13 - Transposons, ICEs and Pathogenicity Islands

Question 1

Transposition

Answer 1

• Mechanism by which a gene moves from one location to another
• Can be found on chromosomal or plasmid DNA

Question 2

Three types of transposable element

Answer 2

• Bacteriophages
• Insertion sequences
• Transposons

Question 3

Common aspects of transposable elements

Answer 3

• Flanked by direct repeats
• Have inverted repeats/direct repeats and encode a transposase
• Has no machinery to replicate itself when it is not inserted into plasmid or chromosome

Question 4

Transposase

Answer 4

Mediates the transposition with high sequence specificity or little sequence specificity

Question 5

Mechanism of movement of transposable elements

Answer 5

• Simple/conservative (cut and paste)
• Replicative (copy and paste)

Question 6

Types of transposable elements

Answer 6

• Insertion elements
• Composite transposon/nonreplicative (cut and paste mechanism)
• Composite transposon/replicative (copy and paste mechanism)

Question 7

Insertion elements

Answer 7

Inverted repeats flanking transposase

Question 8

Composite transposon/ non-replicative (cut and paste mechanism)

Answer 8

Inverted repeats flanking transposase AND accessory genes such as antibiotic resistance or toxin

Question 9

Composite transposon/ replicative (copy and paste mechanism)

Answer 9

Inverted repeats flanking transposase AND resolvase AND accessory genes such as antibiotic resistance or toxin

Question 10

Non replicative (cut and paste) transposition

Answer 10

• Transposon protein (TnpA) is expressed from the Tn gene
• TnpA binds to the IR
• Catalyses cleavage of the dsDNA backbone to release the transposon DNA
• TnpA remains bound to the
  ends of the fragment and creates a circle
• TnpA recognises an attachment site in the target DNA and catalyses insertion of the Tn into this site

Question 11

Conservative transposition (e.g Tn5)

Answer 11

• RecA independent
• TnpA recognizes the IR and the target sequence
• TnpA introduces single strand cuts into the target site and each side of the transposon
• Single strand overhangs
  are created
• TnpA religates dsDNA phosphodiester backbone flanking the transposon
• Results in duplicated target site flanking the transposon

Question 12

Frequency of transposition

Answer 12

1 in 10^4 to 10^7 cells

Question 13

Replicative transposition (e.g Tn3)

Answer 13

• TnpA introduces single strand cuts at the ends of the IR and the target site
• Original and target sites fuse through single stranded copies of the transposon (forming a co-integrate)
• DNA polymerase fills in the
  second strand forming a cointegrate
• TnpR (resolvase) catalyses
  ssDNA exchange between copies of Tn at the resolution (res) site within the transposon
• Co-integrates resolve into two replicons each with
  copy of the Tn

Question 14

Results of inaccurate excision of transposon

Answer 14

• Can move genes to another location in the same genome
• Can move genes onto a resident conjugative plasmid and then move into another
  recipient cell which could be a different strain or a different species
• A compound transposon can acquire all types of functions including it’s own transfer functions so it does not need a plasmid

Question 15

Integrative and Conjugative element (ICE)

Answer 15

Inverted repeats flanking integrase AND excisionase AND accessory genes
such as antibiotic resistance AND transfer genes

Question 16

Genomic islands

Answer 16

Plasmids, bacteriophages and transposons captured in the genome (2/500kb)

Question 17

Pathogenicity islands (PAIs)

Answer 17

• A region of chromosomally located DNA encoding virulence determinants or antibiotic resistance with a different GC% and codon usage to the rest of the chromosome,
• Flanked by direct repeats
• Inserted into specific site (tRNAs most common location)
• Lost ability to move

Question 18

Why have PAIs lost ability to move

Answer 18

Mutations in direct repeats or in intergrase

Question 19

Pathogenicity

Answer 19

Ability to cause disease

Question 20

Virulence

Answer 20

Degree or intensity of pathogenicity

Question 21

Virulence determinant

Answer 21

gene encoding a molecule contributing to pathogenesis

Question 22

Pathogenic potential

Answer 22

Degree of damage caused
to the host (morbidity and mortality)

Question 23

Infectivity

Answer 23

Ability to establish a focal point of infection in the host

Question 24

Invasiveness

Answer 24

Ability of the organism to
spread to adjacent sites in
the body

Question 25

What is evolution of pathogenic bacteria from commensal organisms driven by

Answer 25

• Random mutation
• Acquisition of MGE
• Environmental selection

Question 26

Examples of MGEs

Answer 26

• Bacteriophage
• Plasmids
• Transposons/IS element/integron
• ICE
• Genomic islands (e.g. PAIs)

Question 27

EPEC

Answer 27

• Enteropathogenic E. coli (infant diarrhoea)
• T3SS found on PAI
• EAF plasmid carrying pilus for adherence

Question 28

EHEC

Answer 28

• Hemorrhagic colitis (HC) and Hemolytic Uremic Syndrome (HUS).
• Plasmid that secretes hemolysin
• Bacteriophage that secretes toxins

Question 29

T3SS

Answer 29

• Basal structure in bacteria
• Needle inserts into eukaryotic cell
• Effector proteins are pumped from the bacterium into the eukaryotic cell

Question 30

Uses of T3SS

Answer 30

• Invasion/multiplication within host cell by intracellular pathogens
• Attachment to host cells by extracellular pathogens