Portal de Periódicos da CAPES

Jumping around the Topic of Mobile Genetic Elements

1997; Cell Press; Volume: 88; Issue: 2 Linguagem: Inglês

10.1016/s0092-8674(00)81835-8

1097-4172

Bill Engels, Carlos C. Flores,

Chromosomal and Genetic Variations

Mobile Genetic Elements By David J. Sharrett. New York: IRL Press at Oxford University Press (1995). 179 pp. $105.00, hardcover; $52.00, paperback Genetic information is often compared to the text in a book or to a computer program, but these well-worn analogies break down when we consider mobile DNA. Books don't rewrite themselves while you are trying to read them, and computer programs don't rearrange their code during execution, at least not intentionally. Mobile DNA exists in virtually all organisms, and it is essential to many. It ranges from single-purpose mechanisms such as mating type switching in yeast to the near ubiquity of transposable elements, many of which function equally well in a wide variety of species. While transposable elements are often considered to be molecular parasites, other forms of mobile DNA, such as those which produce antigenic variation, have clear beneficial functions for the organism. Mobile Genetic Elements is a new book on the subject edited by D. Sherratt. If the topic itself is diverse and difficult to define, so is Sherratt's book. Readers looking for an update of Berg and Howe's massive treatment (1989, American Society of Microbiology) will not find it here. Instead, Sherratt offers a much less ambitious, often sketchy, coverage of mobile genetic elements with many areas, such as retrotransposons and retroviruses, mentioned only briefly, and others, such as transposons in yeast, largely untouched. Some chapters, such as Plasterk's excellent review of transposition mechanisms, cover a broad and essential area providing a much-needed review for newcomers to the field. Others, such as the chapter on retrons, focus on narrow issues of interest to specialists. James Shapiro, who edited an earlier book by the same title (1983, Academic Press), opens with an anecdotal chapter about the history of the major discoveries that founded the field of mobile DNA. Many readers will enjoy his account of the events leading to our present understanding, with emphasis on the pioneering work of McClintock. Shapiro struggles, however, when he tries to cast the discovery of mobile elements as bringing about a fundamental change in how the genome is understood. After all, despite the importance of mobile DNA, most pre-McClintock notions of the genome, such as linear genetic maps, still work. Transposable elements, Shapiro says, put an end to the era of the “Constant Genome” and ushered in the paradigm of the “Fluid Genome” (p.1). This will come as a surprise to the many genome project workers who are proceeding with great success on the old-fashioned assumption that the genome structure is more or less constant among members of a species. Shapiro fails to make a convincing argument for his Fluid Genome concept. One example he uses as a case of “major genome restructuring” (p. 11) is that of P elements in Drosophila whose mobilization cause a syndrome of genetic traits called hybrid dysgenesis. P elements invaded the genome of D. melanogaster in historically recent times, but, as Shapiro fails to note, they did not invade the genome of D. simulans, a closely related species. Yet, the genomic organization of these two species remains almost identical. Shapiro's major restructuring is nowhere to be seen. Instead of a Fluid Genome, it is more useful to think of mobile DNA as a small but turbulent component of fluidity within a still mostly constant genome. Another of Shapiro's themes is that of the “biological utility” (p. 8) of transposable elements to their host organisms. Transposable elements, in other words, are good for you. This view stands in sharp contrast to another chapter in the book by John Brookfield who makes the case for transposable elements as genomic parasites. Both authors mention antibiotic resistance factors carried by bacterial transposons as an example of how selection could favor mobile elements. For Shapiro this situation represents the rule, whereas, for Brookfield, it is the exception (unfortunately, neither author mentions the only other clear case of biological