What is the 16S rRNA Gene?

The 16S rRNA gene is a section of prokaryotic DNA found in all bacteria and archaea.
This gene codes for an rRNA, and this rRNA in turn makes up part of the ribosome. The
first 'r' in rRNA stands for ribosomal. The ribosome is composed of two subunits, the large
subunit (LSU) and the small subunit (SSU). These two subunits sandwich the mRNA as it
feeds through the ribosome for translation. While there are also associated proteins helping
to make up the functional units of the ribosome, in general, in bacteria, the SSU is coded for
by the the 16S rRNA gene, and the LSU is coded for by the 23S rRNA & 5S rRNA genes.
Why is it Used?
The 16S rRNA gene is a commonly used tool for identifying bacteria for several reasons.
First, traditional characterization depended upon phenotypic traits like gram positive or gram
negative, bacillus or coccus, etc. Taxonomists today consider analysis of an organism's DNA
more reliable than classification based solely on phenotypes. Secondly, researchers may, for a
number of reasons, want to identify or classify only the bacteria within a given environmental
or medical sample. While there is a homologous gene in eukaryotes, the 18S rRNA gene, it
is distinct, thereby rendering the 16S rRNA gene a useful tool for extracting and identifying
bacteria as separate from plant, animal, fungal, and protist DNA within the same sample.
Thirdly, the 16S rRNA gene is relatively short at 1.5 kb, making it faster and cheaper to
sequence than many other unique bacterial genes.
How is it Used?
Ribosomes (and correspondingly the DNA that codes for them) have been mostly conserved
over time, meaning that their structure has changed very little over time due to their important
function, translating mRNA into proteins. But even within this gene there are parts that have
been conserved more than others. This is due to the structure of the ribosome itself. With
the way the ribosome folds, creating bonds with itself in some places (conserved regions)
while other portions are looped and unbonded (hypervariable regions), the degree to which
any portion of the gene is subject to mutations varies.
Cho em hi v sao dng trnh t DNA trn RNA riboxom xc
nh cy pht sinh loi?
Hin nay ngi ta thng s dng phng php trong sinh hc phn t xy dng cy pht
sinh loi, y l cn c hin i gip so snh s tin ha trong t nhin v trong rRNA c mt
s trnh t c tnh bo tn cao. Nguyn l ca vic xy dng cy pht sinh loi l da vo
nhng thay i( t bin) trn vng bo tn ca rRNA. K thut ny c th m t n gin
nh sau:
Ly rRNA( c th RNA ny c ngun gc t nhn, ti th hoc lc lp) ---> gii trnh t cc
tiu phn ca ribosome ny( thng l 26S)--> dng my tnh so snh cc trnh t ny --->
xy dng cy pht sinh loi.
Bn c th tm cc thng tin trn google da trn nhng t kha: phylogeny, identification...

tm hiu quan h tin ha gia cc loi, ngi ta thng dng cy pht sinh loi phn t
(molecular phylogenic tree), c th l cn c vo mt trnh t kh bo tn cc loi (hoc
gia cc loi trong cng mt chi - genus). Trnh t ny tuy bo tn nhng vn phi p ng
yu cu l c s a dng nht nh, ng thi phi c di va phi , nhng vn cha ng
thng tin. Thng thng, ngi ta dng trc tip trnh t rDNA ch khng phi l rRNA
(tiu phn 16S i vi prokarotes; 18, 26 hoc 28S i vi eukaryote). rDNA ngha l DNA
(nm trn genome) m ha cho rRNA (ribosomal RNA), khuch i trnh t ny v gii m
(sequencing), sau xy dng cy pht sinh loi phn t da trn kt qu gii trnh t.
Khng phi l dng trnh t DNA trn RNA riboxom ( l RNA th lm sao c trnh t DNA
c). Ngi ta s dng phng php phn tch trnh t nucleotit trn RNA riboxom xc
nh cy pht sinh loi do cc trnh t ny c tnh c th rt cao, t b bin i trong qu
trnh pht sinh ca loi.

