Endosymbiosis and the Origin of Eukaryotes: Are mitochondria really just bacterial symbionts?
-
Upload
keely-morrison -
Category
Documents
-
view
33 -
download
0
description
Transcript of Endosymbiosis and the Origin of Eukaryotes: Are mitochondria really just bacterial symbionts?
©1999 Timothy G. Standish
Endosymbiosis and the Endosymbiosis and the Origin of Eukaryotes:Origin of Eukaryotes:Are mitochondria really just Are mitochondria really just
bacterial symbionts?bacterial symbionts?
Timothy G. Standish, Ph. D.
©1999 Timothy G. Standish
OutlineOutline Mitochondria - A very brief overview Endosymbiosis - Theory and evidence Archaezoa - Eukaryotes lacking mitochondria Gene expression - Mitochondrial proteins
coded in the nucleus Mitochondrial genetic codes Gene transport - Mitochondria to nucleus Conclusions
©1999 Timothy G. Standish
MitochondriaMitochondria Mitochondria are organelles found in most
eukaryotic organisms. The site of Krebs cycle and electron transport energy
producing processes during aerobic respiration Are inherited only from the mother during sexual
reproduction in mammals and probably all other vertebrates.
Because of their mode of inheritance genetic material found in mitochondria appears to be useful in determining the maternal lineage of organisms.
©1999 Timothy G. Standish
MitochondriaMitochondria
Matrix
Inter membrane space
Inner membraneOuter membrane
mtDNA
©1999 Timothy G. Standish
Extranuclear DNAExtranuclear DNA Mitochondria and chloroplasts have their own DNA This extranuclear DNA exhibits non-Mendelian inheritance Recombination is known between some mt and ctDNAs Extranuclear DNA may also be called cytoplasmic DNA Generally mtDNA and ctDNA is circular and contains genes
for multimeric proteins, some portion of which are also coded for in the nucleus
Extranuclear DNA has a rate of mutation that is independent of nuclear DNA
Generally, but not always, all the RNAs needed for transcription and translation are found in mtDNA and ctDNA, but only some of the protein genes
©1999 Timothy G. Standish
mtDNAmtDNA Mitochondrial DNA is generally small in animal cells, about
1.65 kb In other organisms sizes can be more than an order of
magnitude larger Plant mtDNA is highly variable in size and content with the
large Arabidopsis mtDNA being 200 kb. The largest known number of mtDNA protein genes is 97 in
the protozoan Riclinomonas mtDNA of 69 kb. “Most of the genetic information for mitochondrial
biogenesis and function resides in the nuclear genome, with import into the organelle of nuclear DNA-specified proteins and in some cases small RNAs.” (Gray et al.,1999)
©1999 Timothy G. Standish
Origin of EukaryotesOrigin of EukaryotesTwo popular theories presupposing naturalism seek to
explain the origin of membrane-bound organelles:1 Endosymbiosis to explain the origin of mitochondria and
chloroplasts (popularized by Lynn Margulis in 1981)
2 Invagination of the plasma membrane to form the endomembrane system
©1999 Timothy G. Standish
Origin of EukaryotesOrigin of EukaryotesTwo popular theories presupposing naturalism seek to
explain the origin of membrane-bound organelles:1 Endosymbiosis to explain the origin of mitochondria and
chloroplasts (popularized by Lynn Margulis in 1981)
2 Invagination of the plasma membrane to form the endomembrane system
Mitochondria
©1999 Timothy G. Standish
Origin of EukaryotesOrigin of EukaryotesTwo popular theories presupposing naturalism seek to
explain the origin of membrane-bound organelles:1 Endosymbiosis to explain the origin of mitochondria and
chloroplasts (popularized by Lynn Margulis in 1981)
2 Invagination of the plasma membrane to form the endomembrane system
Nucleus
Endoplasmic Reticulum
Golgi Body
Mitochondria
Chloroplast
©1999 Timothy G. Standish
Origin of EukaryotesOrigin of EukaryotesTwo popular theories presupposing naturalism seek to
explain the origin of membrane-bound organelles:1 Endosymbiosis to explain the origin of mitochondria and
chloroplasts (popularized by Lynn Margulis in 1981)
2 Invagination of the plasma membrane to form the endomembrane system
Chloroplast
Endoplasmic Reticulum
Nucleus
Golgi Body
Mitochondria
©1999 Timothy G. Standish
How Mitochondria Resemble BacteriaHow Mitochondria Resemble BacteriaMost general biology texts list ways in which mitochondria
resemble bacteria. Campbell et al. (1999) list the following:
Mitochondria resemble bacteria in size and morphology. They are bounded by a double membrane: the outer thought to be
derived from the engulfing vesicle and the inner from bacterial plasma membrane.
