Bacterial Genetics: Bacteria as Model Organisms

Question 1

Why are bacteria used as model organisms? - Medical Topics

Answer 1

• Pathogenesis ( understand diseases better that are caused by bacteria)

Leads to:
- Antibiotic development
- Understanding antimicrobial resistance

Question 2

Why are bacteria used as model organisms? - Biotechnology

Answer 2

Bacteria can be used to manipulate genes
E.coli + Streptomyces speces can be used to understand:

• Screen new activities
• Protein production
• Antibiotic production

Question 3

Why are bacteria used as model organisms? - Fundamental Biology

Answer 3

To understand:
-DNA replication
-Mechanism of transcription
-Transcriptional regulation
-Protein synthesis
-Protein translocation
-Cell stress responses
-Biochemical pathways/Central metab.

Question 4

Why are bacteria used as model organisms? - Environmental Science/Geology

Answer 4

To understand:
- Nitrogen cycle
-Methane production /consumption
-Hydrocarbon consumption
-Oxygen production
-CO2 production

e.g. Geobacter, Rhizobium sp.
Methanogens/-trohps, Cyanobacteria

Question 5

Why are bacteria used as model organisms? - Agriculture

Answer 5

To understand:
- Pesticides
- Livestock health
- Antibiotic production

Question 6

Why not bacteria? - Subcellular compartmentalisation

Answer 6

Bacteria don’t have complex membrane-bound organelles like SER/RER - can’t study all cellular processes to extrapolate such as:

-Phagocytosis
-Nonsense mediated decay
-Subcellular trafficking

Question 7

Why not bacteria - Epigenetics

Answer 7

Do not have histones so can’t study processes like:

• Histone modification
• CpG methylation

Question 8

Why not bacteria? - Lack of complex multicellularity

Answer 8

Doesn’t have the following:
- Animal development
- Plant development
- Locomotion
- Complex reasoning

Question 8

Practical Advantages of using E.coli

Answer 8

• Small size (1-2 micrometers)
• Unicellular & undifferentiated
• Divides by binary fission (limits variation in practical result)
• Simple genome - single circular chromosome
• Simple nutritional requirements (a sugar + some essential salts)
• Grows rapidly ( doubles every 25 mins)
• Each colony on a plate is derived from 1 cell + are clonal
• No ethical considerations

Question 8

How bacterial genetics can be used to investigate a statistically rare event

Answer 8

In E.coli, a rare event is 10^-9 to 10^-10
- In an overnight culture, there is 1 rare cell per 1ml so would be easy to detect
- Ease increases with the more plated poured

Question 9

The Origins of a Typical Bacterial Genome

Answer 9

Caveat - bacteria are incredibly diverse - no ‘typical bacterium)

• Diverged from archaea over 3.5 billion years ago

Evolutionary distance between Bacillus subtilis + E.coli is greater than a plant + human

Question 10

E.coli as a typical bacterium

Answer 10

• Been a model organism for ~90 years
  Typical bacterium refers to E.coli

Question 11

What is a Genome

Answer 11

1. All of genes in an organism
   * Similar to “transcriptome” or “proteome”
2. How those genes are physically encoded and
   inherited

• i.e. the DNA molecule(s) that encode those
  genes
• The chromosome encodes (part of) the genome
• Genome does not equal a chromosome

Question 12

The typical Bacterial genome

Answer 12

• Most bacteria have a single circular chromosome + are haploid
• Has a simple origin of replication
• Very little DNA that is not a gene or genetic element
• Vary substantially in size depending on lifestyle
• Genome can be augmented by plasmids
• Some have linear or multiple chromosomes

Question 13

How Bacterial Genomes are Reductionist + Have Clustered Genes

Answer 13

• Almost all of it encodes for proteins
• Parts that don’t tend to regulate transcription
• Genes in the same metabolic pathway are often organised into polycistronic operons

Question 14

What determines bacterial genome size?

Answer 14

Physical genome size (amount of DNA) correlates well with
number of genes.

• Number of correlates with complexity (morphological,
  physiological, metabolic).
• Large variation in genome size (both amount of DNA and
  number of genes).

Question 15

Small Bacterial Genome means..

Answer 15

Small number of genes.
* Growth often restricted to few specialised niches.
* Often pathogens or endosymbionts

Question 16

Large Bacterial Genome means..

Answer 16

Large number of genes.
* Higher metabolic diversity.
* More complex gene regulation

Question 17

All about plasmids

Answer 17

• DNA molecules with their own origin of replication that are
  not essential for growth and replication of host.
• Usually circular, though can be linear
• High variable size => small (a few kb) to megaplasmids (1000s kb)
• Highly variable variable copy number => low (1-2 per chromosome) to high (50 per)