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GENE221 > Module Two b > Flashcards

Module Two b Flashcards

1
Q

what is the core genome?

A

located on chromosome (s)

Genes including essential genes conserved in all members of a species

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2
Q

what is the accessory genome?

A
  • located on plasmids, chromosomal islands (ICEs), transposons, lysogenic phage
  • Non-essential genes of variable occurrence in a bacterial species
  • Acquired through horizontal transmission
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3
Q

what is the pangenome?

A

core genome + accessory genome

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4
Q

what are the examples of mobile genetic elements?

A

plasmids
transposons
bacteriophage
integrative and conjugative elements (ICEs)

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5
Q

what are plasmids?

A

Extrachromosomal genetic elements

  • capable of autonomous replication
  • not essential to the cell under all circumstances (not required for day-to-day survival)
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6
Q

what is an antibiotic resistance gene?

A
  • encode enzymes that modify or degrade antibiotics
  • Ab genes on plasmids are often carried on transposons
  • significant medically
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7
Q

what must a plasmid do?

A
  • replicate
  • segregate
  • keep host happy
  • keep host under control
  • spread
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8
Q

why do plasmids need to segregate?

A

-must ensure each daughter cell receives at least one copy upon division

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9
Q

how do plasmids keep the host happy?

A
  • 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)
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10
Q

how do plasmids keep the host under control?

A

kill off cells foolish enough to kick them out

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11
Q

why do plasmids need to spread?

A

conjugation: non-conjugative plasmids are often mobilisable

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12
Q

what are the structural features of the F plasmid?

A
  • tra
  • RepF1A
  • oriV
  • par
  • res/fcr
  • ccdA/ccdB
  • hok/sok
  • pif
  • Tn1000, IS2, IS3
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13
Q

what is tra on the F plasmid?

A

mating pore and DNA mobilization functions

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14
Q

what is RepF1A on the F plasmid?

A

determines vegetative replication and incompatibility properties

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15
Q

what is the oriV on the F plasmid?

A

copy number 1 to 2 per cell

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16
Q

what is the par on the F plasmid?

A

partitioning loci

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17
Q

what is the res/fcr on the F plasmid?

A

site-specific recombination system that resolves dimers

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18
Q

what is the ccdA/ccdB on the F plasmid?

A

host-killing system

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19
Q

what is the hok/sok on the F plasmid?

A

Another host-killing system (toxin-antitoxin) - an example of a post-segregational killing system

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20
Q

what is the pif on the F plasmid?

A

Protection against phage T7 by inducing abortive infection

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21
Q

what is the Tn1000, IS2, IS3 on the F plasmid?

A

transposable elements, facilitate interactions between F and other DNA molecules

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22
Q

What are the structural elements of the ColE1 plasmid?

A 
oriV
imm
ColE1
mob
rom
oriT
cer
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23
Q

what is the general principle of plasmid replication control?

A
  • 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
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24
Q

what is a transposon?

A

able to move from one site in the genome to another independent of host recombination system, “jumping genes”

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25
Q

what do transposons do?

A

cause large fraction of spontaneous mutations and chromosome rearrangements (deletions, inversion, replicon fusions)

26
Q

what do transposons enable?

A
  • Enable the rapid acquisition of multiple antibiotic resistances and facilitate the flow of such genes between species
  • provide powerful tools for molecular genetic studies
27
Q

what are the types of bacterial transposons?

A
  • insertion sequences
  • composite transposons
  • non-composite transposons
  • conjugative transposons
28
Q

What is an insertion sequence (IS) element?

A
  • the simplest type of transposon
  • encode only the protein needed for its own transposition
  • ends of all known IS elements have inverted terminal repeats
29
Q

what are P elements?

A

key tools for genetic analysis of Drosophila

30
Q

what are composite transposons?

A
  • 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
31
Q

what are Non-composite (simple) transposons?

A

do not rely on IS modules for transposition

-encode genes for own transposition and accessory funtions and have inverted terminal repeats

32
Q

what does transposition of non-composite (simple) transposons require?

A

transposase and resolvase

33
Q

what is conservative transposition?

A

“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

34
Q

what typeof transposons undergo conservative transposition?

A

IS and composite

35
Q

what is replicative transposition?

A

“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

36
Q

what type of transposons undergoes replicative transposition?

A

non-composite transposons

37
Q

what is a conjugative transposon?

A

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

38
Q

what are conjugative transposons important for?

A

dissemination of antibiotic resistance and virulence

39
Q

how do transposons mediate insertions?

A

transposition or homologous reconbination

40
Q

how do transposons mediate replicon fusions?

A

Hfr formation

41
Q

how do transposons mediate deletions?

A

Homologous recombination between two copies of a transposon present in inverted orientation

42
Q

how are transposons used to generate mutations?

A

Antibiotic resistance gene allows easy selection, Each mutant is likely to only have a single mutation

43
Q

are transposons sued to tag genes for identification?

A

yes

44
Q

what are the two life cycles of temperate bacteriophages?

A

lytic and lysogenic

45
Q

what is the lytic lifecycle?

A
  • the host chromosome is destroyed
  • the phage DNA replicates and assembles into new phages
  • Phages are released into the environment
46
Q

what is the lysogenic lifecycle?

A

The phage DNA integrates into the host chromosome

-the prophage is replicated as part of the bacterial chromosome

47
Q

what does lambda phage integration require?

A
  • attP site on the phage
  • attB on the bacterial chromosome
  • lambda integrase
48
Q

what does lambda phage excision?

A

it is the reverse process to integration and requires lambda integrase and lambda excisionase

49
Q

what are excisionases also called?

A

recombination directionality factors (RDFs)

50
Q

what are the advantages of lysogenic conversion?

A
  • 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

51
Q

what is a genomic island?

A
  • key players in bacterial horizontal gene transfer
  • discrete DNA segments
  • maybe absent from closely related strains
  • usually show evidence of past or present mobility
52
Q

what traits do genomic islands carry?

A

adaptive traits

53
Q

what do genomic islands do?

A

share features of phages and conjugative plasmids

54
Q

where do genomic islands integrate?

A

at specific sites- usually adjacent to a tRNA gene

55
Q

how do genomic islands integrate?

A

similar to lysogenic phages- phage-like integrase near one end of the island

56
Q

is genomic island mobile?

A

most genomic islands have lost mobility and become fixed in the genome

57
Q

what are integrative and conjugative elements?

A

genomic islands that have retained mobility

58
Q

what do integrative and conjugative elements carry?

A

integrase
excisionase
conjugation genes’

59
Q

How do integrative and conjugative elements (ICEs) transfer?

A

by conjugation after excising from the chromosome

60
Q

what is the integration mechanism of ICEs?

A

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
61
Q

how do genomic islands affect bacterial evolution?

A

“fitness” islands that adapt a bacterium with a core chromosome to specific environmental niches

  • pathogenicity
  • resistance to antibiotics
  • symbiosis
  • xenobiotic degradation

GENE221 (6 decks)

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