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B. subtilis versus E. coli
Cell, Vol. 31,499-501,
December
1982
(Part 2), Copyright
0 1982
by MIT
Book Reviews
6. subtilis versus E. coli The Molecular Biology of the Bacilli, 1: Bacillus subtilis. Edited by D. Dubnau. New York: Academic Press. (1982). 378 pp. $44.00.
We practicing scientists are faced with an exponentially increasing avalanche of new material. This problem had already reached a point some years ago which even sociologists could recognize-issues of journals too heavy to carry home, quantities of new journals appropriate only for computers. One way to try to keep up is through textbooks and review books. The book at hand is one of these. Now that the body of knowledge concerning Bacilli has become truly significant, workers in the field have joined to produce the first in a three-volume effort, this one centering on B. subtilis. My purpose is to discuss the choices that have been made and the book in relation to the general usefulness of the genre. First, one can dispose of some of the features that are frequently a subject for comment. As usual, the treatments in the book are uneven and the style disjointed. I am personally unimpressed by this problem; scientific prose is rarely undying, especially since the material changes and expands so quickly. Tolerable clarity is the major requirement, and that is achieved by all the contributions, at least for an appropriate audience. The appropriate audience is a point of some importance. This is not a book for beginning students, and is not meant to be. Background material is frequently skimpy, and only a well informed graduate student or an experienced scientist close to this field will be comfortable with most of the coverage. The price reinforces that point: the all-important Xerox/purchase ratio is 2.3 (that is, one can photocopy the entire book for 43% of its price); and at ratios greater than 1.3, my experience is that books appear almost entirely in libraries, to be selectively borrowed and copied by interested users. The other standard question relates to the choice of authors, and here David Dubnau has picked from the best. Also, in only 2 of 11 chapters do the authors use the occasion for self-glorification (names on request to discrete inquiries). Before turning to the specific contents, I want to indicate some problems that such a set of specialized reviews creates. First, there is the problem of compilation versus review; we want to know the present state of information, but we also want to know what is considered an important question now. A judicious use of some history can also be a great help. Second, there is the major problem of coverage. In this regard, the book is forthright but quite specialized.
It is designed, according to its editor, for “those who are concerned with the use of the 6. subtilis system as a tool for the study of molecular biology and those who wish to increase the medical, veterinary, and industrial usefulness of this and related organisms” (p. xi). Readers should be clear that on its own terms the book equates molecular biology with genetics and recombinant DNA technology. On the other hand, it equates medical, veterinary, and industrial usefulness with genetics and recombinant DNA technology. To be more specific, of 370 pages of text, 103 are directly related to cloning, 210 to gene expression and regulation in normal and sporulating bacteria, and 58 to temperate viruses and specialized transduction, forming a bridge between the first two topics. But the impact of recombinant DNA technology is usually near the surface (Chapter 8 concludes a major section with “the site in 4105 dmetB might prove useful for cloning of DNA” [p. 2641; whereas Chapter 9 concludes in part with “It is not clear whether SPP (or its relatives, or hybrids between them) will also turn out to be useful as a tool for gene cloning.” [p. 3031.1 Since I am most interested in gene expression, I like this approach; but someone interested in the nature of the gram-positive cell wall and the amazing changes during sporulation, or in teichoic acids, will come up short; membranes are mentioned only as a barrier to enzyme secretion or as a possible attachment site for DNA, etc. As for medical relevance, there is no discussion of antibiotic production during sporulation, of how penicillin acts, of sporulation in this system compared to medically important Bacilli, of the possible significance of an SOS system (not mentioned at all!). The other major problem in this type of book is the implicit necessity for a comparative approach. Someone writing about any other bacterium must feel the weight of the literature on E. coli over his head and come to terms with it-as well as with some selective studies of yeast or higher cells in some cases. Some chapters are more successful than others in this regard. To turn briefly to specific contents: -Chapter 1. Henner and Hoch give an up-to-date genetic map. This is well compiled, but comparisons to E. coli, etc., are few. There is no discussion of operons. distribution of sporulation genes, etc.; but interesting points are made about “silent” regions. -Chapter 2. Winston and Sueoka. DNA replication. One of the least comparative chapters. A thorough historical discussion, but I think many readers would first need to review part of A. Kornberg’s book on DNA replication to follow it easily. -Chapter 3. Doi on RNA polymerase. A truly lovely comparative discussion with an attempt to convey the questions he thinks are important. Some overlap with