Some enzymes and inner membrane transport systems resemble prokaryotic plasma membrane systems.
Mitochondrial division resembles bacterial binary fission They contain a small circular loop of genetic material (DNA).
Bacterial DNA is also a circular loop. They produce a small number of proteins using their own ribosomes
which look like bacterial ribosomes. Their ribosomeal RNA resembles eubacterial rRNA.
©1999 Timothy G. Standish
How Mitochondria Don’tHow Mitochondria Don’tResemble BacteriaResemble Bacteria
Mitochondria are not always the size or morphology of bacteria:– In some Trypanosomes (i.e., Trypanosoma brucei)
mitochondria undergo spectacular changes in morphology that do not resemble bacteria during different life cycle stages (Vickermann, 1971)
– Variation in morphology is common in protistans, “Considerable variation in shape and size of the organelle can occur.” (Lloyd, 1974 p 1)
Mitochondrial division and distribution of mitochondria to daughter cells is tightly controlled by even the simplest eukaryotic cells
©1999 Timothy G. Standish
How Mitochondria Don’tHow Mitochondria Don’tResemble BacteriaResemble Bacteria
Circular mtDNA replication via D loops is different from replication of bacterial DNA (Lewin, 1997 p 441).
mtDNA is much smaller than bacterial chromosomes. Mitochondrial DNA may be linear; examples include:
Plasmodium, C. reinhardtii, Ochromonas, Tetrahymena, Jakoba (Gray et al., 1999).
Mitochondrial genes may have introns which eubacterial genes typically lack (these introns are different from nuclear introns so they cannot have come from that source) (Lewin, 1997 p 721, 888).
The genetic code in many mitochondria is slightly different from bacteria (Lewin, 1997).
©1999 Timothy G. Standish
GiardiaGiardia - A “Missing Link”? - A “Missing Link”? The eukaryotic parasite Giardia has been suggested as a
“missing link” between eukaryotes and prokaryotes because it lacks mitochondria (Friend, 1966; Adam, 1991) thus serving as an example of membrane invagination but not endosymbiosis
Giardia also appears to lack smooth endoplasmic reticulum, peroxisomes and nucleoli (Adam, 1991) so these must have either been lost or never evolved
©1999 Timothy G. Standish
A Poor “Missing Link”A Poor “Missing Link” As a “missing link” Giardia is not a strong argument due
to its parasitic life cycle which lacks an independent replicating stage outside of its vertebrate host– Transmission is via cysts excreted in feces followed by
ingestion
– As an obligate parasite, to reproduce, Giardia needs other more derived (advanced?) eukaryotes
Some other free-living Archaezoan may be a better candidate
©1999 Timothy G. Standish
Origin of Origin of GiardiaGiardia Giardia and other eukaryotes lacking mitochondria and
plastids (Metamonada, Microsporidia, and Parabasalia ) have been grouped by some as “Archaezoa” (Cavalier-Smith, 1983; Campbell et al., 1999 p 524-6)
This name reflects the belief that these protozoa split from the group which gained mitochondria prior to that event.
The discovery of a mitochondrial heat shock protein (HSP60) in Giardia lamblia (Soltys and Gupta, 1994) has called this interpretation into question.
Other proteins thought to be unique to mitochondria, HSP70 (Germot et al., 1996), chaperonin 60 (HSP60) (Roger et al., 1996; Horner et al., 1996) and HSP10 (Bui et al., 1996) have shown up in Giardia’s fellow Archaezoans
©1999 Timothy G. Standish
Origin of ArchaezoaOrigin of Archaezoa The authors who reported the presence of mitochondrial
genes in amitochondrial eukaryotes all reinterpreted prevailing theory in saying that mitochondria must have been present then lost after they had transferred some of their genetic information to the nucleus.
