Lecture 2 - Being competitive in the body

Question 1

Why do bacterial genomes contain viral elements?

Answer 1

lamba type bacteriophages are incorperated into the bacterial genome and instead of inducing lysis they pick up mutations over millions of years leading to their inactivation.

Question 2

How can the viral elements of bacterial genomes be utilised?

Answer 2

Can be used as an archaeological record of the evolution of different bacteria.

Question 3

Describe the differences in bacterial genomes

Answer 3

• can have single or multiple chromosomes
• can contain a range of large plamids called megaplasmids or chromids
• chromosome and plasmids can be linear or (more often) circular

Question 4

What is the size range of the bacterial genome?

Answer 4

• 14.3Mb to 0.14Mb
• An extremely large genome: Streptomyces coelicolor (9Mb) [soil bacterium]
• A small gemone: Buchnera aphidicola (0.5Mb) [insect symbiont]
• Middley: E.coli (5Mb)

Question 5

How is the size of the bacterial genome linked to the number of genes and why is this the case?

Answer 5

• The larger the genome, the more genes present and the more complex environment the bacteria lived in
• The use of genomic space in bacterial genomes is incredibly efficient and similar in structure between different bacteria

Question 6

What are prophages/cryptic prophages?

Answer 6

• Remnants of phage attack in the genomes of bacteria
• Often carry important genes
• Prophage: the genetic material of a bacteriophage, incorporated into the genome of a bacterium and able to produce phages if specifically activated
• Cryptic prophage: a non-plaque-forming, defective prophage, stably integrated into the bacterial chromosome. lie in a contiguous group, often provide nutritional benefits or immunity to other phage

Question 7

What is the transformative status of bacteria?

Answer 7

Bacteria are normally transformable and will take up DNA from their environment

Question 8

What is the difference between a core genome and a pan genome?

Answer 8

• Pan genome: totals the complete genome of a particular species of bacteria
• e.g. E.coli Core genome: is the genes that are common to all of a particular species of bacteria, not including the serotype specific genes
• e.g. those that differ between E.coli K-12 MG1655 (commensal) and E.coli O157:H7 (enteropathic strain))
• Necessary to define as there is a lot of variabilty within a species of bacteria

Question 9

What type of bacteria undergo reductive evolution?

Answer 9

Intracellular living bacteria evolving from excisting extracellular living bacteria

Question 10

What is reductive evolution?

Answer 10

• The decreasing in size of a bacteria’s genome as it moves towards being specific to a specific environemt.
• Slowly genes become inactive and unneccessary genes are eventually lost from the genome.
• May go through a period of losing functionality (pseudogenes - inactivated genes, accumulated stop codons) but not decreasing in size

Question 11

What is special about bacterial genomes?

Answer 11

• -have not all evolved from one ancestor
• -represented by organisms across a wide phylogenetic spectrum -
• genome size is generally in the mid range (2-6Mb)

Question 12

What are the special features of bacterial genome dynamics?

Answer 12

1. Gene duplication
   
   • which can then be acted upon by selection pressures to result in a divergence of bacteria
2. . Horizonal gene transfer
   
   • by phages, plasmids and pathogenecity islands
3. Rapid emergence of genetically uniform pathogens from variable ancestral populations
   
   • due to genetic bottlenecking. Small number of individual cells pick up key virulence factors and others are not as effective and are lost from the population
4. Single-nucleotide polymorphisms
5. Patho-adaption
6. Recombination and rearrangement
   
   • have vertical evolution (parent-offspring) alongside spacial, horizontal transfer
7. Accumulation of pseudo-genes and insertion elements after they shift to a new niche
   
   • e.g.mycobacterium leprae: a relatively new pathogen, successful becuase of the presence of humans, can result in leprosy
8. Marked downsizing of the genome in isolated intracellular niches

Question 13

How do bacterial genome dynamics impact bacterial genomes?

Answer 13

• -can see clear patterns of genome dynamics as bacteria become host-adapted
• e.g. smaller genomes for an intracellular parasitic organism as it becomes incorperated as an organelle (mitochondria)

Question 14

What are colonisation dependency factors?

