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Year 3: SGE > Origin of the nucleus > Flashcards

Origin of the nucleus Flashcards

1
Q

List 6 major unique components of the eukaryotic cell.

A
  1. Double nuclear envelope
  2. NPCs
  3. Internal lamina
  4. Nucleolus
  5. Chromatin
  6. Folding of DNA around histones
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2
Q

Is this nuclear envelope a continuous double membrane?

A

No, it is a series of flattened bags

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3
Q

Is the lumen of the nucleus continuous with the ER?

A

Yes

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4
Q

What is open mitosis?

A

Whereby the nuclear membrane completely dissembles and reforms by fusion of the ER vesicles at every division

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5
Q

Did LECA have NPCs?

A

Yes

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6
Q

Did LECA have chromatin?

A

Yes

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7
Q

What did the histones an nucleosomes evolve from?

A

Archaeal structures, e.g. from methanogens

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8
Q

Is eukaryotic RNA polymerase more closely related to archaeal or bacterial polymerase?

A

Archaeal

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9
Q

Is there much homology between archaea and eukaryotes?

A

Yes, much

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10
Q

Are the major unique features of eukaryotic cells conserved across all eukaryotes?

A

Yes

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11
Q

Are the major unique features of eukaryotic cells found in LECA?

A

Yes

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12
Q

Are there any intermediary forms between LECA and current eukaryotes?

A

No, eukaryotes just ‘appeared’

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13
Q

Bacteria have a similar structure to the nucleus. What is it called?

A

The nucleoid that contains the genophore

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14
Q

What is the difference between a eu nucleus and a bacterial nucleoid?

A

The nucleoid is NOT separated from the cytoplasm as it does not have a membrane

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15
Q

Due to the nucleoid what can bacteria do in DNA replication?

A

Couple transcription and translation as the ribosomes can freely interact with the genetic material

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16
Q

Why is there an advantage to the bacterial nucleoid not having a membrane?

A

Because the coupling of transcription/translation allows rapid response to the environment

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17
Q

The nucleus only arose once. True or false?

A

True, as LECA only arose once

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18
Q

What are the 5 hypotheses for the origin of the nucleus?

A
  1. Autogenous invagination
  2. Endokaryosis
  3. Inside-out hypothesis
  4. Viral origin
  5. Intron invasion
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19
Q

Which hypothesis does Nick Lane think is most likely?

A

Intron invasion

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20
Q

What is autogenous invagination?

A

The ‘textbook’ explanation:

Proto-eukaryotes were phagocytic and the nucleus and ER are derived from an invagination of the plasma membrane

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21
Q

What support is there for the autogenous invagination hypothesis? Give 2 reasons.

A
  1. Morphology is correct; nuclear membrane and ER are continuous and evolutionarily related
  2. A phagocyte would need a nucleus to protect the DNA from stretching in phagocytosis
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22
Q

Who found that the nuclear envelope lamina acts as a ‘molecular shock absorber’? How?

A

Dahl et al., 2004:

Nuclear envelope has a network structure that allows elasticity and compressibility. Normally the nucleus is compressed but can expand in phagocytosis.

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23
Q

So the model for autogenous invagination predicts that…

A

The first eukaryote was phagocytic and endosymbiosis came later

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24
Q

What are the 2 major constraints of the autogenous invagination hypothesis?

A
  1. Necessitates a cytoskeleton, yet most prokaryotes have a cytoskeleton, so why hasn’t this happened multiple times?
  2. The loss of the cell wall led to the evolution of eus; L-form bacteria exist without cell walls, so why hasn’t this happened multiple times?
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25
Q

Who was a big advocate for the autogenous invagination hypothesis? What did they say

A

Cavalier-Smith, 1988

Said that the ‘catastrophic loss of the cell wall’ led to eu evolution

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26
Q

What is the endokaryosis hypothesis?

A

The nucleus evolved from an endosymbiont like a methanogen that lost its metabolic machinery over time

Basically there were two endosymbiosis events, one to uptake the nucleus and one for the mitochondria

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27
Q

What support is there for the endokaryosis hypothesis?

A

May explain why information systems (replication, transcription, translation) are archaeal but the membrane systems are bacterial

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28
Q

The nuclear membrane shows homology to the membranes of which group?

