The Regulation of Bacterial Gene Expression

A cell’s genetic and metabolic machineries are integrated and interdependent. The bacterial cell carries out an enormous number of metabolic reactions.

The common feature of all metabolic reactions is that they are catalyzed by enzymes that are proteins synthesized via transcription and translation.

Feedback inhibition stops a cell from performing unneeded chemical reactions by stopping enzymes that have already been synthesized.

• We will now look at mechanisms to prevent synthesis of enzymes that are not needed.

Because protein synthesis requires a huge amount of energy, cells save energy by making only those proteins needed at a particular time. Next we look at how chemical reactions are regulated by controlling gene expression.

Many genes, perhaps 60–80%, are not regulated but are instead constitutive, meaning that their products are con-stantly produced at a fixed rate. Usually these genes, which are effectively turned on all the time, code for enzymes that the cell needs in fairly large amounts for its major life processes. Glycolysis enzymes are examples.

The production of other enzymes is regulated so that they are present only when needed. Trypanosoma, the protozoan parasite that causes African sleeping sickness, has hundreds of genes coding for surface glycoproteins.

Each protozoan cell turns on only one glycoprotein gene at a time. As the host’s immune system kills parasites with one type of surface molecule, parasites expressing a different surface glycoprotein can continue to grow.

Pre-transcriptional Control

Two genetic control mechanisms known as repression and induction regulate the transcription of mRNA and, consequently, the synthesis of enzymes from them.

These mechanisms control the formation and amounts of enzymes in the cell, not the activities of the enzymes.

The Operon Model of Gene Expression

Details of the control of gene expression by induction and repression are described by the operon theory formulated in the 1960s by François Jacob and Jacques Monod. An operon is a group of genes that are transcribed together and controlled by one promoter. We’ll look first at an inducible operon, in which transcription must be turned on.

In E. coli, the enzymes of the lac operon are needed to metabolize lactose. In addition to b-galactosidase, these enzymes include lac permease, which is involved in the transport of lactose into the cell, and trans-acetylase, which metabolizes certain disaccharides other than lactose.

The genes for the three enzymes involved in lactose uptake and utilization are next to each other on the bacterial

These genes, which determine the structures of proteins, are called structural genes to distinguish them from an adjoining control region on the DNA. When lactose is introduced into the culture medium, the lac structural genes are all transcribed and translated rapidly and simultaneously.

We will now see how this regulation occurs :

• In the control region of the lac operon are two relatively short segments of DNA. One, the promoter, is the segment where RNA polymerase initiates transcription. The other is the operator, which is like a traffic light that acts as a go or stop signal for transcription of the structural genes. A set of operator and promoter sites and the structural genes they control define an operon; thus, the combination of the three lac structural genes and the adjoining control regions is called the lac operon.

• A regulatory gene called the I gene encodes a repressor protein that switches inducible and repressible operons on or off.

• The lac operon is an inducible operon. In the absence of lactose, the repressor binds to the operator site, thus preventing transcription. If lactose is present, the repressor binds to a metabolite of lactose instead of to the operator, and lactose-digesting enzymes are transcribed.

• In repressible operons, the structural genes are tran-scribed until they are turned off. The genes for the enzymes involved in the synthesis of tryptophan are reg-ulated in this manner. The structural genes are transcribed and translated, leading to tryptophan synthesis. When excess tryptophan is present, the tryptophan acts as a corepressor binding to the repressor protein. The repressor protein can now bind to the operator, stop-ping further tryptophan synthesis.

Positive Regulation

• Regulation of the lactose operon also depends on the level of glucose in the medium, which in turn controls the intracellular level of the small molecule cyclic AMP (cAMP), a substance derived from ATP that serves as a cellular alarm signal.

• Enzymes that metabolize glucose are constitutive, and cells grow at their maximal rate with glucose as their carbon source because they can use it most efficiently. When glucose is no longer available, cAMP accumulates in the cell.

• The cAMP binds to the allosteric site of catabolic activator protein (CAP). CAP then binds to the lac promoter, which ini-tiates transcription by making it easier for RNA polymerase to bind to the promoter. Thus transcription of the lac operon requires both the presence of lactose and the absence of glucose.

• Cyclic AMP is an example of an alarmone, a chemical alarm signal that promotes a cell’s response to environmental or nutritional stress.

• The same mechanism involving cAMP allows the cell to use other sugars. Inhibition of the metabolism of alternative car-bon sources by glucose is termed catabolite repression (or the glucose effect). When glucose is available, the level of cAMP in the cell is low, and consequently CAP is not bound.

• Epigenetic Control Eukaryotic and bacterial cells can turn genes off by methylating certain nucleotides—that is, by adding a methyl group 1¬CH32. The methylated (off) genes are passed to offspring cells. Unlike mutations, this isn’t permanent, and the genes can be turned on in a later generation. This is called epigenetic inheritance (epigenetic=on genes).

Epigenetics explains why bacteria behave differently in a biofilm...

Post-transcriptional Control

• Some regulatory mechanisms stop protein synthesis after transcription has occurred.

• A part of an mRNA molecule, called a riboswitch, that binds to a substrate can change the mRNA structure. Depending on the type of change, translation can be initiated or stopped.

• Both eukaryotes and prokaryotes use riboswitches to control expression of some genes. Single-stranded RNA molecules of approximately 22 nucleotides, called microRNAs (miRNAs), inhibit protein production in eukaryotic cells. In humans, miRNAs produced during development allow different cells to produce different proteins. Heart cells and skin cells have the same genes, but the cells in each organ produce different proteins because of miRNAs produced in each cell type during development.

• Similar short RNAs in bacteria enable the cell to cope with environmental stresses, such as low temperature or oxidative damage. An miRNA base-pairs with a comple-mentary mRNA, forming a double-stranded RNA. This double-stranded RNA is enzymatically destroyed so that the mRNA-encoded protein is not made .