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Genomics Theory > Evolution of Genomes I & II (lectures 4&5) > Flashcards

Evolution of Genomes I & II (lectures 4&5) Flashcards

1
Q

Factors Influencing Nuclear Genome Evolution: 8

A
  1. Mutation
  2. Gene duplication and loss
  3. Exon (domain) shuffling
  4. Repetitive DNA
    1. Microsatellites
    2. Transposable elements
  5. Horizontal / Lateral gene transfer
    8. Endosymbiosis
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2
Q

Genome Evolution – Gene Duplication

Types of duplications: 3

A

1 *entire genome duplications - polyploidy

2 *partial or entire chromosome duplications

3 *partial or entire gene duplications

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3
Q

Gene duplication allows…

A

Gene duplication allows NOVEL GENE FUNCTIONS and BIOCHEMICAL PATHWAYS to EVOLVE, and the REFINEMENT OF PHYSIOLOGICAL PROCESSES.

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4
Q

Most Eukaryotic Lineages Have Undergone WHOLE GENOME DUPLICATION (WGD) Events:

***Understanding Plant Genomes…

A

1 *appear to have gone through CYCLES OF GENE DUPLICATION EVENTS AND GENE LOSS

2 *leads to INCREASED FITNESS (survival)
ADVANTAGES that are LOST OVER TIME AND FAVOUR NEW WGD

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5
Q

Most Eukaryotic Lineages Have Undergone WHOLE GENOME DUPLICATION (WGD) Events:

***Understanding VERTEBRATE Genomes…

A

1 *ancestor went through 2 WGDs

  1. ‘Saccharomyces cerevisiae’
    (baker’s yeast)
    —-
    *~10% of genes derived from
    WGD event, ~100 million
    years ago
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6
Q

Gene Duplication – Fate of Duplicated Genes EXPLAIN

A
  1. Hypothetical genome with 22 genes
  2. DUPLICATION EVENTS – all genes duplicated; PARALOGUES

3 . Many paralogues obtain DISABLING MUTATIONS, become PSEUDOGENES AND ARE LOST

4 . SECOND DUPLICATION EVENT– ALL paralogues duplicated. MULTIGENE FAMILIES.
– some with 4 copies, others with 2

5 . Again, MANY PARALOGUES OBTAIN DISABLING MUTATIONS, become pseudogenes
and are lost.
(Transpositions and other
duplication events, e.g. single gene duplications can occur)

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7
Q

Eukaryotic Genomes Contain Multiple Segmental Duplications: 4

A
  1. Genomes of multicellular eukaryotes have duplicated regions of more than 1000 bp
      2*INTRAchromosomal (most common) and INTERchromosomal duplications

     3*result in multiple copies of genes

               4*may become ESTABLISHED AS MULTIGENE FAMILIES
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8
Q

Eukaryotic Genomes Contain Multiple Segmental Duplications:

‘Arabidopsis’ genome = 3

A

1 * 30 segmental duplications

2 * intrachromosomal duplications (A) in 3 of the 5
chromosomes

3 * interchromosomal segmental duplications (B)
………*some inverted relative to one another (twisted bands)

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9
Q

Eukaryotic Genomes Contain Multiple Segmental Duplications:

HUMAN GENOME IS COMPOSED OF SEGMENTAL DUPLICATIONS…explain: 2

A
  1. Approximately 4% of the human genome is composed of segmental duplications,
    averaging 15,000 bp in size

2 *duplication events on the LONG ARM of chromosome 22

3 *nearly 200 SEGMENTS (over 10%) of the CHROMOSOME ARM have resulted from duplications

4 *DUPLICATION BIAS toward regions close to the centromere

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10
Q

Eukaryotic Genomes Contain Multiple Segmental Duplications cont’d

Fig 18.16 Brown (2007) Genomes 3

A

SLIDE 9

Centromere to Telomere, DIAGRAM

pink bars = regions duplicated within this chromosome

blue bars = regions duplicated from other chromosomes

black bars = gaps in sequence when analysis was done

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11
Q

Eukaryotic Genomes Contain Multigene Families:

— Single copy genes in multicellular eukaryotes make up

SIMPLE VS COMPLEX GENE FAMILIES

A

1 — Single copy genes in multicellular eukaryotes make up ‘25-50% of protein-coding genes’

2 — SIMPLE (aka classical) gene families
*ALL MEMBERS have IDENTICAL or NEARLY identical SEQUENCES

