Mobile Genetic Elements

Question 1

What are mobile genetic elements (MGEs)?

Answer 1

Section of DNA that can horizontally transfer between bacterial cells

Question 2

What is meant by transmission advantage?
Selfish?

Answer 2

Have transmission advantage compared to most of genome
Chance of getting to next generation is not 100% dependent on cell division

MGE evolutionary interests don’t always align with bacteria so they’re ‘selfish’

Question 3

If a gene imposes a fitness burden on cells that have it, what will happen to that gene?
What happens if that gene is now able to reproduce horizontally?

Answer 3

Frequency of gene becomes smaller as cells without it outcompete these cells

Despite fitness burden the gene still spreads through the population

Question 4

How were yeast used to investigate increased rate of sex and transmission?

Answer 4

Yeast with functional mitochondria bred with yeast with dysfunctional mitochondria
When they increased rate of sex, dysfunctional mitochondria increased in frequency, causing more yeast unable to grow aerobically

Question 5

What are the 3 genes a plasmid needs?

Answer 5

Rep – Control replication of plasmid; Recruits replication components
Par – Partition plasmid into daughter cells as the cell divides
Tra – Construct conjugative pilus and transfer plasmid DNA through

Question 6

What are the 3 types of plasmid?

Answer 6

Conjugative
Mobilisable
Non-mobilisable

Question 7

What genes/features would each plasmid type have? (hint - oriT)

Answer 7

Conjugative would need tra and oriT
Mobilisable - oriT; Parasitise a conjugation plasmids pilus
Non-mobilisable - Neither tra nor oriT so it can transfer

Question 8

What are the -copy types of plasmid?
What do each of them need/don’t need?

Answer 8

Single copy need par to move copies to opposite poles

Multicopy don’t need par and can rely on diffusion to have sufficient copes at each pole

Question 9

Differences between single and multicopy plasmids? (hint - mega)

Answer 9

Single copy are very large with many accessory genes; Can form Megaplasmids

Multicopy tend to be smaller so they can reproduce fast and spread out

Question 10

What is meant by fluid plasmid evolution?
What is a chromid?
If a plasmid gains an essential genes that the chromosome loses, what can we say that plasmid now is?

Answer 10

Accumulate genes over time

Chromid is where a plasmid becomes part of the cell genomes by acquiring essential genes and losing transfer genes

Essential plasmid as it contains only copy of essential gene for survival

Question 11

Explain the phage lysogenic cycle?
What is meant by a temperate phage?

Answer 11

Phage genome infects cells and incorporates into bacterial genome, reproducing alongside

Phage divide with the cell until phage lysis is induced

Question 12

How can lytic cycle be induced? (3 ways)

Answer 12

Environmental (often stress e.g. SOS response)
Quorum sensing; Can detect if new hosts are available
Spontaneously

Question 13

How can temperate phages be useful?

Answer 13

When another population is competing with a prophage infected population

One cell from prophage population can induce lysis and infect competing population
Competitor cells are lysed and prophage population are ‘immune’ as they are already contain phage DNA, so they survive and outcompete

Question 14

What are integrative conjugative elements (ICEs)?
How?
Size and gene count?

Answer 14

Conjugative plasmid that integrates into host genome

Use plasmid genes to conjugate - tra
Use phage genes to integrate

Like plasmids they can be large and carry many genes

Question 15

What are IS elements?
How do they work?

Answer 15

Simplest form of transposons
DNA encodes transposase flanked by terminal inverted repeats

Transposase recognises inverted repeats and cuts out IS element to migrate elsewhere in genome

Question 16

How are transposons more complex than IS elements?

Answer 16

Often carry other genes like antibiotic resistance

Question 17

What is a type I composite transposon?
How does it form?

Answer 17

Non-replicative

2 IS elements close together and the interior inverted repeats are degraded so outermost ones used for jumping
Genes in between are mobilised with the 2 IS elements which now act as one

Question 18

What is a type II complex transposon?

Answer 18

Replicative

Transposase acts on the inverted terminal repeats to cause simultaneous insertion and replication

Question 19

Process of transposon insertion

Answer 19

IS elements are excised and recognise target sequence
Recombination event which causes target sequence to be duplicated
Transposon has integrated

Question 20

How are transposons linked with plasmids?
How can transposons become permanently integrated?

Answer 20

Transposons can carry plasmid accessory genes

Transposons can break and become permanently integrated

Question 21

How do transposons host switch?
What is this concept and what does it amplify?

Answer 21

Bacteria infects host cell and transposon integrate into new host cell genome

Nested MGEs which amplify spread of transposon

Question 22

What are Phage Inducible Chromosomal Islands (PICIs)?

Answer 22

Integrated sections of bacterial genome that exploit phages for their own transfer

Question 23

How does SaPI gene work as a PICI?
How is phage replication reduced?

Answer 23

SaPI sits in the genome and is repressed (silenced) until phage replication is detected
SaPI also excises and replicates and is packaged into the phage head and blocks phage packaging
Phage particles inject the SaPI which integrates

No phage genome is transferred in these infections; Reduces phage replication

Question 24

How does SaPI ensure no phage genome is packaged?

Answer 24

Encodes proteins which force smaller capsid to be made
Phage genome is now too big for capsid and isn’t packaged

Question 25

Why do MGEs carry accessory genes?
What are plasmids and phages more likely to carry?

Answer 25

Express traits in bacteria which benefit the bacteria
Mutualism as both benefit

Phages more likely to carry virulence factor genes (VFG)
Plasmids more likely to carry antimicrobial resistance genes (ARG)

Question 26

How is the genome like an ecosystem? (3 traits)

Answer 26

Collaboration – e.g. Tns hitchhike on plasmids, but carry accessory genes

Parasitism – e.g. PICIs & mobilisable plasmids exploit the transfer machinery of phages and plasmids

Competition – e.g. Many MGEs carry defence systems against other MGEs especially phages

Question 27

How does S. aureus phages use PICIs for defence?

Answer 27

PICI reduces helper phage reproduction
- Helper phage is competing for hosts with other phages

PICI encodes defence systems which target other MGEs (not the helper)

PICI and phage overall benefit each other
- Phage allows PICI to spread to other cells
- In return PICI inhibits competitive phage particles