Answer 14

• important factors neccessary to colonise and compette for a niche in the host
• without this most pathogens would not be pathogens
• therefore are an alternative way of looking at virulence and treatment

Question 15

What is an enteric pathogen?

Answer 15

Lives in the gut

Question 16

Give three examples of enteric pathogens

Answer 16

• Escherichia coli (common commensal with pathogenic strains)
• Shigella dysenteriae (causes bacillary dysentery)
• Salmonella enterica serovar typhimurium (causes food poisoning and gastroenteritis)
• Vibrio cholerae
• Clostridium difficile

Question 17

What is the carbon source for bacteria living in the gut?

Answer 17

• mucin proteins in the gut covered in glycans
• anaerobic bacteria on the lower bowel (Bacteroides thetaiotaomicron and Bifidobacter bifidum) are able to digest these polysaccharides liberate free sugars from the gut
• glycans can be comprised of accumulations of different sugars attached to the glycan backbone, which is a challenge for the bacteria to get access to

Question 18

What are the features of enteric pathogen nutrition in the gut?

Answer 18

Enteric pathogens can only use monosaccharides and some disaccharides but not polysaccharides

Question 19

What is the purpose of the mucus in the gut?

Answer 19

• Mucus is made up of mucin
• sugar coated proteins protect the epithelial cell wall surface from damage

Question 20

How does nutrient availablity change in different parts of the gut?

Answer 20

1. Small intestine - components of the diet (fibre, proteins, starch)
2. Caecum - components of the diet (lactose, hemicellulose)
3. Distal bowel
   
   1. metabolites derived from the diet by bacterial enzymes (glycerol, ethanolamine, ribose)
   2. nutrients dericed from the mucus by bacterial enzymes (galactose, sialic acid, xylose, mannose, BCAA’s, 1,2 - propanediol)

Decreasing carbohydrate availabiity

Question 21

What are the metabolic features of E.coli?

Answer 21

• Metabolically very flexible
• Can use many potential carbon sources in the gut
• commensal strain and pathogenic strain have different uses for their C sources

Question 22

How was it shown that E.coli can utilise a number of carbon sources in the gut?

Answer 22

Two strains of E.coli lines ahow sequential digestion of sugars

Lac operon, glucose v. lactose use (regulation)

Certain sugars are always used before others

Question 23

How was it shown that different E.coli strains access different sugars in the mouse?

Answer 23

1. Tyrrell developed a mouse model of infection to study colonisation
2. Treated with streptomycin (selectively kills the facultative anaerobes leaving the anaerobes (bacteriodes) intact
3. Constructed a series of mutants lacking key growth genes needed for growth on a particular carbon source
4. Found that some carbon sources were used by the commensal strains (K12) such as sialic acid but not the pathogenic strain (EDL)
5. Galactose used by EDL preferentially, Mannose used for K12 preferentially
6. Fucose, arabinose and N-acteylglucosamine important for both

Question 24

How was it shown that in the gut different E.coli are living in different niches?

Answer 24

Looked at overlapping niches for different E.coli in the gut

1. Took particular strain and injected it into an animal model
2. When inject a second strain this accumulates but only has a slight negative effect on the accumulation of the other strain

Shows these strains are not in competition and using different pathways of nutrition

Question 25

How was it shown that precolonisation with some commensal strains protect the mouse against infection by some pathogenic strains?

Answer 25

1. When commensal bacteria input first then pathogenic e.coli get a deacrease in pathogenic colonies

Question 26

What evolutionary forces have shaped pathogen genomes?

Answer 26

• Natural variation in the genome structure, size correlating to the number of genes and the complexity of the bacterial lifecycle (B.aphididia (0.5mb/S. coelicolor 9Mb)
• Phage attack
• Transformation - horiztonal gene transfer
• Core/pan genome (defines the capabilities of a strain e.g. if pathogenic)
• Reductive evolution appropriate to the environment and niche (host adaptation)
• Didn’t evolve from one super ancestor
  
  • Bacterial genome dynamics
  • Wide phylogenetic spectrum