Genes & Signals

IntroductionThe importance of gene regulation in two biological contexts is described. First, during development of a complex organism, genes are switched on and off in elaborate patterns; and second, changes in those patterns of gene regulation drive many evolutionary changes in organisms. The problem is to understand what kinds of molecular interactions, and what kinds of changes in those interactions, drive these processes. The history of certain key ideas, as developed primarily by Jacob, Monod and Lwoff in Paris some 40 years ago is briefly reviewed. A new perspective on the problem is suggested: gene regulation is construed as a process of imposing specificity on an enzyme, RNA polymerase. The most revealing analysis will be of the phenomenon called "gene activation." Chapter 1: Lessons from BacteriaThree mechanisms for activating transcription of specific genes in E.coliare presented. The simplest – and most common – is called "Regulated Recruitment". In this case, the activator – a DNA binding protein that switches on expression of a gene – only has to recruit an enzyme – RNA polymerase – to the gene. Examples of this mechanism (as found at the lacgenes and genes of phage lambda) are described in detail, along with the experimental approaches used to elucidate the mechanism. The other two mechanisms – in which either the polymerase or the gene must undergo a structural change induced by an activator – are again illustrated using examples of each (control of the glnAgene by NtrC; and control of the merTgene by MerR); again, the experimental basis for the proposed mechanisms is in each case described. Where they are used, the roles of repressors – DNA binding proteins that switch off the expression of specific genes – are discussed. How extra-cellular signals control the activities of activators and repressors is examined. Also, the ways in which two activators, or an activator and a repressor, can work together to integrate signals at a given gene is discussed. Often the same regulators can be used in different combinations – a phenomenon called "combinatorial control". The rather simple "adhesive" protein surfaces required for regulated recruitment are emphasized. Other aspects, such as the phenomenon of cooperativity, are discussed in some detail. Chapter 2: Yeast: A Single-celled EukaryoteWhich of the three basic mechanisms of gene activation found in bacteria is used to switch on the typical yeast gene? This is the question asked in this chapter. As in bacteria, genes in yeast can be switched on by activators and switched off by repressors. As in bacteria, these regulatory proteins are controlled by extra-cellular signals. But unlike the bacteria cases – where the "transcription machinery" consisted of a single enzyme (RNA polymerase) – in eukaryotes, even the relatively simple yeast, that machinery is far more complicated. And in addition, the genes themselves are wrapped in histones to form nucleosomes. Despite these complications, many of the same experiments that were revealing in bacteria can be performed in yeast as well. (Control of the GAL1gene by the activator Gal4 is taken as an example). These experiments reveal that, despite the complexities, regulated recruitment is the basic mechanism of activation in yeast. In this case, enzymes that modify the state of nucleosomes in various ways, or that promote transcriptional elongation as well as initiation, are often recruited, along with the basic transcriptional machinery, to switch on genes. Thus a general theme emerges: simple molecular interactions can be reiterated and supplemented by "add ons", as evolution proceeds, to create ever more sophisticated regulatory responses. The role of repressors (e.g. Mig1/TUP1 repression of GAL1) is discussed as well, as are examples of signal integration and combinatorial control (in regulation of the yeast mating type genes; and of the HO gene), and the phenomenon of "gene silencing". Chapter 3: Some Notes on Higher EukaryotesEvidently regulated recruitment explains the action of the typical activator from higher eukaryotes – mammals, flies etc – just as it does that from yeast. The evidence is discussed at the beginning of this brief chapter. But higher eukaryotes use signal integration and combinatorial control to a far greater extent than either yeast or bacteria. This allows them to produce an extraordinary range of patterns of gene expression – something which in turn allows these organisms to be so complex and varied despite the relatively "small" number (and similar types) of genes they each posses. How the activators and repressors achieve this is discussed (using the human interferon-beta gene, and the Drosophila evegene as examples). Finally, one or two other characteristic problems faced by higher eukaryotes – e.g. activation at a distance, imprinting etc – are also described and the extent to which they can be explained in terms of regulated recruitment discussed. Chapter 4: Enzyme Specificity and RegulationIn this final chapter, the principles of regulation uncovered in our survey of transcription are applied to enzymes involved in other processes – signal transduction, protein degradation, the cell cycle, splicing etc. Regulated Recruitment is found to play a large part in how specificity and regulation are imposed on many of these enzymes – e.g. kinases, phosphatases, and ubiquitylating enzymes. The dangers and benefits of regulating enzymes in this way are considered, as are the problems of interpreting certain commonly performed experiments involving enzymes that work in this way. AfterwordThe book ends with some thoughts on how ideas in these areas have developed over time.Ptashne, Mark is the author of 'Genes & Signals', published 2001 under ISBN 9780879696337 and ISBN 0879696338.