Cdl 500
Chapter 6 on possible forms of polymerase provides an interesting case of alternative views of the same evidence by different scientists. -Chapter 4. lssar Smith on translation is very clear where a clear treatment of complex differences between E. coli and B. subtilis is most necessary. -Chapter 5 (Dubnau on transformation), Chapter 7 (Geiduschek and Ito on lytic phages, Chapter 8 (Rutberg on temperate phages) and Chapter 9 (Zahler on specialized transduction) are all useful summaries of fields in which many unique contributions have come from work with B. subtilis. The summaries of gene regulation in SPOl and of the development of hydroxyuracil-containing phages were especially fascinating. -Chapter 6 (Losick on sporulation and its regulation) conveys the extraordinary excitement and historical impact as the study of individual sporulation genes with cloned probes begins (at last!) to tell us much of what is really going on in sporulation. Unfortunately, the text is very repetitive for what is in large part a promissory note; and it would have been nice to cut some repeats in favor of a discussion, for example, of present notions of how spores become heat-resistant (or one of the other topics mentioned above). -Chapters 10 and 11 (Gryczan on cloning and Debalov on industrial uses) are complete summaries of potential use to many readers. To sum up. The authors of this book are the right authors for its purposes; the subject is important; the amount of information has warranted compilation; and I know of nothing comparable available. Because much of the material has not been reviewed elsewhere for some time, the amount of plagiarism seemed very low-most contributors probably borrowing only from their own grant applications. If you want this material, this is the likely book to buy (or Xerox). David Schlessinger Department of Microbiology and Immunology Washington University School of Medicine St. Louis, Missouri 631 10
Codex E. coli Gene Function: E. co/i and Its Heritable Elements. By R. E. Glass. Berkeley: University of California Press. (1982). 487 pp. $40.00-cloth; $20.00-paper.
This is an extensive and generally lucid treatise on the molecular biology of E. coli. As such it inevitably invites comparison with Molecular Genetics, by Stent and Calendar, and with volumes 1 and 3 of Gene Expression, by Lewin. In Glass’s book the discussion is divided into four sections: the cell; the expression
of genetic material; the transfer of genetic material; and the regulation of gene expression. Explanations of the various phenomena of genetic functions are generalized as much as possible into formal, unifying structures. In this sense, Glass has attempted a codification of the molecular genetics of E. coli. For example, a discussion of the operon begins with a strictly theoretical presentation in which all possible variations of negative and positive control systems are included. However, little reference is made subsequently to explicit experimental systems, nor is there much of an attempt to describe the crucial experiments which led to our current state of knowledge. In some respects, this approach is to be welcomed since we all seek the Ultimate Generalization of the Secret of Life, but these generalizations stand in sharp contrast to Lewin’s books, which teem with descriptions of experiments and the questions they answered or posed. Furthermore, though Stent and Calendar’s book is not as encyclopedic as Glass’s or Lewin’s, it is well known for the lively intellectual presentation of ideas and experiments in the context of a way of thinking about biology. Gene Function, nevertheless, will be a very helpful auxiliary text for advanced undergraduate students or for graduate students studying the molecular genetics of procaryotes. In part, this new text is useful because of the currency of its contents (most chapters contain references up to 1980, and some cite even more recent papers) and also because it is, indeed, a comprehensive treatise. However, the book would be improved if it had a more intimate connection to reality, as is found in Lewin’s volumes and in Stent and Calendar’s, as well as some of the spark of the latter book. In an ambitious project of this kind, the author cannot possibly satisfy everyone in his audience. I would still recommend Stent and Calendar to a novice who does not necessarily intend to work in molecular genetics directly. I also have minor objections to the order of presentation of some of the topics and to the omission of experimental data from descriptions of genetic experiments. Among other matters, the absence from the text of any catabolite-regulated operon, apart from the lac operon, is troubling, as is the mistaken identity of the UGG codon in the obligatory table of the code dictionary. A more significant complaint concerns the reproduction of the tables and figures, of which there are many. These illustrations are well planned and useful summaries of information. Unfortunately, many can be read easily only in good light with the aid of a magnifying glass. The publisher would do well to correct this error the next time around. Sidney Altman Department of Biology Yale University New Haven, Connecticut
06520
December
1982
(Part 2), Copyright
0 1982
by MIT
Book Reviews
6. subtilis versus E. coli The Molecular Biology of the Bacilli, 1: Bacillus subtilis. Edited by D. Dubnau. New York: Academic Press. (1982). 378 pp. $44.00.
