Gert Dandanell

Gene-regulatory modules In Escherichia coli: nucleoprotein complexes formed by cAMP-CRP and CytR at the nupG promoter

Repression by CytR depends on the formation of nucleoprotein complexes in which the CytR repressor and the cAMP‐CRP activator complex bind co‐operatively to the DNA. Transcription initiation from CytR‐regulated promoters requires cAMP‐CRP; therefore, the cAMP‐CRP complex functions both as an activator and as a co‐repressor in these promoters. Another interesting aspect of the CytR regulon is that each promoter appears to have individual features. Therefore, structural and functional rules governing the formation of repression and activation complexes in one promoter may not be valid for other promoters of the CytR regulon. Here we show that the Escherichia colinupG gene contains one CytR‐ and four CRP‐binding sites in the control region. Notably, the architecture of the CytR binding site is different from previously described targets. In addition, the CytR repressor triggers a DNA repositioning of a cAMP‐CRP complex in the −35 region upon binding to its operator. Thus, formation of the repression and activation complexes at the nupG promoter involves different subsets of CRP‐binding sites. These findings show that the bacterium uses positive and negative regulatory modules to differentially control the expression of CytR‐ and cAMP‐CRP‐regulated genes.

Nucleotides, Nucleosides, and Nucleobases.

We review literature on the metabolism of ribo- and deoxyribonucleotides, nucleosides, and nucleobases in Escherichia coli and Salmonella,including biosynthesis, degradation, interconversion, and transport. Emphasis is placed on enzymology and regulation of the pathways, at both the level of gene expression and the control of enzyme activity. The paper begins with an overview of the reactions that form and break the N-glycosyl bond, which binds the nucleobase to the ribosyl moiety in nucleotides and nucleosides, and the enzymes involved in the interconversion of the different phosphorylated states of the nucleotides. Next, the de novo pathways for purine and pyrimidine nucleotide biosynthesis are discussed in detail.Finally, the conversion of nucleosides and nucleobases to nucleotides, i.e.,the salvage reactions, are described. The formation of deoxyribonucleotides is discussed, with emphasis on ribonucleotidereductase and pathways involved in fomation of dUMP. At the end, we discuss transport systems for nucleosides and nucleobases and also pathways for breakdown of the nucleobases.

DNA specificity of Escherichia coli deoP1 operator-DeoR repressor recognition.

SummaryWe have studied the importance of the specific DNA sequence of the deo operator site for DeoR repressor binding by introducing symmetrical, single basepair substitutions at all positions in the deo operator and tested the ability of these variants to titrate DeoR in vivo. Our results show that a 16 by palindromic sequence constitutes the deo operator. Positions outside this palindrome (positions ±9, ±10) can be changed without any major effect on DeoR binding. Most of the central 6-8 by of the palindrome (positions ±1, ±2, ± 3) can be substituted with other nucleotides with no or only minor effects on DeoR binding, while changes at position ±4 and ±_5 give a more heterogeneous response. Finally, changes at positions ±6, ± 7 and ±8 severely disrupt DeoR binding.

Xanthosine Utilization in Salmonella enterica Serovar Typhimurium Is Recovered by a Single Aspartate-to-Glycine Substitution in Xanthosine Phosphorylase

xapABR from Salmonella enterica was analyzed and compared with the corresponding Escherichia coli genes. xapB and xapR, but not xapA, encode functional proteins. An S. enterica XapA(Asp72Gly) mutant that restores the phosphorolytic activity was selected. The purified mutant enzyme has different kinetic constants than the E. coli enzyme but similar substrate specificity.

A single-copy galK promoter cloning vector suitable for cloning strong promoters ☆

Abstract We report the construction of lambda galK promoter cloning vectors for cloning and characterization of strong promoters. This phage, which contains a unique Hind III cloning site, was applied to the cloning and analysis of transcription initiations of the regulatory region of the deo -operon of Escherichia coli and the P L promoter of bacteriophage lambda.

Towards a cognitive semiotics of science:: the case of physical chemistry

In chapter 5, Juan Carlos Mendoza Collazos presents an overview of a new approach to signification, known as agentive semiotics, that “links achievements of logic, phenomenology and cognitive sciences” (Nino 2015). As the author states, this clearly aligns this approach with cognitive semiotics. Similarly, agentive semiotics is influenced by enactivism, though it takes a more specific stand on the notion of agency, defining an agent as a being that is animate, situated, and capable of paying attention. This means that artifacts for example only have derived agency, that is, a kind of agency that has been assigned by agents proper, which in the case of artifacts means designers. The bulk of the chapter applies the theory of agentive semiotics precisely to the semiotics of artifact design. Unlike traditional semiotic design analysis, the agentive approach implies focus not on the artifacts themselves, but on acts of production and response. Artifacts have significance (a network of potential responses) and signification (“the actual response an agent activates”), thus paralleling (one version of) the distinction between semantics and pragmatics. The chapter makes a strong case for the application of the theoretical corpus of agentive semiotics to design practice, allowing new insights into the actions and experiences of designers and users. Notions such as agenda, per-agenda, agentive scene, etc. are clearly explained and illustrated, showing how theoretical and “applied” cognitive semiotics can intermix. (Less)