A

Bacteria

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29
Q

What are the constraints of the endokaryosis hypothesis? List 6.

A
  1. No known FL cell with a membrane similar to the nucleus
  2. Why was only one endosymbiont uptaken and not a population like the mitochondria?
  3. FL cells have ATP-generating physiology and nucleus does not
  4. Open mitosis is unique to the nucleus, FL cells don’t do that
  5. No known FL cell is as permeable as the nucleus due to NPCs
  6. Why would all host DNA be transferred to the endosymbiont?
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30
Q

Endokaryosis theory could be described as ‘a frozen accident’. Why?

A

It conveys no selective benefit of the nucleus.

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31
Q

Who put forward the inside-out hypothesis and when?

A

Baum and Baum, 2014

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32
Q

Describe the inside-out hypothesis.

A

The outer membrane of an archaeal cell had protrusions called blebs. NPCs evolved early on in archaeon. The blebs expanded outwards around NPCs and trapped the mitochondria. Energy from the mitochondria was used to further expansion, blebs began to fuse.

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33
Q

During expansion in the inside-out hypothesis, the sides of the blebs began to touch and form what?

A

The ER

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34
Q

During expansion in the inside-out hypothesis, the inner surfaces of the blebs formed what?

A

The outer nuclear membrane

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35
Q

During expansion in the inside-out hypothesis, the archaeal outer membrane formed what?

A

The inner nuclear membrane

36
Q

During expansion in the inside-out hypothesis, external fusion of the blebs formed what?

A

The plasma membrane

37
Q

What are the constraints of the inside-out hypothesis?

A
  1. How does the cell divide? Fission? Division of the central cell + a developmental programme?
  2. Implies NPCs are archaeal in origin (they are not)
  3. Implies position of mitochondria was fixed (it was not)
  4. Implies archaeal membranes were replaced but gives no selective advantage of this
38
Q

Where was the a) original and b) latter position of the mitochondria?

A

a) ER lumen
b) cytosol

They have mixed between

39
Q

What is the viral origin of the nucleus?

A

Viruses and nucleus are both DNA packets surrounded by protein coats

40
Q

Give support for viral origin of the nucleus. List 6 reasons.

A
  1. Red algae: nuclei can move between cells like viruses
  2. Both lack lipid/protein producing pathway
  3. Both contain linear chromosomes, but circular like bacteria/archaea
  4. Both dissemble their membrane in replication
  5. Both transcribe DNA but don’t translate within their boundaries
  6. Similarities w/ poxviruses
41
Q

List 2 similarities of the nucleus w/ poxviruses.

A
  1. PVs make a membrane around their DNA using the ER of the host cell
  2. PV ‘viral factories’ are complex morphological structures, shows PVs can recruit cell-processes to form complex nuclear structures
42
Q

What are the constraints of the viral origin hypothesis. Give

A
  1. Similarities are ANALOGOUS not homologous, no structural/genetic homology
  2. Presupposes existence of ER as the virus uses this to hijack the host
  3. Why would all hosts genes be transferred to viral lumen?
  4. Viral-prokaryote interactions are common, why hasn’t this happened more than once?
43
Q

Can the viral origin of the nucleus be described as a frozen accident theory? Why, why not?

A

Yes, conveys no clear selective advantage of the nucleus

44
Q

What is the most parsimonious assumption for the origin of eus?

A

Endosymbiosis between a host archaeon and a bacterial endosymbiont

45
Q

Who demonstrated there are only two primary domains of life? What are they?

A

Williams et al., 2013

Archaea and bacteria

46
Q

Williams et al., 2013

Where do eus fit on the tree of life?

A

Within the archaea

47
Q

Williams et al., 2013

Which group of archaea are closely related to eus?

A

The lokiarchaea

48
Q

Williams et al., 2013

What are the lokiarchaea?

A

Hydrogen-dependent autotrophs

49
Q

What did Esser et al., 2004 find when looking at eukaryotic genes in yeast? What does this suggest?

A

Yeast genes showed a 75% homology with bacterial genes, implies gene bombardment of the host from the endosymbiont

50
Q

As well as bacterial genes, what can be transferred from endosymbiont to host?

A

Retro-elements

51
Q

What evidence is there in eukaryotic genomes that there was bombardment from retro-elements?

