4. Genomes, diversity and habitats

Question 1

Types of bacterial shapes

Answer 1

Coccus
Rod
Spirillum
Spirochete
Budding and appendaged bacteria
Filamentous bacteria

Question 2

Bacterial genomes

Answer 2

Small, circular, and information-packed.
General size 150kbp (mycoplasma) to >10Mbp (Actinobacteria).
Supplemented by plasmids and other ‘mobile elements’

Question 3

E.coli Bacterial genome

Answer 3

4.6Mbp
4300 genes
Average gene ~1000bp (1kbp)
Single circular molecule
Haploid
No introns
Many genes organised in operons.

Question 4

Plasmids

Answer 4

Extrachromosomal but can be integrated.
Huge size range (<5kbp to >1Mbp)
Often ‘mobile’ (conjugation)
Confer ‘accessory’ functions - resistance, metabolic, virulence and many others.

Question 5

Common mobile genetic elements

Answer 5

Plasmids
Bacteriophage
Transposons and insertion sequences
Integrons

Question 6

Bacteriophages

Answer 6

Bacterial virus
Lytic
Temperature (lysogenic) - Stable insertion in host chromosome.
Can transfer genes - transduction

Question 7

Transposons and insertion sequences

Answer 7

‘Jumping genes’
Hop in and out of chromosomes and plasmids
Often carry resistance genes

Question 8

Integrons

Answer 8

Can pick up and accumulate ‘useful’ genes.

EG Antibiotic resistances

Question 9

‘Mosaic’ bacterial chromosomes

Answer 9

Core genome: ‘Housekeeping’ genes possessed by all strains of a species.
Pan genome: Much larger, totality of genes found across different isolates of a species

Question 10

‘Pathogenicity’ islands

Answer 10

Cluster of genes of 'foreign' appearance.
EG altered G&C content.
Present only in certain strains.
Correllated with virulence.
Various kinds of mobile elements.

Question 11

Genome sequencing

Answer 11

Each spot contains a short DNA fragment.
Coloured tag incorporated at each step.
Massive number of short sequence reads.

Question 12

Genome sequencing - method

Answer 12

1. Prepare genomic DNA
2. Fragment
3. Large scale, random ‘shotgun’ sequencing.
4. 8-10 billion reads of ~150bp
5. Completer genome sequences (96 human genomes in only 48 hours)

Question 13

Sequence assembly of bacterial genome

Answer 13

Overlapping sequences aligned.
Repetitive sequences interfere with assembly.
Complete genome assembly:
Complete with known sequence.
Use long-read sequencing methods (Oxford Nanopore)

Question 14

Bioinformatics

Answer 14

Complex process of interpreting DNA sequence data in terms of gene function.
Computerised algorithms identify sequence features.
Amino acid coding regions (Open reading frames)
ORFs converted to amino acid sequences according to the genetic triplet code.
Amino acid sequence comparisons identify likely protein functions by homology to known sequences in other organisms.
Specialised websites collate information about specific genomes.

Question 15

Impact of genome sequencing

Answer 15

Revolutionise bacterial genetics.
Use comparative genomics to understand bacterial phylogenetics and evolution.
Infectious disease and epidemiology.