The hydrogenosome, a structure involved in carbohydrate metabolism found in some Archaezoans (Muller, 1992), is now thought to represent a mitochondria that has lost its genetic information completely and along with that loss, the ability to do the Krebs cycle (Palmer, 1997).
Alternative explanations include transfer of genetic material from other eukaryotes and the denovo production of hydrogenosomes by primitive eukaryotes.
©1999 Timothy G. Standish
Origin of Archaezoa:Origin of Archaezoa:Mitochondrial AcquisitionMitochondrial Acquisition
©1999 Timothy G. Standish
Origin of Archaezoa:Origin of Archaezoa:Gene Transfer and LossGene Transfer and Loss
mtGenes
Lost genetic
material
©1999 Timothy G. Standish
Origin of Archaezoa:Origin of Archaezoa:Option 1 - Mitochondrial Eukaryote ProductionOption 1 - Mitochondrial Eukaryote Production
©1999 Timothy G. Standish
Origin of Archaezoa:Origin of Archaezoa:Option 2 - Mitochondrial DNA Loss/Option 2 - Mitochondrial DNA Loss/
Hydrogenosome productionHydrogenosome productionHydrogenosome
©1999 Timothy G. Standish
Origin of Archaezoa:Origin of Archaezoa:Option 2A - Mitochondria/Hydrogenosome LossOption 2A - Mitochondria/Hydrogenosome Loss
©1999 Timothy G. Standish
“All in all then, the host nucleus seems to be a tremendous magnet, both for organellar genes and for endosymbiotic nuclear genes.”
Palmer, 1997
©1999 Timothy G. Standish
Steps in Mitochondrial Acquisition:Steps in Mitochondrial Acquisition:The Serial Endosymbiosis TheoryThe Serial Endosymbiosis Theory
Fusion of Rickettsia with either a nucleus containing Archaezoan or
an archaebacteriumRickettsia
DNA reduction/transfer to nucleus
Ancestral eukaryote(assuming a nucleus)
Primitive eukaryote
Host Cell
©1999 Timothy G. Standish
Steps in Mitochondrial Acquisition:Steps in Mitochondrial Acquisition:The Hydrogen HypothesisThe Hydrogen Hypothesis
Fusion of proteobacterium with an archaebacterium
Hydrogen producing proteobacterium
DNA reduction/transfer nucleus production
Hydrogen requiring archaebacterium
Ancestral eukaryoteWith nucleus containing both archaebacterium and proteobacterium genes
©1999 Timothy G. Standish
Metamonada
Hydrogenosome/mitochondria
loss
Hydrogenosome/mitochondria
loss
Microsporidia, and Parabasalia
mtDNAloss
mtDNAloss
mtDNAloss
mtDNAloss
PhylogenyPhylogeny
Eukaryota BacteriaBacteria
Origin of Life
Gene transferGene transfer
Cell fusionCell fusion
©1999 Timothy G. Standish
Timing of Gene TransferTiming of Gene Transfer Because gene transfer occurred in eukaryotes lacking
mitochondria, and these are the lowest branching eukaryotes known:
Gene transfer must have happened very early in the history of eukaryotes.
The length of time for at least some gene transfer following acquisition of mitochondria is greatly shortened.
No plausible mechanism for movement of genes from the mitochondria to the nucleus exists although intraspecies transfer of genes is sometimes invoked to explain the origin of other individual nuclear genes.
