Introduction

1. The Biological Universe
   1. The Bacteria
   2. The Archaea
   3. The Eukaryotes
2. What Is Genetics?
3. Bacterial Genetics
   1. Bacteria Are Haploid
   2. Short Generation Times
   3. Asexual Reproduction
   4. Colony Growth on Agar Plates
   5. Colony Purification
   6. Serial Dilutions
   7. Selections
   8. Storing Stocks of Bacterial Strains
   9. Genetic Exchange
4. Phage Genetics
   1. Phages Are Haploid
   2. Selections with Phages
   3. Crosses with Phages
5. A Brief History of Bacterial Molecular Genetics
   1. Inheritance in Bacteria
   2. Transformation
   3. Conjugation
   4. Transduction
   5. Recombination within Genes
   6. Semiconservative DNA Replication
   7. mRNA
   8. The Genetic Code
   9. The Operon Model
   10. Enzymes for Molecular Biology
   11. Synthetic Genomics
6. What Is Ahead

SEM images of the archaeon “Candidatus Prometheoarchaeum syntrophicum” strain MK-D1. Reprinted fromImachi H, et al, ©2020, Springer Nature, CC-BY 4.0,http://creativecommons.org/licenses/by/4.0/.

THE GOAL OF THIS TEXTBOOK is to introduce the student to the field of bacterial molecular genetics. From the point of view of genetics and genetic manipulation, bacteria are relatively simple organisms. There also exist model bacterial organisms that are easy to grow and easy to manipulate in the laboratory. For these reasons, most methods in molecular biology and recombinant DNA technology that are essential for the study of all forms of life have been developed around bacteria. Bacteria also frequently serve as model systems for understanding cellular functions and developmental processes in more complex organisms. Much of what we know about the basic molecular mechanisms in cells, such as transcription, translation, and DNA replication, has originated with studies of bacteria. This is because such central cellular functions have remained largely unchanged throughout evolution. Core parts of RNA polymerase and many of the translation factors are conserved in all cells, and ribosomes have similar structures in all organisms. The DNA replication apparatuses of all organisms contain features in common, such as sliding clamps and editing functions, which were first described in bacteria and their viruses, called bacteriophages. Chaperones that help other proteins fold and topoisomerases that change the topology of DNA were first discovered in bacteria and their bacteriophages. Studies of repair of DNA damage and mutagenesis in bacteria have also led the way to an understanding of such pathways in eukaryotes. Excision repair systems, mutagenic polymerases, and mismatch repair systems are remarkably similar in all organisms, and defects in these systems are responsible for multiple types of human cancers.

In addition, as our understanding of the molecular biology of bacteria advances, we are finding a level of complexity that was not appreciated previously. Because of the small size of the vast majority of bacteria, it was impossible initially to recognize the high level of organization that exists in bacteria, leading to the misconception that bacteria were merely “bags of enzymes,” where small size allowed passive diffusion to move cellular constituents around. However, it is now clear that movement and positioning within the bacterial cell are highly controlled processes. For example, despite the lack of a specialized membrane structure called the nucleus (the early defining feature of the “prokaryote” [see below]), the genome of bacteria is exquisitely organized to facilitate its repair and expression during DNA replication. In addition, advances facilitated by molecular genetics and microscopy have made it clear tha many cellular processes occur in highly organized subregions within the cell. Once it was appreciated that bacteria evolved in the same basic way as all other living organisms, the relative simplicity of bacteria paved the way for some of the most important scientific advances in any field, ever. It is safe to say that a bright future awaits the fledgling bacterial geneticist, where studies of relatively simple bacteria, with their malleable genetic systems, promise to uncover basic principles of cell biology that are common to all organisms and that we can now only imagine.

However, bacteria are not just important as laboratory tools to understand other organisms; they also are important and interesting in their own right. For instance, they play essential roles in the ecology of Earth. They are the only organisms that can “fix” atmospheric nitrogen, that is, convert N2 to ammonia, which can be used to mak