Bacterial Evolution and Genetics

Question 1

How are bacterial species identified?

Answer 1

16S rRNA sequencing.

Question 2

What are the 2 levels of bacteria identification below species level?

Answer 2

Strain level and isolate level.

Question 3

What is an isolate?

Answer 3

A culture from an infection.

Question 4

What is a strain?

Answer 4

A genetic variant of a microorganism.

Question 5

What are the 3 strain typing techniques and their average nucleotide identity (ANI)?

Answer 5

DNA-DNA hybridisation (>70%)
16S rRNA gene sequencing (>97%)
Whole genome sequencing (>95%)

Question 6

Define average nucleotide identity (ANI).

Answer 6

A measure of nucleotide-level genomic similarity between the coding regions of two genomes.

Question 7

Define epidemiology.

Answer 7

Identification and tracking of disease and infection.

Question 8

Why is it important to study bacteria below species level?

Answer 8

Some strains may cause different diseases or may be more transmissible or deadly.

Question 9

What are the T.RA.D. criteria?

Answer 9

Typeability, reproducibility, accuracy and discriminatory power. All features desired in strain typing.

Question 10

What is typeability?

Answer 10

The number of isolates that can be identified.

Question 11

What is the range in G+C content for bacterial genomes?

Answer 11

20-75%

Question 12

What are bacterial chromosomes like?

Answer 12

1 double-stranded circular DNA chromosome. Can occasionally be linear.

Question 13

How is bacterial DNA organised?

Answer 13

Almost all coding material is on 1 gene (around 1kb). Bacteria possess a core + accessory genome.

Question 14

What are the features of the accessory genome?

Answer 14

Non-essential genes.
Foreign DNA.
Cause of rapid evolutionary change and diversity with and between species.

Question 15

What are the features of the core genome?

Answer 15

Essential genes.
Stable G+C content.
Shared within species.
Slow evolution.

Question 16

What are the 2 drivers of bacterial genome evolution?

Answer 16

Horizontal gene transfer (HGT) and mutation/recombination.

Question 17

Define horizontal gene transfer (HGT).

Answer 17

Transfer of genetic material between organisms not in a parent-offspring relationship.

Question 18

Give 3 examples of horizontal gene transfer (HGT.

Answer 18

Plasmids, bacteriophages and transposable elements (‘jumping genes’).

Question 19

What is a genomic island?

Answer 19

Large DMA regions often integrated into the genome that are not present in all strains of the same species.

Question 20

What are some examples of advantageous accessory genes?

Answer 20

Pathogenecity.
Fitness.
Resistance.
Symbiosis.

Question 21

Define additive evolution.

Answer 21

Gene acquisition, duplication and rearrangement in the accessory genome.

Question 22

Define reductive evolution.

Answer 22

Deletion, inactivation and pseudogene formation in the core genome.

Question 23

Describe a bacterial plasmid.

Answer 23

Circular, self-replicating DNA molecule. Inherited through cell division. Encodes machinery for conjugation.

Question 24

Describe a bacteriophage.

Answer 24

Bacterial viruses that phage genetic material injected into cell. Integrates into genome (lysogeny).

Question 25

Describe a transposable element.

Answer 25

Insertion sequences of 0.7-2.5kb or transposons of 2.5-60kb. A DNA sequence that change its position within a genome.

Question 26

What enzyme binds to the end of a transposon?

Answer 26

Transposase.

Question 27

Define transformation.

Answer 27

The incorporation of foreign DNA into the genome.

Question 28

Define transduction.

Answer 28

Bacteriophage-mediated DNA transfer (virus transfers genetic material).

Question 29

Define conjugation.

Answer 29

The transfer of DNA via cell-to-cell contact.