utility of transposable elements, namely the telomere-forming retrotransposons in Drosophila). Unlike Shapiro, Brookfield places his arguments in the framework of existing data and theory of population genetics. He points out that the low site occupation frequencies for transposons in Drosophila are inconsistent with favorable selection for these sites. He goes on to show how various observations, such as equilibrium distributions and nucleotide sequence phylogenies, fit well to theoretical models in which transposable elements are either neutral or detrimental to their hosts. Brookfield succeeds in explaining these theoretical concepts without relying on mathematical jargon. Shapiro asserts that through transposable elements, “bacteria were engineering their own genomes” (p. 8), and the “raison d'être” (p. 7) of the elements was their ability to move genomic segments. Brookfield's view, however, is that as long as transposable elements can keep a step ahead of natural selection, they need no further raison to exist, and they will engineer the genome whether their host organism likes it or not! One of the most surprising new findings in the area of transposable elements is that of horizontal transfer between species. This topic is relegated to a single paragraph in Brookfield's chapter. Unfortunately, the most striking case of horizontal movement, that of the mariner element which seems to have spread throughout the animal kingdom, is not discussed. Another theme within Mobile Genetic Elements is the molecular mechanisms which underlie these rearrangements. This is an area of intense study which has been transformed in recent years by discoveries that revealed a core similarity in what once seemed disparate mechanisms used by different mobile elements. A chapter by R. Plasterk provides all the fundamentals of the chemistry and mechanics of transposon mobilization as well as the fate of the products afterward. It is written in such a clear and light tone that this complex subject appears quite simple. Mechanisms of a more esoteric field are discussed by Stark and Boocock. They present a useful introduction to “topological selectivity,” which is especially important in site-specific recombination. The mechanics of topological selectivity are vastly more difficult to present without recourse to three-dimensional models than those of transposition, yet the authors do an admirable job. How can a recombination system tell whether two distant recombination sites are on the same molecule or on two different molecules, or if they are oriented in the same way or inverted? Through the use of many diagrams and even a thought experiment involving a tangled pile of string, Stark and Boocock make such difficult concepts tractable. The ability of mobile elements to recombine DNA has been harnessed to produce hundreds of resources that are now indispensable in the tool kits of geneticists and cell and molecular biologists. A chapter by Berg and Berg and one by Kaiser, Sentry, and Finnegan outline the tools crafted from mobile elements that are now available for use in bacteria and eukaryotes respectively. The chapter on transposons as tools in bacteria by C. and D. Berg is not intended for the casual reader. It will, however, be an indispensable aid to researchers planning experiments that will employ these tools. This chapter will serve as a guide to select the best element for various applications such as mutagenesis of chromosomal genes verses genes cloned in plasmids, or making “nested” deletions for DNA sequencing. It will also help experimenters select an appropriate element for a given bacterial species and compare the relative merits of different transposon delivery systems. Kaiser, Sentry, and Finnegan review the many uses of mobile elements in eukaryotic systems. They emphasize transposons, especially the P element of Drosophila melanogaster. The heavy focus on Drosophila technology reflects the authors field of expertise and also the fact that Drosophila researchers are uniquely reliant on transposons as the principal means of transformation, mutagenesis, and gene replacement. Transposons used in other model organisms are also discussed, but in significantly less depth. The authors mention, for example, that the Tc1 insertions in C. elegans often cause little or no