Hello.
I'm Bob Leske of Johns Hopkins.
We will examine the bacterial genome in
this short lecture.
Be sure to focus on the polycistronic
nature of some transcripts.
Unlike eukaryotes, most bacteria have a
single chromosome.
And in most but not all cases, that
chromosome is circular.
Polycistronic is an important term,
meaning that there can be
more than one protein coding reagent on an
mRNA transcript.
Examining that transcript more closely.
You will find two untranslated regions
that are not protein coated.
Those come at either end of the sequence.
We will look at the lactose operon, made
famous by Jacob and Monod in the 1960s.
And then to bring it back to
bioinformatics, we will look to
identify operons on an NCBI sequence
record and on a gene prediction.
[bbb] First, let's be aware that bacteria
tend to have much smaller genomes than
eukaryotes.
Escherichia coli or what we call E.
coli has a 4.6 megabase genome.
That's 4.6 million base pairs.
One of the simplest eukaryotes budding
yeast has a genome of 12.1 megabases.
Almost three times the size of E coli.
And that's a very small eukaryotic genome.
The human genome is 3.2 gigabases.
That's 3.3 billion based pairs.
And that's not even the largest genome.
Some plants are even bigger in genome size
than humans.
Bacteria usually had a single circular
chromosome.
There are exceptions.
Many also have extrachromosomal plasmids.
Those are small, usually circular pieces
of additional DNA.
Here's a site map of the E coli genome.
Look at the top where you see a zero.
The 0 position represents what's called
the origin of replication.
Then the numbers increase clockwise and
there
are about 4 million 600 thousand or so.
Now
remember, there are still two strands of
DNA.
What we call the plus strand is arranged
in this diagram, clockwise.
However, there are genes on the minus or
complimentary strand and they run in the
other direction.
So, I've mentioned polycistronic.
In eukaryotes, the final splice mRNA
usually only has one protein coding
region.
That means that only one protein is
derived from the mRNA.
Actually many copies of that same single
protein.
In bacteria, while mRNA splicing usually
does not occur.
There are often, but not always, more than
one protein coding region in a prokaryotic
mRNA.
If say, an mRNA has five protein coding
regions, then
translation makes many molecules of each
of those five proteins.
And here's what it looks like.
The diagram's a bit fuzzy but it displays
the concept well.
Prokaryote is at the top and the eukaryote
is at the bottom.
Prokaryotes tend to do it this way for
efficiency.
Here is a similar diagram.
But you can see the untranslated regions
or UTRs at either end.
The one at the left of the mRNA is called
the 5' UTR.
The 5' refers to the chemistry of which
carbon that phosphate attaches to on the
sugar.
Or to put it in another way, protein
sequences go from N terminus to C
terminus.
DNA and RNA sequences go from 5' to 3',
and both involve chemistry.
The 5' UTR is everything to the left of
the first AUG start codon.
The 3' UTR is on the right.
It's everything that is untranslated after
the stop codon.
Both UTRs are found in eukaryotes as well.
So, from left to right on a bacterial
mRNA, you have a 5' UTR.
One or more codon regions then a 3' UTR.
Here is the well-studied lactose operon.
Bacteria prefer glucose as an energy
source, but if there
is no glucose to be found they'll deal
with lactose.
So they have to find away to turn on the
genes involved in lactose synthesis.
This describes some complex regulation and
shows what's called the
regulatory region of the gene, or in this
case the operon.
That's the term for the multiple genes on
a single mRNA.
Look primarily at the numbers below the
first graphic.
The +1 position is called the
transcription start site.
That is no the start codon.
It is the start of the mRNA, transcription
not translation.
The mRNA is to the right of that +1
position.
Or think of it this way.
+1 refers to the beginning of the 5' UTR
of the mRNA.
The region to the left of the +1 is called
the regulatory region.
Here is where proteins bind that help
control the level of transcription.
A need for lactose digestion ultimately
determines whether if
the transcription of the lactose enzymes
is on or off.
The direction to the left, or to the 5'
side, is frequently called upstream.
The minus 35 position, is 35 bases
upstream of the transcription start site.
And to the right or to the 3' side is
called downstream.
In prokaryotes, you can have a single mRNA
that contains more than one coding region.
That would be very rare in eukaryotes, but
very common in bacteria and archaea.
This operon goes from position 70 to 6338.
The
mRNA would be larger since it would
include the untranslated regions of the
mRNA that come before the start codon and
after the last dot codon.
If you look at the annotation, you will
see that this operon has four CDS regions.
[bbb].
Here is an output for
fgenesb@softberry.com.
This is explained in a separate video on
bacterial gene prediction.
Note that there are four transcription
units, meaning that
four mRNAs come out of this region of
genomic DNA.
Of those four transcription unit, two are
operons, which
each have more than one CDS on that mRNA.
The first mRNA.
Has three CDS regions, Op 1, Op 2, and Op
3.
Next are two single CDS transcription
units, Tu 1and Tu 1.
Why not Tu 2?
That would imply a second CDS on an mRNA,
that's how that numbering works.
The last mRNA has 2 CDS regions, Op 1 and
Op 2.
Hopefully that explains the notation.
To
summarize, bacteria usually has circular
genomes.
Eukaryotes tend to have linear chromosomes
and more than one.
With prokaryotic genes, you don't have to
deal with the splicing issue, usually.
However, one complication is that multiple
coding
reagents often occur on a bacterial mRNA
transcript.
Finally, why do it this way?
Bacteria waste little space in their
genome.
Efficiency allows for genes in a certain
pathway to be transcribed onto one
mRNA molecule so that all necessary
enzymes can be translated into one shot.
That's it for now.