Mobile Genetics Elements & Antimicrobial Suscptibilit

Question 1

Why is bacterial evolution rapid?

Answer 1

Due to their large population size and to their short generation times.

Question 2

What are factors that contribute to bacterial evolution and adaptation?

Answer 2

Mutations and horisontal gene transfer (HGT)

Question 3

What are mechanisms for horisontal gene transfer (HGT)?

Answer 3

1) Transduction
2) Conjugation
3) Transformation

Question 4

How does transduction occur?

Answer 4

1) Bacteriophages infect bacterial cells
2) Can remove a portion of the host cells DNA upon excision
3) Infection of new host - foreign DNA is incorporated

= Transfer of genetic material from one bacterium to another

Question 5

What is conjugation?

Answer 5

A donor transfers genetic material to recipient through direct contact.
Requires production of a pilus. The pilus draws the two bacteria together.
Requires independently replication genetic elements called conjugative plasmids, or chromosomally integrated conjugative elements (ICEs). These genetic elements encode proteins that facilitate their own transfer and occasionally the transfer of other cellular DNA from the donor plasmid-carrying cell to the recipient cell that lacks the plasmid or ICE.

Question 6

What is transformation?

Answer 6

The direct uptake of exogenous genetic material into a cell, often from a dead bacterium.
Recipient bacterium must be competent.
The process involves the transfer of cellular DNA between closely related bacteria and is mediated by chromosomally encoded proteins that are found in some naturally transformable bacteria.

Question 7

What is natural and induced competence, in the eye of transformation?

Answer 7

Natural competence: response to environmental conditions. Uptake specific sequence (USS) recognized by receptors on the cell surface.
Induced competence: disruption of the cell membrane.

Question 8

What is advantages of HGT?

Answer 8

• Gain new genes with new functions
• More rapid evolution
• Positive for adaptive evolution of the population

Question 9

What is disadvantages of HGT?

Answer 9

• Larger genome needs to be replicated and maintained
• Biosynthetic resources for new functions
• Potential for loss of function and cell death
• “Burden” on the bacterial cell

Question 10

What are the general barriers to genetic exchange?

Answer 10

1) Donor-recipient similarity barrier: most HGT between closely related species
2) Ecological barrier: most transfers within habitats
3) Functional barrier: deletion of non-functional DNA

Question 11

What is the difference between conjugative plasmids and mobilizable plasmids?

Answer 11

Conjugative plasmids (F+) encode all genes required for conjugation:
- Mobility (MOB) genes (relaxase + T4CP)
- A membrane-associated mating pair formation (MPF) complex (=T4SS)

Mobilizable plasmids can use the MPF of another genetic element present in the cell.

Question 12

How does the transfer of plasmids occur between two bacterial cells?

Answer 12

A pilus (T4SS) is formed between a donor cell (F+) and a recipient cell (F-)

Question 13

What is the life cycle of bacteriophages?

Answer 13

1) Phage injects its DNA into cytoplasm
2a) Phage DNA directs the synthesis of many new phages
3a) Cell lyses and releases the new phages
4a) New phages can bind to bacterial cells

1) Phage injects its DNA into cytoplasm
2b) Phage DNA integrates into host chromosome
3b) Prophage DNA is copied when cell divides
4b) On rare occasions, a prophage may be excised from host chromosomes

Question 14

How is transduction performed in bacteriophages?

Answer 14

Generalized transduction:
1) Bacterial host cell (donor cell) infected by phage
2) Host cell DNA is broken down into smaller pieces. Proteins and phage DNA is also synthesized
3) Bacterial host DNA is packaged in one of the viral capsids that are released through lysis of the bacterial cell
4) Transducing phage with host DNA infest new recipient cell. Recombination also occurs here
5) Recombinant new cell has a mixture of the donor DNA (1) and of its own DNA. Its genotype is different

Specialized transduction:
1) Prophage DNA integrated into the bacterial DNA
2) Prophage DNA cuts incorrectly and exchanges its DNA to that of the bacterial host cell
3) Phage capsids contain bacterial host DNA, which is transferred to a new bacterial recipient cell
4) Transduced phage is transferred to a new cell and recombination occur
5) The recombinant cell DNA has a different genotype, which is different from the donor or recipient cell genotype

Question 15

What is a transposon?

Answer 15

Transposable elements (TEs) - also known as “jumping genes” - are DNA sequences that move from one location on the genome to another.
They are always maintained in an integrated site in the genome.

Question 16

What are different types of MGEs (mobile genetic elements)?

Answer 16

It includes plasmids, bacteriophages, IS-elements and transposons, and pathogenicity islands.

Question 17

What genes are encoded in MGEs?

Answer 17

In addition to their core genes, MGEs typically carry several different accessory genes that provide their host cell with a selective advantage, such as antibiotic resistance, virulence factors, or unusual metabolic pathways.
Indeed, most medically and economically important bacterial phenotypes are encoded by MGEs.

Question 18

What is mobile genetic elements (MGEs)?

Answer 18

MGEs are segments of DNA that encode enzymes and other proteins that mediate the movement of DNA within genomes (intracellular mobility) or between bacterial cells (intercellular mobility).

Question 19

What is a plasmid?

Answer 19

A plasmid is a collection of functional genetic modules that are organized into a stable, self-replicating entity or “replicon”, which is smaller that the cellular chromosome and which usually does not contain genes required for essential cellular functions.
The classic plasmids are covalently closed, circular double-stranded DNA molecules.

Question 20

What is partitioning?

Answer 20

A process in which plasmids must replicate, control their copy number, and ensure their inheritance at each cell-division.

Question 21

What is the main steps in conjugation?

Answer 21

1) Mating-pair formation (Mpf)
2) A signalling event that transfer can occur
3) The transfer of DNA (Dtr)

Question 22

What is the function of the relaxase in conjugative systems?

Answer 22

It nicks DNA to give a signle-stranded substrate that is suitable for transfer. This nicking occurs in a strand- and site-specific manner at a nic site, allowing self-transmissible og miobilizable systems to be classified by their relaxase and nic sequences.

Question 23

What is the main difference between virulent bacteriophages and temperate bacteriophages?

Answer 23

Virulent bacteriophages replicate vigorously and lyse the host bacteria.
Temperate bacteriophages have an alternative, quiescent, non-lytic growth mode called lysogeny. In most known cases of lysogeny, the phage genome integrates into the bacterial chromosome and replicates with it as a prophage, but in a few cases, the phage genome replicates autonomously as a circular or linear plasmid.

Question 24

What is a insertion sequence (IS)?

Answer 24

A type of short transposon

Question 25

What are the two main challenges in the genomic analysis of any organism?

Answer 25

1) Developing suitable information management and computational analysis resources
2) Generating sufficient new sequence data so that the important scientific questions that face the field can be addressed