Bacterial Genetics Flashcards
how can bacteria transfer info horizaontally
to another bactiera - end up with recombinant cell
bacteria can harbor genes on extra chromosomal elements called
plasmids
describe plasmids
much smaller than chromosome
encodes up to 100 genes
holoenzyme =
RNAP + Sigma factor
what does RNAP stand for
RNA polymerase
there are receptors that bind what during translation
N-formyl methionine (fMet)
operon concept
wasteful to produce enzymes if there is nothing for enzymes to work on. in operon they will be induced when needed or enzymes repressed when not needed
quorum sensing
Ability to establish cell-to-cell communication
Important for survival
e.g. biofilm production
draw organization of lac operon in e. coli
pg 7
gene that will encode repressor in lac operon
LacI
polycistornic mRNA
very long single RNA in lac operon
if lactose isn’t present, repressor protein does what
binds to operator site
if there is no lactose present was does RNA pol do
it can still bind to promoter but respresor is on operator so it doesn’t transcribe
when lactose is present
lactose binds to repressor so repressor can’t bind to operator site so RNA polymerase can ranscribe
quorum sensing
inductoin of gene expression in response to critical gene desnity
what is exxample of genes that are used with quorum sensing
biofilm
toxin genes
apathogenetic state regarding quarum sensing
QS regulated genes not on
as population of bacteria increases what stage
sufficient concentration of inducers and critical mass of baceria able to respond to inducers
what do inducers do
bind to receptor complex and turn on transcription of the regulated gene
what will the binding of inducer do
virulence gene - changes it from being harmless to being harmful
what is biofilm
mucopolysacharide layer that provide protection against
Phagocytosis
Dehydration
Antibiotic penetration
antigenic variation in regards to immunology
can give bacteria an advantage, can help them invade ongoing immune response
if bacteria can alter its structure the immunes systems antibiotic resistance may not longer be effective
genetic diversity allows bacteria to
have advantage if enviornment changes
name one way diversity helps bacteria
antibiotics - can aquire antibiotic resistance genes
four main mechanisms for gene transfer
Transposition, Transformation, Transduction, Conjugation
flagella are targets of what
why is this important
antibodies
salmonella (or other bacteria) can turn off gene that makes flagella to evade antibiotic response
how do flagella give bacteria advantage
allows them to invade
in some cases antibiotic resistance is due to mutation in
chromosome
what is another qy antibiotic resistance can happen
acquisition of mobile genetic elements:
plasmid
transpoon
plasmids usually encode
enzymes to degrade antibiotics
transposon
move pieces of DNA within the chrom. or from a plasmid
in many caese the DNA aquired by bacteria via horizontal gene transfer has to be
stabiized or else it will bedegraded
what are 2 mechanisms of recombination for bacteria to stabilize
homologous
non-homologous
homologous DNA recombination
Involves major bacterial DNA repair process (requires recombination enzymes (RecA))
dna recombined via homologous is usually
sort, linear pieces fo DNA
what does hologous DNA recombination require
substantial sequence homology between transferred DNA and target site
what will usually happen with homologous recombination
gene replacement
is all DNA uptaken in homologous recombination
no - the stuff taht isn’t is degraded
site specific recombination is also called
illegitimate or non-homologous recombination
what is requirement for site-specific recmobination
Requires only a small region of homology between transferred DNA and target site
foreign DNA in site-specific recombination is:
circular plasmid, phage, transposons
Requires restriction endonucleases (site-specific recombinases)
how are transposons integraded
site-specific recomination
what does site specific recombination result in
integraded DNA - all is taken up nothign is lost
is all DNA integrated in homologous recombination
no some is loss, what isn’t taken up is degraded
temperate phages integrate
dna into chromosome of cell that they infect
draw example of site-specific recombination and the steps
pg 19
what is result of site-specific recombination
gene insertion
what are four main mechanisms of gene transfer
transposition
transformation
conjugation
transduction
transposition is mediated by
transposons “jumping genes”
transposons
can jump to different genes and plasmids
transofmration
uptake of “naked” DNA
conjugation
one bacteria to another following cell-cell contact
two type of conjugation
transfer via what is on plasmid
transfer bacterial chromosomal change
transduction
mediated by bacterial phages
some of the phages make mistake and package wrong DNA
avirulent bacteria can be conferted to
virulent bacteria
what si the significance of gene transfer (one significance)
converstion to virulence
presentation of disease
what are common places converstion will take place that would cause virulence
pilli - promote adherance
toxins
enzymes that degrade basement membranes
transposons are flakned by
intdirect repeats
indirect repeats
sequence of nucleotides followed by that sequence in reverse
how can you get mutation due to transposon
b/c they insert themsef into genetic info, can cause mutation
PAI stand for
pathogenicity islands
PAi
find direct repeats, indicating there are transposons
they often contain virulence factors
they can be mobilized from one bacteria to another
examples of PAI
toxins
adhesins
antibiotic resistance genes
describe some properties of transposon
- Random movement: Transposable genetic elements can move from any DNA molecule to other DNA molecules. The movement is not totally random; there are preferred sites in a DNA molecule at which the transposable genetic element will insert.