phenotype because the majority of insertions are into introns. However, another reason, not mentioned, is that most Tc1 insertions in exons are spliced out of the pre-mRNA. Another missing topic is the use of Agrobacterium-mediated T-DNA transfer as a tool for the mutagenesis and transformation of plants. This important technique has often been overlooked as a form of mobile DNA. A chapter on retrons (bizarre bacterial elements that produce conjoined RNA–DNA molecules) is included to give a taste of the diversity that exists out there but which could not be covered. Although this chapter is quite fascinating, we would have preferred an attempt to survey the spectrum of mobile DNA, and at least briefly describe the other types of mobile genetic elements. When the first Mobile Genetic Elements book came out in 1983 it defined the field as it existed at the time. Six years later, the much larger volumeMobile DNA, did the same thing for its time. Since then, the field has grown considerably, perhaps beyond the point where a single volume can encompass existing knowledge. The present work, and others that have appeared recently (McDonald, 1992, Genetica; Saedler and Gierl, 1996, Springer-Verlag) do not come close to this kind of comprehensive coverage. However, they do serve a useful function by sampling a field that often seems as much a moving target as the transposable elements with which it deals. Behe Michael J., Darwin's Black Box, 1996, Free Press, New York, 289, $25.00 Bell, R.M., Exton, J.H., Prescott, S.M., Handbook of Lipid Research, 1996, Plenum Press, New York, 316, $89.50 Birren, B., Lai, E., Nonmammalian Genomic Analysis, A Practical Guide, , 1996, Academic Press, San Diego, California, 353, $39.95 Biswas, B.B., Biswas, S., Subcellular Biochemistry, Vol 26, myo-Inositol Phosphates, Phosphoinositides/ and Signal Transduction, 1996, Plenum Press, New York, 421, $125.00 Boyce, A.J., Mascie-Taylor, C.G.N., Molecular Biology and Human Diversity, 1996, Cambridge University Press, New York, 305, $64.95 Brabec, V., Walz, D., Milazzo, G., Experimental Techniques in Bio Electrochemistry, 1996, Birkhauser, Boston, Massachusetts, 558, $269.50 Carey, P.R., Protein Engineering and Design, 1996, Academic Press, San Diego, California, 361, $79.95 Chiu, S.-W., Moore, D., Patterns in Fungal Development, 1996, Cambridge University Press, New York, 226, $54.95 Christou, P., Particle Bombardment For Genetic Engineering of Plants, 1996, R.G. Landes Company, Austin, Texas, 199, $69.95 Collado-Vides, J., Magasanik, B., Smith, T.F., Integrative Approaches To Molecular Biology, 1996, MIT Press, Cambridge, Massachusetts, 345, $50.00 Cotter, T.J., Martin, S.J., Techniques in Apoptosis, A User's Guide, , 1996, Portland Press Ltd, London, 333, $120.00 Cotter, E.F., Methods in Molecular Medicine, Molecular Diagnosis of Cancer, , 1996, Humana Press, Totowa, New Jersey, 218, $69.50 DePamphilis, M.L., DNA Replication In Eukaryotic Cells, 1996, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1058, $125.00 Diamandis, E.P., Christopoulos, T.K., Immunoassay, 1996, Academic Press, San Diego, California, 579, $69.95 Eckstein, F., Lilley, D.M.J., Catalytic RNA, 1996, Springer-Verlag, New York, 417, $197.00 Elles, R., Molecular Diagnosis of Genetic Diseases, 1996, Humana Press, Totowa, New Jersey, 356, $69.50 Eun, H.-M., Enzymology Primer for Recombinant DNA Technology, 1996, Academic Press, San Diego, California, 702, $125.00 Fiskum, G., Neurodegenerative Diseases Molecular and Cellular Mechanisms and Therapeutic Advances, 1996, Plenum Publishing, New York, 482, $135.00 Fletcher, M., Bacterial Adhesion, Molecular And Ecological Diversity, , 1996, Wiley-Liss, New York, 361, $95.00 Friedman, H., Rose, N.R., Bendinelli, M., Microorganisms And Autoimmune Diseases, 1996, Plenum Press, New York, 298, $79.50 Griffin, D.H., Fungal Physiology, 1996, Wiley Publishers, New York, 458, $42.95 Grossblatt, N., Upstream, Salmon & Society in the Pacific Northwest, , 1996, National Academy Press, Washington, D.C., 452, $44.95 Grossblatt, N., Careers in Science and Engineering, 1996, National Academy Press, Washington, D.C., 134, $11.95 Hawkins, J.D., Gene Structure and Expression, 1996, Cambridge University Press, New York, 212, $19.95 Hidaka, H., Nairn, A.C., Intracellular Signal Transduction, 