Bioinformatics of Mitochondria, a topdown lecture

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Bioinformatics of Mitochondria,a top-down
lecture
Martijn Huynen

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Central role of mitochondria in metabolism
Calcium signaling
Coenzyme synthesis
Citric acid cycle
Urea cycle
Heme synthesis
FeS clusters
Apoptosis
Electrical signaling
ATP production
Fatty acids oxidation
Heat generation
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Endosymbiotic origin of mitochondria
16S Ribosomal RNA
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Original rationales for the endosymbiosis

• 1 ATP ? (MCF family is strictly eukaryotic)
• 2 Oxygen sink ? (Andersson Kurland)
• 3 H2 ? (Martin Muller)

O2
ATP
H2
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Free-living, alpha-proteobacterial ancestor
Gene transfer
Gene loss
Gain (Andersson Kurland) and retargeting of
proteins
Rickettsia
Mitochondria
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Identifying eukaryotic proteins with an
alpha-proteobacterial origin based on their
phylogeny
A
B
Alpha-proteobacterial proteins with the rest of
the bacteria and archaea
Eukaryotic alpha-proteobacterial proteinsg in
the same branch
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Detecting eukaryotic genes of alpha-proteobacteria
l ancestry
GENOME
6 alpha-proteobacteria (22 500 genes)
6 alpha-proteobacteria 9 eukaryotes 56
BacteriaArchaea
TREE SCANNING
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Alpha-proteobacterial genes monophyletic with
eukaryotic genes
446
630
Non redundant orthologous groups
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Estimating false positives and false
negatives,630 orthologous groups appears a lower
bound

• False positives Of the unrelated Deinococcus
  radiodurans the algorithm selects 1.3
• False negatives Of the 66 proteins encoded in
  the mitochondrial genome of Reclinomonas
  americana the procedure selects 49

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Saturation in the estimated size of the
proto-mitochondrial proteome with an increasing
number of sequenced alpha-proteobacterial genomes
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Increasing the number of genomes leads to more
accurate results less false negatives, less
false positives
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Proto-mitochondrial metabolism

• Catabolism of fatty acids, glycerol and amino
  acids-Some pathways are not mitochondrial in
  present day mitochondria

non-mitoch..
mitochondrial
not in yeast/human
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The majority of the proto-mitochondrial proteome
is not mitochondrial (anymore)
566
Yeast mitochondrial proteome
Proto-mitochondrial proteins in S.cerevisiae
Eric Schon, Methods Cell Biol 2001 (manually
curated)
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303
59
293
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Huh et al., Nature 2003 (green fluorescent
genomics)
527
Proto-mitochondrial proteins in H.sapiens
755
Human mitochondrial proteome
Eric Schon, Methods Cell Biol 2001
508
113
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From endosymbiont to organell, not only loss and
gain of proteins but also retargeting
proteins
loss
re-targeting
Ancestor
Modern mitochondria
gain
t
Gabaldon and Huynen, Science 2003
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Original rationales for the endosymbiosis

• Aerobic (no hydrogenosomal eukaryotes have been
  published yet.)
• Catabolizing lipids, glycerol and amino-acids,
  incomplete TCA
• Benefit for host wider than either H2, ATP or O2
  consumption iron-sulfur clusters and a variety
  of metabolic pathways

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From endosymbiont to organell a turnover of
protein in functional classes and an increase in
specialization (middle columns yeast, right
columns human)
COG functional classification
F Nucleotide metabolism G Carbohydrate
metabolism M Cell envelope biogenesis
C Energy conversion O Protein turnover,
chaperones J Translation, Ribosomal structure
Very low throughout D Cell division
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Gene loss in the evolution of mitochondria
Mitochondrial FtsZ in a chromophyte alga.Beech
PL, Nheu T, Schultz T, Herbert S, Lithgow T,
Gilson PR, McFadden GI Science 2000 A homolog
of the bacterial cell division gene ftsZ was
isolated from the alga Mallomonas splendens. The
nuclear-encoded protein (MsFtsZ-mt) was closely
related to FtsZs of the alpha-proteobacteria,
possessed a mitochondrial targeting signal, and
localized in a pattern consistent with a role in
mitochondrial division. Although FtsZs are known
to act in the division of chloroplasts, MsFtsZ-mt
appears to be a mitochondrial FtsZ and may
represent a mitochondrial division protein.
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Kiefel BR Gilson PR Beech PL.Diverse eukaryotes
have retained mitochondrial homologues of the
bacterial division protein FtsZ. Protist. 2004
Mar155(1)105-15.Mitochondrial fission requires
the division of both the inner and outer
mitochondrial membranes. Dynamin-related proteins
operate in division of the outer membrane of
probably all mitochondria, and also that of
chloroplasts--organelles that have a bacterial
origin like mitochondria. How the inner
mitochondrial membrane divides is less well
established. Homologues of the major bacterial
division protein, FtsZ, are known to reside
inside mitochondria of the chromophyte alga
Mallomonas, a red alga, and the slime mould
Dictyostelium discoideum, where these proteins
are likely to act in division of the organelle.
Mitochondrial FtsZ is, however, absent from the
genomes of higher eukaryotes (animals, fungi, and
plants), even though FtsZs are known to be
essential for the division of probably all
chloroplasts. To begin to understand why higher
eukaryotes have lost mitochondrial FtsZ, we have
sampled various diverse protists to determine
which groups have retained the gene. Database
searches and degenerate PCR uncovered genes for
likely mitochondrial FtsZs from the
glaucocystophyte Cyanophora paradoxa, the
oomycete Phytophthora infestans, two haptophyte
algae, and two diatoms--one being Thalassiosira
pseudonana, the draft genome of which is now
available. From Thalassiosira we also identified
two chloroplast FtsZs, one of which appears to be
undergoing a C-terminal shortening that may be
common to many organellar FtsZs. Our data
indicate that many protists still employ the
FtsZ-based ancestral mitochondrial division
mechanism, and that mitochondrial FtsZ has been
lost numerous times in the evolution of
eukaryotes.
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Zooming in on one mitochondrial complex,
NADHubiquinone oxidoreductase (Complex I), and
using gene loss for function prediction