- Not capable of self replication: The transposable genetic elements do not exist autonomously and thus, to be replicated they must be a part of some other replicon.
- Transposition mediated by site-specific recombination: Transposition requires little sequence homology. Transposition is mediated by an enzyme transposase that is encoded by the transposon.
- Transposition can be accompanied by duplication: For some transposons, transposition results in removal of the transposon from the original site and insertion at a new site. For other transposons, transposition is accompanied by the duplication of the transposon with one copy remaining at the original site and the other transposed to a new site.
what are the two methods of transposons
cut and paste
copy and paste
describe cut and paste and copy and paste of transposons
pg 26
transformation
Most important mechanism of
genetic exchange in gram
positive microorganisms
such as Streptococcus pneumoniae
to be able to take up DNA from enviornemtn bactiera has to be
competent
to become competent a bacteria has to be
stressed in some way
what is competence controlled by
competence factor (CF)
what does CF stand for
competence factor
CF makes
gram positive bacteria capable of taking up DNA from enviornemnt
what DNA is taken up by competenct bacteria
single strand
dna plasmid can be taken up bia transofmration, does it require integration
no
conjugation is most well studied in what kind of bacteria
most known in gram neg.
conjugal plasmid encodes
fertility factor
conjugal plasmid refered to
f factor
f factor plasmid
to be donor bacterium have to have
f pillus (sex pillus) F posiive
recepient has to have
NOT F pillus
is F negative
there will only be conjugation b/w
f negative recipient
F positive donor
conjugal plasmid has a number of important genes including
Tram operon
oriT
bacterial chromosome
tra operon codes for
F pillus
to be donor cell need what operon
tra
where will be nicked for conjugation
Origin of transfer site
what does Hfr stand for
high frequency recombinant
f plasmid can also integrate by what
site specific recombination into bacterial chromosome
when plasmid integrates via site specific recombination what is it called
Hfr cell
Hfr will make (in conjugation)
f pillus (hfr is still donor cell)
draw F factor plasmid and all components
pg 30
what is considered male in bacteria
has f pilus
draw out a F+ and F- cross
pg 31
what kind of cleavage in conjugation
single strand
so both stands have conjugal plasmid and then both cells will be F+
aquisition of conjugal plasmid is called
conjugation
if there is no selective pressure for maintaining plasmid
they will get rid of the plasmid
site specific recombination will be where
at insertion sequence
where will single strand cleavage always be
oriT
what is the last thing transferred
tra operon
is the tra operon actually transferred
no it breaks down before that
what will be transferred in integrated f plasmid single strand cleavage
the genes closest to OriT including bacterial chrom. genes
draw out integrated conjugal plasmid and where it is cut
pg 34 & 35
what is first step of Hfr conjugation
conjugal plasmid integrates into bacterial chromosome
in Hfr conjugation where is it nicked
origin of transfer
what has to happen to conjugation in order for their to be phenotypic change
it has to be incorporated/integrated into chrom. of recipient
can transfer genes in Hfr conjugation that lie close to
oriT
receipient in Hfr conjugation will always be
recipient
how many genes are contained in bacterial chromosome
about 3000 genes
different sigma factors allow expression of what
different sets of genes
In order for RNA polymerase to bind to promoters, what is needed
sigma factor
what does PAMP stand for
Pathogen-Associated Molecular Pattern
N-formyl methionine is soluble
PAMP
to evade the immune system, what can salmonella do
switch b/w two distinct flagellin proteins
cassette switching
what happens in phase 2 of cassette switching
won’t have H1 being made b/c you’re making repressor that will block H1 bein gmade
what happens in phase 1 of cassette switching
won’t make H2 or repressor of H1 but you will make H1
draw out phase 2 of cassette switching
pg 13
draw out phase 1 of cassette switching
pg 13
what is another name for cassette switching
site-specific inversion
where is tra operon on f factor plasmid
on opposite side of where cut is made (cut is made by oriT)
what are the steps in conjugation
1- Donor cell produces pilus;
2- Pilus attaches to recipient cell, brings the two cells together;
3- The mobile plasmid is nicked and a single strand of DNA is then transferred to the recipient cell;
4- Both cells re circularize their plasmids, synthesize second strands, and reproduce pili. Both cells are now viable donors.
