Transcription in Prokaryotes - Online Tutor, Practice Problems & Exam Prep

Prokaryotic transcription begins with the initiation phase, where RNA polymerase holoenzyme binds to consensus promoter sequences, including the Pribnow box. The sigma factor within the holoenzyme ensures specificity for different RNA types. Transcription elongates within a transcription bubble until a termination sequence signals the end. Prokaryotes can produce polycistronic mRNA, containing multiple genes, requiring further processing into individual mRNAs. Key terminators include rho-dependent and rho-independent types, with intrinsic termination occurring less frequently due to weak uracil bonds. Understanding these processes is crucial for grasping gene expression in prokaryotes.

Prokaryotic Transcription

Hi. In this video, we're going to be talking about prokaryotic transcription. So prokaryotic transcription is different or differs from eukaryotic transcription. They're similar in a lot of ways, but there are important differences. So, first, let's talk about the first step of transcription, which is always initiation. Now, prokaryotic transcription initiation requires certain factors, of course. One of these factors is called a promoter, and this promoter is actually a DNA sequence, and this lies upstream of the transcription start site. Remember, before the gene, and it's a DNA sequence that signals for transcription start. And how it signals is because it recruits proteins to that area that will trigger transcription initiation. So we call the promoter sequence in prokaryotes consensus sequences. This means that they're not the exact same. They're not conserved sequences, meaning that it's pretty much the same sequence across many different organisms, but consensus sequence just means that they're similar. They're not exact, they're not even close enough to be exact, but they're pretty similar across many different prokaryotic species. So promoters in prokaryotes are consensus sequences, and this is one major difference because in eukaryotic transcription that's not the case. Now, one of these sequences that acts as a promoter is called the prim now box, or sometimes you don't see it as this, but you see it as just the 10 base pair sequence, because it lies 10 base pairs upstream of the transcription start site. So this is the sequence here, you don't necessarily need to know that, but just know that the prim prim prim now box, lies 10 base pairs upstream of the start site and is a very common prokaryotic promoter. Now, in addition to the prim Now box, there's another 35 base pair consensus sequence that doesn't necessarily have a fancy name but is also present. So you have one at the 10 base pair and one at the 35 base pair upstream. And then, occasionally, you get another sequence that is 40 to 60 base pairs upstream. And I write notice here that I'm writing this as negative 40, negative 60. That suggests that it's upstream of the sequence. So here are the 3 potential promoters. These 2 are very commonly here, and this one is mainly optional; it's occasionally there. Now you have these promoters, so what comes in, I said proteins come in and bind to the promoter. Well, what this is called is called the RNA polymerase holoenzyme, and the holoenzyme just means that it has the region of the protein that's going to catalyze the reaction, so the catalytic core, the enzyme is doing its job, but it also has other factors as well. So the RNA polymerase holoenzyme for prokaryotes has the core enzyme, which is going to be doing the transcription part, but it also has an important factor called the sigma factor. And the sigma factor is a short peptide sequence, and this controls specificity. So RNA polymerase in prokaryotes transcribes all RNA. And so, in order to specify what type is needed, whether ribosomes are needed or whether this is being used for protein synthesis, The part that controls that is the sigma factor, and the sigma factor is kind of just this exchangeable factor. So there are many different types of sigma factors, and each one is specific for a different type of RNA. And so whenever the cell needs to transcribe, say, ribosomal RNA, it brings in the appropriate sigma factor. If it needs to transcribe protein or transcribe RNA that will be used for protein, it brings in the appropriate sigma factor. And so the sigma factor is important for specificity, what RNA is actually being transcribed. So if we look at this, here's initiation of transcription. Remember, we have a DNA double helix. We have the RNA factor or RNA polymerase, and the sigma factor is inside, and that can be exchanged, depending on the RNA that needs to be transcribed. And although it's written here in a really horrible yellow color, I don't know who made this image, but the yellow represents the promoter. So you can see the RNA polymerase is coming, it's binding this promoter, and this will initiate transcription. So after transcription is initiated, what happens is the transcript has to be elongated, so that occurs after initiation, and the region that's being transcribed at the time is called the transcription bubble. This is a short sequence of DNA. It's around 18 nucleotides long, and this is what's actively being transcribed. So only about 8 nucleotides are being transcribed at any given moment, but you need 10 more to fit the proteins that are being associated, the RNA polymerase, the sigma factor, the unwound DNA, so it creates this light bubble that's a transcription where transcription is occurring or about to occur or have just occurred, and we call that bubble the transcription bubble. Now, the transcription bubble continues along the whole way. Right? It transcribes the DNA until it reaches a certain, sequence, and that sequence is where termination occurs. So, there are many different types of sequences, and the sequence is called the termination sequence, also called the terminator, depending on the book that you use. I like terminator just because it sounds real fancy, but essentially it's just a DNA sequence that says, hey, stop here, and, it's found upstream of where it's actually terminated, and the termination sequence signals for proteins to come in and help terminate it. So it's not going to terminate it there, right? Because that would get rid of the sequence and it needs that sequence. It terminates it sort of, downstream, of that sequence. Now there are different types of proteins that come in to help terminate. There are some called the rho dependent terminators. You may also see rho written in fancy way, but essentially it's pronounced rho. And this, terminates the transcript in the presence of a rho protein. Then, of course, there's rho independent terminators and do it in the absence of the rho protein, and then there's this fancy type these are the 2 most common, and then there's this fancy type called intrinsic termination, and this happens, much more rarely, but what happens is that you have an RNA with a bunch of uracil in it, and uracil is not, you know, in DNA, a binds with t. It doesn't bind with u. So if you have a transcript that has a bunch of uracils, you have a binding with u on the template strand, and that bond is weak. It's definitely not as weak as the a t pair. So a is u, it's weak. So what happens is that RNA polymerase, these this transcript have a bunch of uracils, these are weak bonds, and it can cause disassociation of that transcript and the RNA polymerase and result in transcript termination. Now, oftentimes that happens, it's too early and it shouldn't be happening like that, but sometimes it happens when it's supposed to. But again, like I said, the intrinsic termination is more rare than the rho dependent or rho independent terminators. Now, finally, let's talk about this last little bit, and this is very important, because this is a big difference between prokaryotic and eukaryotic transcription. So prokaryotic transcription can result in polycistronic mRNA. What polycistronic mRNA is, it's actually RNA that has a group of genes. So there's been, there's DNA, there's a group of genes in order, and all of it has been transcribed into RNA in a single strand, instead of each RNA represents each gene. So you have a single RNA and it has 4, 5, 10, 15, 50 genes on it, and this means that there is only one terminator and that was present at the end of the group of genes. So the RNA polymerase just kept transcribing, kept transcribing until it reached the terminator, and that happened to be after a few genes were already present. And so the prokaryotic, this doesn't happen in eukaryotic transcription, but in prokaryotic transcription, that means that the RNA that's produced has to be processed further so that each gene is cut out individually, processed into individual genes and individual proteins instead of just one long mRNA transcript or polycistronic mRNA that contains multiple genes. So here we have an example, we have initiation, which I showed you before. You have your RNA polymerase, your sigma factor binding to your promoter. Then you have your transcription bubble as it's being transcribed. Remember, this is the 5 prime end and the 3 prime end is over here. And, because this is, because it's, yeah, 3 prime and 5 prime because it's doing the RNA strand as the template sequence, and then there's some type of termination sequence here in green. And so when the RNA polymerase actually reaches this sequence, it dissociates, the sigma factor dissociates, and now you have, mRNA. And sometimes this mRNA, if it's polycistronic mRNA, can contain multiple genes on it, but here there are 3, and each one will have to be processed so that they eventually become separate mRNAs and separate proteins. So that is prokaryotic transcription, let's now move on.

