Chapter 13: The Prokaryotic Chromosome: Genetic Analysis in
Bacteria
Outline
I.
A general overview of prokaryotes
A. Numbers, sizes, life styles, and metabolic diversity of bacteria
1. Bacteria outnumber all other organisms on earth by many orders of magnitude
2. Researchers have identified 10,000 species of bacteria with an amazing range of sizes and life
styles
3. Bacteria display a remarkable metabolic diversity that enables them to live almost anywhere
4. Despite their diversity, bacterial cells have a number of features in common
B. The power of bacterial genetics is the potential for studying rare events
1. Researchers grow bacteria in liquid media or on media solidified by agar
2. Focus on E. coli
II.
The bacterial genome
A. One circular chromosome
1. The representation of genes, genotype, and phenotype depends on an understanding of
mutations
2. Structure and organization of the E. coli chromosome
3. Insertion sequences dot the E. coli chromosome
4. Transcription in E. coli
5. DNA replication in E. coli
6. Chromosomal evolution: comparing different strains of E. coli, and E. coli with Salmonella
typhimurium
B. Plasmids: smaller circles of DNA that do not carry essential genes
III. Gene transfer in bacteria
A. Transformation: fragments of donor DNA in the immediate environment enter the recipient
and alter its genotype
1. In natural transformation, the recipient cell has the enzymatic machinery for DNA import
2. In artificial transformation, damage to recipient cell walls allows donor DNA to enter the cells
B. Conjugation: donor cells carrying specialized plasmids establish contact with and transfer
DNA to recipients
1. The F plasmid and conjugation
2. The F plasmid occasionally integrates into the E. coli chromosome where it promotes the
conjugational transfer of essential chromosomal genes
3. Analyses of Hfr transfers help map genes
4. Comparisons of interrupted mating studies using different Hfr strains confirm that the bacterial
chromosome is a circle
5. Recombination analyses of Hfr crosses improve mapping accuracy
6. Bacterial geneticists can use a special type of F plasmid known as F’ for genetic
complementation studies
C. Transduction: gene transfer via bacteriophage
1. Bacteriophage particles are produced by the lytic cycle
2. Generalized transduction
3. Mapping genes by generalized transduction
4. Temperate phage can integrate into the bacterial chromosome
5. Phage lambda (O): a model temperate phage
6. Lysogens are immune to further infection by the same phage
7. Events that damage DNA may induce prophage to enter the lytic cycle
8. During induction, phage may acquire the capacity for specialized transduction
9. Summary: comparing generalized and specialized transduction
D. Many naturally occurring mechanisms of gene transfer have been adapted for genetic analysis
1. Mutant isolation
2. Mapping
IV. Comprehensive example: genetic dissection helps explain how bacteria move
A. How bacteria move to Achieve Chemotaxis Rotating flagella are the mechanical basis of the
random walk
B. Many Bacterial Mutants Cannot Carry Out Chemotaxis
1. Flagellum mutants
2. Motor mutants
3. Signal transduction mutants
4. Receptor mutants
Essential Concepts

Bacteria are prokaryotic cells with no membrane-enclosed nucleus or other cell organelles.
The bacterial genome consists of a single circular chromosome in which the genes are tightly
packed, with about one gene per kilobase pair.

During transcription in E. coli, different strands of DNA serve as the template for different
genes, with the most frequently transcribed genes oriented in the direction of replication fork
movement. Replication begins at the origin of chromosomal replication (oriC) and proceeds
bidirectionally around the circular genome to the termination region (terC).

Some bacteria carry, in addition to their chromosome, plasmids: small circles of doublestranded DNA. Plasmids may include genes that benefit the bacterial host under certain
conditions. One important group of plasmids promotes conjugative gene transfer between two
bacteria.

Bacterial genomes contain IS and Tn elements, transposons that can move between sites on
any DNA molecule in the cell.

Transformation is a form of gene transfer in which donor DNA that is floating free in the
growth medium enters a recipient cell. Some bacteria have cellular machinery that supports
efficient natural transformation. Species that do not undergo natural transformation can be
induced to take up DNA by treatments that disrupt their cell walls in a process known as
artificial transformation.

Conjugation is a second form of gene transfer. It depends on direct cell-to-cell contact
between a donor carrying a conjugative plasmid (the F plasmid is one example) and a
recipient lacking such a plasmid. In crosses between F + and F - strains, only the plasmid is
transferred. In crosses between Hfr and F - strains or between F’ and F - strains, the plasmid
also transfers chromosomal genes.

Transduction is a third form of gene transfer in bacteria. It depends on the packaging of
bacterial donor DNA in the protein coat of a bacteriophage. In generalized transduction,
phage can package any part of the donor genome. Specialized transduction is a property of
lysogenic bacteriophage, which can only package host genes adjacent to the integrated
prophage genome.

It is possible to map bacterial genes using any of the three forms of gene transfer. Interrupted
mating experiments can map the approximate positions of genes. Measures of frequencies of
cotransformation or cotransduction provide better resolution: the closer two genes are, the
more likely they are to appear on the same short DNA fragment. Sequences of complete
bacterial genomes are becoming increasingly important as mapping resources.