as a F- cell obtains a copy of F factor, what does it become
F+
what is the end result of a conjugation (one F+ cell giving copy of F factor to the F- cell)
both cells will be F+ males
what does curing mean
F+ bacteria becomes F-
conjugation vs. curing
conjucation: F- becomes F+
curing F+ becomes F-
how can we promote curing
removing plasmids via chemical agents like acridine orange
in quorum sensing what happens with a low density of inducers
they diffuse before they can act on QS receptor
how can bacteria utilize antigenic variation
mutation
phase variation
uptake of new info (plasmid/antibiotic resistance)
donor cells are (“sex”)
male
recepient cells are (“sex”)
female
why will the tra operon not be copied in an integrated conjugal plasmid
the conjugal core breaks down before it because of force
Hfr cell will make contact with what cell
F- cell
once contact from Hfr cell to F- cell is made, what happens
single strand cleavage at origin of transfer
where is single strand cleavage always going to occur
origin of transfer (OriT)
will the entire bacterial chromosome ever be transferred in conjugation
no
what will receipient cell aquire in Hfr cross
chromosomal genes that lie closes to site of integration of F plasmid (opposite from F+ to F- cross)
to be stabilized the donor DNA into recipient DNA has to be
stabilized
pathogenicity islands are regions where there is concentration of
virulence factors
when plasmids insert into the bacterial genome they have propencity for doing it at where
pathogenicity islands
at the end of F+ to F- cross what happens
entire plasmid is transferred but NO chromosomal DNA and the receipient cell has become a F+ b/c of the plasmid it received
at end of Hfr cross what happens
recipient still receipient b/c it doesn’t receive genes that encode for F pillus. the recipient can aquire chromosomal genes from donor.
if the conjugation from Hfr is recombined vs. not recombined what happens
if recombined it will be incoroprated to genome if not recombined will be degraded
what is transduction mediated by
viruses that infect bactera
phages
viruses that infect bactera
generalized transduction
mediated by lytic bacteria phages
: transfer of any bacterial gene from the disrupted cell
specialized transduction
not a straight lytic cycle
bacterial phage integrates its genome into the bacterial chromosome
specialized transduction mediated by
temperate phage or lysogenic phage (both bacterial phage)
differnece b/w lysogenic and lytic phage
in lysogenic the phage is actually incorporated into the host chromosome. in lytic some DNA is incorporated into host chromosome but it doesn’t incorporate itself to replicate
when lysogenic phage itegrates its bacteria into chromosome its called a
lysogen
both form of transductio happen b/c during packing/assembly of bacteria phage, the bacteria phage makes a mistake
packages some bacteria chromosomal DNA instead of complete viral genome
list steps of lytic infection (generalized transduction)
pg 41
most of bacteria phages will encapsalate the
viral genome
some bacteria phage (transducing phages) do what
make a mistake in packaging
package part of bacteria chromosomal DNA so when they infect another bacterial cell they inject some bacteria chromosomal DNA so it won’t go into lytic cycle
if bacterial/chromosomal DNA (from bacteria lytic phage) is stabilized by recombination it can lead to
aquisition of genes by the receipient from the donor cell that was originally infected
in specialized transduction the temperate/lysogenic phage initially
integrates self into chromosome of recipient cell
what can reactivate bacteria phage from latent stage
stress
when proviral DNA is excised from the chromosome it isn’t excised exactly he right way, so what comes out of chromosome (specialized transduction, lysogenic cycle)
part phage and part bacterial chromosomal DNA
the part phage and part bacterial phage is packaged as what
transducing phage in some phage heads
most important aspect of lysogenic cycle
during provirus phase itself
anythign encoding on proviral DNA (and many virulence factors are!) and can be expressed during latent stage
compare generalized and specialized
pg 43
generalized transduction goes straight into
straight into lytic cycle
transducing phage
generated b/c during assembly we mispackage bacterial chromosomal DNA instead of phage DNA
in specialized transduction what is first step
integration of phage DNA as provirus (or prophage) into chromosome of infected cell
main diff. b/w lysogenic and lytic cycle
lytic phase in lysogenic cycle doens’t hapen immediatley, only after prophage is re-activated after latency
lytic phage goes straight into
lytic cycle
draw out lytic and lysogenic cycle
pg 44
lysogenic
integration of phage dna as provirus
really imporatnt feature of lysogenic/tempreate phages
lysogenic conversion
when prophage Dna integrated dna is now called
lysogen
lysogen harbors dna of
lysogenic phage
anythign encoded on phage dna can
be expressed in lysogen
what is example of what lysogen can express
toxin, etc
Once integrated into the bacterial chromosome, these genes can cause the bacteria to produce the encoded
virulence factors (Lysogenic Conversion) resulting in disease.
site where bacteria phages tend to integrate are
PAI (pathogenicity islands)
pathogenicity islands are highly
mobilizable
transposons pop out
after death the islands can be taken up via transofmration
regions where phages insert by site specific recombination
draw out gene transfer comparison b/w transformation conjugation & transduction
pg 48
when phage has combination of host cell and its own DNA, what happens when it infects another cell
it won’t go into infectious cycle but the bacterial chromosomal genes can be stabilized by recombination into chromosome of receipient so receipient cell would aquire bacterial chromosomal DNA from donor cell originally infected
to release transducing phase have to go into
lytic cycle
