BIS2C_2020. Lecture 13 Organelles and Endosymbiosis

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BIS2C
Biodiversity & the Tree of Life
Spring 2020
Lecture 13:
Organelles and Endosymbiosis
Prof. Jonathan Eisen

Black necked stilt

Yellow headed blackbird

Sora

Calidrid

Great horned owl

Ruddy Duck

American avocet

White tailed kite

Anna’s hummingbird

Black chinned hummingbird

White faced ibis

Hover fly

Skipper

Gulf fritillary

Tiger swallowtail

Mytila crescent

Damsel fly

River otter

Learning Goals
• Understand the models and the evidence that
supports those models, that explain the origin of
the nucleus, mitochondria and chloroplasts
• Understand the differences between primary,
secondary and tertiary endosymbioses
• Understand how to track the multiple
evolutionary histories within eukaryotic genomes
that result from endosymbioses

!12: Mutualisms and Microbiomes
!13: Endosymbiosis and Organelles
!14: Plants
Lecture 13 Context

Lecture 13 Outline
• Background and Context
• Endosymbiosis and Organelles
!Origin and evolution of the nucleus
!Origin and evolution of mitochondria
!Origin and evolution of chloroplasts

Background: Lab
• Many parts of Lab 3

Background: Lecture 12 Review

Lecture 12 Outline
• Background and Context
• Mutualisms
• The Human Microbiome

Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +

Mutualistic Symbioses of Bacteria w/ Eukaryotes
• Digestive
! Ruminants
! Cellulolytic insects
• Defensive
• Behavioral
! Squid light organs
• Autotrophic
! Photosynthetic (many)
! Chemosynthetic in deep sea
• Nutritional
! Aphids
! Nitrogen fixation in legumes

These worms with their symbionts function as
chemolithoautotrophs. This is weird because
“normal" worms and most other animals are
A: Chemolithoheterotrophs
B: Chemoorganoautotrophs
C: Chemoorganoheterotrophs
D: Photolithoautotrophs
Thought Question

Organism
Mutualism + +
Commensalism + 0
Microbes in human microbiome likely benefit.
Many interactions with human microbiome likely
“commensalism” because we do not know effect on humans

Organism
Mutualism + +
Some associations in the human microbiome
appear to be mutualistic

Story 1: The Obese Mouse

Story 2: Disturbing the Microbiome
Antibiotics
Diet Changes
Hygiene
C-sections
Story 2: Disturbing the Microbiome (vs expected)

Story 3: Restoring the Microbiome
• C-section story is an example of attempting
to restore a disturbed microbiome
• Many other examples

Nucleus: An organelle found in all eukaryotes

Common Features of Eukaryotic Cells

Additional Traits Common To Eukaryotes
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing

An ancestor of all eukaryotes
Cell
membrane
Genome

Cell
membrane
Genome
Nucleus

Cell
membrane
Genome
Other Eukaryotic Features
Nucleus

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Formation of nucleus &
invention of many eukaryotic
traits
1
1

Traits Shared by Eukaryotes and Asgard Archaea
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
traits
1
1
Some key
traits may
have
originated
here

Lecture 13 Outline
• Introduction
• Origin and evolution of the nucleus
• Origin and evolution of mitochondria
• Origin and evolution of chloroplasts

Mitochondrion: Organelle in (Almost) All Eukaryotes
Respiration and
production of
ATP for
eukaryotes

Many
similarities to
bacteria /
prokaryotic
archaea
But morphology
not useful for
phylogeny of
bacteria &
prokaryotic
archaea
Origin and evolution of mitochondria

DNA

Thought Question
• T/F
• The fact that mitochondria have DNA
genomes shows that they are derived from
bacteria

Thought Question
• T/F
• The fact that mitochondria have DNA
genomes shows that they are derived from
bacteria
• Prokaryotic Archaea have DNA genomes too
and some look a lot like mitochondria

rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
PB AMito B

PB AMito B
All mitochondrial trace
a common ancestry to a
single lineage within the
alpha subgroup of the
Proteobacteria phylum
of Bacteria

