16S ribosomal RNA



16S ribosomal RNA (or 16S rRNA) is a component of the 30S subunit of prokaryotic ribosomes. It is 1,542 nucleotides in length. The genes coding for it are referred to as 16S rDNA and are used in reconstructing phylogenies.

Multiple sequences of 16S rRNA can exist within a single bacterium.

Functions
It has several functions:
 * Like the large (23S) ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal protein
 * 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 known to be involved in iniitation of protein synthesis; RNA-protein cross-linking by A.P. Czernilofsky et al. (FEBS Lett. Vol 58, pp 281–284, 1975).
 * Interacts with 23S, aiding in the binding of the two ribosomal subunits (50S+30S)
 * Stabilizes correct codon-anticodon pairing in the A site, via a hydrogen bond formation between the N1 atom of Adenine (see image of Purine chemical structure) residues 1492 and 1493 and the 2'OH group of the mRNA backbone

Universal Primers
The 16SrRNA gene is used for phylogenetic studies as it is highly conserved between different species of bacteria and archaea. Carl Woese pioneered this use of 16S rRNA. In addition to these, mitochondrial and chloroplastic rRNA are also amplified.

Universal (or quasi-universal as it does not pick up some recently discovered hydrothermal archaea species belonging to the phylum Nanoarchaeota ) PCR primers are used to amplify the 16SrRNA gene providing the phylogenetic information, the most common universal primer pair was devised by Weisburg et al. and are currently referred to 27F and 1492R, however, for some applications shorter amplicons may be necessary for example for 454 sequencing with Titanium chemistry (500-ish reads are ideal) the primer pair 27F-534R covering V1 to V3.

Sequence analysis of the 16S rRNA sequences is done with the help of several primers, called "universal primers." These primers target the conserved region of 16S rRNA gene and amplify the target in parts. Finally the several amplified parts could be assembled together to have the entire sequence of the complete 16S rRNA. Some of the primers are listed below:

PCR applications
In addition to highly conserved primer binding sites, 16S rRNA gene sequences contain hypervariable regions that can provide species-specific signature sequences useful for bacterial identification. As a result, 16S rRNA gene sequencing has become prevalent in medical microbiology as a rapid, accurate 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.