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16S rRNA Identification

16S ribosomal RNA (or 16S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The genes coding for it are referred to as 16S rRNA gene and are used in reconstructing phylogenies, due to the slow rates of evolution of this region of the gene. Carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA in phylogenetics in 1977. Multiple sequences of the 16S rRNA gene can exist within a single bacterium. Functions 1. Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. 2. The 3′-end contains the anti-Shine-Dalgarno sequence, which binds upstream to the AUG start codon on the mRNA. The 3′-end of 16S RNA binds to the proteins S1 and S21 which are known to be involved in initiation of protein synthesis[5] 3. Interacts with 23S, aiding in the binding of the two ribosomal subunits (50S and 30S) 4. Stabilizes correct codon-anticodon pairing in the A-site by forming a hydrogen bond between the N1 atom of adenine residues 1492 and 1493 and the 2′OH group of the mRNA backbone. In addition to highly conserved primer binding sites, 16S rRNA gene sequences contain hypervariable regions that can provide species-specific signature sequences useful for identification of bacteria. As a result, 16S rRNA gene sequencing has become prevalent in medical microbiology as a rapid and cheap alternative to phenotypic methods of bacterial identification. Although it was originally used to identify bacteria, 16S sequencing was subsequently found to be capable of reclassifying bacteria into completely new species, or even genera. It has also been used to describe new species that have never been successfully cultured. With third-generation sequencing coming to many labs, simultaneous identification of thousands of 16S rRNA sequences is possible within hours, allowing metagenomic studies, for example of gut flora. Database: The 16S rRNA gene is used as the standard for classification and identification of microbes, because it is present in most microbes and shows proper changes. Type strains of 16S rRNA gene sequences for most bacteria and archaea are available on public databases, such as NCBI. However, the quality of the sequences found on these databases is often not validated. Therefore, secondary databases that collect only 16S rRNA sequences are widely used.