Lynn Margulis
Konstantin Mereschkowski
Endosymbiotic Theory

A common ancestor of eukaryotes
Cell
membrane
Genome
Nucleus

A Proteobacterium
αProteo
Genome
Bacterial cell envelope

Proteobacteria are Gram negative
• Two major ways it is
used in bacteria
• Gram-positive bacteria -
thick peptidoglycan layer
outside 1 cell membrane
• Gram-negative bacteria
- thin peptidoglycan
layer outside between
two cell membranes
• This has many impacts
on biology, including
sensitivity to antibiotics

A Symbiosis Between Eukaryote and a Proteobacterium
Genome
Cell
membrane
Genome
Nucleus
αProteo

Engulfment
Nucleus
Cell
membrane
Genome
Genome
αProteo

Endosymbiosis
Cell
membrane
Genome
Genome
Host
membrane
αProteo
Endosymbiosis: when an organism
(the host) bring another organism (the
symbiont) inside of its cell.
Nucleus

Endosymbiosis
Cell
membrane
Genome
Genome
Host
membrane
Is a “Primary symbiosis” because symbiont
has not experienced a prior symbiosis
Nucleus
αProteo

Endosymbiosis
Cell
membrane
Genome
Genome
Host
membrane
αProteo
Lost a membrane
Nucleus

Endosymbiosis
Cell
membrane
Genome
Genome
Host
membrane
αProteo
Lost cell wall
Nucleus

Eukaryote with a Mitochondrion
N
Mitochondrion
Genome
M
Nucleus
Cell
membrane
Genome

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
traits
1
Endosymbiosis with a
Proteobacterium that
became the mitochondrion
2
2
1
Note - Proteobacteria
were already diverse
at this point even
though this tree does
not show this

Eukaryotic Parts Have Different Histories
Nucleus
A model
of a
eukaryotic
cell
Bacteria Eukaryotes“Prok. Archaea”
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria “Prok. Archaea”PB
Mitochondrion

Eukaryotic Parts Have Different Histories
Nucleus
MitochondrionA model
of a
eukaryotic
cell
Bacteria Eukaryotes“Prok. Archaea”
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria “Prok. Archaea”PB

More Detailed Phylogeny of Eukaryotes
Phylogeny of Eukaryotic
Groups
The exact phylogeny here
does not matter and you do
not need to know this full
phylogeny.

N M
N M
N M
N M
N M
N M
N M
N M
N
+
+
+
+
-
+
+
+
+
Presence/Absence of Mitochondria
Some eukaryotes
do not have
mitochondria
Giardia = Diplomonad
Trichomonas = Parabisalid
Best explanation is
that they lost their
mitochondria

Chloroplast: Organelle Found in Photosynthetic Eukarya

Many
similarities to
bacteria /
prokaryotic
archaea
But morphology
not useful for
phylogeny of
bacteria &
prokaryotic
archaea
Origin and evolution of chloroplasts

DNA

rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Cyano “pA”CPST B

Chloroplast Phylogeny
Conclusion: All Chloroplasts Have a Common Ancestry and Are Derived from A
Single Cyanobacterial Lineage

Extending the Endosymbiosis Model …

Eukaryotic Cell
N
M
Mitochondrion
Mitochondrial
Genome
Nucleus
Cell membrane
Nuclear Genome

Cyanobacterium
Cyano

Cyanobacteria are Gram negative
• Two major ways it is
used in bacteria
• Gram-positive bacteria -
thick peptidoglycan layer
outside 1 cell membrane
• Gram-negative bacteria
- thin peptidoglycan
layer outside between
two cell membranes
• This has many impacts
on biology, including
sensitivity to antibiotics

Symbiosis with Free Living Cyanobacterium
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano

Engulfment
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome Cyano

Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Cyanobacterial
Cell envelope
Cyanobacterial
Genome
Cyano
Is a “Primary symbiosis” because the symbiont has not
experienced a prior symbiosis.

Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast
Becomes the Chloroplast

Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast
Outer chloroplast membrane lost in some

Endosymbiosis
N
Mitochondrion
Mitochondrial
Genome
M
Nucleus
Cell membrane
Nuclear Genome
Chloroplast
Cell envelope
Chloroplast
Genome
Chloroplast
Chloroplast cell wall lost in some

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
traits
1
2
2
1

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
traits
1
2
Cyanobacterium that became
the chloroplast
3
3
2
1

Eukaryotes with Chloroplasts: Three Histories
Nucleus
MITO
CPST
Bacteria “Pr. Archaea” Eukaryotes
Nuclear
Tree
Mitochondrial
Tree
Eukaryotes Bacteria “Pr. Archaea”PB
Chloroplast
Tree
Bacteria CBEukaryotes “Pr. Archaea”

Scattered distribution of chloroplasts

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
Hypothesis 1:
Ancestral AND Loss

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
Hypothesis 1:
Ancestral AND Loss
Not supported by analysis
of phylogeny of
chloroplasts.
X

N M
C
N M
N M
N M
N M
N M
Hypothesis 2:
Diversification of Major
Lineages
Symbiosis in Plantae
Ancestor
And then other organisms
with chloroplasts got them
later …

The Plantae consist of
several clades; all
chloroplasts trace back
to a single incidence of
endosymbiosis.
Plantae group w/in Eukaryotes

Plantae group only
have “simple”
membrane around their
chloroplasts

N M
C
N M
C
N M
C
N M
C
Each lineage accumulates
some unique properties,
such as sequences of some
of their genes (N, M or C
genes).
N M
C
N M
C
N M
C
N M
C
N M
C

N M
C
Hypothesis 2:
Diversification of Major
Lineages
Symbiosis in Plantae
Ancestor
And then “Secondary
Symbiosis” in other
lineages

Models and Examples
• For the following topic you need to know the
general models for additional symbioses in
the history of chloroplasts and how to infer
history of symbioses
• You should also know which taxa are
involved in the main examples covered

Model for “Secondary” Symbiosis

Symbiosis between two eukaryotic cells
N
M
“Normal” eukaryote
Blue
membranes
to help track

Plantae representative with chloroplast
Black
Membranes to
Help Track
N M
C

N
M
“Normal” eukaryote
Plantae representative with chloroplast
N M
C

Engulfment
N
M
N M
C

Endosymbiosis
N
M
N
M
C
Symbiont
Host
Endosymbiosis: when an organism (the host) bring another organism (the

Endosymbiosis
N
M
N
M
C
Symbiont
Host
This is a “secondary” symbioses because the symbiont itself already was a
host of other symbionts.

Thought Question
N
M
N
M
C
Symbiont
Host
How many different histories could there be after a secondary endosymbiosis?

N
M
N
M
C
Symbiont
Host
How many different histories could there be after a secondary endosymbiosis?
Thought Question

N
M
N
M
C
Symbiont
Host
Loss of components
Second mitochondria often lost

Endosymbiosis
N
M
N
C
Symbiont
Host
Second mitochondria often lost

Endosymbiosis
N
M
N
C
Symbiont
Host
Second nucleus often lost

Endosymbiosis
N
M
C
Symbiont
Host
Second nucleus often lost

Endosymbiosis
N
M
C
Symbiont
Host
Symbiont membrane sometimes lost

Examples

Excavates: Euglenids
• Have flagella.
• Some are
photosynthetic,
some always
heterotrophic, and
some can switch.
Movement in the euglenoid Eutreptia

N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Euglena Nuclear DNA tells
us what its phylogenetic
backbone is
Excavates: Euglenid Chloroplast Origins

Euglena plastid
DNA says its plastid
is related to those of
chlorophytes

Model to explain this …
130

A lonely Excavate ...
131
N
M

N M
C
Chlorophyte

N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
Chlorophyte

Symbiosis
N
M
N M
C

Endosymbiosis
N
M
N M
C

N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C

Stramenopiles: Diatoms
A colony of the diatom,
Bacillaria paradoxa
•Unicellular, but many associate in
filaments.
•Have carotenoids and appear yellow or
brown.
•Excellent fossil record
•Most are photoautotrophic
•Responsible for 20% of all carbon fixation.
•Oil, gas source