3 — COMPLEX gene families

*members have SIMILAR SEQUENCES

*DIFFERENT ENOUGH TO CODE for gene products with different properties

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12
Q

Gene Duplication – Fate of Duplicated Genes: DIAGRAM IMPORTANT

A

SLIDE 11

LOOK AND STUDY THE DIAGRAM

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13
Q

Orthologues and Paralogues

= IMPORTANT DIAGRAM

3 PROCESSES

A
  1. Gene G
  2. SPECIATION TO GIVE TWO SEPARATE SPECIES

…. GENE DUPLICATION AND DIVERGENCEN

…GENE DUPLICATION AND DIVERGENCE

LOOK AT DIAGRAM IMPORTANT …SLIDE 12

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14
Q

What are Isozymes…example?

A

Isozymes = enzymes that catalyse the same biochemical reaction, but in different tissues, or at different times, or with different properties (e.g.
kinetics)

e.g. lactate dehydrogenase (LDH) isozyme expression during rat heart development
* as heart develops, isoenzymes with largely B
subunits (associated with aerobically active
tissues) are expressed

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15
Q

Multigene Families – Fine-tuning & Expansion of Physiology: explain ..5

A
  1. Gene LOSSES and GENE FAMILY EXPANSIONS IN DIFFERENT EVOLUTIONARY LINEAGES RESULTED IN VARIABILITY IN THE RELATIVE CONTRIBUTIONS OF INDIVIDUAL GENE FAMILIES TO THE TOTAL CODING DNA SEEN ACROSS SPECIES.

2 *e.g. human vs mouse genomes

3 *roles in cellular ion and metabolite transport

4 *second messenger signaling

5 *synaptic transmission

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16
Q

Genome Evolution –

Polypeptide Domain
Shuffling = 5

A

1 *domains may be either STRUCTURAL OR FUNCTIONAL

2 *involves COMBINING EXISTING DOMAINS INTO GENE ARCHITECTURES

3 *may involve domain DUPLICATION – leads to
ELONGATION of gene; EVOLUTION of novel
domain through mutation

4 *may involve domain INSERTION from a
different gene – leads to MOSAIC GENES

5 *~20% of eukaryotic exons involved

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17
Q

DOMIAN DUPLICATION AND DOMAIN SHUFFLING …DIAGRAM

A

LOOK AT SLIDE 15

SHUFFLING PROCESS

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18
Q

Domain Shuffling - Increasing Gene Architecture Complexity = 3

A
  1. Gene architecture COMPLEXITY INCREASES WITH ORGANISM COMPLEXITY

2 *Drosophila, vertebrate, and flowering plant genes have ACCUMULATED more
DOMAINS and EVOLVED MORE COMPLEX ARCHITECTURES than genes of worms or fungi

3 *Think about GENOME EVOLUTION = evolution of DOMAINS MAKING UP GENES.

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19
Q

Domain Shuffling – Increasing Gene Architecture Complexity DIAGRAM

A

SLIDE 16

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20
Q

Domain Shuffling – Increasing Gene Architecture Complexity:

TISUE PLASMINOGEN ACTIVATOR (TPA) = 6

A

Tissue plasminogen activator (TPA)

1 * involved in BLOOD CLOTTING

2 * one of the first discovered MOSAIC PROTEINS

3 * TPA gene has four exons:

……. *1st derived from from gene encoding FIBRONECTIN

……..2nd derived from EPIDERMAL GROWTH factor gene
……..3rd and 4th derived from gene encoding PLASMINOGEN

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21
Q

Explain BORDERS OF PROTEIN DOMAINS….

A

borders of the protein domains match perfectly with EXON-INTRON BOUNDARIES – supporting idea that DURING EVOLUTION EXONS MAY BE TRANSFERRED FROM ONE GENE TO ANOTHER

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22
Q

Domain Shuffling – Increasing Gene Architecture Complexity cont’d…DIAGARAM

A

SLIDE 17

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23
Q

Origin of the Eukaryotic Genome – Endosymbiosis

DIAGRAM

A

SLIDE 18

Nucleus
Mitochondrion
Chloroplast

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24
Q

Origin of the Nucleus: + DIAGRAM

A

LOOK AT DIAGRAM SLIDE 19

Highly debated

Prior to or concurrent with the acquisition of mitochondrion?

