Why 16S rRNA gene?

16S rRNA gene is considered as an important tool for bacterial phylogenetics. I have here hinted at some of the facets which gave the gene a genetic marker status.
A bacterial chromosome has 5S, 16S and 23S rRNA genes interlinked by an intergenic spacer to form a gene cluster known as the ribosomal RNA operon.  The number of rRNA operon copy differs for every bacterial species and this is an important chronometer deciding the phylogeny of a bacterium.
Though the 16S rRNA gene sequence was first obtained in 1972, the sequence was used for phylogenetic purpose in the year 1985 [1].
The 16S rRNA gene, to face divergence of 1 to 2 % takes almost 50 million years, says Moran et al. [2] and for this reason the gene is considered as highly conserved.
The sequence of 16S rRNA gene has 9 highly conserved regions and 9 hyper-variable regions. The conserved regions are used to design primers while the variable regions paves way to undergo phylogenetic study and thus 16S rRNA gene is considered as marker gene for bacterial profiling [3].
Phylogenetic trees are widely used to elucidate systematic relationships between different species, in particular, the novel microbial lineages [1]. ExTaxon is an automated system for phylogenetic analysis and one of the easy to handle and standard tools for species identification based on 16S rRNA gene sequence.

Schematic representation of bacterial ribosomal RNA operon, variable regions and primers for 16S rDNA sequencing.
[1] Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985 Oct; 82(20): 6955-6959.
[2] Moran NA, Munson MA, Baumann P, Ishikawa H. Proc R Soc London Ser B. 1993; 253: 167–171.
[3] Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol. 2008 Oct; 11(5): 442-446.


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