We practicing scientists are faced with an exponentially increasing avalanche of new material. This problem had already reached a point some years ago which even sociologists could recognize-issues of journals too heavy to carry home, quantities of new journals appropriate only for computers. One way to try to keep up is through textbooks and review books. The book at hand is one of these. Now that the body of knowledge concerning Bacilli has become truly significant, workers in the field have joined to produce the first in a three-volume effort, this one centering on B. subtilis. My purpose is to discuss the choices that have been made and the book in relation to the general usefulness of the genre. First, one can dispose of some of the features that are frequently a subject for comment. As usual, the treatments in the book are uneven and the style disjointed. I am personally unimpressed by this problem; scientific prose is rarely undying, especially since the material changes and expands so quickly. Tolerable clarity is the major requirement, and that is achieved by all the contributions, at least for an appropriate audience. The appropriate audience is a point of some importance. This is not a book for beginning students, and is not meant to be. Background material is frequently skimpy, and only a well informed graduate student or an experienced scientist close to this field will be comfortable with most of the coverage. The price reinforces that point: the all-important Xerox/purchase ratio is 2.3 (that is, one can photocopy the entire book for 43% of its price); and at ratios greater than 1.3, my experience is that books appear almost entirely in libraries, to be selectively borrowed and copied by interested users. The other standard question relates to the choice of authors, and here David Dubnau has picked from the best. Also, in only 2 of 11 chapters do the authors use the occasion for self-glorification (names on request to discrete inquiries). Before turning to the specific contents, I want to indicate some problems that such a set of specialized reviews creates. First, there is the problem of compilation versus review; we want to know the present state of information, but we also want to know what is considered an important question now. A judicious use of some history can also be a great help. Second, there is the major problem of coverage. In this regard, the book is forthright but quite specialized.
It is designed, according to its editor, for “those who are concerned with the use of the 6. subtilis system as a tool for the study of molecular biology and those who wish to increase the medical, veterinary, and industrial usefulness of this and related organisms” (p. xi). Readers should be clear that on its own terms the book equates molecular biology with genetics and recombinant DNA technology. On the other hand, it equates medical, veterinary, and industrial usefulness with genetics and recombinant DNA technology. To be more specific, of 370 pages of text, 103 are directly related to cloning, 210 to gene expression and regulation in normal and sporulating bacteria, and 58 to temperate viruses and specialized transduction, forming a bridge between the first two topics. But the impact of recombinant DNA technology is usually near the surface (Chapter 8 concludes a major section with “the site in 4105 dmetB might prove useful for cloning of DNA” [p. 2641; whereas Chapter 9 concludes in part with “It is not clear whether SPP (or its relatives, or hybrids between them) will also turn out to be useful as a tool for gene cloning.” [p. 3031.1 Since I am most interested in gene expression, I like this approach; but someone interested in the nature of the gram-positive cell wall and the amazing changes during sporulation, or in teichoic acids, will come up short; membranes are mentioned only as a barrier to enzyme secretion or as a possible attachment site for DNA, etc. As for medical relevance, there is no discussion of antibiotic production during sporulation, of how penicillin acts, of sporulation in this system compared to medically important Bacilli, of the possible significance of an SOS system (not mentioned at all!). The other major problem in this type of book is the implicit necessity for a comparative approach. Someone writing about any other bacterium must feel the weight of the literature on E. coli over his head and come to terms with it-as well as with some selective studies of yeast or higher cells in some cases. Some chapters are more successful than others in this regard. To turn briefly to specific contents: -Chapter 1. Henner and Hoch give an up-to-date genetic map. This is well compiled, but comparisons to E. coli, etc., are few. There is no discussion of operons. distribution of sporulation genes, etc.; but interesting points are made about “silent” regions. -Chapter 2. Winston and Sueoka. DNA replication. One of the least comparative chapters. A thorough historical discussion, but I think many readers would first need to review part of A. Kornberg’s book on DNA replication to follow it easily. -Chapter 3. Doi on RNA polymerase. A truly lovely comparative discussion with an attempt to convey the questions he thinks are important. Some overlap with