©1999 Timothy G. Standish
Cytoplasmic Production of Cytoplasmic Production of Mitochondrial ProteinsMitochondrial Proteins
Mitochondria produce only a small subset of the proteins used in the Krebs cycle and electron transport. The balance come from the nucleus
As mitochondrial genomes vary spectacularly between different groups of organisms, some of which may be fairly closely related, if all came from a common ancestor, different genes coding for mitochondrial proteins must have been passed between the nucleus and mitochondria multiple times
©1999 Timothy G. Standish
The Unlikely Movement of Genes The Unlikely Movement of Genes Between Mitochondria and the NucleusBetween Mitochondria and the Nucleus
Movement of genes between the mitochondria and nucleus seems unlikely for at least two reasons:
1 Mitochondria do not always share the same genetic code with the cell they are in
2 Mechanisms for transportation of proteins coded in the nucleus into mitochondria seem to preclude easy movement of genes from mitochondria to the nucleus
©1999 Timothy G. Standish
Cytoplasm
Nucleus
Protein Production Protein Production Mitochondria and ChloroplastsMitochondria and Chloroplasts
G AAAAAA
Export
ChloroplastMitochondrion
©1999 Timothy G. Standish
Cytoplasm
Nucleus
ChloroplastMitochondrion
Protein Production Protein Production Mitochondria and ChloroplastsMitochondria and Chloroplasts
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane space
Inner membraneOuter membrane
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
ML
SLR
QS
IRF
FK
PA
TR
TL
CS
SRY
LL
P +ADP
ATP
P +ADP
ATP
©1999 Timothy G. StandishMatrix
Inner membrane
Outer membrane
MLSLR
QSIR
FFKPA
TRTLC
SSRY
LL
Inter membrane
space
Leader sequence binding receptor
Protein Production Protein Production MitochondriaMitochondria
Peptidease cleaves off the leader
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inner membrane
Outer membrane
MLSLRQSIRFFKPATRTLCSSRYLL
Inter membrane
space
Leader sequence binding receptor
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inner membrane
Outer membrane
Inter membrane
space
Leader sequence binding receptor
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inner membrane
Outer membrane
Inter membrane
space
Leader sequence binding receptor
Hsp60
Hsp60
Chaperones
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inner membrane
Outer membrane
Inter membrane
space
Leader sequence binding receptor
Mature protein
©1999 Timothy G. Standish
Yeast Cytochrome C Yeast Cytochrome C Oxidase Subunit IV LeaderOxidase Subunit IV Leader
MLSLRQSIRFFKPATRTLCSSRYLL
PolarPolar
PolarPolar
Non-Non-polarpolar
RY
PL
T
CS
R
L
S
T
I
KP
R
F
A
F
M
RQ
L
L
S
S
This leader does not resemble other eukaryotic leader sequences, or other mtProtein leader sequences.
Probably forms an helix This would localize specific classes of amino
acids in specific parts of the helix There are about 3.6 amino acids per turn of the
helix with a rise of 0.54 nm per turn
First 12 residues are sufficient for transport to the mitochondria
Neutral Non-polarPolarBasicAcidic
Recognized by peptidase?
©1999 Timothy G. Standish
Yeast Cytochrome C1 LeaderYeast Cytochrome C1 Leader
MFSNLSKRWAQRTLSKTLKGSKSAAGTATSYFE-KLVTAGVAAAGITASTLLYANSLTAGA--------------
Cytochrome c functions in electron transport and is thus associated with the inner membrane on the intermembrane space side
Cytochrome c1 holds an iron containing heme group and is part of the B-C1 (III) complex
C1 accepts electrons from the Reiske protein and passes them to cytochrome c
Neutral Non-polarPolarBasicAcidic
Second cut
First cut
Uncharged second leader sequence signals for transport across inner membrane into the intermembrane space
Charged leader sequence signals for transport to mitochondria
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane space
Inner membraneOuter membrane
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
P +ADP
ATP
P +ADP
ATP
Peptidease cleaves off the leader
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
Peptidease cleaves off the second leader
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
©1999 Timothy G. Standish
Protein Production Protein Production MitochondriaMitochondria
Matrix
Inter membrane
space
Inner membrane
Outer membrane
Leader sequence binding receptor
Mature protein
©1999 Timothy G. Standish
Nuclear DNA
Building a Minimally Functional Building a Minimally Functional Nuclear Mitochondrial GeneNuclear Mitochondrial Gene
Given that a fragment of DNA travels from the mitochondria to the nucleus and is inserted into the nuclear DNA
Additional hurdles may include: Resolution of problems resulting from differences between
mitochondrial and nuclear introns Resolution of problems resulting from differences between
mitochondiral and nuclear genetic codes
Mitochondrial Gene
Signal Sequence
Control Sequence
Mitochondrial GeneSignal SequenceControl Sequence
©1999 Timothy G. Standish
Additional RequirementsAdditional RequirementsIn addition to addition of appropriate control and
leader sequences to mitochondrial genes, the following would be needed:
Recognition and transport mechanisms in the cytoplasm
Leader sequence binding receptors Peptidases that recognize leader sequences and
remove them
©1999 Timothy G. Standish
No Plausible Mechanism ExistsNo Plausible Mechanism Exists If genes were to move from the mitochondria to the nucleus they
would have to somehow pick up the leader sequences necessary to signal for transport before they could be functional
While leader sequences seem to have meaningful portions on them, according to Lewin (1997, p 251) sequence homology between different sequences is not evident, thus there could be no standard sequence that was tacked on as genes were moved from mitochondria to nucleus
Alternatively, if genes for mitochondrial proteins existed in the nucleus prior to loss of genes in the mitochondria, the problem remains, where did the signal sequences come from? And where did the mechanism to move proteins with signal sequences on them come from?
