Design principles for elementary gene circuits: Elements, methods,and examplesMichael A. Savageaua)Department of Microbiology and Immunology, University of Michigan Medical School,5641 Medical Science Building II, Ann Arbor, Michigan 48109-0620共Received 25 July 2000; accepted for publication 19 December 2000兲The control of gene expression involves complex circuits that exhibit enormous variation in design.For years the most convenient explanation for these variations was historical accident. According tothis view, evolution is a haphazard process in which many different designs are generated bychance; there are many ways to accomplish the same thing, and so no further meaning can beattached to such different but equivalent designs. In recent years a more satisfying explanation basedon design principles has been found for at least certain aspects of gene circuitry. By design principlewe mean a rule that characterizes some biological feature exhibited by a class of systems such thatdiscovery of the rule allows one not only to understand known instances but also to predict newinstances within the class. The central importance of gene regulation in modern molecular biologyprovides strong motivation to search for more of these underlying design principles. The search isin its infancy and there are undoubtedly many design principles that remain to be discovered. Thefocus of this three-part review will be the class of elementary gene circuits in bacteria. The first partreviews several elements of design that enter into the characterization of elementary gene circuits inprokaryotic organisms. Each of these elements exhibits a variety of realizations whose meaning isgenerally unclear. The second part reviews mathematical methods used to represent, analyze, andcompare alternative designs. Emphasis is placed on particular methods that have been usedsuccessfully to identify design principles for elementary gene circuits. The third part reviews fourdesign principles that make specific predictions regarding 共1兲 two alternative modes of gene control,共2兲 three patterns of coupling gene expression in elementary circuits, 共3兲 two types of switches ininducible gene circuits, and 共4兲 the realizability of alternative gene circuits and their response tophased environmental cues. In each case, the predictions are supported by experimental evidence.These results are important for understanding the function, design, and evolution of elementary genecircuits. © 2001 American Institute of Physics. 关DOI: 10.1063/1.1349892兴Gene circuits sense their environmental context and or-chestrate the expression of a set of genes to produce ap-propriate patterns of cellular response. The importanceof this role has made the experimental study of generegulation central to nearly all areas of modern molecu-lar biology. The fruits of several decades of intensive in-vestigation have been the discovery of a plethora of bothmolecular mechanisms and circuitry by which these areinterconnected. Despite this impressive progress we areat a loss to understand the integrated behavior of mostgene circuits. Our understanding is still fragmentary anddescriptive; we know little of the underlying design prin-ciples. Several elements of design, each exhibiting a vari-ety of realizations, have been identified among elemen-tary gene circuits in prokaryotic organisms. The use ofwell-controlled mathematical comparisons has revealeddesign principles that appear to govern the realization ofthese elements. These design principles, which make spe-cific predictions supported by experimental data, are im-portant for understanding the normal function of genecircuits; they also are potentially important for develop-ing judicious methods to redirect normal expression forbiotechnological purposes or to correct pathological ex-pression for therapeutic purposes.I. INTRODUCTIONThe gene circuitry of an organism connects its gene set共genome兲 to its patterns of phenotypic expression. The geno-type is determined by the information encoded in the DNAsequence, the phenotype is determined by the context-dependent expression of the genome, and the circuitry inter-prets the context and orchestrates the patterns of expression.From this perspective it is clear that gene circuitry is at theheart of modern molecular biology. However, the situation isconsiderably more complex than this simple overview wouldsuggest. Experimental studies of specific gene systems bymolecular biologists have revealed an immense variety ofmolecular mechanisms that are combined into complex genecircuits, and the patterns of gene expression observed in re-sponse to environmental and developmental signals areequally diverse.The enormous variety of mechanisms and circuitryraises questions about the bases for this diversity. Are thesevariations in design the result of historical accident or havethey been selected for specific functional reasons? Are theredesign principles that can be discovered? By design principlea兲Electronic mail: [email protected] VOLUME 11, NUMBER 1 MARCH 20011421054-1500/2001/11(1)/142/18/$18.00 © 2001 American Institute of PhysicsDownloaded 01 May 2002 to 131.215.135.10. Redistribution subject to AIP license or copyright, see http://ojps.aip.org/chaos/chocr.jspwe mean a rule that characterizes some biological featureexhibited by a class of systems such that discovery of therule allows one not only to understand known instances butalso to predict new instances within the class. For manyyears, most molecular biologists assumed that accidentplayed the dominant role, and the search for rules receivedlittle attention. More recently, simple rules have been iden-tified for a few variations in design. Accident and rule bothhave a role in evolution and their interplay has becomeclearer in these well-studied cases. This area of investigationis in its infancy and many such questions remain unan-swered.This review article addresses the search for design prin-ciples among elementary gene circuits. It reviews first sev-eral elements of design for gene circuits, then mathematicalmethods used to study variations in design, and finally ex-amples of design principles that have been discovered forelementary gene circuits in prokaryotes.II. ELEMENTS OF DESIGN AND THE NEED FORDESIGN PRINCIPLESThe behavior of an intact biological system can seldombe related directly to its underlying genome. There are sev-eral different levels of hierarchical organization