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Genomes and Genomics 3 > 2. E. coli genome > Flashcards

2. E. coli genome Flashcards

1
Q

What is the smallest genome difference needed for two bacteria to be different species?

A

1 nt change in the genome can be enough for 2 bacteria to be different species

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2
Q

Explain the structure of a diagram representing complete sequenced bacterial genome

A
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3
Q

What genomic components are used to describe prokaryotic genomes?

A

Prokaryotic genomes described:
- composition and regions of diverging parts
- biological inventory
- evolutionary considerations (HGT, gene ancestry)

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4
Q

Explain what is a GC skew

A

GC skew - region of genome which has a distorted base composition compared to other regions

+ GC skew on leading strand
- GC skew on lagging strand

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5
Q

Why is GC skew different in leading and lagging strands?

A

Higher GC index in leading than lagging because of ss cytosine deamination:
- in replication leading strand template has longer exposed ssDNA fragment than lagging strand
- ssDNA more unstable - Cs get deadinated - become U - in replication recognised as T -> loss of GC residues

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6
Q

What are the common features of bacterial genomic composition that are considered?

A

Bacterial genome composition features:
- base composition (% C, G, A, T)
- GC skew
- over/under-representation of specific sequences (words) - ex: under-representation of CTAG (causes DNA bend - can interfere with transcription)
- repeated sequences - ex: REP

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7
Q

What are the recognisable sequences in E. coli genomes?

A
  • under-represented words - CTAG (causes DNA bend - replication problems)
  • skewed words: Chi, 8-mer
  • repeated sequences: Rhs elements (large repeats in genome rearrangements by HR, potential contact-dependent growth inhibition system - produce surface proteins that inhibit neighbouring bacteria after contact), Repetitive Extragenic Palindromic (REP) sequences (small inverted repeats downstream of genes - modulate transcription in repsonse to stress)
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8
Q

What are Chi sites used for?

A

Chi sites mark recombination hotspots - used by RecBCD for HR to repair dsDNA breaks

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9
Q

What are the types of genes based on function?

A
  • Informational genes - small porportion - involved in transcription, translation, and related processes
  • Operational genes - provide function inside the cell - housekeeping genes
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10
Q

What is comparative genomics?

A

Comparative genomics - direct comparison of complete genome of one organism against another to infer how species evolved + determine functions of genes and noncoding regions

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11
Q

Define orthologues and paralogues

A

Orthologues: descendant gene from a common ancestral gene before species diverged - homologues between organisms

Paralogues: related genes in the same organism

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12
Q

What are the three example E. coli strains compared in the lectures? Describe them

A

Commensal E. coli K-12: in GI tract but can become pathogenic if transported else / in immunocompromised

Enterohaemorrhagic E. coli O157: in cow rectum - can contaminate beef - not cooked well can cause internal bleeding -> death

Uropathogenic E. coli CFT073: causes UTI

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13
Q

How is enterohaemorrhagic E. coli O157 strain genome different from commensal E. coli K-12?

A

Larger genome - some specific genes that are not found in K-12 - acquired pathogenicity by HGT - acquired toxins from bacteriophages + T3SS

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14
Q

How is uropathogenic E. coli CFT073 strain genome different from commensal E. coli K-12?

A

Larger genome - common backbone but some specific genes (CFT073 specific islands) - 60 pathogenicity islands - allow to colonise urinary tract - better adhesion to epithelium

UTI - blood in urine because E. coli want to retrieve iron from RBCs:
pilus used to adhere to urinary tract epithelial cells -> cytotoxic necrozing factor degrades capillaries -> RBCs released -> haemolysin lyses RBCs -> iron released

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15
Q

How are horizontally acquired islands represented in a diagram?

A

Diagram: comparing two strains one on top of the line - one on bottom, the higher the peak - larger insertion

HGT genes often inserted near tRNA genes for am a transport in protein synthesis

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16
Q

Genomic comparison of E. coli K-12, E. coli O157 and E. coli CFT073

A
17
Q

Lecture summary

A
18
Q

What is a pan-genome?

A

Pan-genome - represents the entire set of genes within a species, consisting of a core + ‘dispensable’ genome.

19
Q

What is the function of rpoB gene in E. coli?

A
  • rpoB gene encodes the beta-subunit of RNA polymerase
  • has emerged as a core gene candidate for phylogenetic analyses and identification of related bacteria

Genomes and Genomics 3 (13 decks)

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