• -Complex I deficiency is a severe hereditary
  disease (patients lt 5 year) without therapy
• -For 60 of the patients no mutation is found in
  known CI genes

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Tracing the evolution of Complex I from 14
subunits in the Bacteria to 46 subunits in the
Mammals by comparative genome analysis
Fungi 37
Mammals 46
Bacteria 14 subunits
Plants 30
Algae 30
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Issues in homology detection that we do not
detect sequence similarity does not mean that
proteins are not homologous. Latest developments
in homology detection profile vs. profile
searches
The fungal ComplexI subunit NUVM is homologous to
the Bovine subunit NB5M (B15), This homology can
only be detected by profile vs. profile searches
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Beyond Blastology, Cogoly Phylogenies for
orthology prediction
The Complex I assembly protein CI30 has been
duplicated in the Fungi. This can explain the
presence of a CIA30-homolog in Complex I-less
S.pombe
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Mining the proto-mitochondrion for new Complex I
proteins

Metazoa

Fungi

Alpha-proteobacteria
A methyltransferase derived from the
alpha-proteobacterial ancestor of the
mitochondria has a phylogenetic distribution
identical to Complex I proteins, suggesting
involvement of this protein in Complex I
Gabaldon and Huynen, Bioinformatics 2005
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Function prediction of Complex I proteins
NUEM
Eukaryotes
CIA30
Cyanobacteria
CIA30 is inserted in NueM in Cyanobacteria,
suggesting an interaction between CIA30 and NueM
in the eukaryotes as well.
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Plants,algae
Mammals
Insects
Nematode
Fungi
Fish
Distribution of Complex I subunits among model
species
Experimentally verified
Homolog present in genome, predicted gene
Homolog present in genome, not predicted
Absent from genome
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Reconstructing Complex I evolution by mapping the
variation onto a phylogenetic tree. After an
initial surge in complexity (from 14 to 35
subunits in early eukaryotic evolution) new
subunits have been gradually added and
incidentally lost.
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Tinkering in the eukaryotic evolution of Complex
I new subunits have been added all over the
complex
Gabaldon et al. (2005) J. Mol. Biol. See also
Science (2005) 308, 167
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Deconstructing protein complexes by tracing their
evolution The phylogenetic distribution of
Complex I subunits suggests the presence of
submodules and the functions of the individual
proteins In eukaryotes evolution appears less
sub-modular than in prokaryotes
T. Friedrichs model
Huynen et al., FEBS lett. 2005
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How about the origin of the peroxisome? Like
mitochondria an organell involved in oxidative
metabolism, but without a genome. Multiplication
by fission has suggested an endosymbiotic origin.
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Scenarios for the origin of the peroxisome and
mitochondria
A) Independent endosymbiotic origins
B) A single origin followed by fission
C) Retargeting of mitochondrial proteins
Time
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The yeast and rat peroxisomal proteomes contain a
large fraction of proteins of alpha-proteobacteria
l origin (18-19), besides a large fraction of
proteins of eukaryotic origin (37-38)
Alpha-proteobact
unresolved
Yeast (61 proteins)
Rat (50 proteins)
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Most (90) of the peroxisomal proteins of
alpha-proteobacterial origin have paralogs in the
mitochondria

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The retargeting of mitochondrial proteins to the
peroxisome has continued in recent evolution

Peroxisomal
Mitoch.
Signal peptide cleavage site
Within the Cit1/2 protein family all proteins
have a mitochondrial location (exp. data and/or
predictions), expect Cit2p which is peroxisomal,
and has lost the cleavage site (YS)
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Tracing the evolution of the peroxisome a
continuous retargeting of proteins from various
origins. (yellow eukaryotic, green
alphaprot, red actinomyc., blue
cyanobact.) The ancestral peroxisome
was likely involved in b-oxidation, harboring
Catalase to detoxify hydrogen peroxide.
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Scenarios for the origin of the peroxisome and
mitochondria
A) Independent endosymbiotic origins
B) A single origin followed by fission
C) Retargeting of mitochondrial proteins
Time
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Studying evolution of organellar proteomes is not
only interesting in itself, it also provides us
with clues about the functions of proteins