Molecular Biology Gene Regulation in Prokaryotes

Hello, and welcome back to www.educator.com.0000

Today, we are going to talk about gene regulation in prokaryotes.0003

As an overview, we will first talk about transcription and regulation.0009

And then, we will move into the regulation of translation.0014

We are going to focus mainly on transcription and regulation because that is most often where gene regulation occurs.0017

We will talk about bacterial operons.0023

We will focus on two of the most popular ones taught in many university classes which is the lactose operon and the tryptophan operon.0026

And then, I will talk to you about the virus bacteriophage λ.0035

We will talk about its lytic or lysogenic growth phases.0039

Finally, as I said, we will talk about the regulation or translation.0044

What is gene regulation?0051

It is the regulation of the amount of RNA that is made from each individual gene DNA sequence.0053

This is transcriptional regulation.0062

This is often tied in the amount of protein that is produced from that gene.0066

Usually, if you decrease the amount of mRNA made, you will decrease the overall amount of protein that can be made.0069

Regulatory proteins control our gene expression.0078

Most of that regulation occurs at the step of the initiation of transcription.0082

That is important.0088

Example, you could increase or decrease the binding ability of the RNA polymerase to its gene promoters.0094

Regulation can also occur during the elongation or termination steps on transcription, as well as during translation.0103

Let us jump right in, the bacterial operons.0120

What is an operon?0123

It is a functional unit of DNA that contains several genes, all under the control of a single promoter.0125

This is important, several genes all under the control of a single promoter.0135

That means all genes will be transcribed in equal quantities.0144

The first operon we are going to talk about, the lac operon or the lactose operon.0149

This is found in E. coli.0154

The whole purpose is to metabolize lactose.0156

This particular operon is regulated at the initiation step of transcription.0169

This is very common.0176

There are three genes contained in this operon, lacZ, lacY, and lacA.0178

It is what is called an enduciple system, meaning there is little or no transcription.0185

It can be induced to have high transcription.0197

When there is high lactose concentration, there will be high transcription.0200

If there is no lactose concentration, there will be no transcription.0206

Let us draw this out, what does it look like?0213

First of all, what does an operon look like?0217

We are not even specific, we are going to talk about the lactose one yet.0219

What is an operon look like, let us see.0222

If we check out our DNA, 5 prime, 3 prime.0225

We will say we have 4 genes here, the A gene and the B gene, the C gene and the D gene, all under a single promoter.0236

If we make the mRNA from that, we have what is called the polycistronic gene.0253

It is multiple genes on same mRNA.0263

We have our A, B, C, D genes.0267

What we have here is that, this is a fixed ratio of A to B to C to D because it is all under the control of the same gene promoter.0275

What this will make is then, for example, what this will make is protein A, protein B, protein C, and protein D.0294

Usually, what makes an operon is that all of the genes under the control of the single promoter, act together in a certain way.0337

They act in concert.0346

An example of that would be turning, let us say, we have substrate.0347

Let us go purple.0360

Protein A might work on substrate 1.0368

Protein A might be responsible for turning substrate 1 into substrate 2.0388

And then, protein B would be responsible for turning substrate 2 into 3, protein C, 3 into 4.0406

Protein D, 4 into 5.0414

What this entire operon does, what the entire operon does is turn substrate 1 into the final product of whatever product 5 is.0416

This is the ultimate goal of this entire operon.0429

It works in concert to do that.0434

Back to our specifics, let us look at the lac operon again.0438

We have the 3 genes, lacZ, that is going to encode an enzyme named β galactosidase.0442

That is the enzyme that cleaves lactose which is a disaccharide, into glucose and galactose, two monosaccharide.0451

We then have lacy which encodes lactose permeates,0460

that is a membrane protein responsible for allowing lactose to get into the cell.0465

It allows you to get from the outside to the inside.0473

And then, we have lacA encoding an enzyme called galactoside O acetyl transferase.0476

That is an enzyme involved in detoxification of the cell.0484

Also part of the lac operon is an upstream gene, it is not under the same promoter.0488

It is not being made in equal quantities of lacZ, Y, and A, in the normal thing.0495

LacI is our upstream gene that encodes a repressor protein, a transcription or repressor protein.0501

What this will do, it all bind lactose, if lactose is available.0508

Otherwise, it will bind the operator DNA sequence.0514

If this repressor binds the operator sequent, there is no transcription.0517

Basically, if lactose is available, the repressor is binding lactose and not the DNA operator.0525

