Although different cells in a multicellular organism contain the same genes, cells in one tissue are often specialized to perform specific functions that distinguish them from cells in another tissue. For example, nerve cells transmit signals whereas red blood cells carry oxygen. These differences in cellular function are due to the expression of specific subsets of genes.
How do cells regulate the expression of some genes while silencing others?
Similarly, the fertilized egg has a full complement of genetic information that is copied and distributed to every cell in the body, but only a fraction of the genes are expressed in any given cell. Even single-celled organisms, such as bacteria, have a full complement of genes, but again, different genes are turned on at different times depending on the ambient conditions or the nutrients available.
This tight control of gene expression is necessary both for the remarkable adaptability of cells and for their proper functioning. In multicellular organisms, differential gene expression is a central feature of development and evolution, allowing genes turned on in one region of an embryo to be turned off in another, thereby yielding new developmental patterns. Gene expression also contributes to diseases, including cancer, and about 10 percent of all drugs, including steroid hormone analogs, act by targeting one or another of the mechanisms leading to gene expression.
This blog describes how prokaryotic and eukaryotic cells control gene expression to make specific RNAs and proteins on an as needed basis. Much of what we have learned about gene regulation has been from experiments measuring the expression from individual genes. However, more recently the development of new technologies and completion of several genome sequences have enabled global analyses of how large groups of genes are regulated.
Bacterial Genomes
The prokaryotic genomes, as in bacteria, generally contain one or more circular double-stranded DNA molecules with the barest minimum of non-coding sequences. Because compactness is so extreme in prokaryotes, virtually every DNA segment codes for proteins or RNAs. In addition, there are very few non-coding gaps between different transcription units. Rather frequently, genes whose ultimate function in controlling a biological process is related will cluster together and be coordinately regulated. For instance, genes encoding flagella synthesis may lie close enough to genes involved in the metabolism of sugars that rigorous control of both transcription and translation are required.
The Bacterial Operon
Bacterial cells are in direct contact with the environment and must respond rapidly to changes in nutritional conditions. When bacteria are growing in minimal medium and are transferred to a medium containing lactose or tryptophan, for example, gene expression changes rapidly.
Lactose Utilization:
Lactose is a disaccharide composed of glucose and galactose that provides a source of energy and metabolic intermediates. Under conditions of low growth, bacteria do not synthesize β-galactosidase, an enzyme involved in lactose digestion. In the presence of lactose, on the other hand, the production of β-galactosidase is greatly increased by the induction process triggered by lactose.
Tryptophan Synthesis:
Tryptophan is an amino acid that can be synthesized by bacteria. In the absence of tryptophan, the bacteria begin to synthesize the enzymes required to produce tryptophan, by turning on the genes that code for these enzymes. Conversely, when sufficient tryptophan is present, these genes are turned off.
The Operon Model
Bacterial genes that code for proteins within a single metabolic pathway are often grouped together and transcribed into one mRNA molecule. These groups are known as operons. An operon includes:
Structural genes code for enzymes involved in the pathway. They are transcribed into one polycistronic mRNA and then into various enzymes. The promoter is the binding site of RNA polymerase, where transcription begins. In DNA, there is a region called an operator where a repressor protein will bind and halt transcription when necessary. A regulatory gene codes for the repressor protein binding to the operator.
Trp Operon:
The trp operon is a repressible operon. An inactive repressor binds to the operator region of the operon only when complexed with tryptophan, acting as a co-repressor. When tryptophan is not available, RNA polymerase transcribes the genes of the operon, leading to biosynthesis of tryptophan. When tryptophan levels rise, the tryptophan-repressor complex binds to the operator, reducing transcription.
The Lac Operon:
The lac operon controls lactose breakdown. This is an inducible operon because the presence of lactose induces transcription. The lactose binds to an intracellular receptor called the lac repressor, which undergoes an internal shape change, enabling it to no longer bind to the operator. Under these conditions RNA polymerase transcribes the genes encoding β-galactosidase and other enzymes required for lactose metabolism. When lactose levels fall the repressor again binds to the operator, terminating transcription.
Catabolite Repression
In the process of regulating bacterial genes, repressors, including those of the lac and trp operons, typically function as negative regulators, inhibiting gene expression by binding to DNA and blocking transcription. The lac operon, however, is similarly controlled through positive means, which was a concept initially grasped when research on the glucose effect was done. When glucose is available, together with other sugars such as lactose or galactose, the bacterium metabolizes glucose only and ignores the presence of the other sugars. Consequently, it represses the enzymes that would deal with the other sugars, including β-galactosidase.
In 1965, it was discovered that cyclic AMP (cAMP), until that time known only in eukaryotic cells, is present in E. coli. The amount of cAMP depends inversely on the glucose levels: the more glucose available, the lower the level of cAMP. Indeed, if cAMP is added to a glucose-rich medium, bacteria begin synthesizing normally repressed catabolic enzymes.
Although the mechanism by which glucose inhibits cAMP is not yet understood, the role of cAMP in countering the effect of glucose is very well understood. The complex of cAMP with the receptor protein CRP binds to a specific site in the control region of the lac operon, and, by altering the conformation of DNA, allows RNA polymerase to initiate transcription. This cAMP-CRP complex is required to have efficient transcription even in the presence of lactose when the lac repressor is unable to inhibit the RNA polymerase. Thus, glucose levels indirectly impact lac operon transcription through cAMP levels.
Attenuation
The trp operon also employs attenuation, a feedback control mechanism involving premature transcription termination. If high levels of tryptophan are available, RNA polymerase begins transcription, but terminates shortly after starting in the leader sequence. If tryptophan levels are low, transcription continues through the leader sequence into the structural genes of the operon.
Attenuation is a form of transcription termination. In this case, the process involves alternative RNA secondary structures being produced following transcription. One of the structures inhibits further transcription by halting the RNA polymerase and the other does not. The structure produced depends on whether tryptophan is available, thereby dictating whether the process would be an early termination of transcription or continuation to synthesize the complete mRNA for all structural genes.
Riboswitches
Other regulatory mechanism involves the binding of small metabolites to bacterial mRNAs with high specificity. This occurs for mRNAs with a structured 5′ noncoding region whose conformation is changed in the presence of the metabolite. The change in conformation influences gene expression associated with the synthesis of the metabolite.
Riboswitches usually turn off gene expression by influencing one step either in transcription termination or translation initiation. Unlike the protein-based repressors, riboswitches work purely through RNA and thus represent a possible ancestral mechanism from an RNA world.
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