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Biosynthesis and Genetics of Lipopolysaccharide Core
Published in Helmut Brade, Steven M. Opal, Stefanie N. Vogel, David C. Morrison, Endotoxin in Health and Disease, 2020
David E. Heinrichs, Chris Whitfield, Miguel A. Valvano
The rfaH locus is required for expression of a number of systems in E. coli and Salmonella. These include hemolysin (122), F-factor (123,124), LPS (120,121,124,125), and group II capsules (126,127). There is now overwhelming data to indicate that RfaH is a transcriptional antiterminator (153). Transcription of the traYZ operon (part of the F factor) is prematurely terminated in rfaH mutants compared with rfaH+ cells (128,129), and suppressors of rfaH map to rho and rpoBC indicating that RfaH operates at rho-dependent termination sites (130). Whether or not RfaH acts at rho-independent termination sites is still in question. Reporter fusions throughout the waaQ operon indicate that expression of most, if not all of the genes of the operon are regulated by rfaH (125,131). The effect of rfaH mutations is more dramatic on promoter-distal gene fusions (125). Although initial findings indicated the possible existence of secondary promoters within the waaQ-operon (132), a more recent study using polar mutations has more or less ruled this out (47). Further, Brazas et al. have reported the presence of multiple termination sequences throughout the waaQ operon (131). Thus it would appear that there is a requirement for an antitermination mechanism that would allow transcription of distal genes in the operon.
Ribosomal RNA Processing Sites
Published in S. K. Dutta, DNA Systematics, 2019
Robert J. Crouch, Jean-Pierre Bachellerie
The Box A sequence is a part of an apparatus that affects transcription. Together with other cell factors36 (and in some cases, phage-encoded factors), the Box A sequence acts to antiterminate transcription. It may be to ensure complete transcription of bacterial rRNA genes, an antitermination mechanism must be triggered. The location of the “Box A-like” sequences upstream from both 16S and 23 S rRNA37 (Figure 2) may reflect yet another common feature of rRNA transcription, not a simple sequence recognized as a processing site (i.e., there may be more information in the primary sequence than mature rRNAs and processing sites).
Regulation of Synthesis of the β & β′ Subunits of RNA Polymerase of Escherichia Coli
Published in James F. Kane, Multifunctional Proteins: Catalytic/Structural and Regulatory, 2019
Rudolph Spangler, Geoffrey Zubay
Bacterial cells contain at least 1,000 copies of RNA polymerase. This single multiprotein complex is responsible for most of the transcription in Escherichia coli. It is also used in an unmodified or modified form for transcription of a large number of bacteriophage genes. The polymerase recognizes about a thousand different promoters on the bacterial chromosome with different efficiencies that depend upon the sequences of these promoters as well as more or less specific regulatory factors whose concentrations vary with the physiological state of the cell. This differential response in certain cases also extends to the sites of provisional terminators (attenuators) found in host and viral genes which are modulated by a variety of antiterminator factors. The complexity of the bacterial polymerase shown by its response to a wide variety of situations stretches the imagination to the very limits of biochemical reality. Superimposed on this functional complexity is the growing realization that the synthesis of the RNA polymerase itself is one of the more intricately regulated gene expression processes in E. coli. At the present time the regulatory processes which control RNA polymerase synthesis are only partly understood. As will be argued below, the regulatory mechanism which controls the amount of RNA polymerase reflects the desirability for RNA polymerase levels to be coupled with the cell’s needs for ribosomal proteins.1 The primary object of this paper is to describe the regulatory mechanism which controls the synthesis of the β and β′ subunits of RNA polymerase.
Promoter orientation of the immunomodulatory Bacteroides fragilis capsular polysaccharide A (PSA) is off in individuals with inflammatory bowel disease (IBD)
Published in Gut Microbes, 2019
Lucy E. Blandford, Emma L. Johnston, Jeremy D. Sanderson, William G. Wade, Alistair J. Lax
The first gene of all eight PS biosynthetic loci is the upxY gene where x is replaced by a to h depending on the specific PS locus. The UpxY family of proteins share homology amongst individual proteins, but contain a region of amino acid sequence in the N terminal half that are specific for the individual biosynthetic loci (a-h).12 The UpxY proteins are able to associate with RNA polymerase in the 5' untranslated region (UTR) to prevent premature termination of transcription. The adjacent upxZ genes code for a family of proteins able to prevent the transcriptional antitermination function of other PS loci UpxY proteins. Altogether the UpxZ proteins prevent simultaneous synthesis of PS types in a single bacterial cell by a hierarchical system of regulation, with PSC the default locked ‘ON’ promoter.13
Inhibition of Shiga toxin-converting bacteriophage development by novel antioxidant compounds
Published in Journal of Enzyme Inhibition and Medicinal Chemistry, 2018
Sylwia Bloch, Bożena Nejman-Faleńczyk, Karolina Pierzynowska, Ewa Piotrowska, Alicja Węgrzyn, Christelle Marminon, Zouhair Bouaziz, Pascal Nebois, Joachim Jose, Marc Le Borgne, Luciano Saso, Grzegorz Węgrzyn
In the absence of the prophage inducing agent, the influence of compounds CM092, CM032D, and CM3186B on expression of bacterial genes involved in the oxidative stress response, as well as of bacteriophage genes crucial for either lytic (N, Q) or lysogenic (cI, cII) development was negligible (Figure 9(A)). However, addition of hydrogen peroxide caused activation of the host genes coding for the oxidative stress proteins, and phage genes coding for antitermination proteins (as expected), while having little effects on phage lysogenic proteins (also as expected) (Figure 9(B)). Importantly, simultaneous presence of hydrogen peroxide and any of the tested compounds caused a significant decrease of the efficiency of expression of the oxidative stress genes as well as phage genes (N, Q) supporting the lytic development (Figure 9(B)). In contrast to these genes, expression of the gene coding for the cI repressor was enhanced under these conditions. These results suggest that compounds CM092, CM032D, and CM3186B impair expression of bacterial genes involved in the oxidative stress response, or ameliorate the effects of oxidative stress. This leads to prevention of the prophage induction by hydrogen peroxide.
Strategies for targeting RNA with small molecule drugs
Published in Expert Opinion on Drug Discovery, 2023
Christopher L. Haga, Donald G. Phinney
Riboswitches are naturally occurring RNA aptamers that bind specific small molecules to regulate gene expression, most often in bacteria [39]. These structured RNA sequences are usually found in the untranslated region of mRNA and consist of an evolutionarily conserved ligand-binding aptamer domain working in conjunction with a variable sequence expression platform domain that serves to regulate downstream expression. Upon binding to a cognate ligand, conformation changes occur within the RNA, inducing or inhibiting gene expression, through several mechanisms such as transcription and translation termination, transcription antitermination, translational activation, and alternative splicing.