In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of itself, such as tRNA or rRNA. Promoters are located near the transcription start sites of genes, upstream on the DNA . Promoters can be about 100–1000 base pairs long, the sequence of which is highly dependent on the gene and product of transcription, type or class of RNA polymerase recruited to the site, and species of organism.
Streptococcus pyogenes is a species of Gram-positive, aerotolerant bacteria in the genus Streptococcus. These bacteria are extracellular, and made up of non-motile and non-sporing cocci that tend to link in chains. They are clinically important for humans, as they are an infrequent, but usually pathogenic, part of the skin microbiota that can cause group A streptococcal infection. S. pyogenes is the predominant species harboring the Lancefield group A antigen, and is often called group A Streptococcus (GAS). However, both Streptococcus dysgalactiae and the Streptococcus anginosus group can possess group A antigen as well. Group A streptococci, when grown on blood agar, typically produce small (2–3 mm) zones of beta-hemolysis, a complete destruction of red blood cells. The name group A (beta-hemolytic) Streptococcus is thus also used.
In molecular biology, a riboswitch is a regulatory segment of a messenger RNA molecule that binds a small molecule, resulting in a change in production of the proteins encoded by the mRNA. Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its effector molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, expanded the known natural capabilities of RNA beyond its ability to code for proteins, catalyze reactions, or to bind other RNA or protein macromolecules.
Virulence factors are cellular structures, molecules and regulatory systems that enable microbial pathogens to achieve the following:
In the field of molecular biology the 6S RNA is a non-coding RNA that was one of the first to be identified and sequenced. What it does in the bacterial cell was unknown until recently. In the early 2000s scientists found out the function of 6S RNA to be as a regulator of sigma 70-dependent gene transcription. All bacterial RNA polymerases have a subunit called a sigma factor. The sigma factors are important because they control how DNA promoter binding and RNA transcription start sites. Sigma 70 was the first one to be discovered in Escherichia coli.
Spot 42 (spf) RNA is a regulatory non-coding bacterial small RNA encoded by the spf gene. Spf is found in gammaproteobacteria and the majority of experimental work on Spot42 has been performed in Escherichia coli and recently in Aliivibrio salmonicida. In the cell Spot42 plays essential roles as a regulator in carbohydrate metabolism and uptake, and its expression is activated by glucose, and inhibited by the cAMP-CRP complex.
In molecular biology the ArcZ RNA is a small non-coding RNA (ncRNA). It is the functional product of a gene which is not translated into protein. ArcZ is an Hfq binding RNA that functions as an antisense regulator of a number of protein coding genes.
The Bacteroidales-1 RNA motif is a conserved RNA structure identified by bioinformatics. It has been identified only in bacteria within the order (biology) Bacteroidales. Its presumed length is marked by a promoter on one end that conforms to an alternate consensus sequence that is common in the phylum Bacteroidota, and its 3′ end is indicated by predicted transcription terminators. It is often located downstream of a gene that encodes the L20 ribosomal subunit, although it is unclear whether there is a functional reason underlying this apparent association.
The c4 antisense RNA is a non-coding RNA used by certain phages that infect bacteria. It was initially identified in the P1 and P7 phages of E. coli. The identification of c4 antisense RNAs solved the mystery of the mechanism for regulation of the ant gene, which is an anti-repressor.
The fluoride riboswitch is a conserved RNA structure identified by bioinformatics in a wide variety of bacteria and archaea. These RNAs were later shown to function as riboswitches that sense fluoride ions. These "fluoride riboswitches" increase expression of downstream genes when fluoride levels are elevated, and the genes are proposed to help mitigate the toxic effects of very high levels of fluoride.
The Downstream-peptide motif refers to a conserved RNA structure identified by bioinformatics in the cyanobacterial genera Synechococcus and Prochlorococcus and one phage that infects such bacteria. It was also detected in marine samples of DNA from uncultivated bacteria, which are presumably other species of cyanobacteria.
