13th week:

Chapter 10.
Genetics of Bacteria and Archaea
(Bacteria와 Archaea의 유전학)
 Chapter 10

Chapter 11
(12th Edition)
Genetics of Bacteria and Archaea
(Bacteria와 Archaea의 유전학)
 Genetic Map of the Escherichia coli
Chromosome
• Escherichia coli is a useful model organism for the study of
biochemistry, genetics, and bacterial physiology
• The E. coli chromosome from strain MG1655 has been mapped using
conjugation, transduction, molecular cloning, and sequencing
• Some Features of the E. coli Chromosome
– Many genes encoding enzymes of a single biochemical pathway are clustered
into operons
– Operons equally distributed on both strands
– ~ 5 Mbp in size
– ~ 40% of predicted proteins are of unknown function
– Average protein contains ~ 300 amino acids
– Insertion sequences (IS elements)
Circular Linkage Map of the Chromosome of E. coli K-12

Source: Brock Biology of Microorganisms 12th edition.

Figure 11.1
 Plasmids
• Plasmids: genetic elements that replicate independently of the host
chromosome
– Small circular or linear DNA molecules
– Range in size from 1 kbp to > 1 Mbp; typically less than 5% of the size of the
chromosome
– Carry a variety of nonessential, but often very helpful, genes
– Abundance (copy number) is variable
• A cell can contain more than one plasmid, but it cannot be closely
related genetically due to plasmid incompatibility
– Many Incompatibility (Inc) groups recognized
– Plasmids belonging to same Inc group exclude each other from replicating in
the same cell but can coexist with plasmids from other groups
 Plasmids
• Some plasmids (episomes) can integrate into the cell chromosome;
similar to situation seen with prophages
• Removal (curing) plasmids from host cells can result from various
treatments
• Conjugative plasmids can be transferred between suitable organisms
via cell-to-cell contact
– Conjugal transfer controlled by tra genes on plasmid
– Genetic information encoded on plasmids is not essential for cell function
under all conditions but may confer a selective growth advantage under certain
conditions
• R plasmids
– Resistance plasmids; confer resistance to antibiotics and other growth
inhibitors
– Widespread and well-studied group of plasmids
– Many are conjugative
Genetic Map of the Resistance Plasmid R100

Source: Brock Biology of Microorganisms 12th edition.

Figure 11.3
 Mutation
• Mutation
– Heritable change in DNA sequence that can lead to a change in phenotype (observable
properties of an organism)
• Mutant
– A strain of any cell or virus differing from parental strain in genotype (nucleotide sequence of
genome)
• Wild-type strain
– Typically refers to strain isolated from nature
• Selectable mutations
– Those that give the mutant a growth advantage under certain environmental conditions
– Useful in genetic research
• Nonselectable mutations
– Those that usually have neither an advantage nor a disadvantage over the parent
– Detection of such mutations requires examining a large number of colonies and looking for
differences (screening)
 Mutation
• Screening is always more tedious than selection
• Methods available to facilitate screening
– E.g., replica plating
• Replica plating is useful for identification of cells with a nutritional
requirement for growth (auxotroph)
• Induced mutations
– Those made deliberately

• Spontaneous mutations
– Those that occur without human intervention
– Can result from exposure to natural radiation or oxygen radicals

• Point mutations
– Mutations that change only one base pair
– Can lead to single amino acid change in a protein or no change at all
Screening for Nutritional Auxotrophs