Metagenomics cho php chng ta nghin cu cc vi sinh vt bng cch gii m thng tin di
truyn ca chng t DNA m c trch rt trc tip t cc cng ng ca cc vi sinh vt
mi trng, do tng bc vt qua s cn thit ca vic phn lp hay nui cy. Mn hc
ny c xy dng trn nhng thnh cng ca cc cuc nghin cu 16S rRNA cc mu mi
trng nui cy c lp (Olsen, Lane et al., 1986). N cung cp nhng hiu bit v lch s
tin ha cng nh cc kh nng cha bit t trc ca cng ng vi sinh vt chuyn sng
trong mi trng. l, cc cu hi sau c th c gii p vi sinh vt no ?, vi sinh
vt ang lm g? v vi sinh vt hot ng nh th no?. Kt qu phong ph ca gene v
cu trc phn t c gii m t cc vi sinh vt ko nui cy c c tim nng to ln trong
s pht trin cht xc tc sinh hc (biocatalysts) mi cho ng dng cng nghip v dc
phm.
Metagenomics l vic gii trnh t v phn tch DNA ca cc vi sinh vt ly t mi trng
m khng cn nui cy chng. Metagenomics cn c bit n nh l "h gene cng ng"
hay "h gene mi trng".

Hin nay, chng ta c rt t thng tin v i a s cc vi sinh vt hin din trong cc mi
trng khc nhau trn tri t, ch yu l do chng ta khng th nui cy chng trong phng
th nghim - ngi ta c lng c rng, di 1% ca tt c cc loi vi khun c nui
cy. Trong thi gian qua, chng ta khng nui cy cc vi sinh vt c l do thiu kin thc
v sinh l hc ca chng v cc tn hiu mi trng m da vo chng ta c th thit k
mi trng nui cy ph hp, tuy nhin cc cng ngh nui cy mi bt u gii quyt nhng
vn ny (Zengler, Walcher et al., 2005). Tuy nhin, hu ht tri thc ca chng ta c thu
lm t mt phn nh vi sinh vt c phn lp. N ging nh, nu ngi ngoi hnh tinh h
cnh lc a Antarctica v thc hin nghin cu v chim cnh ct, v coi nh l i din
y cho ton b sinh vt trn tri t.
Mt s mc tiu c th ca d n metagenomics c th gm:

Xc nh tnh a dng phn loi s dng 16S rRNA v cc mu gene a dng v cy phn
loi ca vi sinh vt c th c s dng theo di v d on cc iu kin v bin i mi
trng.
Xc nh gene hay operon cho cc ng vin enzyme cn thit (nh cellulases, chitinases,
lipases, thuc khng sinh, cc sn phm t nhin khc); nhng enzyme ny c th c ng
dng trong cng nghip hoc dc phm.
Xc nh bin th hoc a dng trong gen cho cc enzyme quan trng, gip xc nh hoc
thit k ti u cc cht xc tc.
Xc nh cc c ch bi tit, iu ha v truyn tn hiu ca cc mu hoc cc gene quan tm.
Bit c cch cc c ch ny c t chc v iu ha gip nng cao cc hot tnh enzyme.
Xc nh cc h thng vn chuyn (transporter systems) - chng ta c th d on g v cc
ngun thc n hoc cc cht m c th bt gp trong mi trng?
Xc nh vi khun hoc cc trnh t plasmid. Nhng kh nng nh hng n s a dng v
cu trc ca cc cng ng vi sinh vt.
Xc nh cc s kin chuyn giao gene mun tim nng. Hiu bit v tnh mm do ca
genome c th cho chng ta mt tng v cc p lc chn lc gene v s tin ha trong
mi trng sng.
Xc nh gene/operons cho vic thu thp dinh dng, t kch thch (nhm cm nhn), trung
tm trao i cht trung gian, iu ny c th cung cp nhng hiu bit cho tng tc
syntrophic hoc khm ph nn tng thnh cng ca vi sinh vt trong mi trng ca chng.
Xc nh con ng trao i cht. S hiu bit r rng v con ng trao i cht c th dn
ti hng tip cn thit k mi trng nui cy tng trng cho cc loi vi sinh vt cha th
nui cy c.
Xc nh cc gene chim u th trong mt mi trng nht nh so vi nhng gene khc.
Nhn dng c cc gene c trng trong mt mi trng c th gip ch cho vic pht trin
cc phng thc tm hiu cc qu trnh, tng tc v phn ng ca cng ng vi sinh vt.
Cui cng, d liu v siu d liu metagenomics c th c tn dng thit k cc th
nghim thng lng cao v thng lng thp, cc th nghim ny tp trung vo vic xc nh
vai tr ca cc gene v cc vi sinh vt trong vic thnh lp cng ng vi sinh vt ng.