The hopC RNA motif is a predicted cis-regulatory element identified by a bioinformatic screen for conserved RNA secondary structures. hopC RNAs are exclusively found within bacteria classified within the genus Helicobacter, some of which are human pathogens that infect the stomach and can cause ulcers.
The JUMPstart RNA motif describes a conserved RNA-based secondary structure associated with JUMPstart elements. The 39-base-pair JUMPstart sequence describes a conserved element upstream of genes that participate in polysaccharide synthesis. The JUMPstart element has been shown to function as an RNA, and is present in the 5' untranslated regions of the genes it regulates.
The L17 downstream element RNA motif is a conserved RNA structure identified in bacteria by bioinformatics. All known L17 downstream elements were detected immediately downstream of genes encoding the L17 subunit of the ribosome, and therefore might be in the 3' untranslated regions of these genes. The element is found in a variety of lactic acid bacteria and in the genus Listeria.
The Pseudomon-1 RNA motif is a conserved RNA identified by bioinformatics. It is used by most species whose genomes have been sequenced and that are classified within the genus Pseudomonas, and is also present in Azotobacter vinelandii, a closely related species. It is presumed to function as a non-coding RNA. Pseudomon-1 RNAs consistently have a downstream rho-independent transcription terminator.
Bacterial small RNAs are small RNAs produced by bacteria; they are 50- to 500-nucleotide non-coding RNA molecules, highly structured and containing several stem-loops. Numerous sRNAs have been identified using both computational analysis and laboratory-based techniques such as Northern blotting, microarrays and RNA-Seq in a number of bacterial species including Escherichia coli, the model pathogen Salmonella, the nitrogen-fixing alphaproteobacterium Sinorhizobium meliloti, marine cyanobacteria, Francisella tularensis, Streptococcus pyogenes, the pathogen Staphylococcus aureus, and the plant pathogen Xanthomonas oryzae pathovar oryzae. Bacterial sRNAs affect how genes are expressed within bacterial cells via interaction with mRNA or protein, and thus can affect a variety of bacterial functions like metabolism, virulence, environmental stress response, and structure.
RivX sRNA is a non-coding RNA molecule involved in the interface between two key regulators of virulence in the human pathogen Streptococcus pyogenes : the CovR/S system and Mga regulator. This RNA, along with its downstream protein-coding gene RivR, are the first discovered links between these two important regulation networks. An extra protein linking the two pathways, TrxR, was described a year later. The adjoining of these two pathways could allow a consistently high virulence of S. pyogenes despite a variety of environmental conditions.
In molecular biology, Streptococcus sRNAs are small RNAs produced by species of Streptococcus bacteria. Several screens have identified numerous sRNAs in different species and strains of Streptococcus including S. pneumoniae, S. pyogenes, S. agalactiae and S.mutans. The function of most of these is currently unknown, however a few have been characterised including FasX small RNA. Many sRNAs have roles in pathogenesis.
The uup RNA motif is a conserved RNA structure that was discovered by bioinformatics. uup motif RNAs are found in Bacillota and Gammaproteobacteria.
RopB transcriptional regulator, also known as RopB/Rgg transcriptional regulator is a transcriptional regulator protein that regulates expression of the extracellularly secreted cysteine protease streptococcal pyrogenic exotoxin B, which is an important virulence factor of Streptococcus pyogenes and is responsible for the dissemination of a host of infectious diseases including strep throat, impetigo, streptococcal toxic shock syndrome, necrotizing fasciitis, and scarlet fever. Functional studies suggest that the ropB multigene regulon is responsible for not only global regulation of virulence but also a wide range of functions from stress response, metabolic function, and two-component signaling. Structural studies implicate ropB's regulatory action being reliant on a complex interaction involving quorum sensing with the leaderless peptide signal speB-inducing peptide (SIP) acting in conjunction with a pH sensitive histidine switch.
