bacterial evolution

Question 1

what is the rate for a point mutation? and can this rate ever change?

Answer 1

Rate = 10-6 to 10-9 per nt per generation in bacteria growing under normal culture condition.
1. yes, under stress the rate can increase 10000 fold

Question 2

what are examples of point mutations?

Answer 2

Indels, SNPs

Question 3

What is DNA recombination?

Answer 3

physical change of DNA between genetic elements

Question 4

What can result from recombination?

Answer 4

• deletion or insertion (think about during replication when there are 2 chromosomes)
• inversion (rearrangement) (think about the loop)

Question 5

where does recombination occur?

Answer 5

rearrangement: inverted repeats

deletion/insertion: direct repeats

Question 6

what is antigenic variation?

Answer 6

• the pathogens can change its antigen

- it can do this through phase variation,

Question 7

what is phase variation and what is an example?

Answer 7

phase variation is when there are two states for a phenotype and the bacteria can switch between these states.
Example: Salmonella is able to switch between two type of flagella, H1 and H2, at a frequency of 10-4.

Question 8

what is a slipped-strand misrepair and its 2 mechanisms? Where might this occur

Answer 8

-during transcription and replication the two strands are separated. when they rehybridize the bases don’t line up properly resulting in a loss or gain of genetic material
1. excision of the loops - small increment deletions
2. incision opposite the loops - small increment insertions
found in areas of REPEATS

Question 9

Gene shuffling - antigenic variation example

Answer 9

pilS is a copy of pilE without the promoter. only one pilE in a cell and multiple pilS (10-20 all with different variants, antigens (epitopes)). pilS and pilE can recombine and produce many different pilE- N. gonorrhoeae
-pilS and pilE are very similar, but not the same

Question 10

phase variation: salmonella specifics

Answer 10

promotor region is located within 2 inverted repeats, so it has the potential to cause a rearrangement (inversion). Normally the promoter is located upstream of H2 and repressor of H1. when it is inverted it cannot express H2 and the repressor of H1, so H1 is expressed.

Question 11

slip-strand misrepair example: Opa protein

Answer 11

each Opa protein has a different amount of CTCTT repeats before the protein (which has 1 semivariable region and 2 multivariable regions). depending on the amount of repeats the frame will be different, creating truncated Opa proteins
-everyone has their own Opa protein and even then your Opa protein can change

Question 12

can slip strand misrepair cause phase variation?

Answer 12

yes

Question 13

two component system

Answer 13

when virulence is regulated by two genes, forming a system that regulates gene expression

Question 14

example of two component system and slip strand misrepair

Answer 14

• promotes chronic infection
• example is bvgS. Gs (or Cs) can be added to the gene, which results in a truncated protein and then the virulence gene is not expressed. These bacteria wait to join the fight later when the GC pair is removed.

Question 15

HGT

Answer 15

acquisition of DNA from the outside (intergenic variation)

• transformation: pick up DNA (usually random) from outside
• conjugation: specific transfer of a plasmid
• transduction (mediated by phage, which transports DNA into the cell)

Question 16

transformants

Answer 16

cells that have acquired foreign DNA through transformation

Question 17

competent

Answer 17

describes bacteria that can pick up DNA from their environment and incorporate it into their genome

Question 18

DUS

Answer 18

DNA uptake sequence: some bacteria are only competent for DNA sequences from their own species. specific sequences

Question 19

mouse experiment for natural transformation

Answer 19

1. smooth strain (capsule) mouse - dead
2. rough strain mouse - alive
3. heat killed smooth - alive
4. heat killed smooth and rough strain - dead

ie the rough acquired the virulence factor (capsule) that allowed it to survive and kill the host

Question 20

what is competence regulated by

Answer 20

stress - may acquire new function that will help you deal with that stress. (sometimes competent cells will kill non-competent cells to steal their DNA )

Question 21

conjugation

Answer 21

when plasmids are transferred from a donor cell to a recipient cell.

Question 22

what is a self-transmissible plasmid?

Answer 22

a plasmid is an accessory genes(200,000bp limit)

• have everything they need for transfer
• formation of a pili, formation of a mechanism for transfer, and transfer of the plasmid as a single strand, recipient synthesizes second strand
• Result: both cells have the plasmid

Question 23

what is a mobilizable plasmid

Answer 23

• miss some of the genes required for transmission (ie genes to form the pili)
• needs to require a transmissible plasmid
  result: both have the mobilizable plasmid (and of course one still has the self-transmissible plasmid

Question 24

transposon

Answer 24

• jumping genes
• a gene with inverted repeats on both sides. the gene usually is for a benefit for the bac ie drug resistance
• encodes transposase
• can insert itself into another DNA molecule
• can jump from the bac chromosome to the plasmid

Question 25

composite transposon

Answer 25

• if there are two transposons very close to each other they can potentially jump together and take any genes that are between them.
• allows the transfer of a large portion of the genome to other bacteria

Question 26

PAI

Answer 26

PAIs can constitute 10-20% of a bacterial genome.
• PAIs can be visualized in the genome as a “scar” resulting from a HGT event.
• PAIs usually have a different %GC content than the rest of the genome and are bordered by direct repeats or contains genes of mobile DNA elements.
• Many PAIs encode genes that give the bacteria virulence function (Secretion system, LPS modification, iron acquisition, capsule, etc).
ie: high GC content, near tRNA, usually encode a gene with a virulence function