Snyder and Champness Molecular Genetics of Bacteria. Tina M. Henkin

Chapter 13 further presents an expanded picture of numerous systems that bacteria use to guard against horizontal gene transfer. Although horizontal gene transfer is by far the most important mechanism for evolution in bacteria and archaea, it also provides the greatest vulnerability, with the relentless onslaught of bacteriophages and mobile elements that can sap cellular resources or inactivate important or essential host genes. Significantly, host defense systems also provide the most important tools ever developed for molecular biology. The new chapter provides expanded background on diverse restriction endonucleases and the important roles they play in molecular biology. We cover the variety of tools that are available for cloning and gene assembly, as well as the advantages and disadvantages of these techniques to help guide the investigator. These techniques allow never-imagined possibilities for quickly and accurately constructing synthetic DNA fragments for testing ideas or allowing advances in engineering, including assembling entire bacterial genomes. We greatly expanded the section on CRISPR/Cas systems and chose the Cas9 system, important in many applications in a multitude of model systems and human genome engineering, to illustrate on the book’s cover. CRISPR/Cas systems are very diverse, falling into six distinct types and tens of subtypes. We provide the reader with the background needed to understand how these fascinating systems evolved, the role they play in the natural environment, and the massive promise they hold in genome engineering.

Acknowledgments

      We continue to be indebted to a large number of individuals for their help, talking through ideas, sharing insights from their area of expertise, or reading over sections for accuracy and clarity. Other individuals have alerted us to errors, suggested areas to include, or provided graphics. However, if errors remain in the text, they are our own.

      We acknowledge those whose comments on earlier editions have carried over to the current edition. In addition, we thank Esther Angert, Melanie Berkmen, Briana Burton, Druba Chattoraj, Mick Chandler, Pete Christie, Alan Grossman, Alba Guarné, Claudia Guldimann (and the Zürich book club), John Helmann, Laura Hug, Ailong Ke, Bénédicte Michel, Kit Pogliano, Lise Raleigh, Phoebe Rice, Jim Samuelson, Mark Sutton, Anthony Vecchiarelli, Bob Wiess, Steve Winans, Wei Yang, and Steve Zinder.

      It was a great pleasure to work with Director Christine Charlip and ASM Press, and we look forward to the new partnership with John Wiley & Sons, Inc. We enjoyed working first with Production Manager Larry Klein and then transitioning to Developmental Editor Ellie Tupper, who coordinated the project to the finish line. We continue to be grateful for the professional and patient work of Patrick Lane of ScEYEence Studios for making our visions come to life in these illustrations.

About the Authors

      Tina M. Henkin is a Professor of Microbiology, Robert W. and Estelle S. Bingham Professor of Biological Sciences, and Distinguished University Professor at The Ohio State University, where she has been teaching microbiology and bacterial genetics since 1995. She received her B.A. in biology at Swarthmore College and her Ph.D. in genetics at the University of Wisconsin-Madison, and did postdoctoral work in molecular microbiology at Tufts University Medical School. Her research focuses on gene regulation in Gram-positive bacteria, primarily using Bacillus subtilis as a model. Her laboratory uncovered the T-box regulatory mechanism, in which the leader RNAs of bacterial genes bind a specific uncharged tRNA to modulate expression of the downstream genes. This work led to the discovery of riboswitch RNAs that bind cellular metabolites to mediate similar regulatory responses. Current work focuses on elucidating the basis for specific ligand recognition and molecular mechanisms for ligand-mediated changes in RNA structure in a variety of riboswitch classes. She is a Fellow of the American Academy of Microbiology, the American Association for the Advancement of Science, and the American Academy of Arts and Sciences, a member of the National Academy of Sciences, and co-winner of the National Academy of Sciences Pfizer Prize in Molecular Biology for her work on riboswitch RNAs.

      Joseph E. Peters is a Professor of microbiology at Cornell University, where he has been teaching bacterial genetics and microbiology at the graduate and undergraduate level since 2002. He received his B.S. from Stony Brook University and his Ph.D. from the University of Maryland at College Park. He did postdoctoral work at the Johns Hopkins University School of Medicine, in part as an NSF-Alfred P. Sloan Foundation postdoctoral research fellow in molecular evolution. His research has focused on the intersection between DNA replication, recombination, and repair and how it relates to evolution, especially in the area of transposition. Most recently he has been interested in the evolution of defense systems like CRISPR/Cas systems and how they can be repurposed by mobile elements for new tasks. Research in his lab is funded by the National Science Foundation, the U.S. Department of Agriculture, and the National Institutes of Health. He is the director of graduate studies for the field of microbiology at Cornell.

Introduction

      1  The Biological Universe The Bacteria The Archaea The Eukaryotes

      2  What Is Genetics?

      3  Bacterial Genetics Bacteria Are Haploid Short Generation Times Asexual Reproduction Colony Growth on Agar Plates Colony Purification Serial Dilutions Selections Storing Stocks of Bacterial Strains Genetic Exchange

      4  Phage Genetics Phages Are Haploid Selections with Phages Crosses with Phages

      5  A Brief History of Bacterial Molecular Genetics Inheritance in Bacteria Transformation Conjugation Transduction Recombination within Genes Semiconservative

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