Regulation of Gene Expression in Prokaryotes

LMS is currently down (due to a lightning strike or something), so at first I thought that it'd be a good excuse to not study. But then someone pointed out to me that the app (Blackboard Mobile Learn) is still useable, so here I am.

Describe and give examples of positive and negative regulation of prokaryotic gene expression

I've done this before in two previous posts: The Lactose Operon and Positive Regulation of the Lactose Operon.

Describe and give examples of how some bacterial gene regulatory proteins can act as repressors or activators

Well, since nothing in the body likes to be simple, proteins can have different functions depending on where they bind and so forth. If a protein binds in a way that makes it harder for the polymerase to get to the gene, then the protein is acting as a repressor. If the protein binds in a way that facilitates the polymerase binding to the gene, then the protein is acting as an activator.

The bacteriophage lambda repressor is an example of a regulatory protein that can act as either a repressor or an activator (which is pretty confusing, given the name). Like other proteins, it can repress by preventing binding of RNA polymerase, or activate by facilitating binding of RNA polymerase.

Describe and give examples of the roles of alternative sigma factors in prokaryotic gene expression

I've mentioned sigma factors in an earlier post, but just a quick refresher: in prokaryotic cells such as E. coli, the core enzyme of RNA polymerase has five subunits, which a special protein known as sigma factor can bind to in order to form a holoenzyme (core enzyme plus sigma factor). Ultimately, it's sigma factor that helps the polymerase to bind to the promoter. The sigma factor dissociates soon after transcription has begun.

There are different sigma factors which recognise different promoters. This helps to coordinate transcription of different genes. The most common sigma factor is sigma 70. Another important sigma factor is sigma 54, which tends to bind to genes that have enhancer regions (i.e. activators far away from the transcription start site).

Describe and give examples of two-component regulatory systems in prokaryotes

A "two-component regulatory system" is, to my understanding, essentially the use of two components (a sensor and a response regulator) to regulate genes. The sensor protein senses a change in the environment, which causes it to react with the response regulator protein (usually by phosphorylation, but there are other ways), which in turn causes a gene to be activated or repressed. The functional domain of the sensor protein is called the transmitter domain, and it's responsible for phosphorylating or otherwise activating the response regulator. The functional domain of the response regulator protein is called the receiver domain, and it's the part that gets phosphorylated or whatever.

Example number 1: NtrB and NtrC. NtrB is a kinase (i.e. a protein that tacks phosphate groups onto other stuff) that is activated when glutamine levels are low. When glutamine levels are low, NtrB phosphorylates NtrC, which stimulates the transcription of the gln gene which codes for glutamine synthetase. Glutamine synthetase, as its name suggests, catalyses the synthesis of glutamine, restoring glutamine levels in the cell.

Example number 2: PhoR and PhoB. PhoR is a transmembrane protein which senses phosphate in the periplasmic space (i.e. between the inner and outer membranes). When phosphate levels in the periplasmic space is high, some of it binds to the periplasmic domain of PhoR, keeping it inactivated. When phosphate levels drop, however, phosphate dissociates from PhoR, activating it. PhoR then transfers a phosphate from ATP to PhoB, a protein in the cytosol. This activates PhoB, allowing it to act as a transcription factor for several genes.

Describe and give examples of phase variation as a mechanism controlling gene expression

Phase variation basically involves inversion of genes (i.e. taking it out and putting it back in backwards). I've mentioned inversion briefly in an earlier post. The consequences of inversion include "switching off" promoters, if it's a promoter region that is inverted. Phase variation isn't a very common way of controlling genes, but it does happen.

An example in where phase variation is used is in flagellin genes in salmonella. Salmonella has plenty of flagella that help it to move around, but these flagella make them way too obvious to immune system cells in people that they're trying to kill. Phase variation, which switches off the H2 flagellin gene, allows them to sneak around much more effectively.