Figure 11.5
Source: Brock Biology of Microorganisms 12th edition.
Figure 11.5
 Mutation
• Silent mutation
– Does not affect amino acid sequence
• Missense mutation
– Amino acid changed; polypeptide altered
• Nonsense mutation
– Codon becomes stop codon; polypeptide is incomplete
• Deletions and insertions cause more dramatic changes in DNA
• Frameshift mutations
– Deletions or insertions that result in a shift in the reading frame
– Often result in complete loss of gene function
Genetic engineering allows for the introduction of specific mutations (site-directed
mutagenesis)
 Mutation
• Point mutations are typically reversible
• Reversion
– Alteration in DNA that reverses the effects of a prior
mutation
• Revertant
– Strain in which original phenotype that was changed in the
mutant is restored
– Two types
• Same-site revertant: mutation restoration activity is at the
same site as original mutation
• Second-site revertant: mutation is at a different site in the
DNA
 Mutation
• Several forms of radiation are highly mutagenic
• Two main categories of mutagenic electromagnetic radiation
– Non-ionizing (i.e., UV radiation)
• Purines and pyrimidines strongly absorb UV
• Pyrimidine dimers is one effect of UV radiation
– Ionizing (i.e., X-rays, cosmic rays, and gamma rays)
• Ionize water and produce free radicals
• Free radicals damage macromolecules in the cell
• Three Types of DNA Repair Systems
– Direct reversal: mutated base is still recognizable and can be repaired without
referring to other strand
– Repair of single strand damage: damaged DNA is removed and repaired using
opposite strand as template
– Repair of double strand damage: a break in the DNA
• Requires more error-prone repair mechanisms
 Genetic Exchange in Prokaryotes
(원핵생물에서 유전물질의 교환)
• Recombination
– Physical exchange of DNA between genetic elements

• Homologous recombination
– Process that results in genetic exchange between homologous DNA from two different sources

• Selective medium can be used to detect rare genetic recombinants

• Plant viruses

• Transformation
– Genetic transfer process by which DNA is incorporated into a recipient cell and brings about
genetic change
• Discovered by Fredrick Griffith in the late 1920s
– Worked with Streptococcus pneumococcus
• This process set the stage for the discovery of DNA
• Competent: cells capable of taking up DNA and being transformed
– In naturally transformable bacteria, competence is regulated
– In other strains, specific procedures are necessary to make cells competent and electricity can
be used to force cells to take up DNA (electroporation)
Griffith’s Experiments with Pneumococcus

Source: Brock Biology of Microorganisms 12th edition.

Figure 11.15
Mechanisms of Transformation in Gram-Positive Bacteria

Source: Brock Biology of Microorganisms 12th edition.

Figure 11.16
 Genetic Exchange in Prokaryotes
(원핵생물에서 유전물질의 교환)
• Transduction
– Transfer of DNA from one cell to another is mediated by a bacteriophage
– Two modes
• Generalized transduction: DNA derived from virtually any portion of the host genome is
packaged inside the mature virion
• Specialized transduction: DNA from a specific region of the host chromosome is integrated
directly in the virus genome
• Generalized transduction: DNA derived from virtually any portion of the
host genome is packaged inside the mature virion
– Defective virus particle incorporates fragment of the cell’s chromosome
randomly
– Can be temperate or virulent
– Low efficiency
 Genetic Exchange in Prokaryotes
(원핵생물에서 유전물질의 교환)
• Specialized transduction: DNA from a specific region of the host
chromosome is integrated directly in the virus genome
– DNA of temperate virus excises incorrectly and takes adjacent host genes along with it
– Transducing efficiency can be high
• Bacterial conjugation (mating): mechanism of genetic transfer that
involves cell-to-cell contact
– Plasmid encoded mechanism
– Donor cell: contains conjugative plasmid
– Recipient cell: does not contain plasmid
• F (fertility) plasmid
– Circular DNA molecule; ~ 100 kbp
– Contains genes that regulate DNA replication
– Contains several transposable elements that allow the plasmid to integrate into the host
chromosome
– Contains tra genes that encode transfer functions
Generalized Transduction

Source: Brock Biology of Microorganisms 12th edition.

Figure 11.17
Specialized Transduction

Source: Brock Biology of Microorganisms 12th edition.

Figure 11.18
Genetic Map of the F (Fertility) Plasmid of E. coli

Source: Brock Biology of Microorganisms 12th edition.

Figure 11.19