RISA Technique – RISA analysis of ribosomal inter-gene sequences 2nd February 2023 – Tags: gene, gene sequences, RISA, RISA Technique
What is RISA?
RISA, or ribosomal intergenic sequence analysis, is used in the analysis of different types of micro-organisms. It is used to compare bacterial cultures that are distinguished by the type of environment in which they live or the method of treatment. It is a method that works without bias in culture-dependent approaches. It is also known as ‘community fingerprinting’
The RISA technique is based on PCR amplification of the region of the rRNA gene operon located between the small (16s) and large (23s) ribosomal subunits. This is the so-called intergenic spacer region (ISR). By using oligonucleotide primers targeting conserved regions in the 16S and 23S, we can generate RISA fragments from most dominant bacterial genes in an environmental sample.
Unlike most of the rRNA operon, which has a structural function, RISA fragments can encode tRNAs depending on the bacterial species. However, the taxonomic value of ISRs lies in too much heterogeneity in both length and nucleotide sequence.
In RISA, we exploit the heterogeneity of ISR length, which has been shown to range from 150 to 1500 bp.
The product obtained by PCR is a mixture of fragments provided by several dominant individuals of a species. This product is then subjected to polyacrylamide gel electrophoresis and the DNA is visualised after staining.
The result of the electrophoresis is a complex pattern of bands that provides a species-specific profile, where each DNA band corresponds to the corresponding bacterial population.
What is the fingerprint technique?
The fingerprint technique is a laboratory technique used to determine the probability in a person’s identity based on the nucleotide sequences of certain regions of human DNA that are unique to individuals. DNA sampling is used in a variety of situations such as criminal investigations, other forensic purposes and paternity tests. In these situations, a match is sought between two DNA samples.
The use of fingerprint techniques offers the possibility to assess the presence of differences between microbial populations, but does not provide a direct determination of taxonomic affiliation
What can we identify with RISA?
With RISA, we can identify Enterococcus cecorum. It belongs to the group of opportunistic pathogens and can play a role as an aetiological agent of diseases in humans (mainly nosocomial infections), chickens and pigeons. Recently, this bacterium appears to be a threat to the poultry industry worldwide. Infection with this bacterium in chickens can cause septicaemia, endocarditis or, in severe cases, brain necrosis and encephalomalacia.
The bacterium rarely attacks the human body, but there are cases of infection of the post-operative hernia plate and colonisation in the urinary tract.