Heat shock proteins (HSP) are a family of proteins produced by cells in response to exposure to stressful conditions. They were first described in relation to heat shock, but are now known to also be expressed during other stresses including exposure to cold, UV light and during wound healing or tissue remodeling. Many members of this group perform chaperone functions by stabilizing new proteins to ensure correct folding or by helping to refold proteins that were damaged by the cell stress. This increase in expression is transcriptionally regulated. The dramatic upregulation of the heat shock proteins is a key part of the heat shock response and is induced primarily by heat shock factor (HSF). HSPs are found in virtually all living organisms, from bacteria to humans.
In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation termination codon. The 3′-UTR often contains regulatory regions that post-transcriptionally influence gene expression.
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.
The PrfA thermoregulator UTR is an RNA thermometer found in the 5' UTR of the prfA gene. In Listeria monocytogenes, virulence genes are maximally expressed at 37 °C but are almost silent at 30 °C. The genes are controlled by PrfA, a transcriptional activator whose expression is thermoregulated. It has been shown that the untranslated mRNA (UTR) preceding prfA, forms a secondary structure, which masks the ribosome binding region. It is thought that at 37 °C, the hairpin structure 'melts' and the SD sequence is unmasked.
The Hsp90 cis regulatory element is an RNA element found in the 5' UTR of the Drosophila hsp90 mRNA. It is required for increased translational efficiency during the heat shock response.
In molecular biology, heat shock factors (HSF), are the transcription factors that regulate the expression of the heat shock proteins. A typical example is the heat shock factor of Drosophila melanogaster.
Pseudomonas sRNA are non-coding RNAs (ncRNA) that were predicted by the bioinformatic program SRNApredict2. This program identifies putative sRNAs by searching for co-localization of genetic features commonly associated with sRNA-encoding genes and the expression of the predicted sRNAs was subsequently confirmed by Northern blot analysis. These sRNAs have been shown to be conserved across several pseudomonas species but their function is yet to be determined. Using Tet-Trap genetic approach RNAT genes post-transcriptionally regulated by temperature upshift were identified: ptxS and PA5194.
The Pseudomon-groES RNA motif is a conserved RNA structure identified in certain bacteria using bioinformatics. It is found in most species within the family Pseudomonadaceae, and is consistently located in the 5' untranslated regions of operons that contain groES genes. RNA transcripts of the groES genes in Pseudomonas aeruginosa where shown experimentally to be initiated at one of two start sites, from promoters called "P1" and "P2". The Pseudomon-groES RNA is in the 5' UTR of transcripts initiated from the P1 site, but is truncated in P2 transcripts. groES genes are involved in the cellular response to heat shock, but it is not thought that the Pseudomonas-groES RNA motif is involved in heat shock regulation. However, it is thought that the motif might regulate groES genes in response to other stimuli.
FourU thermometers are a class of non-coding RNA thermometers found in Salmonella. They are named 'FourU' due to the four highly conserved uridine nucleotides found directly opposite the Shine-Dalgarno sequence on hairpin II (pictured). RNA thermometers such as FourU control regulation of temperature via heat shock proteins in many prokaryotes. FourU thermometers are relatively small RNA molecules, only 57 nucleotides in length, and have a simple two-hairpin structure.
cspA mRNA 5' UTR is the untranslated region of the cspA gene, which is important in the cold shock response in Enterobacteriales such as E. coli. The 5' UTR element acts as an RNA thermometer, regulating the expression of cspA in response to temperature. By regulating temperature, cspA proteins carry out the vital function of homeostasis.
An RNA thermometer is a temperature-sensitive non-coding RNA molecule which regulates gene expression. RNA thermometers often regulate genes required during either a heat shock or cold shock response, but have been implicated in other regulatory roles such as in pathogenicity and starvation.
The IbpB thermometer is an RNA thermometer element found in the ibpAB operon. The operon contains two heat-shock genes, encoding inclusion body binding proteins A and B (IbpA/B), and is the most drastically upregulated operon under heat-shock in Escherichia coli.
