Genome reduction and gene duplication Flashcards

1
Q

Why would microbes shrink?

A
  • Generalist
  • less costly
  • minimalistic lifestyle an advantage
  • Habitat provides limited substrates and nutrients
  • Habitat is stable sp support limited metabolic range
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2
Q

Why would microbes expand?

A
  • Specialist
  • costly but flexible lifestyle.
  • Habitat provides substrates and nutrients
  • Habitat is unpredictable but requiring large flexible metabolic capacity
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3
Q

The relationship between lifestyle and large genome size?

A
  • Free-living organisms
  • Host-associated/ Facultative symbionts
  • High per cent GC and large Genome size.
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4
Q

The relationship between lifestyle and small genome size?

A
  • Free-living auxotrophs
  • Obligate symbionts
  • intracellular parasites
  • Smaller genomes and low Genome size.
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5
Q

What are auxotrophs?

A

Organisms inability to produce certain organic compound for its growth.

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6
Q

Types of dependent lifestyles and small cells works (small genome).

A
  • Free-living auxotroph has no host
  • Obligate episymbiont living on the host.
  • Obligate endosymbiont or intracellular pathogen living inside the host.
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7
Q

Why genome reduction in free-living bacteria/ archaea (auxotrophy)?

A
  • Loss of genes for essential biosynthetic pathways

- depends on other organisms to grow

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8
Q

What is genome stream-lining in free-living bacteria?

A

The leaky bacterial helpers (larger genomes) and auxotrophic beneficiaries (smaller genomes). The smaller genome will lose gene (mutation) as it relies on a larger genome. Resulting in the mutated small genome will dependent on the large genome.

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9
Q

What is obligate episymbiont?

A

The host Ignicaccus can grow with N. equitans, but the N. equitans cant without ignicaccus.

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10
Q

What is endosymbiont or intracellular pathogen?

A

The parasite lives in host with a highly stable environment.

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11
Q

The implication of genome stream-lining: low GC

A

Guanine and cytosine are energetically more costly. Smaller genome have fewer DNA repairs genes, which mean an increase in common point mutation ( Cytosine -> Uracil -> Thymine).

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12
Q

What are pseudogenes?

A

non-functional genes.

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13
Q

How does a genome shrink?

A
  • creation of pseudogenes

- gene deletion

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14
Q

How is the creation of pseudogenes?

A

The initial stage of genome streamlining:
- Genes: unneeded
- The mutation occurs, and are not selected against
- loss of function of unneeded genes.
The final stage of genome streamlining:
- Loss of gene > genes gained

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15
Q

what are the extreme examples of genome streamlining?

A

Cyanobacteria to chloroplast

Alphaproteobacteria to mitochrondria.

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16
Q

Types of lifestyle with a larger genome?

A

Free-living (no host)
Host-associated:
- Not dependent
- Not obligate (facultative), eg. facultative endosymbiont

17
Q

How does a genome expand?

A

Gene gains > gene loss.

Genes gained through horizontal gene transfer from other organisms and gene duplications.

18
Q

Expansion: many duplicated genes

A

Duplicate weakly functional genes, this higher chance of attaining a positive mutation. Select for positive mutation and lose weaker duplicates.

19
Q

Expansion: diverse mechanisms

A
  • Have genes for alternative metabolisms
  • Have many genes for similar important functions optimized for different conditions
  • Diverse genes to tolerate environmental stress