  • for latest, see Tria et al. (2021) Genome Biol. Evol. 13: 1
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25
Q

Origin of the Nucleus:

A

Comparison of yeast nuclear open reading frames (excluding those encoding
mitochondrial proteins) with those of eight archea and 12 eubacteria.

26
Q

Origin of the Nucleus:

‘ORF groups originating from archea’

A
  • cell cycle control
  • assembly of protein complexes
  • nuclear organisation
  • endoplasmic reticulum organisation
  • DNA repair
  • replication
  • transcription to RNA
  • Translation Ribosomal Protein
27
Q

Origin of the Nucleus:

‘ORF groups originating from eubacteria’

A
  • metabolism
  • energy
  • detoxification
  • stress response
  • signal transduction
  • ionic homeostasis
  • protein folding and stabilisation
  • organisation of cytoplasm
  • organisation of plasma membrane
28
Q

Origin of the Nucleus: DIAGRAM

A

SLIDE 20

29
Q

Origin of the Nucleus cont’d

Comparison of yeast nuclear open reading frames (excluding those encoding
mitochondrial proteins) with those of eight archea and 12 eubacteria

CONCLUSION:

A

Concluded: an archeal
cell entered a eubacterial
cell and evolved into a
nucleus

30
Q

Origin of Mitochondria?
SIZES?

…4

A
  1. Free-living α-PROTEOBACTERIUM
    - typical genome size - 1 to 9 Mbp
  2. Mitochondrial genome size:
    - typically 15-60 kbp
    extremes
    …..‘Plasmodium’ sp. - 6 kbp
    ……    ‘curcubit plants’ - 2000 kbp
  3. Mitochondrial genome coding capacity:
    on average - 50-60 genes
  4. REDUCTION IN GENOME CONTENT DUE TO GENE TRANSFER AND GENE LOSS
31
Q

ORIGIN OF CHLOROPLASTS AND MITOCHONDRIA DIAGRAM:

A

SLIDE 21-22

32
Q

Origin of Chloroplasts:

A
  1. Free-living CYANOBACTERIUM
    …… *typical genome size - 1.5 to 8 Mbp
  2. Chloroplast genome size:
    typically 120-160 kbp
    extremes
  3. Chloroplast genome coding capacity:
    on average – 50-200 genes
  4. REDUCTION IN GENOME CONTENT DUE TO GENE TRANSFER AND GENE LOSS
33
Q

Secondary and Tertiary Origins of Chloroplasts!

A

Eukaryote-eukaryote symbioses

Common in the photosynthetic protists (algae)

34
Q

Secondary and Tertiary Origins of Chloroplasts!

IMPORTANT DIAGRAM

A

SLIDE 23

35
Q

Evolution of Nuclear and Organelle Genomes:

The “product specificity corollary” of the endosymbiotic theory:

A

The “product specificity corollary” of the
endosymbiotic theory:

Nuclear-encoded gene products are RE-TARGETED TO THE ORGANELLE FROM WHOSE GENOME THEY ORIGINATED

36
Q

Evolution of Nuclear and Organelle Genomes: DIAGRAM

A

SLIDE 24

37
Q

Evolution of Nuclear and Organelle Genomes:

’ Chloroplasts and mitochondria’ = 5

A
  1. Chloroplasts and mitochondria import ~90% of their proteins from the cytosol
  2. HOWEVER: many mitochondrial proteins are not of α-proteobacterial origin, and many
    chloroplast proteins are not of cyanobacterial origin!
  3. The product specificity corollary of the Endosymbiotic theory is NOT supported

4….. <30% of the proteins encoded by genes originating from α-proteobacterium are predicted to be targeted to yeast and human mitochondria

5….. <50% of the proteins encoded by genes originating from cyanobacterium are predicted to be targeted to ‘Arabidopsis’ chloroplasts

38
Q
A

Calvin cycle

  1. *CO2 fixation pathway in plant chloroplasts
  2. *enzymes of pathway are encoded by nuclear genes of cyanobacterial and α- proteobacterial origin
  3. Cytosolic isoforms of these enzymes are typically encoded by genes of endosymbiont origin!
39
Q

Evolution of Nuclear and Organelle Genomes = CALVIN CYCLE OUTCOMES…

A

Outcomes

1 - opportunity for evolution of novel function

2 - co-evolution of nuclear,
mitochondrial and chloroplast genomes in eukaryotic cells

40
Q

‘Evolution of Nuclear and Organelle Genomes’

