Molecular Genetics of Bacteria 5th Edition

Book Preface

In the preface to the fourth edition (published in 2004) we referred to the revolution in bacterial genetics that was started by gene cloning and sequencing, coupled with related techniques such as the polymerase chain reaction (PCR) and microarrays, and culminated in knowledge of genome sequences of a rapidly expanding range of bacteria. This posed a dilemma. How could we accommodate these new techniques, and the wealth of exciting new information they provided, while not losing sight of classical bacterial genetics? This dilemma has become even more acute.

True, many of the older methods are now no longer used, and could be relegated to the pages of history. But there is a danger of throwing out the baby with the bathwater. Not only is there a need to maintain some sense of how the subject has got to the stage we are now at, but also a discussion of some of these methods is useful in establishing an understanding of how bacterial genetics operates in natural environments. Genetics is not just about how we find out about bacteria: it is about how bacteria have evolved, and continue to evolve, and continue to adapt to changing environments. Molecular genetics, in isolation, is essentially reductionist. Even genome sequencing, and global analysis of gene expression, by themselves merely provide catalogues of genes. Ultimately, those lists have to be related to the behaviour of the whole organism, and from there to how organisms interact with one another and with their environment.

So we have continued with a compromise approach, slimming down even further the description of classical bacterial genetics to allow space not only for some of the new technological advances but also for some of the advances that these methods have allowed in understanding important aspects of bacterial behaviour.

One further aspect needs a word of explanation. What is a bacterium? It is now clear that there are two distinct types of prokaryote: the bacteria proper and the Archea. Most of this book concerns the bacteria in the proper taxonomic sense, but some aspects are also relevant to Archea, especially where we consider the differences between prokaryotes and eukaryotes. It complicates the text too much to make this distinction, so we apologize if anyone is offended by occasional blurring of the lines between bacteria and prokaryotes.

As with the earlier editions, the choice of what to include and what to leave out is very much a personal one. We hope that the final product will remain accessible for a non-specialist reader, and will succeed in introducing them to both the exciting and rapidly developing field of molecular genetics and also the fascinating world of bacteria.

Jeremy W. Dale
Simon F. Park

In this book it is assumed that you will already have a working knowledge of the essentials of molecular biology, especially the structure and synthesis of nucleic acids and proteins. The purpose of this chapter therefore is to serve as a reminder of some of the most relevant points, and to highlight those features that are particularly essential for an understanding of later chapters.

n bacteria, the genetic material is double-stranded DNA, although bacterio-phages (viruses that infect bacteria; see Chapter 4) may have double-stranded or single-stranded DNA, or RNA. The components of DNA (Figure 1.1) are
2-deoxyribose (forming a backbone in which they are linked by phosphate residues) and four heterocyclic bases: two purines (adenine, A, and guanine,
G) and two pyrimidines (thymine, T, and cytosine, C). The sugar residues are linked by phosphodiester bonds between the 5 position of one deoxyribose and the 3 position of the next (Figure 1.2), while one of the four bases is attached to the 1 position of each deoxyribose. It is the sequence of these four bases that carries the genetic information.

The two strands are twisted around each other in the now familiar double helix, with the bases in the centre and the sugar-phosphate backbone on the outside. The two strands are linked by hydrogen bonds between the bases. The only arrangement of these bases that is consistent with maintaining the helix in its correct conformation is when adenine is paired with thymine and guanine with cytosine. One strand therefore consists of an image of the other; the two strands are said to be complementary. Note that the purines are larger than the pyrimidines, and that this arrangement involves one purine opposite a pyrimidine at each position, so the distance separating the strands remains constant The structure of RNA differs from that of DNA in that it contains the sugar ribose instead of deoxyribose, and uracil instead of thymine (Figure 1.1). It is usually described as single-stranded, but only because the complementary strand is not normally made. There is nothing inherent in the structure of RNA that prevents it forming a double-stranded structure: an RNA strand will pair with (hybridize to) a complementary RNA strand, or with a complementary strand of DNA. Even a single strand of RNA will fold back on itself to form double-stranded regions. In particular, transfer RNA (tRNA), and ribosomal RNA (rRNA) both form complex patterns of base-paired regions. The formation of secondary and tertiary structures in RNA via base-pairing can also influence gene expression and this is considered in further detail in Chapter 3.