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Composition of E. Coli (Neidhardt) Copyright © 1987 American Society for Microbiology 1913 I St., N.W. Washington, DC 20006 Library of Congress Cataloging-in-Publication Data Escherichia coli and Salmonella typhimurium. Includes index. 1. Escherichia coli. 2. Salmonella typhimurium. I. Neidhardt, Frederick C. QR82.E6E83 1987 589.9'5 87-1065 ISBN 0-914826-89-1 ISBN 0-914826-85-9 (soft) All Rights Reserved Printed in the United States of America 1. Introduction MOSELIO SCHAECHTER AND FREDERICK C. NEIDHARDT Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109 Escherichia coli and Salmonella typhimurium are most biosynthetic pathways, the refinement of the gram-negative rods of the family Enterobacteriaceae. concept of the gene, the solution of the genetic code, They resemble each other in most ways but differ in the discovery of molecular mechanisms of gene regu­ some essential details. Like many of the eubacteria, lation, and the molecular portrayal of viral morpho­ neither species is well delineated. E. coli represents a genesis. wide cluster of biotypes, whereas S. typhimurium is Today, E. coli and S. typhimurium are special to us more circumscribed. Both species have been known because more is known about them than about any since the early days of bacteriology, E. coli as a other cellular form of life. To give an idea of the common member of the intestinal flora and S. typhi­ current extent of this knowledge, about 1/3 of the gene murium as a frequent agent of gastroenteritis. products of E. coli have been studied in some bio­ These organisms have been preeminent in research chemical detail, and their genes have been identified; laboratories for nearly a century. At first glance this of the order of 10% of the E. coli genome has been may seem surprising because neither is a particularly sequenced; and map positions have been determined good model for studying some of the more exciting for approximately half its genes. The rest are not far phenomena in cell biology. They do not differentiate behind. We know perhaps 80% of the organism's (like Caulobacter), sporulate (like Bacillus), fix nitro­ metabolic pathways. We have a remarkably detailed gen (like the closely related Klebsiella), photosynthe­ picture of how its macromolecules are made, and we size (like Rhodospirillum), chemosynthesize (like can use purified cell components to construct reason­ Nitrosomonas), excrete large amounts of protein (like able facsimiles of these molecules in the test tube. Bacillus), or grow in exotic environments (like Thermus Less complete is our knowledge of how gene expres­ or Thiobacillus). sion is regulated, for this turns out to be quite a rococo The reason for the popularity of these two species in business. Nonetheless the main features of regulation microbiological research is not quite lost in antiquity, can be described for many operons, and the list of but is somewhat complex. Since the early days, bac­ control mechanisms that has been described is im­ terial physiologists chose organisms that were easily pressive, if somewhat daunting. Considerably less is accessible, were not highly virulent, and grew readily known about how the component parts "talk" to each on defined media. E. coli emerged only gradually as other to result in regulated growth or in rapid re­ the undisputed winner. By the late 1930s, it was the sponses to changes in the environment. organism of choice, thanks to the work done on its Much of the work done with E.coli and S. typhimu­ bacteriophages by investigators like the Wollmans rium has been under defined laboratory conditions. and Bronfenbrenner. This was followed by the crucial Increasingly, we have become aware that this gives research of Monod on growth physiology and enzy­ only a partial picture and that to understand many of matic adaptation and that of Delbruck and Luria on the properties of these organisms we must take into phage genetics. In the late 1940s its fate was sealed by account how they function in their natural environ­ the discoveries of conjugation by Lederberg and of ments. Alas, these environments are very complex, transduction by Zinder and Lederberg. S. typhimuri­ and it is difficult to assess the properties that are um became the popular organism for genetic and relevant from the eye view of the organism. In broad biochemical experiments that relied on transduction. strokes, we know that strains of E. coli are found Genetic analysis of cellular function became possible habitually in the large intestine of vertebrates, usually and was used to take full advantage of other conve­ as minority members of the normal flora. They can nient properties of these species. These include rela­ cause diseases in other body sites, and they spread tive ease of preparing enzymatically active cell ex­ between individual hosts, often after a relatively short tracts and the flexible ways with which both small