A

Eu genes are in pieces, coding exons are separated by junk introns

52
Q

How do eus cope with bacterial introns in their DNA?

A

Introns are spliced out by a splicosome during transcription

53
Q

On the basis of mechanistic similarity, which group can we assume eu introns to be derived from?

A

Bacterial group II mobile self-splicing introns

54
Q

From which group are group II mobile self-splicing introns derived from? Why is this unsurprising?

A

alpha-proteobacteria

The mitochondria are descendants of alpha-proteobacteria

55
Q

Are group II mobile self-splicing introns parasitic?

A

Yes

56
Q

Why are group II mobile self-splicing introns maintained in low densities in pro populations?

A

They do not splice their genomes and so removal would disrupt gene function

57
Q

How might group II mobile self-splicing introns have been released into the host in proto-eukaryotes?

A

Through lysis of the endosymbiont

58
Q

Introns proliferated throughout the eukaryotic genome as parasitic elements. True or false?

A

True

59
Q

Why was intron proliferation a problem in the proto-eukaryote?

A

During DNA replication, splicing of introns is slow, but ribosomal translation is fast. Creates a timing mismatch.

60
Q

Transcription and translation needed to be separated in the proto-eukaryote. Why?

A

Because otherwise abnormal proteins containing translated introns will be synthesised on the ribosomes

61
Q

Is there a lot of evidence for intron invasion theory?

A

No, but what exists is compelling

62
Q

Who looked at the conservation of intron positions across major eu groups? What did they find?

A

Kersanach et al., 1994:

Intron positions are highly conserved across groups, indicates common ancestry.

For example there are 5 conserved introns in the GADPH gene.

63
Q

There was intron proliferation before LECA. Who studied this?

What did they find?

How did they propose this happened?

What did this show?

A

Sverdlov et al., 2007:

Position of ancient paralogues not conserved.
Position of recent paralogues conserved.

In ancient paralogues, duplication happened first. The intron insertion meant it would be different across paralogues OR
Intron invasion first, then duplication, then introns removed as is reverse-transcriptase dependent. Means introns would be different across paralogues.
In recent paralogues, intron invasion happened first then duplication, intron position would be conserved.

Basically that recent paralogues shared common ancestry, i.e. intron invasion happened first while cell was evolving, then duplication occurred in common ancestor so position is conserved across all descendants.

Basically support for the fact that intron invasion came first, then LECA evolved.

64
Q

The acquisition of mitochondria preceded the evolution of the nucleus. How do we know this?

A

The nuclear proteome of eus is chimeric, comprising eu, archaeal and bacterial components.

Nulceolus, nuclear envelope and NPCs are chimeric. This suggests they evolved under endosymbiosis.

65
Q

The nuclear membrane is derived from the ER and yet is composed of bacterial lipids. How might the host archaeal lipids have been replaced?

A

Gene transfer from the endosymbiont to host led to uncontrolled expression of lipids.

These lipids were repelled by the water of the cytoplasm (phase separatation) and began to deposit.

Lipids clumped together into distinct structures, producing an early nuclear membrane and ER.

66
Q

Does uncontrolled lipid formation of the nuclear envelope/ER require a cytoskeleton? Why is this in support of intron invasion theory?

A

No cytoskeleton is required, which is good bc it hadn’t evolved yet

67
Q

Why is the disorderly precipitation of lipids to orm the nuclear envelope/ER advantageous?

A

It separates transcription and translation

68
Q

Eventually bacterial lipids replaced archaeal membranes. How do we know that hybrid membranes were unviable?

A

If they existed they have gone extinct

69
Q

Eventually bacterial lipids replaced archaeal membranes. What is an advantage of this?

A

Host cell was autotrophic. To evolve heterotrophy membrane transporters were necessary. Endosymbiont had membrane transporters; co-option by the host led to evolution of heterotrophy in eus.

THIS CONVEYS A SELECTIVE ADVANTAGE OF CHANGING MEMBRANES

70
Q

Summarise the evidence for intron invasion theory or origin of the nucleus. Give 4 points.