Cdl 500
Chapter 6 on possible forms of polymerase provides an interesting case of alternative views of the same evidence by different scientists. -Chapter 4. lssar Smith on translation is very clear where a clear treatment of complex differences between E. coli and B. subtilis is most necessary. -Chapter 5 (Dubnau on transformation), Chapter 7 (Geiduschek and Ito on lytic phages, Chapter 8 (Rutberg on temperate phages) and Chapter 9 (Zahler on specialized transduction) are all useful summaries of fields in which many unique contributions have come from work with B. subtilis. The summaries of gene regulation in SPOl and of the development of hydroxyuracil-containing phages were especially fascinating. -Chapter 6 (Losick on sporulation and its regulation) conveys the extraordinary excitement and historical impact as the study of individual sporulation genes with cloned probes begins (at last!) to tell us much of what is really going on in sporulation. Unfortunately, the text is very repetitive for what is in large part a promissory note; and it would have been nice to cut some repeats in favor of a discussion, for example, of present notions of how spores become heat-resistant (or one of the other topics mentioned above). -Chapters 10 and 11 (Gryczan on cloning and Debalov on industrial uses) are complete summaries of potential use to many readers. To sum up. The authors of this book are the right authors for its purposes; the subject is important; the amount of information has warranted compilation; and I know of nothing comparable available. Because much of the material has not been reviewed elsewhere for some time, the amount of plagiarism seemed very low-most contributors probably borrowing only from their own grant applications. If you want this material, this is the likely book to buy (or Xerox). David Schlessinger Department of Microbiology and Immunology Washington University School of Medicine St. Louis, Missouri 631 10
Codex E. coli Gene Function: E. co/i and Its Heritable Elements. By R. E. Glass. Berkeley: University of California Press. (1982). 487 pp. $40.00-cloth; $20.00-paper.
This is an extensive and generally lucid treatise on the molecular biology of E. coli. As such it inevitably invites comparison with Molecular Genetics, by Stent and Calendar, and with volumes 1 and 3 of Gene Expression, by Lewin. In Glass’s book the discussion is divided into four sections: the cell; the expression
of genetic material; the transfer of genetic material; and the regulation of gene expression. Explanations of the various phenomena of genetic functions are generalized as much as possible into formal, unifying structures. In this sense, Glass has attempted a codification of the molecular genetics of E. coli. For example, a discussion of the operon begins with a strictly theoretical presentation in which all possible variations of negative and positive control systems are included. However, little reference is made subsequently to explicit experimental systems, nor is there much of an attempt to describe the crucial experiments which led to our current state of knowledge. In some respects, this approach is to be welcomed since we all seek the Ultimate Generalization of the Secret of Life, but these generalizations stand in sharp contrast to Lewin’s books, which teem with descriptions of experiments and the questions they answered or posed. Furthermore, though Stent and Calendar’s book is not as encyclopedic as Glass’s or Lewin’s, it is well known for the lively intellectual presentation of ideas and experiments in the context of a way of thinking about biology. Gene Function, nevertheless, will be a very helpful auxiliary text for advanced undergraduate students or for graduate students studying the molecular genetics of procaryotes. In part, this new text is useful because of the currency of its contents (most chapters contain references up to 1980, and some cite even more recent papers) and also because it is, indeed, a comprehensive treatise. However, the book would be improved if it had a more intimate connection to reality, as is found in Lewin’s volumes and in Stent and Calendar’s, as well as some of the spark of the latter book. In an ambitious project of this kind, the author cannot possibly satisfy everyone in his audience. I would still recommend Stent and Calendar to a novice who does not necessarily intend to work in molecular genetics directly. I also have minor objections to the order of presentation of some of the topics and to the omission of experimental data from descriptions of genetic experiments. Among other matters, the absence from the text of any catabolite-regulated operon, apart from the lac operon, is troubling, as is the mistaken identity of the UGG codon in the obligatory table of the code dictionary. A more significant complaint concerns the reproduction of the tables and figures, of which there are many. These illustrations are well planned and useful summaries of information. Unfortunately, many can be read easily only in good light with the aid of a magnifying glass. The publisher would do well to correct this error the next time around. Sidney Altman Department of Biology Yale University New Haven, Connecticut
06520