N M
N M
N M
N M
N M
Many lines of evidence indicate that it occurred in the
common ancestor of the “Plantae” lineage.
One line of evidence for this is that all organisms on this
branch have chloroplasts and the cells of these organisms
resemble the “primary” symbiotic cell.
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Diatom nuclear DNA tells us
what its phylogenetic
backbone is
Diatom Chloroplast Origins

Diatom plastid DNA
says its plastid is
related to those of
red algae

A lonely Stramenopile ...
142
N
M

A lonely red algae ...
143
N M
C

Red algae
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C
N M
C

A lonely red algae ...
145
N M
C

N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C

N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Many other secondary endosymbioses
Apicomplexans
Dinoflagellates
Amoebozoans

•Most are marine and are important
photoautotrophic primary producers
•Mixture of pigments give them a golden brown
color.
•Have two flagella, one in an equatorial groove,
the other in a longitudinal groove.
Alveolates: Dinoflagellates
Certium
tenue
Coral symbiont
Tour - Don’t Need to
Know These Details

Alveolates: Apicomplexans
• All parasitic
• Have a mass of organelles at one tip
—the apical complex that help the
parasite enter the host’s cells.
Apical complex • Plasmodium falciparum-
Malaria kills 700,000-2,000,000
people per year—75% of them
are African children
152
Know These Details

• Not colonial; live as single cells
• Some secrete shells or glue sand
grains together to form a casing.
• Many pathogens
Amoebozoans: Loboseans Tour - Don’t Need to
Know These Details

Rhizaria: Cercozoans
Some cercozoans are aquatic, others
live in soil.
They have diverse forms and habitats.
One group has chloroplasts derived
from a green alga by secondary
endosymbiosis.
Euglyphid
Chlorarachnion reptans
Know These Details

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
traits
1
2
the chloroplast
3
3
2
1
Secondary

Still Can’t Fit Model to Some Eukaryotes

Dinoflagellate Kryptoperidinium foliaceum
http://onlinelibrary.wiley.com/doi/10.1111/j.1550-7408.2007.00245.x/full

•All are multicellular; some get very large (e.g.,
giant kelp).
•The carotenoid fucoxanthin imparts the brown
color.
•Almost exclusively marine.
Stramenopiles: Brown Algae
A community of brown algae: The marine kelp forest

Model to Explain These

Diatom Doing It’s Thing
N
M
N M
C
Diatom

N
M
A Lonely Stramenopile
Stramenopile

N
M
Symbiosis
N
M
N M
C
Stramenopile
Diatom

N
M
Engulfment
N
M
N M
C

N
M
Endosymbsiosis
Host
Symbiont
This is a “tertiary” symbiosis because the symbiont itself already underwent a
secondary symbiosis.
N
M
N M
C

N
M
Endosymbsiosis
Host
Symbiont
Note - many of these organelles and genomes will have been lost sometime in
the history of such tertiary symbioses. I am showing all of them here so that
you can track where they would go IF everything was kept
N
M
N M
C

N
M
Thought Question
Host
Symbiont
How many different histories could thereby after a tertiary symbiosis?
N
M
N M
C

N
M
Many of the genomes and components frequently lost
Host
Symbiont
Can end up like this
C

N M
N M
N M
N M
N M
N M
C
N M
C
N M
C N M
C N M
C
N M
C
N M
C
N M
C
N M
C
Tertiary endosymbioses?
Brown Algae
Tertiary Endosymbsiosis

Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
traits
1
2
the chloroplast
3
3
2
1
Secondary
Tertiary

Past, Present and Future
!12: Mutualisms and Microbiomes
!13: Endosymbiosis and Organelles
!14: Plants

Thistle

Poppy

Salsify

BIS2C_2020. Lecture 13 Organelles and Endosymbiosis

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BIS2C_2020. Lecture 13 Organelles and Endosymbiosis