Which of the following is not an example of a prokaryotic promoter sequence?

• A. TATA Box
• B. Pribnow Box
• C. 35bp consensus sequence
• D. -40-60 upstream consensus sequence

What is the purpose of a sigma factor in prokaryotic transcription?

• A. The sigma factor serves as a transcription initiator sequence
• B. The sigma factor controls the specificity of the polymerase
• C. The sigma factor forms the transcription bubble
• D. The sigma factor controls transcription termination

Prokaryotic transcription can create polycistronic mRNA.

• A. True
• B. False

Here’s what students ask on this topic:

What is the role of the sigma factor in prokaryotic transcription?

The sigma factor is a crucial component of the RNA polymerase holoenzyme in prokaryotic transcription. It is a short peptide sequence that ensures the specificity of transcription. The sigma factor helps the RNA polymerase recognize and bind to the promoter regions of DNA, initiating transcription. Different sigma factors are specific to different types of RNA, such as ribosomal RNA or mRNA for protein synthesis. This specificity allows the cell to transcribe the appropriate type of RNA needed at any given time. Once transcription is initiated, the sigma factor can be exchanged for another, depending on the RNA type required.

What are consensus sequences in prokaryotic transcription?

Consensus sequences in prokaryotic transcription are DNA sequences that are similar but not identical across different prokaryotic species. These sequences act as promoters, signaling the start of transcription. The most common consensus sequences include the Pribnow box, located 10 base pairs upstream of the transcription start site, and another sequence located 35 base pairs upstream. Occasionally, a sequence 40 to 60 base pairs upstream may also act as a promoter. These sequences recruit proteins, including the RNA polymerase holoenzyme, to initiate transcription.

What is the transcription bubble in prokaryotic transcription?

The transcription bubble is a region of unwound DNA where active transcription occurs. It is approximately 18 nucleotides long, with about 8 nucleotides being transcribed at any given moment. The transcription bubble forms as the RNA polymerase moves along the DNA, separating the strands to allow RNA synthesis. This bubble contains the RNA polymerase, the sigma factor, and the unwound DNA, facilitating the elongation of the RNA transcript until a termination sequence is reached.

What is polycistronic mRNA in prokaryotic transcription?

Polycistronic mRNA is a type of mRNA found in prokaryotes that contains multiple genes within a single RNA molecule. This occurs because prokaryotic transcription can transcribe a group of genes in one continuous strand of RNA. The resulting polycistronic mRNA must be further processed to separate the individual genes into distinct mRNAs, each coding for a specific protein. This is a significant difference from eukaryotic transcription, where each mRNA typically corresponds to a single gene.

What are the different types of termination sequences in prokaryotic transcription?

In prokaryotic transcription, termination sequences signal the end of transcription. There are several types of termination sequences: rho-dependent terminators, which require the rho protein to terminate transcription; rho-independent terminators, which do not require the rho protein; and intrinsic terminators, which involve weak uracil bonds in the RNA causing disassociation. Rho-dependent and rho-independent terminators are the most common, while intrinsic termination is less frequent but can occur when the RNA transcript contains a series of uracil residues.