A
  1. Conservation of intron positions in recent paralogues indicates an evolutionary bottleneck that LECA overcame (restricting intron movement)
  2. The acquisition of mitochondria preceded nucleus evolution, gives evidence that intron bombardment from endosymbiont could have caused evolution
  3. Nuclear membrane is derived from bacterial lipids as intron invasion caused uncontrolled gene expression. This has a selective advantage of separating transcription/translation and allowed host co-option of endosymbiont membrane transporters for heterotrophy
  4. Introns show homology to group II mobile self-splicing introns derived from alpha-proteobacteria (which they mitochondria are)
71
Q

Proteonomic analyses of nucleolar, nuclear envelope and NPCs shows they are chimeric. What does this mean?

A

They evolved AFTER the acquisition of mitochondria.

72
Q

Esser et al., 2004:

Yeast genome has 75% bacterial homology.

Archaeal-derived genes are of which origin?
Bacterial-derived genes are of which origin?

A

Methanogen

alpha-proteobacteria (like the endosymbiont)

73
Q

Who estimated the percentage of introns in early eukaryotes?

What was the percentage?

How many introns were predicted per kb of DNA?

How did he propose these heavily-invaded organisms survived?

A

Koonin, 2009:

80% of DNA was introns in early eus

2+ introns per kb

Could only have survived under a severe population bottleneck

74
Q

Define a population bottleneck.

A

A severe reduction in population size caused by chance events.

75
Q

Who suggested that lokiarchaeota was the host cell in proto-eukaryotes? Why?

A

Spang et al., 2015

Loki and eus form a monophyletic group.
Loki shows evidence of membrane remodelling/vesicular transport, which is close to phagocytosis.

76
Q

What are the two traditional schools of thought with regards to origin of the nucleus? Which main hypotheses does this refer to?

A

Mitochondria first vs. phagocytosis first

Mito first = intron invasion, inside-out hypothesis, possibly endokaryosis
Phagocytosis = autogenous invagination

77
Q

Which theories can be thought of as ‘frozen accident theories’ as they convey no clear benefit of the nucleus?

A

Inside-out
Endokaryosis
Viral origin

78
Q

Why is it parsimonious to assume that endosymbiosis of the mitochondria came first?

A

All eukaryotes have them

79
Q

Who put forward the hydrogen hypothesis? What is it?

A

Martin and Muller, 1998

In proto-eukaryotes, the host was an anaerobic hydrogen-dependent, autotrophic archaeon and the endosymbiont was a facultatively anaerobic bacterium that produced hydrogen as a by-product.

80
Q

What recent study found support for the hydrogen hypothesis? Why?

A

Sousa et al., 2016

Found lokiarchaeon is hydrogen-dependent

81
Q

How do Spang et al., 2015 and Sousa et al., 2016 match up?

Why do they not fully agree?

A

Both think host was Loki

Spang et al., 2015; host was Loki because it displays membrane remodelling capabilities, favours PHAGOCYTE FIRST HYPOTHESIS
Sousa et al., 2016; Loki was hydrogen-dependent, fits the hydrogen hypothesis, MITOCHONDRIA FIRST HYPOTHESIS

82
Q

Why is the acquisition of the mitochondria relevant to intron invasion?

A

That has to come first, without an endosymbiont there is no intron invasion

83
Q

Muller and Martin, 1998:

What evidence is there for the eubacterial origin of the mitochondria?

What does this suggest?

A

Hydrogenosomes and mitochondria share a common ancestry.

Hydrogenosomes are organelles in anaerobic organisms

Obligate aerobe nature of eukaryotes is derived

84
Q

Who looked at lipid proliferation in B. subtilis?

What is L-form?

What did they find?

What does this show?

Which hypothesis does this support?

A

Mercier et al., 2013

A cell wall-less state of bacteria, B. subtilis can do this

That mutations leading to increased membrane synthesis are sufficient to drive evolution of the L-form in bacteria

Lots of lipids = don’t need a cell wall as forms the cell membrane

Intron invasion, increased lipid proliferation is sufficient to create a membrane

85
Q

Who showed that the nucleolar proteome and associated ribosome assembly is chimeric?

A

Staub et al., 2004

86
Q

Who showed that the nuclear envelope and NPCs are chimeric?

A

Mans et al., 2004

87
Q

Who first proposed intron invasion theory?

They said that the advantage was the separation of slow splicing and fast translation, driven by the selective pressure of intron invasion from the endosymbiont

A

Martin and Koonin, 2006

Year 3: SGE (11 decks)

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