16S rRNA sequencing is research method used to identify different types of bacteria or archaea within a biological sample. For this reason, it is an extremely useful tool in microbiome research studies, however it also has a number of other applications:
16S rRNA is a type of rRNA involved in making the small subunit of the prokaryotic
ribosome; these are components of the 30S subunit (prokaryotic ribosome). In
general, it has a structural function alike the rRNA in the larger subunit, to hold the
proteins of ribosomes in set positions. They are also involved in promoting the fusion
of the small subunits to the larger subunits by the interaction with the 23s rRNA in
the larger subunit. The small ribosomal units in Archaea, Bacteria, Chloroplasts and
Bacteria contain the 16S.
The “S” in 16S is the sedimentation coefficient – an index that indicates the
macromolecule’s downward velocity in the centrifugal field. The 16S rRNA gene is
the sequence of DNA that corresponds to the rRNA encoding bacteria seen in the
genome of bacteria. These are specific and highly conserved; their gene sequence is
lengthy enough.
In prokaryotes, the ribosomal RNAs are as follows –
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Features of 16S rRNA
Number of copies
Bacteria comprise approximately 5 to 10 copies of the 16S rRNA, making the
detection extremely sensitive.
Size
The size of the 16S rRNA coding gene is close to 1500bp containing 50 functional
domains.
Information
The internal structure of 16S rRNA gene comprises conserved and variable regions.
The universal primers of different bacteria could be framed as per the conservative
region, and particular primers of particular bacteria could be framed as per the
variable region. The interspecific variation of information in the different areas of the
16S rRNA makes the recognition specific.
16s rRNA Function
The following are the functionalities of the 16s rRNA –
They interact with the 23S helping in the integration of the two units of ribosomal
subunits (50S+30S)
3’end comprises a reverse SD sequence used in binding the AUG codon (initiation)
of the mRNA. The 16S rRNA’s 3’ terminal with S1 and S21 combination was seen to
be associated with the initiation of the synthesis of proteins
Immobilisation of ribosomal proteins serves as scaffoldings. Hence, they have a
structural role in defining the positions of the ribosomal proteins
It stabilises the accurate codon-anticodon pairing in the A-site to form a hydrogen
bond between the N1 atoms of the adenine residues, and the 2′OH group of the
backbone of the mRNA
Gene detection – 16S rRNA
The technique of 16S rRNA gene detection has emerged to have become the most
widely used tool to identify and detect pathogens as a result of the PCR technology,
and sustained advancements in nucleic acid research technology.
The technology is applicable to recognize, categorise and find pathogens at a faster
pace and with accuracy. It involves these steps – genomic DNA is gathered,
collecting 16S rRNA gene fragments, and analysing the gene sequence of 16S
rRNA.
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