Therefore, the operon is active.0533

Let us draw out this lac operon.0539

What is it look like, let us look at the DNA.0544

This is a way just to show that there is a lot of distance in the DNA.0571

It does not necessarily have to be very close.0575

This is the +1 site shown right here.0609

What we can make from that is our mRNA.0616

Our mRNA will have our lacZ, our lacY, and our lacA.0632

Right here, lacI, that is our repressor.0643

Cap, that is our cap binding sequence.0645

P is the promoter, always the operator.0649

Lac Z, Y, and A are our lac operon.0653

In times of high lactose, we will just write this out here.0659

We have high transcription.0671

In times of no lactose, we have no transcription.0676

For the promoter to be active, the cap protein must bind the cap DNA sequence.0689

For cap to bind, CAMP, cyclic AMP needs to be bound to the cap protein.0710

If there is no CAMP, then we have no cap DNA binding which means we have no transcription.0729

What is important is that, I will show you with the star.0761

As your glucose concentration increases, CAMP concentration decreases.0767

And that is going to lead to lower transcription.0798

Where does glucose come into play?0807

Remember, glucose is a breakdown product of lactose.0810

If I write this down here, lactose gets broken down by β galactosidase into glucose and galactose.0815

Glucose, in fact, blocks an enzyme called adenylyl cyclase.0843

That enzyme is responsible for turning ATP into CAMP.0864

As glucose concentration goes up, we block more of the enzyme that turned CAMP, that turns ATP into CAMP.0877

Therefore, as glucose concentration goes up, CAMP concentration goes down.0887

We see that CAMP needs to bind the cap protein, for the cap protein to bind the DNA sequence.0891

The cap protein is bind the DNA sequence, for transcription to occur.0902

It is all interrelated.0906

This is all important, we also know that lacI, the repressor protein that would be made,0910

normally binds the operator sequence right here, which will turn off transcription.0917

We do not get any mRNA, this is all blocked off, we would not do that.0923

If there is a bunch of lactose present, that lacI will actually bind the lactose,0932

therefore, freeing up the operator on so that transcription can occur.0939

There are couple caveats to this that I want to point out about the operator.0948

If the DNA sequence is mutated, then the repressor lacI cannot bind,0953

no matter what the lactose concentration in the cell is.0961

If the operator sequence is mutated and lacI cannot bind no matter what,0965

this is what would be called constitutively active or on, meaning high transcription.0970

That is if operator sequence is muted.0993

Another thing that can be altered is that, if the lacI gene is mutated,1007

then it does not matter how much lactose is present because the lacI gene would not be able to bind the operator sequence.1022

Therefore, we have the same result as up here, constitutively on, leading to high transcription.1037

These obviously are not under normal circumstances, that is when we have a mutation.1049

But this is just a couple other ways to see how this lac operon can be regulated or actually lose regulation.1057

Our second bacterial operon that we are going to talk about today is the tryptophan operon or the trp operon.1069

This is also found in E. coli, its purpose is to produce tryptophan from chrismic acid.1076

It is also regulated at the initiation step of transcription.1083

This one contains 5 genes instead of 3 and it is derepressible,1088

meaning that it is normally in a repressed state and you can take that repression off.1093

If you have very low tryptophan concentration around, this will become active because you are going to want to produce tryptophan.1100

Let us draw out the trp operon.1113

It has its own version of a repressor, that is upstream.1131

We have the promoter, we have the operator.1136

We have these reasons called 1, 2, 3, and 4 which are part of in attenuation region.1139

Then, we jump into the operon trp-E, trp-D, trp-C, trp-B, trp-A, obviously more DNA.1148

What does our mRNA look like?1170

The +1 site is right here.1174

We can get two different mRNAs.1178

This right here, remember, I said was called the attenuation region.1183

This will affect whether we get a small mRNA or a large mRNA.1190

And that will be due to the fact that, one thing I want to point out is that all of these are inverted repeats.1196

A thing about inverted repeat, they can bind to each other, causing intramolecular base pairing.1210

Another thing I want to point out is that sequence 1 contains 14 codons, 2 of which are tryptophan.1216

That is called the attenuation region.1238

First things first, we have our mRNA.1252

Here is our 5 prime, we have all the way through.1262

We have trp-B, trp-D, trp-C, trp-E, trp-A.1271

We will get this transcript, this is called an mRNA variant.1291

This one, when we have low tryptophan concentration.1296

When we have low tryptophan concentration, we get this.1307

The reason being, what happens is that we actually get this attenuation region looking like this.1310

We have 1, 2, 3, 4.1331

What this is, we call it a tennis racket or whatever you may want to call it.1342

We have intramolecular base pairing between region 2 and region 3.1347

Because we have low tryptophan, we are having this intramolecular base pairing between 2 and 3.1352

This leads to a ρ-dependent termination.1362

This mRNA is over 6,000 bases long and we know it is poly cystronic because it has all these genes.1374

