Lecture 6 - horizontal gene transfer (pre-midterm) Flashcards
Core genome
Set of genes found in every strain of a given bacterial species. In E. coli, approximately 450 genes
Pan genome
Set of all genes found in all strains of a given bacterial species. In E. coli, approximately 55 thousand genes.
Genomic island
Block of genes found in one strain of bacteria but not another; sometimes can be transferred between bacteria thru horizontal gene transfer
Base pair difference between E. coli O157:H7 and K12
500 base pairs are present in O157:H7 that aren’t in K12
Sources of DNA for horizontal gene transfer?
Transposons, genomic islands, phages, plasmids
Where did the gene sequence for shiga toxin come from?
Encoded by a lysogenic phage (integrates into the host genome)
What is the source of most toxins found in bacteria?
Genes encoded by horizontally transferred genes
What is a PAI?
Pathogenic associated island; genomic island that can encode one of multiple toxins
Three main methods of horizontal gene transfer
- Transformation
- Transduction
- Conjugation
Transformation
Direct uptake of naked/free DNA into bacterial cells
Transduction
Bacteriophage mediated transfer of DNA (usually DNA from one host cell to another)
Conjugation
Transfer of DNA using mating pili
Competent bacteria
Bacteria that are able to take up naked DNA from their environment
How is competence achieved in bacteria?
- natural competency
- artificially achieve by chemical (use Ca + low temps to make membrane brittle) or physical (voltage drops to punch holes) means
Observations of Griffith’s experiments with streptococcus pneumoniae
Rough (non-virulent) strain was able to take up virulence factors from heat-killed smooth (virulent) strain
Competence in Gram negative bacteria
Machinery related to type IV pilus from N. gonorrhoeae
- DNA receptor recognizes certain DNA
- pilus pulls DNA to the cell
- dsDNA degraded to ssDNA
- ssDNA imported into cell
Competence in Gram positive bacteria
Uses a pseudo-pilus that performs a similar action to Gram neg pilus. Grabs dsDNA, brings in ssDNA
Requirements of bacterial conjugation
- mediated by conjugation pili assembled by donor cell
- requires cell-cell contact
What is F factor?
Fertility factor. Low-copy plasmid that encodes proteins for the conjugation pilus.
Where was F factor discovered?
F+ E. coli cells
Replication origins in conjugative plasmids
- oriV: “vegetative” used for replication during the cell cycle
- oriT: “transfer” used during DNA transfer (conjugation)
Method of replication from oriV in conjugative plasmids
Similar mechanism to theta replication. Bidirectional
Method of replication from oriT in conjugative plasmids
Similar mechanism to rolling circle. Unidirectional, sends a single strand to recipient cell
General mechanism of conjugation
- Pilus forms between donor and recipient, contracts to bring cells together
- Bridge forms between donor and recipient
- Conjugative plasmid nicked at oriT and begins sending ssDNA through the bridge
- Transferred strand re-circularizes and replicates
Hfr strains
“High frequency recombination”
Strains of E. coli in which the F plasmid has integrated into the chromosome
What is unique about Hfr cells?
- capable of transferring large segments of the chromosome into recipient cells via conjugation
- entire chromosome can be transferred in about 100 minutes
Generalized recombination
Requires that the two recombining molecules have a considerable stretch of homologous DNA sequences
Site-specific recombination
Requires a short specific sequence recognized by the integrase/recombinase enzyme
Example of site-specific recombination
XerC resolution of catenated chromosomes
Recombination with RecA
RecA finds the homology between two strands and mediates strand invasion
Example of gene transfer into eukaryotes
Agrobacterium tumefaciens
- causes crown gall disease in plants
- contains a tumor inducing plasmid (Ti) that can be transferred via conjugation to plant cells
Transduction vs generalized transduction
Transduction: transfer of genes between cells using bacteriophage particles
Generalized: transfer of any gene between bacteria
Mechanism of generalized transduction
- Phage DNA inserted into bacteria
- Host chromosome degraded
- New phages assembled with host DNA instead of phage DNA
- Host DNA phage infects a new host
- Bacterial DNA integrated into new host genome