©1999 Timothy G. Standish
Variation In Codon MeaningVariation In Codon Meaning Lack of variation in codon meanings across almost all phyla is
taken as an indicator that initial assignment must have occurred early during evolution and all organisms must have descended from just one individual with the current codon assignments
Exceptions to the universal code are known in a few single-celled eukaryotes, mitochondria and at least one prokaryote
Most exceptions are modifications of the stop codons UAA, UAG and UGA
serine
Stop
Stop
Common Meaning
Stop
CandidaA yeast
Euplotes octacarinatusA ciliate
ParameciumA ciliate
OrganismTetrahymena thermophila
A ciliate
leucine
cysteine
glutamine
Modified Meaning
CUG
UGA
UAA UAG
Codon/sUAA UAG
glutamine
StopMycoplasma capricolumA bacteria tryptophanUGA
Neutral Non-polar, Polar
©1999 Timothy G. Standish
Variation in Mitochondrial Variation in Mitochondrial Codon AssignmentCodon Assignment
UGA/G=Stop
UniversalCode
Cyt
opla
sm/
Nu
cleu
s
Pla
nts
Yea
st/
Mol
ds
Pla
tyh
elm
ith
s
Ech
inod
erm
s
Mol
lusc
s
Inse
cts
Ver
teb
rate
s
UGA=Trp
AGA/G=Ser
AUA=Met
AUA=MetCUN=Thr
AUA=IleAAA=Asn
AAA=AsnN
emat
odes
NOTE - This would mean AUA changed from Ile to Met, then changed back to Ile in the Echinoderms
UGA must have changed to Trp then back to stop Differences in mtDNA lower the number of tRNAs needed
AAA must have changed from Lys to Asn twice
©1999 Timothy G. Standish
Problems Resulting From Problems Resulting From Differences in Genetic CodesDifferences in Genetic Codes
Changing the genetic code, even of the most simple genome is very difficult.
Because differences exist in the mitochondrial genomes of groups following changes in the mitochondrial genetic code, mitochondrial genes coding differently must have been transported to the nucleus.
These mitochondrial genes must have been edited to remove any problems caused by differences in the respective genetic codes.
©1999 Timothy G. Standish
No Modern ExamplesNo Modern ExamplesUnfortunately for Margulis and S.E.T. [the serial endosymbiotic theory], no
modern examples of prokaryotic endocytosis or endosymbioses exist . . . She discusses any number of prokaryotes endosymbiotic in eukaryotes and uses Bdellovibrio as a model for prokaryotic endocytosis. Bdellovibrios are predatory (or parasitoid) bacteria that feed on E. coli by penetrating the cell wall of the latter and then removing nutrient molecules from E. coli while attached to the outer surface of its plasma membrane. Although it is perfectly obvious that this is not an example of one prokaryote being engulfed by another Margulis continually implies that it is.
P.J. Whitfield, review of “Symbiosis in Cell Evolution,” Biological Journal of the Linnean Society 18 [1982]:77-78; p 78)
©1999 Timothy G. Standish
ConclusionsConclusions Presence of mitochondrial genes in nuclear DNA reduces
the window of time available for mitochondrial acquisition in eukaryotes.
Understanding the structure of mitochondrial genes in the nucleus and how they are expressed makes the transfer of genes from protomitochondria to the nucleus appear complex.
Differences between mitochondrial genetic codes and nuclear genetic codes adds to the complexity of gene transfer between mitochondria and nucleus.
As molecular data accumulates, the endosymbiotic origin of mitochondria appears less probable.