Lecture 14: Information flow - DNA transfer

Question 1

which bacteria has the smallest genome?

Answer 1

Nasuia deltocephalinicola

Question 2

which bacteria has the largest genome?

Answer 2

Minicystis rosea

Question 3

what are PAIs?

Answer 3

pathogenicity assocaited islands where genes with related function cluster together on the genome

Question 4

what are the features of a bacterial genome?

Answer 4

• mostly circular
• supercoiled by DNA gyrase
• no nucleus or nuclear membrane
• no introns and exons

Question 5

how is the E.coli genome arranged?

Answer 5

several supercoiled domains that associate with histone like proteins

Question 6

what does a lack of nucleus allow for?

Answer 6

transcription and translation to be coupled

Question 7

what do plasmids consist of?

Answer 7

double stranded circular DNA

Question 8

what may plasmids carry?

Answer 8

insertion sequences or transposons

Question 9

how are circular genomes replicated?

Answer 9

bi-directionally creating a theta structure

Question 10

how are plasmids replicated?

Answer 10

theta (either bi or unidirectionally) or rolling circle

Question 11

what is HGT?

Answer 11

horizontal gene transfer that is the direct transfer of genetic material between cells

Question 12

what 3 things does HGT allow for?

Answer 12

• acquire new genetic material rapidly
• evolve new traits to adapt to environment/stresses
• accelerated rate of evolution

Question 13

what 3 ways does HGT differ from sexual reproduction?

Answer 13

• unidirectional (donor -> recipient)
• asymmetrical
• not constrained by species boundary

Question 14

what are the 3 main mechanisms of HGT?

Answer 14

• transformation
• transduction
• conjugation

Question 15

what is HGT mediated by?

Answer 15

RecA protein

Question 16

what are the 2 possible outcomes of HGT?

Answer 16

• patches -+– +-++
• splices –++ ++–

Question 17

what is another name for the transformation mechanism in HGT?

Answer 17

Natural competence

Question 18

what is the HGT transformation mediated by?

Answer 18

pilus or pseudopilus that reach for DNA and pull it into the cell

Question 19

what is HGT transformation regulated by?

Answer 19

quorum sensing mechanisms

Question 20

what is HGT transduction mediated by?

Answer 20

bacteriophages

Question 21

what are the 2 methods of HGT transduction?

Answer 21

generalised and specialised

Question 22

what are the 4 steps in generalised phage transduction?

Answer 22

1. phage attaches to host cell
2. phage injects DNA
3. homologous recombination of phage and host DNA
4. host cell in transduced

Question 23

what occurs in specialised transduction?

Answer 23

only a small region of the bacterial chromosome is transferred

Question 24

what does HGT conjugation require?

Answer 24

cell to cell contact via conjugative pilus

Question 25

what is HGT conjugation mediated by?

Answer 25

plasmids

Question 26

what are the 5 steps of HGT conjugation?

Answer 26

1. pilus binds and retracts causing cells to have a pathway between each other 2. F plasmid is nicked on one strand opening it 3. one of the plasmid strands is transferred and replicated in the other cell 4. synthesis of complimentary strand in other cell 5. plasmids are synthesised and DNA transfer is complete

Question 27

what are 3 barriers to HGT?

Answer 27

1. genomes between different species differentiating in GC content and codon usage 2. expression of restriction enzymes 3. CRISPR-cas9

Question 28

what are transposable elements?

Answer 28

discrete segments of DNA that move from one location to another

Question 29

what are transposable elements mobilised by?

Answer 29

transposase enzyme via inverted repeat sequences

Question 30

what are the 2 types of transposable elements?

Answer 30

insertion sequences and transposons

Question 31

how does transposase work?

Answer 31

- recognises a specific sequence - cuts and ligates DNA leading to duplication of target sequence

Question 32

what are 3 facts about insertion sequences?

Answer 32

- may be present in mutiple copies on host genomes/plasmids - can lead to widespread DNA rearrangements - responsible for mobilisation of vancomycin resistance genes

Question 33

what are 3 facts about transposons?

Answer 33

- larger than IS - comprise IS elements flanking antibiotic resistance genes - encode Tra genes enabling mobilisation via conjugation