16S ribosomal RNA: Wikis

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Categories: Ribosomal RNA

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Atomic structure of the 30S Subunit from Thermus thermophilus. Proteins are shown in blue and the single RNA strand in orange.^[1]

The 16S rRNA is a part of the ribosomal RNA −-- a 1542 nt long component of the small prokaryotic ribosomal subunit (30S).

It is possible for multiple sequences to exist in a single bacterium.^[2]

1 Functions
2 Universal Primers
- 2.1 PCR applications
3 References
4 External links

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.
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 1943 and the 2'OH group of the mRNA backbone.

Universal Primers

The 16srRNA gene is used for phylogenetic studies^[3] as it is highly conserved between different species of bacteria and archaea.^[4] 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^[5])PCR primers are used to amplify the 16srRNA gene to provide phylogenetic information.

Comparative analysis of the 16S rRNA sequences is done with the help of primers, called "universal primers" which have the sequences:

forward: AGA GTT TGA TCC TGG CTC AG
reverse: ACG GCT ACC TTG TTA CGA CTT

PCR applications

In addition to highly conserved primer binding sites, 16S rRNA gene sequences contain hypervariable regions which 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.

References

^ Schluenzen F, Tocilj A, Zarivach R, Harms J, Gluehmann M, Janell D, Bashan A, Bartels H, Agmon I, Franceschi F, Yonath A (2000). "Structure of functionally activated small ribosomal subunit at 3.3 angstroms resolution". Cell 102 (5): 615–23. doi:10.1016/S0092-8674(00)00084-2. PMID 11007480.
^ Case RJ, Boucher Y, Dahllöf I, Holmström C, Doolittle WF, Kjelleberg S (January 2007). "Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies". Appl. Environ. Microbiol. 73 (1): 278–88. doi:10.1128/AEM.01177-06. PMID 17071787. PMC 1797146. http://aem.asm.org/cgi/pmidlookup?view=long&pmid=17071787.
^ 16S ribosomal DNA amplification for phylogenetic study W G Weisburg, S M Barns, D A Pelletier and D J Lane; J Bacteriol. 1991 January; 173(2): 697-703
^ Coenye T, Vandamme P (November 2003). "Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes". FEMS Microbiol. Lett. 228 (1): 45–9. doi:10.1016/S0378-1097(03)00717-1. PMID 14612235. http://linkinghub.elsevier.com/retrieve/pii/S0378109703007171.
^ Huber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, Stetter KO (2002). "A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont". Nature 417 (6884): 63–7. doi:10.1038/417063a. PMID 11986665.