Module Two b Flashcards
what is the core genome?
located on chromosome (s)
Genes including essential genes conserved in all members of a species
what is the accessory genome?
- located on plasmids, chromosomal islands (ICEs), transposons, lysogenic phage
- Non-essential genes of variable occurrence in a bacterial species
- Acquired through horizontal transmission
what is the pangenome?
core genome + accessory genome
what are the examples of mobile genetic elements?
plasmids
transposons
bacteriophage
integrative and conjugative elements (ICEs)
what are plasmids?
Extrachromosomal genetic elements
- capable of autonomous replication
- not essential to the cell under all circumstances (not required for day-to-day survival)
what is an antibiotic resistance gene?
- encode enzymes that modify or degrade antibiotics
- Ab genes on plasmids are often carried on transposons
- significant medically
what must a plasmid do?
- replicate
- segregate
- keep host happy
- keep host under control
- spread
why do plasmids need to segregate?
-must ensure each daughter cell receives at least one copy upon division
how do plasmids keep the host happy?
- constrain metabolic load by regulating copy number
- large plasmids typically only 1-5 copies/cell (low copy number)
- small plasmids ~15-50 copies/cell (high copy number)
how do plasmids keep the host under control?
kill off cells foolish enough to kick them out
why do plasmids need to spread?
conjugation: non-conjugative plasmids are often mobilisable
what are the structural features of the F plasmid?
- tra
- RepF1A
- oriV
- par
- res/fcr
- ccdA/ccdB
- hok/sok
- pif
- Tn1000, IS2, IS3
what is tra on the F plasmid?
mating pore and DNA mobilization functions
what is RepF1A on the F plasmid?
determines vegetative replication and incompatibility properties
what is the oriV on the F plasmid?
copy number 1 to 2 per cell
what is the par on the F plasmid?
partitioning loci
what is the res/fcr on the F plasmid?
site-specific recombination system that resolves dimers
what is the ccdA/ccdB on the F plasmid?
host-killing system
what is the hok/sok on the F plasmid?
Another host-killing system (toxin-antitoxin) - an example of a post-segregational killing system
what is the pif on the F plasmid?
Protection against phage T7 by inducing abortive infection
what is the Tn1000, IS2, IS3 on the F plasmid?
transposable elements, facilitate interactions between F and other DNA molecules
What are the structural elements of the ColE1 plasmid?
oriV imm ColE1 mob rom oriT cer
what is the general principle of plasmid replication control?
- Plasmid DNA replication is controlled by a plasmid-encoded inhibitor that acts at oriV
- as cell size increases, inhibitor concentration decreases, and plasmid replication initiated
- replication results in further copies of inhibitor gene and more inhibitors which limits plasmid replication again
what is a transposon?
able to move from one site in the genome to another independent of host recombination system, “jumping genes”
what do transposons do?
cause large fraction of spontaneous mutations and chromosome rearrangements (deletions, inversion, replicon fusions)
what do transposons enable?
- Enable the rapid acquisition of multiple antibiotic resistances and facilitate the flow of such genes between species
- provide powerful tools for molecular genetic studies
what are the types of bacterial transposons?
- insertion sequences
- composite transposons
- non-composite transposons
- conjugative transposons
What is an insertion sequence (IS) element?
- the simplest type of transposon
- encode only the protein needed for its own transposition
- ends of all known IS elements have inverted terminal repeats
what are P elements?
key tools for genetic analysis of Drosophila
what are composite transposons?
- Consist of two IS elements flanking a central region carrying other genes
- IS elements supply transposase and ITP recognition signals
- Often only one IS module makes active transposase
what are Non-composite (simple) transposons?
do not rely on IS modules for transposition
-encode genes for own transposition and accessory funtions and have inverted terminal repeats
what does transposition of non-composite (simple) transposons require?
transposase and resolvase
what is conservative transposition?
“Cut-and-Paste”
Transposase makes , 1. dsDNA cuts in donor
Staggered cuts in target
there is a small direct repeat sequence on either side of the transposon
what typeof transposons undergo conservative transposition?
IS and composite
what is replicative transposition?
“copy and paste”
Transposases make:
-two ssDNA cuts in donor
-Staggered cuts in the target
resolution of cointegrate requires the resolvase (catalyzes recombination like event
what type of transposons undergoes replicative transposition?
non-composite transposons
what is a conjugative transposon?
able to excise from the genome and transpose from one cell to another via a conjugative intermediate
-insert randomly into the recipient and also reinsert into donor genome
what are conjugative transposons important for?
dissemination of antibiotic resistance and virulence
how do transposons mediate insertions?
transposition or homologous reconbination
how do transposons mediate replicon fusions?
Hfr formation
how do transposons mediate deletions?
Homologous recombination between two copies of a transposon present in inverted orientation
how are transposons used to generate mutations?
Antibiotic resistance gene allows easy selection, Each mutant is likely to only have a single mutation
are transposons sued to tag genes for identification?
yes
what are the two life cycles of temperate bacteriophages?
lytic and lysogenic
what is the lytic lifecycle?
- the host chromosome is destroyed
- the phage DNA replicates and assembles into new phages
- Phages are released into the environment
what is the lysogenic lifecycle?
The phage DNA integrates into the host chromosome
-the prophage is replicated as part of the bacterial chromosome
what does lambda phage integration require?
- attP site on the phage
- attB on the bacterial chromosome
- lambda integrase
what does lambda phage excision?
it is the reverse process to integration and requires lambda integrase and lambda excisionase
what are excisionases also called?
recombination directionality factors (RDFs)
what are the advantages of lysogenic conversion?
- is efficient
- does not require cell-to-cell contact
- incorporation not homology-dependent
can act at a population level
can survive harsh conditions that eliminate bacteria
what is a genomic island?
- key players in bacterial horizontal gene transfer
- discrete DNA segments
- maybe absent from closely related strains
- usually show evidence of past or present mobility
what traits do genomic islands carry?
adaptive traits
what do genomic islands do?
share features of phages and conjugative plasmids
where do genomic islands integrate?
at specific sites- usually adjacent to a tRNA gene
how do genomic islands integrate?
similar to lysogenic phages- phage-like integrase near one end of the island
is genomic island mobile?
most genomic islands have lost mobility and become fixed in the genome
what are integrative and conjugative elements?
genomic islands that have retained mobility
what do integrative and conjugative elements carry?
integrase
excisionase
conjugation genes’
How do integrative and conjugative elements (ICEs) transfer?
by conjugation after excising from the chromosome
what is the integration mechanism of ICEs?
mechanism like that of phage lambda
-ICE integrated between attL and attR sites
- recombination between attL and attR excises a circular island
- gives attP (in the ICE) and attB (in the chromosome)
- ICE-free cell can be a recipient for conjugative transfer
- Recombination between attP and attB results in integration
how do genomic islands affect bacterial evolution?
“fitness” islands that adapt a bacterium with a core chromosome to specific environmental niches
- pathogenicity
- resistance to antibiotics
- symbiosis
- xenobiotic degradation
