Gene Regulation

What biochemical processes control initiation of gene transcription?

● Gene regulation is mediated by proteins called transacting factors (or, more commonly, transcription factors) that bind to specific sites on DNA called cis-acting sites. Transcription factor protein binding to cis-acting sequences occurs primarily via interaction between amino acid side chains on the protein and the nucleotide bases.

● Binding of transcription factors to sites near each other is often cooperative, where the binding of one protein to a region of DNA assists in the binding of another.

● The activity of transcription factors can be affected in many ways. For instance, their synthesis can be regulated, their activity can be modulated allosterically by the binding of small-molecule ligands, they can undergo posttranslational modification, and they can be degraded in a controlled manner.

● The two major types of gene regulation are positive control and negative control. In positive control, transcriptional activator proteins stimulate the transcription of target genes, whereas in negative control, transcriptional repressor proteins inhibit transcription.

What mechanisms control prokaryotic gene expression?

● In prokaryotes, genes involved in common pathways are often organized into single transcription units called operons. Expression of the entire set of genes can then be regulated by action at a single promoter.

● Genes are commonly regulated in ways that appear to be economical uses of cellular resources. Proteins involved in catabolic pathways are only expressed when those nutrients are available, and proteins involved in biosynthetic pathways are only made when the end product is not abundant in the environment.

● The lac operon is subject to two types of control. It is expressed only when lactose (or IPTG) is present in the environment and when glucose is absent.

● In the presence of lactose, the lac repressor dissociates from a site near the promoter, allowing RNA polymerase access to the promoter. In the absence of glucose, the level of cAMP is high, cAMP binds to the CRP activator, and the cAMP–CRP complex binds near the lac promoter to stimulate its expression.

● The lac repressor is a tetramer, and it binds to two sites near the promoter, leading to much more complete repression than if only one site were present. DNA-bound cAMP–CRP protein makes contacts with RNA polymerase to facilitate its binding to the promoter.

What mechanisms control eukaryotic gene expression?

● Eukaryotic DNA is packaged into DNA–protein structures called nucleosomes, in which 147 bp of DNA wrap around a protein core called a histone octamer. Nucleosomes can be further compacted into higher-order structures, some of which inhibit gene expression.

● The default state of eukaryotic genes is that they are unavailable for transcription because they are packaged in chromatin. Expression of eukaryotic genes is an active process that modifies chromatin in various ways to allow access by the transcription machinery.

● Eukaryotic transcriptional activator proteins do not interact directly with RNA polymerase II. Instead, they act to recruit other proteins to the genes being regulated. RNA polymerase II becomes part of the pre-initiation complex at a late stage.

● Nucleosomes can be laterally moved along the DNA or removed from it by chromatin remodeling machines, which are recruited to genes by activator proteins. These machines are large multiprotein complexes and require ATP. Their action usually results in exposure of cis-acting sites for other transcription factors.

● Transcriptional activator proteins often bind at cis-acting sites called enhancers, which can function at variable distances from the promoter and in either orientation. They interact with the promoter by looping the DNA to assemble the pre-initiation complex.