Chapter 9: Genetics of Bacteria and Archaea

Mutations are heritable alterations in DNA sequence that arise either spontaneously through replication errors or through exposure to mutagens such as chemical agents or radiation. The chapter explains the molecular basis of mutation, including point mutations that produce missense, nonsense, or silent substitutions, as well as frameshift mutations caused by insertions or deletions that disrupt the reading frame of genes. Additional genetic events such as reversions and suppressor mutations illustrate how secondary mutations can restore or modify phenotypic outcomes. Microbial cells also possess DNA repair systems that maintain genomic stability, although some repair pathways such as the SOS response introduce additional mutations during damage recovery. The chapter then examines genetic recombination and the mechanisms of horizontal gene transfer that allow microorganisms to exchange genetic information independently of reproduction. Transformation involves the uptake of free DNA from the environment by competent cells and its integration into the chromosome through homologous recombination mediated by proteins such as RecA. Transduction occurs when bacteriophages transfer bacterial DNA between cells during infection cycles, while conjugation requires direct cell to cell contact and typically involves conjugative plasmids such as the F plasmid that mediate DNA transfer through a conjugative pilus. Integration of the F plasmid into the chromosome produces Hfr strains capable of transferring chromosomal genes, and excision events can generate F prime plasmids carrying host DNA. The chapter also describes mobile genetic elements such as insertion sequences and transposons that move within genomes through transposition, contributing to genome rearrangement and the spread of traits such as antibiotic resistance. Finally, microbial defense systems that protect genomic integrity are discussed, including restriction endonucleases that degrade foreign DNA and CRISPR Cas adaptive immune systems that recognize and cleave previously encountered viral or plasmid sequences.