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A short guide to the E coli operons

This page contains background material to the course Quantitative Systems Biology at KTH. Many of the examples used in the book followed in the 2012 year, and earlier years,

Uri Alon, 2007
An Introduction to Systems Biology: Design Principles of Biological Circuits
Chapman & Hall/CRC Mathematical and Computational Biology Series
ISBN-10: 1-58488-642-0
ISBN-13: 978-158488-642-6

are very well known, but not summarized in an Appendix to the book (as they could perhaps have been). This page is intended to be a living document and material will be added to with no fixed schedule.

The operon concept

The term operon was coined by Monod and Jacob in 1960, and several E coli operons are described in detail in their still very readable review from 1961 (unfortunately this link can be slow, but it exists): The classical coli operons comprise a group of genes, organized in one polycistronic transcript, and an operator where one or several transcription factors can bind a regulate the trancription rate of the transcript. The proteins coded for in the genes typically do different tasks related to bringing in a substance to the cell and using it as an energy source or for other purposes. Most of the operons used as examples in the book are described in Wikipedia, to which I will refer below.

The lac operon

The lac operon regulates the transport and metabolism of lactose and is treated in the book in Fig 2.5 (page 17), Fig 4.9 (page 55), and in the evolutionary experiments described in Fig 10.1 (page 196), Fig 10.2 (page 197) and in Figs 10.4 and 10.5 (page 200). Lactose is a sugar of two carbon rings (a disaccharide sugar) that is found most notably in milk and made from galactose and glucose. Glucose and galactose are simple sugars (monosaccharides) where glucose is very common while galactose is also mainly found in milk products. The lac operon codes lacZ, which cleaves lactose into glucose and galactose, lacY, which pumps lactose into the cell, and lacA. The lac operon is regulated by the lac repressor which represses transcription of the lac genes when it binds to a binding site in the operon. The lac operon is also regulated by the catabolite activator protein (CAP) (also known as cAMP receptor protein) which enhances the expression of the lac genes when it binds to its binding site in the operon. lac repressor depends on the signal allolactose (of which IPTG is an experimental substitute) and only binds DNA when allolactose is not present. Similarly, CAP depends on the signal cAMP and only binds DNA when cAMP is present. The concentration of cAMP varies inversely to that of glucose. The lac operon therefore (roughly) executes the logical function NOT(glucose) AND NOT(NOT(lactose)). In words this means that the lac genes are mainly expressed when glucose is not present in the medium but lactose is.

The gal operon

The gal operon regulates the metabolism of galactose and is mentioned in the book in Fig 4.14 (page 64). The gal operon is regulated by CRP-cAMP as the lac operon, and also by the gal repressor (galR) and gal isorepressor (galS). Regulation is quite complex and involves looping of DNA between two different repressor sites. The regulation is galR and galS is described in where it was shown that galR is constitutively expressed while galS is negatively auto-regulated and positively regulated by CRP-cAMP. The two genes CRP and galS and the gal genes galETK hence together form a feed-forward loop (with negative auto-regulation on the "Y") as described in Alon Fig 4.14.

The ara operon

The ara operon regulates the transport and metabolism of arabinose and is treated in the book in Fig 4.9 (page 55). Arabinose is a sugar of one five-carbon ring and has its name from gum arabic, a natural gum made of hardened sap historically cultivated in Arabia. The ara operon codes for araB, araA and araD and is regulated by CRP-cAMP and the araC repressor. This system was reviewed quite recently (to be continued...)
Copyright © Sidansvarig: Erik Aurell <eaurell@kth.se>
Uppdaterad 2015-01-20