Chapter 9 Flashcards
Genomic analysis shows that microbes undergo extensive gene loss and gain
result of?
20% of E. coli genome may have originated in other microbes
horizontal gene transfer, recombinations, and a variety of mutagenic and DNA repair strategies
Horizontal gene transfer
movement of genes between species or genera
vertical gene transfer
generational passing of genes from parent to offspring (cell division)
transformation
importing DNA into cells
• At least 82 known naturally competent (capable of importing DNA) species
• Gram-positive (Streptococcus, Bacillus)
• Gram-negative (Haemophilus, Nisseria)
Requires specific protein complexes called transformasomes
• Why is natural transformation useful?
- Use as ”food”
- DNA repair
- Influence evolution – species adjust to new envir. by new genes.
Gram-positive – growth phase dependent competence
- Triggered by quorum sensing
- Each cell secretes a small peptide called competence factor (CF) – unique to each species
- CF increases as population increases
- Above a certain concentration CF activates a phosphorylation cascade that activates transcription of transformasome
Gram-negative
•no CF-always competent (Nisseria) or become comp. when starved (Haemophilus)
•Have a similar transformasome
•Outer membrane barrier
-Neisseria use pilus assembly-when pilus disassembles it drags DNA into cell
-Pilus naturally assembles and disassembles during growth
Transformation is species and sequence specific
limits exchange between genera
conjugation
cell-cell contact w sex pilus sticking out from a donor cell
Hfr strain
high-frequency recombination strain – F-
factor integrated into chromosome
Generalized transduction
take gene from donor cell to recipient
• Uses rolling circle-makes long copy of dna (concatemers)
• pac site to cut them into indiv. pieces
Specialized transduction
transfer only a few closely linked genes b/w cells
• Example (E. coli)
• integrates into host chromosome(lysogenic)
• Improper excision by host recombination enzymes – take host genes adjacent to attachment site
What is the fate of new DNA that has entered the cell?
- Plasmid capable of autonomous replication
- May be incorporated into chromosome
- Degraded by nucleases –seen as foreign DNA bc lack of methylation or by CRISPR
Generalized recombination
two recombining molecules w significant homology (crossing over in sections of dna)
Site specific recombination
little sequence homology – requires short (10-20 bp) sequence recognized by recombination enzyme
Why is recombination advantageous?
- DNA repair mechanism
- Cells w/ damaged chromosomes use DNA donated by others from same species to repair damaged genes
- “Self-improvement” program – samples genes from other organisms to enhance fitness of cell
Mutation
• change in base sequence and failure for cell to repair the change
point mutation
change in a single nucleotide
silent mutation
does not change AA sequence. lys–>lys (degenerate codon)
Missense mutation
changes aa sequence
Loss-of-function mutation
decreases or eliminates protein activity
gain-of-function mutation
increases or gain new activity
knockout mutation
eliminates function
Frameshift mutation
insertion or deletion of 1-2 bp (not multiple of 3). ribosome reads wrong triplets. sometimes stop codon.
mutagens
ex. uv light
chemical agents that can damage DNA
for pyrimidine-creates pyrimidine dimer that blocks replication/transcription
spontaneous mutations
• Rare bc DNA repair/proofreading is efficient
• Tautomeric shifts- C binds to A
• Deamination reactions – C change to U
• Damage by reactive oxygen species (H2O2, superoxide/hydroxyl radicals)
-interfere w/ polymerases and stops replication/transcription
Methyl mismatch repair
deoxyadenosine methylase (Dam) –methylates GATC
• Only parent strand methylated
• Mut proteins-cut out incorrect base, DNA Pol I fills in correct base
DNA repair – Error proof repair
• Photoreactivation
Photolyase binds pyrimidine dimer and cleaves cyclobutane ring linking damaged nucleotides
DNA repair – Error proof repair
• Nucleotide excision repair
- removes 12-13 nucleotides
* DNA Pol I repairs gap
DNA repair – Error proof repair
• Base excision repair
• Glycosylase clip damaged bases -U fromC deamination -Deamination of A to hypoxanthine • Cuts out single base • Endonuclease cleaves the backbone • DNA Pol I repairs strand
• E. coli’s genome is rife with
genomic islands, inversions, deletions, paralogs and orthologs
Transposable elements
enzyme that copies sequence from one dna into anther (tranasposase enzyme makes this happen)
• Not autonomous – cant exist outside of larger DNA molecule
insertion sequences (FOR TRANSPOSABLE ELEMENTS)
simple transposable element (700- 1500 bp)
Transposons
carry other genes plus those required for transposition
transposition
moving a transposable element b/w DNA
stop codons
uaa, uga, uag
F’ factor
takes some chromosomal dna
DNA repair – Error proof repair
Recombinational repair
•both strand/one strand is damaged
-DNA Pol III skips over damaged regions
• RecA binds gap and w/ piece of undamaged DNA
• Damage can be repaired by other mechanisms
DNA repair – Error proof repair
• SOS (“save our ship”) repair
extensive damage
• RecA binds ssDNA (stimulates autodig. of LexA repressor)
“sloppy ”polymerases w/ NO proofreading- insert whatever is available
DNA repair – Error proof repair
Nonhomologous end joining
Double stranded breaks are
dangerous. Ku and LigD recombine them. can be errors.
