CspA mRNA 5' UTR
Encyclopedia
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.
The 5' UTR was first suspected to be significant when mutations within this region of cspA significantly increased the stability of the transcript at 37°C.
The secondary structure of cspA mRNA changes in response to temperature; at 37°C the transcript is unstable and less efficiently translated
than at lower temperatures. Unlike other RNA thermometers (such as FourU
), the secondary structure is not reliant on the melting of a hairpin
in order to affect gene expression
. Instead, in temperatures below 20°C a cis-regulatory region of ncRNA in the 5' UTR of cspA presents the Shine-Dalgarno sequence
and AUG start codon
to the ribosome
in a more accessible way. The precise mechanism for changing the mRNA conformation is unknown. cspA protein is then produced in significantly higher quantities, making up over 2% of the cell's proteome
during cold shock. cspA protein binds Hfq, which upregulates production of sigma factor
s which mediate a stress response.
RNA thermometer
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.In...
, regulating the expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
of cspA in response to temperature.
The 5' UTR was first suspected to be significant when mutations within this region of cspA significantly increased the stability of the transcript at 37°C.
The secondary structure of cspA mRNA changes in response to temperature; at 37°C the transcript is unstable and less efficiently translated
Translation (genetics)
In molecular biology and genetics, translation is the third stage of protein biosynthesis . In translation, messenger RNA produced by transcription is decoded by the ribosome to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein...
than at lower temperatures. Unlike other RNA thermometers (such as FourU
FourU thermometer
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 ....
), the secondary structure is not reliant on the melting of a hairpin
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions,...
in order to affect gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
. Instead, in temperatures below 20°C a cis-regulatory region of ncRNA in the 5' UTR of cspA presents the Shine-Dalgarno sequence
Shine-Dalgarno sequence
The Shine-Dalgarno sequence , proposed by Australian scientists John Shine and Lynn Dalgarno , is a ribosomal binding site in the mRNA, generally located 8 basepairs upstream of the start codon AUG. The Shine-Dalgarno sequence exists only in prokaryotes. The six-base consensus sequence is AGGAGG;...
and AUG start codon
Start codon
The start codon is generally defined as the point, sequence, at which a ribosome begins to translate a sequence of RNA into amino acids.When an RNA transcript is "read" from the 5' carbon to the 3' carbon by the ribosome the start codon is the first codon on which the tRNA bound to Met,...
to the ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
in a more accessible way. The precise mechanism for changing the mRNA conformation is unknown. cspA protein is then produced in significantly higher quantities, making up over 2% of the cell's proteome
Proteome
The proteome is the entire set of proteins expressed by a genome, cell, tissue or organism. More specifically, it is the set of expressed proteins in a given type of cells or an organism at a given time under defined conditions. The term is a portmanteau of proteins and genome.The term has been...
during cold shock. cspA protein binds Hfq, which upregulates production of sigma factor
Sigma factor
A sigma factor is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. Different sigma factors are activated in response to different environmental conditions...
s which mediate a stress response.