There is the other variant that can be made when we have high tryptophan.1388

It will end here.1417

It is actually only 139 bases long.1419

This right here is the +139, right there is the +161 spot.1429

This will end up making a 34 hairpin.1442

Here I forgot to write out here.1455

What we have is EDCPA.1456

This is what we call the attenuated version.1481

This would undergo low independent termination.1484

This right here, this type of hairpin between the 3 and 4 actually causes the mRNA to pull out of the RNA polymerase.1494

It pulls it off the DNA resulting into an attenuated or shortened mRNA.1507

Whereas, the one up here, the hairpin between the 2 and 3 region is ρ-dependent.1512

It would not pull out until the ρ factor comes, after recognizing the stop sequence at the end of the mRNA.1518

That is the difference here.1526

When we have low trp, you have a 2 and 3 hairpin that allows you to transcribe all the way through to the end of the sequence.1527

We have high tryptophan concentration, you have a 3 -4 hairpin, up here in these attenuation regions,1538

which causes ρ-independent release of that mRNA.1545

In an attenuated, only 139 base mRNA.1549

One thing is important to mention is that, when we have this high tryptophan concentration,1556

the repressor will bind the operator sequence leading to no transcription.1565

Up here, when we have low tryptophan concentration,1576

the repressor does not bind the operator sequence which leads to transcription.1581

One thing to point out, remember, I said in this one sequence right here in the attenuation region,1594

it contains two tryptophan codons.1601

If you have absolutely 0 tryptophan, the ribosome will stall at that attenuation sequence 1 because it has 2 trp codons.1605

If you cannot put in trp right there, the ribosome cannot continue on synthesizing new protein.1634

This attenuation is a way to regulate gene transcription, about 8 to 10 fold.1644

You can do repression using that repressor protein gives you regulation about 70 fold.1654

Attenuation and regulation together can give you overall gene regulation, anywhere from around 600 folds.1659

These are just different ways between the lac operon and the trp operon of regulating gene expression.1667

In two completely different ways, even though they are both regulating at the same part of transcription which is the initiation.1674

Let us move away from our bacterial operons and let us switch gears to looking at how a virus works through its life cycle.1694

We have bacteriophage λ and that is a virus.1705

It infects the bacterium E. coli.1709

It has what is called a temperate lifecycle.1712

It can either be lysogenic which means its DNA genome.1714

Here is an example of a bacteriophage, it will latch onto an E. coli cell, this is E. coli with E. coli’s chromosome,1721

we will just say that.1736

The lambdaphage will shoot or inject its DNA into the E. coli.1739

It will make a circularized genome inside the E. coli.1748

This is the λ DNA.1753

There are two things that can be done.1761

Either this DNA can integrate into the host genome, becoming one with the E. coli DNA.1763

It can just stay there dormant or silent, kind of just outside of you.1773

Or the lambdaphage can just replicate its genome separately, over and over again.1778

Hijacking the E. coli cell machinery, making many new viruses.1789

It will just twice the bacterial cell and which in fact kills it and release more viruses to the environment.1795

In which case, those can do the same thing.1804

They can be infecting more E. coli.1806

Based on what they want to do, they can either integrate with the genome for lysogeny.1813

Or they can just hijack the cell machinery and use it to produce more viruses and lies the E. coli.1817

This is how the bacteriophage can affectively regulate its transcription to do one or the other.1825

Let us draw it out, it is a complex process.1835

I’m only going to draw out a simple part of it.1838

We are going to look here.1841

This would be the DNA of lamdaphage.1848

This is the λ DNA.1896

There is much more to it, we are just going to focus on this.1902

Right here, I’m just going to write it on then I will explain it.1908

Remember, this is DNA.1916

The cro protein than can be made from the cro DNA sequence will bind at this spot.1918

When cro binds here, this PL PRM PR PRE, those are all promoters and that is why they have their directionality.1937

It is which way they will promote transcription.1954

We have 3 of them pointing in the leftward direction.1957

Just PR pointing in the right direction.1959

If cro binds this region, this all of our 3 region, then that will block the PRM promoter.1961

This will lead to PR and PL, PR right here and PL.1977

They will be the promoters in charge of transcription.1991

This will lead to lysis of the bacterial cell.1996

C1 which is a protein that can be made from this DNA sequence, will bind to this sequence.2015

If C1 binds, the PR promoter is blocked.2034

And then, we will have PRN being the one that is transcribing.2045

This will lead to lysogeny, entering into the bacterial DNA.2058

Why would this occur?2075

This is important, I will write it with a star.2078

C1 concentration must be kept high to stay in lysogenic phase.2086

How it does that is, we have the pre-promoter helping out in this, helps keep C1 concentration high.2111

C1 is under control of this pre-promoter.2145

Basically, if the pre-promoter is active, C1 is produced quite highly.2150

If C1 is produced, we have it binding to this spot, blocking the PR promoter, which keeps this PRM promoter active.2157