αr9 is a family of bacterial small non-coding RNAs with representatives in a broad group of α-proteobacteria from the order Hyphomicrobiales. The first member of this family (Smr9C) was found in a Sinorhizobium meliloti 1021 locus located in the chromosome (C). Further homology and structure conservation analysis have identified full-length Smr9C homologs in several nitrogen-fixing symbiotic rhizobia, in the plant pathogens belonging to Agrobacterium species as well as in a broad spectrum of Brucella species. αr9C RNA species are 144-158 nt long and share a well defined common secondary structure consisting of seven conserved regions. Most of the αr9 transcripts can be catalogued as trans-acting sRNAs expressed from well-defined promoter regions of independent transcription units within intergenic regions (IGRs) of the α-proteobacterial genomes.
In molecular biology, the Hsp17 thermometer is an RNA element found in the 5' UTR of Hsp17 mRNA. Hsp17 is a cyanobacterial heat shock protein belonging to the Hsp20 family.
RcsR1 trans-acting sRNA, formerly known as SmelC587, is a stress-related riboregulator, conserved in Sinorhizobium, Rhizobium and Agrobacterium. It contains highly conserved stem-loops involved in the interaction with several target mRNAs. In Sinorhizobium meliloti RcsR1 less conserved central region is responsible for the species-specific interaction with the 5’UTR of autoinducer synthase encoding mRNA sinI. The interaction negatively influences sinI translation.
The first cyanobacterial RNA thermometer (RNAT) Hsp17 was found in the 5'UTR of Synechocystis heat shock hsp17 mRNA. Further study demonstrated that cyanobacteria commonly use RNATs to control the translation of their heat shock genes. HspA is a homolog of Hsp17 in thermophilic Thermosynechococcus elongatus. Two more thermometers were found in the 5'UTRs of mesophilic cyanobacteria A. variabilis and Nostocsp. The first RNAT called avashort was shown to regulate translation by masking the AUG translation start site. The second RNAT called avalong, as it has an extended initial hairpin, might involve tertiary interactions and has similarities to the ROSE element.
RNA thermometers regulate gene expression in response to temperature allowing pathogens like Yersinia to switch on silent genes after entering the host organism. Usually, RNA thermometers are located in the 5'UTR, but an intergenic RNA thermometer was found in Yersinia pseudotuberculosis. The LcrFRNA thermometer together with the thermo-labile YmoA protein activates synthesis of the most crucial virulence activator LcrF (VirF). The RNA thermosensor sequence is 100% identical in all human pathogenic Yersinia species.
RNA thermometers (RNATs) regulate gene expression in response to temperature, allowing pathogens such as Neisseria meningitidis to switch on silent genes after entering the host organism. However the temperature for expression of Neisseria virulence-associated traits is 42 °C while other bacterial pathogen RNATs require 37 °C. This is probably because N. meningitidis is an obligate commensal of the human nasopharynx and becomes pathogenic during inflammation due to viral infection. Three independent RNA thermosensors were identified in the 5′UTRs of genes needed for: capsule biosynthesis (cssA), the expression of factor H binding protein (fHbp) and sialylation of lipopolysaccharide, which is essential for bacterial resistance against immune killing (lst). The very different nucleotide sequence and predicted inhibitory structures of the three RNATs indicate that they have evolved independently.
Lig RNA thermometer is a cis-acting non-coding RNA element that controls ligA and ligB gene expression in Leptospira interrogans in response to temperature change. The lipoproteins LigA and LigB stimulate adhesion of the element and then hosting proteins. The RNA that composes of 175-nucleotide 5'UTR and the first six lig codons folds into two distinct-stem loop structures. Lig expression is limited by these double-stranded RNA structures because they occludes the ribosome-binding site. At higher temperatures, the ribosome binding site is exposed to promote translation initiation.
