Bacterial Genetics II (Ch. 9, Lec. 11)
Wednesday, October 28, 2020 12:47 AM
• Silent mutation: does not change the amino acid sequence.
• Missense mutation: results in an amino acid substitution.
• Nonsense mutation: changes the amino acid sequence to a stop codon.
• Frame-shift mutation: changes the open reading frame of the gene.
• Spontaneous mutations are rare b/c of DNA efficiency in proofreading and repair:
○ Arise from tautomeric shifts in DNA bases that alter bp properties, oxidative deamination of
bases, formation of apurinic sites, and damage caused by reactive O2 species.
• Mutagens: chemical agents (base analogs/modifiers, intercalators) and EM radiation (X-rays and
gamma rays break up the DNA, UV rays form pyrimidine dimers->block replication/transcription)
that cause mutations.
• Mutagen testing: test for whether a certain chemical causes mutations in the DNA of the test
organism.
○ Ex. Mixing potential mutagens w/ rat liver homogenate mimics effect of human liver on these
mutagens.
○ Growth = reversion mutations incurred by the hisG mutant bacteria. -> Growth indicates that
a compound is potentially mutagenic.
9.2: DNA Repair
• DNA repair types:
1. Error-proof repair pathways: prevent mutations thru methyl mismatch repair, photoreactivation,
nucleotide excision repair, base excision repair, and recombinational repair.
2. Error-prone repair pathways: risk introducing mutations in near-death situations.
9.3: Gene Transfer--Mechanisms and Barriers
• Microbial genomes have a mosaic nature-- taking up foreign DNA can be beneficial.
○ Imported DNA can be sued as an alt food source, repair damaged chromosomes, and drive
genome evolution.
• Conjugation: DNA transfer from one bacterium to another, requiring cell-to-cell contact. Initiated
by pilus protruding from the donor cell.
○ Ex. Bacteria that causes crown gall disease contains a tumor-inducing plasmid that can be
transferred via conjugation to plant cells. -> bacteria can transfer genes across domains.
○ Requires transferable plasmids. Ex. E. coli has a fertility factor (F factor), which contains 2
replication origins:
• oriV: used in non-conjugating cells.
• oriT: used during DNA transfer.
○ Begins when the F+ (donor cell) comes in contact w/ the F- cell.
○ F-factor plasmid can integrate into the chromosome. -> cell is now Hfr, or high-freq
recombination strain.
○ Hfr cell is capable of transferring parts of the chromosome into a recipient cell. Genes are
transferred in order.
○ An integrated F factor excise from the chromosome via host recombination. -> Aberrant
excision results in an F' factor / F' plasmid, which carries the chromosomal genes. ->
• Partial diploid: F' plasmid that can express these extra chromosomal genes.
• Transduction: bacteriophages carry host DNA from one cell to another.
1. Generalized transduction: transfers ANY gene from a donor to a recipient cell.
2. Specialized transduction: transfers ONLY a few closely linked genes to the phage insertion site
b/w cells.
• CONs of bacterial DNA transfer-- harms the host cell. To protect themselves:
○ Restriction endonucleases cleave alien DNA.
○ Host DNA is methylated, preventing restriction enzymes from cutting into it.
• Transformation: importing free DNA into the bacterial/archaeal cell.
○ Competent cells: cells that are capable of taking up foreign DNA from their environment.
○ Ex. Gram-negative bacterium V. chloerae extends a type IV pilus, which can actively take up
free DNA.
• GI tract is ideal place for DNA transfer: high-density biofilms allow for close contact required for
conjugation, GI tract contains many phage that can mediate transduction.
• Restriction endonucleases Type I and III have restriction and modification activities. -> cleave
DNA some dist away from the recognition site.
• Type II endonucleases possess only endonuclease activity.
• In general, endonucleases recognize palindromic DNA sequences and cleave at those sites.
Wednesday, October 28, 2020 12:47 AM
• Silent mutation: does not change the amino acid sequence.
• Missense mutation: results in an amino acid substitution.
• Nonsense mutation: changes the amino acid sequence to a stop codon.
• Frame-shift mutation: changes the open reading frame of the gene.
• Spontaneous mutations are rare b/c of DNA efficiency in proofreading and repair:
○ Arise from tautomeric shifts in DNA bases that alter bp properties, oxidative deamination of
bases, formation of apurinic sites, and damage caused by reactive O2 species.
• Mutagens: chemical agents (base analogs/modifiers, intercalators) and EM radiation (X-rays and
gamma rays break up the DNA, UV rays form pyrimidine dimers->block replication/transcription)
that cause mutations.
• Mutagen testing: test for whether a certain chemical causes mutations in the DNA of the test
organism.
○ Ex. Mixing potential mutagens w/ rat liver homogenate mimics effect of human liver on these
mutagens.
○ Growth = reversion mutations incurred by the hisG mutant bacteria. -> Growth indicates that
a compound is potentially mutagenic.
9.2: DNA Repair
• DNA repair types:
1. Error-proof repair pathways: prevent mutations thru methyl mismatch repair, photoreactivation,
nucleotide excision repair, base excision repair, and recombinational repair.
2. Error-prone repair pathways: risk introducing mutations in near-death situations.
9.3: Gene Transfer--Mechanisms and Barriers
• Microbial genomes have a mosaic nature-- taking up foreign DNA can be beneficial.
○ Imported DNA can be sued as an alt food source, repair damaged chromosomes, and drive
genome evolution.
• Conjugation: DNA transfer from one bacterium to another, requiring cell-to-cell contact. Initiated
by pilus protruding from the donor cell.
○ Ex. Bacteria that causes crown gall disease contains a tumor-inducing plasmid that can be
transferred via conjugation to plant cells. -> bacteria can transfer genes across domains.
○ Requires transferable plasmids. Ex. E. coli has a fertility factor (F factor), which contains 2
replication origins:
• oriV: used in non-conjugating cells.
• oriT: used during DNA transfer.
○ Begins when the F+ (donor cell) comes in contact w/ the F- cell.
○ F-factor plasmid can integrate into the chromosome. -> cell is now Hfr, or high-freq
recombination strain.
○ Hfr cell is capable of transferring parts of the chromosome into a recipient cell. Genes are
transferred in order.
○ An integrated F factor excise from the chromosome via host recombination. -> Aberrant
excision results in an F' factor / F' plasmid, which carries the chromosomal genes. ->
• Partial diploid: F' plasmid that can express these extra chromosomal genes.
• Transduction: bacteriophages carry host DNA from one cell to another.
1. Generalized transduction: transfers ANY gene from a donor to a recipient cell.
2. Specialized transduction: transfers ONLY a few closely linked genes to the phage insertion site
b/w cells.
• CONs of bacterial DNA transfer-- harms the host cell. To protect themselves:
○ Restriction endonucleases cleave alien DNA.
○ Host DNA is methylated, preventing restriction enzymes from cutting into it.
• Transformation: importing free DNA into the bacterial/archaeal cell.
○ Competent cells: cells that are capable of taking up foreign DNA from their environment.
○ Ex. Gram-negative bacterium V. chloerae extends a type IV pilus, which can actively take up
free DNA.
• GI tract is ideal place for DNA transfer: high-density biofilms allow for close contact required for
conjugation, GI tract contains many phage that can mediate transduction.
• Restriction endonucleases Type I and III have restriction and modification activities. -> cleave
DNA some dist away from the recognition site.
• Type II endonucleases possess only endonuclease activity.
• In general, endonucleases recognize palindromic DNA sequences and cleave at those sites.
