Horizontal Gene Transfer

examples of mobile genetic elements

• transposons

• integrated phage DNA

• plasmids

• pathogenicity islands

what is the size of a plasmid

1 kbp to more than 1 mbp

• less than 5% of the size of the chromosome

what type of genetic information is on a plasmid

non-essential genes, commonly accessory

• heavy metal resistance

• antibiotic resistance

• toxins

• virulence factors

do all members of the same species have the same plasmids

no

what is conjugation

ability for plasmids to transfer themselves, or other DNA, from one cell to another

who discovered conjugation

lederberg and tatum

what was Strain A positive and negative for in the U tube experiment

positive

• met

• bio

• thr

negative

• leu

• thi

explain the U tube experiment

demonstrated that cell-to-cell contact is needed to transfer genetic material by conjugation. in the tube, there was a filter separating cells A and cells B that would allow only chemicals to pass. cells from the tube were plated, but nothing grew. when cells A and cells B were mixed together and cell-to-cell contact was allowed, they were able to exchange genetic material. As a result, they were able to support each others growth on plate

what is a transconjugant

a recipient cell that has completed conjugation and now has the plasmid

how many tra genes are on the F plasmid

at least 20

OriV vs OriT

OriV is used for vegetative replication while OriT is used for transfer during conjugation

explain how DNA is transferred via F plasmid conjugation

1. the recipient is reocgnized by the donor cell, and MPF coupling protein confirms the pair is established

2. MPF coupling protein will signal to relaxase to cut at the OriT

3. relaxase will hold on to the 5’ end of one strand of DNA and bring it to the recipient cell as helicase unwinds the DS DNA

4. relaxase will make sure the SS DNA forms a circle

5. the SS plasmid in the donor cell has a 3’ end that serves as a primer, while the SS plasmid in the recipient cell needs primase

6. the complimentary strand will be synthesized in both cells to make DS plasmid

7. there will be the donor cell and the transconjugant at the end

self-transmissible plasmid vs mobilizable plasmid

• self-transmissible plasmids can transfer themselves (e.g. F plasmid uses its tra genes for transfer)

• mobilizable plasmids can be transferred to another self, but only with the help of self-transmissble plasmids

how are mobilizable plasmids transferred

1. the tra genes on the F plasmid will help contact the recipient cell

2. the MPF coupling system of the F plasmid will signal to the relaxase of the mobilizable plasmid

3. the transfer of the mobilizable plasmid to the recipient can begin

4. only the mobilizable plasmid is transferred, not the F plasmid

which part of the Ti plasmid is transferred from A. tumefaciens

T-DNA, which consists of oncogenes and opine synthesis genes

what else is on the Ti plasmid

vir genes, T-DNA, opine catabolism genes

how is the T-DNA transferred to the wounded plant cell

1. VirA will autophosphorylate upon sensing phenolic compounds from a wounded plant

2. it will then transfer its phosphate group to VirG

3. VirG~P will activate other vir genes

4. VirD endonuclease will cut on both sides of the T-DNA region

5. VirE will bind to the nicked plasmid and transfers it to VirB

6. VirB will transfer the plasmid to the plant cell

what must happen for the T-DNA to work

• the single stranded T-DNA must be DS

• the T-DNA must enter the nucleus, and then integrate into the plant chromosome

what is transposon

DNA elements that can jump from DNA site to another

which organisms have transposon

all

type 1 composite transposons

• have IS elements on both ends of genes that carry benefit

• transposase is in IS elements

type 2 complex transposons

• No IS elements

• transposase within other genes that carry benefit

how long are IS elements

750 - 2000 bp

how many IS elements in e.coli

• 6 copies of IS1

• 7 copies IS2

• several of IS3 and IS4

how was the first IS element discovered

E. coli was unable to grow on galactose because an IS element had jumped in a gal gene

how many phages are there

1 × 10³¹

examples of phages

T2, lambda, MS2

are phages obligate parasites

yes, they need a host to replicate in

basic pattern of phage replication

1. adsorb to cell surface

2. inject genetic material into host

3. host genetic material is replicated and phage proteins are made

4. assembly to be released

explain the lytic phage infection

1. the phage will attach to cell and inject genetic material into host

2. phage DNA will replicate independent of the host

3. the phage particles will begin to assemble and its DNA will enter the head

4. the phages will lyse the host cell to leave

explain the lysogenic phage infection

1. phage will attach to host cell and inject genetic material

2. the DNA will be integrated into the host DNA and will be undetected by the host

3. if severe damage happens to the host cell, the lysogenic phage will become lytic

phage vs prophage

• phages are viruses that infect bacteria

• prophages are phage DNA in lysogenic state

what is a lysogen

this is the name given to a bacterial cell that houses a prophage

(e.g. prophage = P2, thus, lysogen = P2 lysogen)

how to tell if a bacterium is a lysogen

if it is resistant to an infection by the same phage

andre lwoff

• discovered lysogenic phages

• observed that seemingly uninfected e. coli were able to produce phages after suffering UV damage

phage induction

prophages (e.g. phage lambda) can enter lytic state when the cell encounters UV or chemical damage

how does C1 repression work in phage lambda

1. the C1 protein functions as a DNA-binding dimer

2. it will bind to the promoter to repress the expression of lytic genes if the phage is in its lysogenic state

how is C1 repression relieved

1. SS DNA will build up in the cell after the cell encounters UV damage

2. RecA will bind to SS DNA and cause C1 to autocleave itself

3. this will allow lytic genes to be expressed

morons

when phage is in its lysogenic state, and integrates its DNA into host chromosome, it can provide genes that help host cell increase virulence

lysogenic conversion

a lysogenic phage that changes host cell behavior

chromosomal or pathogenicity islands

region of bacterial chromosome that is of foreign origin that contains clusters of genes that provide pathogenic advantage

how can you tell that it is a pathogenicity island

• its GC content

• its preferred codon for a particular amino acid

why are some pathogenicity islands found next to Phe-tRNA

this tRNA is highly conserved, so this locus is easy to find

can pathogenicity islands replicate on their own

no

what is on S. aureus pathogenicity island 1 (SaPI1)

has gene for toxic shock syndrome 1 which leads to multi-organ failure

how is SaPI1 transferred from cell to cell

1. the 80a phage will infect a cell that has SaPI1

2. SaPI1 will remove itself from the chromosome and generate more copies of the pathogenicity island using phage replication proteins

3. SaPI1 will then be packaged into tiny-headed 80a phage particles

4. the 80a phages will leave and infect other bacteria with SaPI1

what are the 4 defenses bacteria have against viruses

1. prevent adsorption

2. prevent DNA injection

3. DNA cleavage

4. cell death

what does it mean when a virus is parasatized

when a pathogenicity island hijacks a virus’s replication proteins to replicate the PI and force the virus to carry the PI in its tiny head

what is bacterial innate immunity

• restriction modification system

• block adsorption/ injection

• abortive infection

what is acquired immunity

CRIPSR/ Cas

restriction modification systems

• first line of intracellular defense

• methyltransferase is used to methylate host DNA to protect it from restriction endonucleases

• this means foreign DNA (virus) will be cut

what does CRISPR/ Cas stand for

clustered regularly interspaced short palindromic repeats/ CRISPR associated (proteins)

what does CRISPR/ Cas protect bacteria from

virus and plasmids

how does CRISPR work

1. when foregin DNA enters, Cas proteins will cut DNA and insert chunk into CRISPR array, looks like black diamonds

2. if the same virus tries to infect again, the cell will use the chunk to scan for foreign DNA and destroy it

is CRISPR array passed down to next generation

yes, unlike in humans