16S ribosomal RNA
Encyclopedia
Svedberg
A svedberg is a non-SI physical unit used for sedimentation coefficients. It characterizes the behaviour of a particle type in sedimentation processes, notably centrifugation. The svedberg is technically a measure of time, and is defined as exactly 10-13 seconds A svedberg (symbol S, sometimes...
rRNA) is a component of the 30S
30S
30S is the smaller subunit of the 70S ribosome of prokaryotes. It is a complex of ribosomal RNA and ribonucleoproteins that functions in mRNA translation...
subunit of prokaryotic ribosome
Ribosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
s. It is approximately 1.5kb (or 1500 nucleotide
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
s) 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 RNA23S ribosomal RNAThe 23S rRNA is a 2904 nt long component of the large prokaryotic subunit The ribosomal peptidyl transferase activity resides in this rRNA...
, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteinRibosomal proteinA ribosomal protein is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. A large part of the knowledge about these organic molecules has come from the study of E. coli ribosomes. Most ribosomic proteins have been... - The 3' end contains the anti-Shine-Dalgarno sequenceShine-Dalgarno sequenceThe Shine-Dalgarno sequence , proposed by Australian scientists John Shine and Lynn Dalgarno , is a ribosomal binding site in the mRNA, generally located 8 basepairs upstream of the start codon AUG. The Shine-Dalgarno sequence exists only in prokaryotes. The six-base consensus sequence is AGGAGG;...
, 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 initation 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 (50S50S50S is the larger subunit of the 70S ribosome of prokaryotes. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the subunits 5S and 23S.-Structure:...
+30S30S30S is the smaller subunit of the 70S ribosome of prokaryotes. It is a complex of ribosomal RNA and ribonucleoproteins that functions in mRNA translation...
) - 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 structurePurineA purine is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring. Purines, including substituted purines and their tautomers, are the most widely distributed kind of nitrogen-containing heterocycle in nature....
) residues 1492 and 1493 and the 2'OH group of the mRNA backbone
Universal Primers
The 16SrRNA gene is used for phylogeneticPhylogenetics
In biology, phylogenetics is the study of evolutionary relatedness among groups of organisms , which is discovered through molecular sequencing data and morphological data matrices...
studies as it is highly conserved between different species of bacteria and archaea. Carl Woese
Carl Woese
Carl Richard Woese is an American microbiologist and physicist. Woese is famous for defining the Archaea in 1977 by phylogenetic taxonomy of 16S ribosomal RNA, a technique pioneered by Woese and which is now standard practice. He was also the originator of the RNA world hypothesis in 1977,...
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
Archaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
species belonging to the phylum Nanoarchaeota
Nanoarchaeota
In taxonomy, the Nanoarchaeota are a phylum of the Archaea. This phylum currently has only one representative, Nanoarchaeum equitans.-External links:...
) PCR primers
Primer (molecular biology)
A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. They are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA...
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
Primer (molecular biology)
A primer is a strand of nucleic acid that serves as a starting point for DNA synthesis. They are required for DNA replication because the enzymes that catalyze this process, DNA polymerases, can only add new nucleotides to an existing strand of DNA...
, 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:
| Primer name | Sequence (5'-3') | Reference |
|---|---|---|
| B27F | AGA GTT TGA TCC TGG CTC AG | |
| U1492R | GGT TAC CTT GTT ACG ACT T | same as above |
| 928F | TAA AAC TYA AAK GAA TTG ACG GG | |
| 336R | ACT GCT GCS YCC CGT AGG AGT CT | as above |
| 1100F | YAA CGA GCG CAA CCC | |
| 1100R | GGG TTG CGC TCG TTG | |
| 337F | GAC TCC TAC GGG AGG CWG CAG | |
| 907R | CCG TCA ATT CCT TTR AGT TT | |
| 785F | GGA TTA GAT ACC CTG GTA | |
| 805R | GAC TAC CAG GGT ATC TAA TC | |
| 533F | GTG CCA GCM GCC GCG GTA A | |
| 518R | GTA TTA CCG CGG CTG CTG G |
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 microbiologyMedical microbiology
Medical microbiology is both a branch of medicine and microbiology which deals with the study of microorganisms including bacteria, viruses, fungi and parasites which are of medical importance and are capable of causing infectious diseases in human beings...
as a rapid, accurate alternative to phenotypic
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...
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.