It allows you to stay hidden inside the E. coli cell.2169

If you do not have C1 been made very high, we have cro being mixed.2175

If you are not going in the leftward direction, the leftward direction is producing C1, the rightward direction, the PRM PL.2180

The rightward is making cro.2197

If you are going rightward, we have a lot of cro around, cro protein.2201

That is going to bind this one, blocking the PRM.2204

The PRM and PRE are going to help with the C1.2208

Therefore, this is going to end up going through a lysis phase.2212

It is going to end up just hijacking the cell machinery, killing the bacteria and exiting out.2215

If you do not regulate transcription and translation properly, then you are not going to be able to contain,2222

whether you are going through lysogeny or lysis.2231

Other than transcriptional regulation, DNA damage can play into this.2234

For example, if we have bacterial DNA damage that can actually shift you from lysogeny to the lytic phase.2242

How does it do that?2268

When you have damage, you have DNA gaps occurring.2269

DNA gaps are bound by recA, binding the single stranded DNA.2279

RecA gets activated to recA*.2293

RecA* causes auto cleavage of the C1 protein which leads to lysis.2312

Not just transcription regulation, but actually DNA damage can affect2342

whether you have the lytic lifecycle or the lysogenic lifecycle of the bacteriophage.2347

This is just separate from an operon but it is a very involved DNA sequence that goes through transcription and regulation.2355

Depending on which protein is found in higher quantity, C1 or cro will tell you2364

whether you are going through lysogenic phase for C1 or lysis phase for cro protein.2372

I briefly want to go over the fact that we can be regulated at translation.2384

What that is normally looking like is that you bind the RNA, by proteins near the site that the ribosome will normally bind.2389

Therefore, the ribosome cannot even bind the mRNA.2399

This does not allow the 30S ribosomal subunit to bind RNA.2405

Another way that you can regulate translation is if you have intramolecular base pairing of mRNA.2411

The mRNA itself could be hiding its normal ribosome binding site.2416

Maybe it is right here, but because it is base paired to itself, the ribosome cannot bind the mRNA.2424

There is also post-transcriptional regulation of rRNA folding via translation repression of the ribosomal protein synthesis.2434

Basically, if you have rRNAs not folded correctly, they cannot interact properly2446

with the proteins to make the nuclear protein that we know as the ribosome.2453

I’m not going to go in any one of these specifically, but these are all options and possibilities how you can regulate translation.2459

For the last slide, I want to give you an example of something that is actually pretty cool phenomenon.2470

We have this thing, this piece of nucleic acid called the ssraRNA.2477

This is a really important RNA found in prokaryotes, that can rescue ribosomes2486

that are translating broken mRNAs or an mRNA galactose stop codon.2493

This is really important because if we have a ribosome and it is translating the mRNA, this is our eukaryote or prokaryotic.2500

This is the 50S and the 30S to make the 70S ribosome.2520

If we have an mRNA that is stuck in a ribosome, the broken mRNA, it gets stuck in the ribosome.2526

That ribosome will continue to try to translate it.2533

It is basically not happening.2538

Basically, what this does is it takes that ribosome out of commission and tell that mRNA can be released.2541

The ribosome is no longer useful for translating any functional proteins.2552

Same thing that if an mRNA does not have a stop codon, that can be problematic.2558

Our ribosomes need to be fully functional.2564

If we are translating broken mRNA, the ribosome is basically going to stall there and wait until something can be fixed.2568

Since that normally does not happen, we have this special RNA coming in and it will rescue that.2576

It is what is called a tmRNA.2581

It is part tRNA, part mRNA.2585

It can be charged with an alanine amino acid.2588

What happens is, if it is stalled right here, this tmRNA can come into the A site.2593

It can be charged with an alanine.2605

It can come into the A site, allow translocation to go to that P site.2613

The ribosome will be going that way which means that this will go to the P site.2624

What it does is translocation is able to occur.2631

And then, it is followed by 10 codons and a stop codon.2634

The protein is coming out, maybe it is stalled right there.2638

But then, you have this tag that is added.2645

It is 10 then a stop codon.2651

This is a very important piece.2659

This acts as a tag that directs the destruction of the mRNA by the cellular proteases.2663

That directs the overall protein that was produced, not the mRNA.2672

That protein gets it to the prodiuzome and gets destroyed.2683

This is really important, it allows the mRNA to be released from the ribosome.2686

Now, the ribosome can pick up on another mRNA and be functional, making a functional protein on that.2693

As well as, this messed up protein that was made from a broken mRNA or an mRNA without a stop codon,2698

can then be just degraded and thrown away.2706

That it does not fold into a protein and maybe become a protein that screws everything up.2709

Maybe has a function that was unintended.2716

This is a pretty cool RNA feature and a protective feature that is found for translational regulation in prokaryotes.2720

I hope that you enjoyed the lecture today.2732

Thank you for being here at www.educator.com and I hope to see you again.2735