extracorporeal residence. Almost never do they find and large molecules can be tagged with radioactive themselves in a constant, unchanging environment. isotopes. Labeling with different precursors was car­ Rather, they feed only intermittently in the large ried out extensively by a group of investigators at the intestine and undergo partial desiccation when void­ Department of Terrestrial Magnetism of the Carnegie ed from their host. If deposited in a body of water they Institution of Washington. They published the earliest face the problems of nutrition at low concentrations of "E. coli bible" (1). foodstuff. Between hosts they undergo shifts in tem­ With these major advantages it is no wonder that E. perature, some subtle, some drastic. These circum­ coli, S. typhimurium, and their bacteriophages led to stances, plus some new ones, are sometimes faced by major triumphs of biology such as the elucidation of these organisms when they are grown in laboratory 2 SCHAECHTER AND NEIDHARDT media and intermittently saved in Bijou bottles, evolved a series of "alarm reactions" which permit dunked in glycerol, and placed in a freezer, or lyophil­ them to repair damaged DNA, shut off the synthesis of ized. unwanted RNA, or protect their membranes. Most of Given such a varied existence, it can be expected these responses lead to the selective shut-off or turn­ that E. coli and S. typhimurium are highly adaptive. on of specific macromolecules. The number of regula­ This is, in fact, the case. These species and many of tory devices used is very large and possibly beyond their relatives can synthesize the preponderance of our current comprehension. Shut-off of gene expres­ their constituents, often from a single organic com­ sion at transcription or translation take on a bewil­ pound and a few minerals. Their repertoire of nutri­ dering number of versions. Even after proteins are tional abilities is quite impressive. If anything, it is made, their activity or stability can be modified. We surprising that they have not yet learned to live on know that our knowledge in this area is incomplete Tris buffer. They respond to changes in temperature and that we have much to learn. and available nutrients by making rapid adjustments The impression gained is that the demands from in the synthesis of regulatory molecules. As a conse­ selective pressure for efficiency and adaptability have quence, they can vary considerably in size and chem­ resulted in a complex network of regulatory interac­ ical composition. Unamuno's dictum, "Yo soy yo y mi tions. The constraints of space and speed do not circunstancia" ("I am I and my circumstance"), ap­ permit the physical separation of different metabolic plies to them very well. activities that is seen in higher cells. "Spaceship E. As expected from organisms that grow in competi­ coli" is not a large space station with many compart­ tion with others, E. coli and S. typhimurium are also ments and with the luxury of many redundant parts highly efficient in the way they husband their energy and back-up systems. It must make do with fewer resources. When presented with different kinds of parts and make multiple use of many of them. If this nutrients, they grow at different rates. The richer the is so, individual macromolecules can be expected to array of nutrients provided, the faster they grow, function in several ways. We have a few examples that sparing themselves the task of synthesizing many of suggest this: many proteins have not only an enzymat­ the compounds provided exogenously. Under condi­ ic or controlling function but they also regulate their tions of active growth they synthesize the quantities of own synthesis (autorepression); some polypeptides small and large molecules they require and very little act as subunits of different enzymes or structural extra. Only under conditions of starvation or other proteins. If this turns out to be true on a large scale, it stresses do they accumulate constituents that they will make it difficult to ascribe the regulatory proper­ cannot use immediately. Under such conditions, a ties of a given protein or nucleic acid to their proper certain amount of energy is expended "inefficiently" place in the overall scheme. Pleiotropy reigns su­ for the sake of adaptation. For instance, nongrowing preme! For this reason alone the task ahead is not cells contain a small but significant number of ribo­ trivial, although in our opinion it can be faced with somes that are not engaged in protein synthesis. optimism. Although the making of these ribosomes is at a cost, A central goal in biology is the achievement of a their presence at the time of refeeding allows the cells cellular paradigm. Until we understand thoroughly to resume growth faster. the growth of one cell, we shall be handicapped in The grand strategy that allows these organisms to imagining the nature of our understanding of any cell.
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