Why were endosymbiont genes transferred to the host cell nucleus? = 3

A
  1. Evolutionarily advantageous to:
  2. *isolate genes from sites where mutagenic
    radicals are formed
  3. *have genes in a sexual population instead of
    asexual population (avoidance of Muller’s
    Ratchet)
41
Q

‘Evolution of Nuclear and Organelle Genomes’

Why have not all endosymbiont genes been transferred to the host cell nucleus? = 3

A
  1. Hydrophobicity Hypothesis (HH):
    - Some gene products are too hydrophobic to be imported into organelles.
  2. Code Disparity Hypothesis (CDH):
    - Genetic code used in organelles and nucleus differ, which would lead to incorrectly translated proteins.
  3. Co-location for Redox Regulation (CORR):
    - Proximity of genes to their products’ sites of activity allows a rapid response in gene expression to changes in metabolism.
42
Q

Evolution of Nuclear and Organelle Genomes DIAGRAM = SLIDES 27 AND 28

A

INTERACTION BETWEEN MITOCHONDRION, PLASMID, NUCLEUS

SLIDES 27 AND 28

43
Q

What is Left in Organelle Genomes?

Two main functional categories of genes retained:

A

Two main functional categories of genes retained:

1) PROTEINS OF THE BIOENERGETIC MEMBRANES
* photosynthetic
* respiratory

2) COMPONENTS OF GENE EXPRESSION
* rRNAs
* tRNAs

‘So do these data support any one hypothesis over
the others?’

44
Q

‘Evolution of Nuclear and Organelle Genomes:’

Why have not all endosymbiont genes been transferred to the host cell nucleus? = ‘Hydrophobicity Hypothesis (HH)’ = 3

A

Hydrophobicity Hypothesis (HH):
1 - Some gene products are too hydrophobic to be imported into organelles.

  1. Animal and fungal proteins encoded in the
    mitochondrion support this hypothesis.
  2. Nuclear-encoded proteins of the mitochondrial respiratory chain and
    chloroplast light harvesting proteins argue against this hypothesis
45
Q

‘Evolution of Nuclear and Organelle Genomes:’

Why have not all endosymbiont genes been transferred to the host cell nucleus? =
‘ Code Disparity Hypothesis (CDH)’ = 2

A
  1. Code Disparity Hypothesis (CDH):
    Genetic code used in organelles and nucleus differ, which would lead to incorrectly translated proteins.
  2. Most organelle genomes use the standard
    code;
    - however, disparity exists between nuclear and mitochondrial codes in animals and protists
46
Q

‘Evolution of Nuclear and Organelle Genomes:’

Why have not all endosymbiont genes been transferred to the host cell nucleus? = ‘Co-location for Redox Regulation (CORR)’ = 2

A
  1. Co-location for Redox Regulation (CORR):
    - Proximity of genes to their products’ sites of activity allows a rapid response in gene expression to changes in metabolism.
  2. Evidence supporting this comes from studying the effects on gene transcription
    when the redox poise of the chloroplast changes.
47
Q

Transfer of Organelle DNA to the Nucleus Continues: Promiscuous DNA!

‘Comparative genomics has identified:’…4

A

Comparative genomics has identified:

  1. Copies of genes still in organelle genomes are also in other cellular compartments

…..2 *NUMTs – nuclear mitochondrial DNAs

…..3 *NUPTs – nuclear plastid DNAs

  1. RANGE OF SEQUENCE SIMILARITY INDICATES RECURRENT TRANSFERS—FRAGMENTS WITH MOST SIMILAR SEQUENCES ARE MOST RECENT TRANSFERS
48
Q

Transfer of Organelle DNA to the Nucleus Continues: ‘Promiscuous DNA!’

EXAMPLES = 3
- size of fragments etc

A
  1. ‘yeast nuclear genome’
    * fragments with 80-100% similarity to mitochondrial genes
    * size range: 22 to 230 bp
    * integrated at 34 sites
  2. ‘rice nuclear genome’
    * chromosome 10 contains 33 kb insert of chloroplast DNA and a 131 kb insertion that represents nearly the entire chloroplast genome
  3. ‘human nuclear genome’
  • 59 fragments of mitochondrial DNA >2 kb in length totaling 280 kb

*one 14.6 kb fragment encoding nearly the entire human mitochondrial
genom

49
Q

How is DNA Transferred Between Intracellular Compartments? = 4

A

1.) LYSIS OF ORGANELLES AND RELEASE OF DNA

2.) FUSION OF ORGANELLES (lateral gene transfer)

3.) PHYSICAL CONTACT BETWEEN ORGANELLES, or INCLUSION of MITOCHONDRIA in NUCLEI

  1. ) PLASTIDS (e.g. chloroplasts) form
    CONNECTIONS, called STROMULES, WITH OTHER ORGANELLES
50
Q

Nonhomologous end-joining (NHEJ)?

