Genetics and Biosynthesis of Lipopolysaccharide O-Antigens
Helmut Brade, Steven M. Opal, Stefanie N. Vogel, David C. Morrison in Endotoxin in Health and Disease, 2020
The JUMPstart sequence is always found in the same orientation to the direction of transcription, an observation that, combined with its position upstream of transcription start sites, suggests a possible role in transcription. The ops subsequence is also found in the regulatory regions of a number of gram-negative operons involved in toxin production and conjugal transfer of DNA. Studies on the involvement of ops in expression of the E. coli hemolysin operon have provided an insight into a possible mechanism of transcriptional regulation and have implicated the product of the rfaH gene in this process. By examining transcription of promoter-distal genes and mRNA transcript lengths in various ops and rfaH mutants, two groups (162,163) reported evidence to support the idea that the E. coli RfaH protein interacts with ops to suppress transcription polarity. Bailey et al. (163) also reported a structural relationship between RfaH and the essential transcription/termination cofactor NusG. Based on their experimental data and this homology, these workers have proposed that RfaH regulates expression of the ops-containing operons by interacting with the cis-acting ops element and the RNA polymerase, suppressing polarity and enabling transcription to continue through the operon. More recently, Leeds and Welch (164) speculated that RfaH might interact with the RNA polymerase to help create a termination-resistant complex in a manner similar to λ N-mediated antitermination at the λnut site (165).
Regulation of Synthesis of the β & β′ Subunits of RNA Polymerase of Escherichia Coli
James F. Kane in Multifunctional Proteins: Catalytic/Structural and Regulatory, 2019
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.
Ribosomal RNA Processing Sites
S. K. Dutta in DNA Systematics, 2019
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).
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
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.
Intestinal phages interact with bacteria and are involved in human diseases
Published in Gut Microbes, 2022
Phages can spread virulence factors between strains, including toxin-coding genes that cause many diseases, such as diphtheria, cholera, dysentery, and scarlet fever.29Vibrio cholerae, the pathogen of cholera, requires two coordinating regulators to achieve full virulence: cholera toxin and toxin-coregulated pilus. The structural genes of cholera toxin are encoded by the filamentous phage CTXφ, and the CTXφ genome acts as a plasmid for chromosome integration or replication. The El Tor mutation of the phage CTXφ destroys XerC and XerD, two bacterial-encoded tyrosine recombinases. These two enzymes usually play a role in the decomposition of chromosomal dimers. CTXφ phages integrate at the decomposition site DIF1 of the larger dimer of the two chromosomes of V. cholerae, leading to the genetic diversity of cholera epidemic strains and further affecting the release of cholera toxin by V. cholerae.30,31 The toxin in Shiga toxigenic E. coli (STEC) is encoded by resident temperate lambdoid bacteriophages. Temperate lambdoid bacteriophages might contain toxin structural genes or regulators of toxin structural genes transduced by host bacteria. The Shiga toxin (Stx) gene is expressed when the phage is induced to leave its dormant state and begin replication. Extensive phage replication results in the release of large amounts of Stx from E. coli.32,33 The Stx gene is located downstream of the phage PR promoter, and the transcription of the promoter and the expression of Stx are controlled by the Q antitermination protein. Q antitermination protein is expressed only during phage lysis-mediated growth, so phages carrying the Q21 subtype produce a lower amount of Stx.32
Related Knowledge Centers
- Bacteriophage
- Escherichia Coli
- Nucleotide
- Prokaryote
- Rna
- Termination Factor
- Transcription
- Rna Polymerase
- Lambda Phage
- Arginine