1996, Academic Press, San Diego, California, 310, $69.00 Hoch, H.C., Jelinski, L.W., Craighead, H.G., Nanofabrication and Biosystems, Integrating Materials Science, Engineering, and Biology, , 1996, Cambridge University Press, New York, 423, $125.00 Hoffman, S.L., Malaria Vaccine Development, A Multi- Immune Response Approach, , 1996, ASM Press, Washington, D.C., 310, $75.00 Jolles, P., Lysozymes, Model Enzymes in Biochemistry and Biology, , 1996, Birkhauser Verlag, Boston, Massachusetts, 449, $189.95 Kibbler, C., Mackenzie, D., Odds, F., Principles and Practices of Clinical Mycology, 1996, Wiley Publishers, New York, 276, $80.00 Lancaster, J., Nitric Oxide, Principles and Actions, , 1996, Academic Press, San Diego, California, 355, $79.95 Leigh, I.M., Newton Bishop, J.A., Kripke, M.L., Tooze, J., Skin Cancer, 1996, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 361, $80.00 Lonai, P., Mammalian Development, 1996, Hardwood Academic, Amsterdam, 387, $190.00 Maines, M.D., Nitric Oxide Synthase, Characterization And Functional Analysis, , 1996, Academic Press, San Diego, California, 354, $89.00 Maragoudakis, M.E., Molecular, Cellular, and Clinical Aspects of Angiogenesis, 1996, Plenum Press, New York, 298, $105.00 Maulik, S., Patel, S.D., Molecular Biotechnology, Therapeutic Applications and Strategies, , 1996, Wiley-Liss Inc, New York, 223, $42.50 Miller, J.M., A Guide To Specimen Management In Clinical Microbiology, 1996, ASM Press, Washington, D.C., 153, $24.95 Murray, P.R., ASM Pocket Guide To Clinical Microbiology, 1996, ASM Press, Washington, D.C., 274, $26.95 Narahashi, T., Ion Channels, 1996, Plenum Press, New York, 457, $110.00 Paradise, L.J., Bendinelli, M., Friedman, H., Enteric Infections and Immunity, 1996, Plenum Publishing, New York, 272, $79.50 Paul, E.A., Clark, F.E., Soil Microbiology and Biochemistry, 1996, Academic Press, San Diego, California, 340, $39.95 Persing, D.H., PCR Protocols For Emerging Infectious Diseases, 1996, ASM Press, Washington, D.C., 180, $34.95 Purich, D.L., Contemporary Enzyme Kinetics And Mechanisms, 1996, Academic Press, San Diego, California, 541, $59.95 Raizada, M.K., Phillips, M.I., Summers, C., Advances in Experimental Medicine and Biology Vol. 396, Recent Advances in Cellular and Molecular Aspects of Angiotensin Receptors, , 1996, Plenum Press, New York, 270, $85.00 Reiss, M.J., Straughan, R., Improving Nature?, 1996, The Science And Ethics of Genetic Engineering. Cambridge University Press, New York, 288, $24.95 Rissler, J., Mellon, M., The Ecological Risks of Engineered Crops, 1996, The MIT Press, Cambridge, Massachusetts, 159, $16.95 Rudolph, F.B., McIntire, L.V., Biotechnology, Science, Engineering, and Ethical Challenges for the 21st Century, , 1996, Joseph Henry Press, Washington, D.C., 278, $34.95 Setlow, J.K., Genetic Engineering, Principles and Methods, , 1996, Plenum Press, New York, 289, $79.50 Shultz, S.G., Andreoli, T.E., Brown, A.M., Fambrough, D.M., Hoffman, J.F., Welsh, M.J., Molecular Biology of Membrane Transport Disorders, 1996, Plenum Press, New York, 681, $149.50 Smolensky, M.H., Rensing, L., Chronobiology International The Journal of Biological and Medical Rhythm Research, 1996, Marcel Dekker, Monticello, New York, 80, $175.00 Thomasma, D.C., Kushner, T., Birth To Death, Science and Bioethics, , 1996, University Press, Cambridge, 382, $64.95 Tomiuk, J., Wohrmann, K., Sentker, A., Transgenic Organisms, Biological and Social Implications, , 1996, Birkhauser, Basel, Switzerland, 263, $83.95 Tovee, M.J., An Introduction to the Visual System, 1996, Cambridge University Press, New York, 202, $22.95 Tsonis, P.A., Limb Regeneration, 1996, Cambridge University Press, New York, 241, $74.95 Weinberg, R.A., Racing to the Beginning of the Road, The Search for the Origin of Cancer, , 1996, Harmony Books, New York, 270, $27.50 Whetton, A.D., Gordon, J., Blood Cell BioChemistry 7, Hematopoietic Cell Growth Factors and Their Receptors, , 1996, Plenum Press, New York, 419, $110.00 Wirth, J., Color Atlas of Genetics, 1996, Thieme, New York, 411, $29.00 Wolfram, S., The Mathematica Book, 1996, Cambridge University Press, New York, 1403, $44.95 Wunderlich, G.S., Sloan, F.A., Davis, C.K., Nursing Staff in Hospitals and Nursing Homes, Is It Adequate?, , 1996, National Academy Press, Washington, D.C., 542, $59.95