A

double-stranded-break (DSB) repair mechanism that requires no homology between ends (illegitimate
repair)

51
Q

How is Organelle DNA Integrated into the Nuclear Genome?

A

Nonhomologous end-joining (NHEJ):

  • double-stranded-break (DSB) repair mechanism that requires no homology between ends (illegitimate
    repair)
52
Q

How is Organelle DNA Integrated into the Nuclear Genome?

Nonhomologous end-joining (NHEJ): TYPES… 2

A

Two general types of insertions identified:

i) RELATIVELY LONG FRAGMENTS OF ORGANELLE

ii) MOSAICS OF ORGANELLE DNA FRAGMENTS

53
Q

How is Organelle DNA Integrated into the Nuclear Genome? DIAGRAM

A

SLIDE 35

54
Q

Effects of Organelle DNA on Nuclear Integrity: 4

A
  1. MOST present-day TRANSFERS GENERATE NON-CODING SEQUENCES (pseudogenes).
  2. Some recent NUMTs show preferential insertion into genes – changes in exon-intron patterns.
    * NUMTs associated with human disease, e.g. 251 bp insertion in coagulation factor VII gene – NOVEL SPLICE SITE, DEFECTIVE PROTEIN, BLEEDING DISORDER
  3. Insertions into non-protein-coding regions may affect gene regulation.
  4. One study found ~40 nuclear genes across 4 species (yeast, rice, ‘Arabidopsis’ and
    human) that have been remodeled by organelle DNA.
55
Q

Effects of Organelle DNA on Nuclear Integrity:

’ Three outcomes of remodeling observed:…’

A

1) partial conservation of the original organelle ORF

2) replacement of the original ORF by a novel ORF

3) high rate of nonsynonomous substitutions – sequence diversification

56
Q

Genome Evolution – Horizontal (Lateral) Gene Transfer EXAMPLES

A

“The transmission of genetic material between the genomes of two individuals
(that may belong to different species) by nonvertical inheritance”

Feschotte & Pritham
(07) Annu Rev Genet 41:331

57
Q

Genome Evolution – Horizontal (Lateral) Gene Transfer..EXAMPLES: 5

A

1 * endosymbiont genes transferred to host nucleus

2 * retroviruses in vertebrate genomes acquired through infection of the germ
line

3 * prokaryote to prokaryote transmission of antibiotic resistance and virulence
genes, and the genes for nitrogen fixation and photosynthesis

4 * acquisition of transposons

  1. Few clear examples of genes transferred between unrelated multicellular
    eukaryotes
58
Q

Horizontal Gene Transfer – Photosynthesising Sea Slugs(!) = 10

A
  1. Sea slugs (‘Elysia chlorotica’) acquire chloroplasts through feeding on an alga (‘Vaucheria litorea’)

2 * the chloroplasts

3 *inside cells lining the slug’s gut

4 *continue to photosynthesise, even without nuclei that normally provide >90% of their proteins

5 *provide carbohydrates to slugs for >10 months

6 * numerous algal chloroplast and nuclear genes are expressed

7 * transcriptome data

  1. BUT sequencing of sea slug egg cell genome
    indicates no algal sequences in the germ line
  2. A current hypothesis – algal genes exist as
    extrachromosomal DNA in feeding adult sea
    slugs
  3. KLEPTOPLASTY
59
Q

KLEPTOPLASTY = That was 2013

A

that was 2013. but in 2014…

60
Q

Horizontal Gene Transfer – Photosynthesising Sea Slugs(!)… in 2014

= 3

A
  1. ‘in situ’ hybridsation of metaphase chromosome spreads from unhatched sea slug larvae (prior to feeding)

…..2 * DIG-labelled probe for ‘Vaucheria litorea prk’ gene

…..3 * ‘prk’ = phosphoribulokinase – an enzyme in the CO2 fixation pathway

Genomics Theory (10 decks)

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