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Transcript
Coping with cold and aging:
the genome of
Pseudoalteromonas
haloplanktis
1 August 2006
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Authors
Génétique des Génomes Bactériens
Gang Fang
Evelyne Krin
Etienne Larsabal
Géraldine Pascal
Eduardo Rocha
Agnieszka Sekowska
Genoscope
Valérie Barbe
Stéphane Cruveiller
Sophie Mangenot
Géraldine Pascal
Zoé Rouy
David Vallenet
Claudine Médigue
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
University of Hong Kong
Christine Ho
Frankie Cheung
University of Liège
Georges Feller
University of Naples
Luisa Tutino
University of Strasbourg
Philippe Bertin
University of Stockholm
Gunnar von Heijne
[email protected]
The first discovery of
genomics
In 1991, at the EU meeting on genome programs in Elounda,
Greece, the presentation of the yeast chromosome III and the first
100 kb of the Bacillus subtilis genome revealed that, contrary to
expectation (the only cases where this had been observed were
phages, for obvious reasons), at least half of the genes uncovered
were totally unknown, whether in structure or in function
Among reasons for that is our present lack of deep knowledge of
metabolism, as well as our lack of knowledge of the way new
genes are created, selecting function first, then recruiting a
structure that will be improved as it is submitted to natural
selection for increased fitness of its host (acquisitive evolution)
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Genome projects
2045 ongoing projects, 348 completed, mostly from
microbes (228 with more than 1500 genes, more or
less correctly annotated)
144,116,054,623 nucleotides at International Nucleotide
Sequence Database Collaboration (INSDC)
Microbes make 50% of the Earth protoplasm
40-50% coding DNA sequences (CDSs) do not
correspond to known functions; 10% correspond to
the core genome ( « persistent » genes)
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
From sequence to
function?
Inductive reasoning combines sequence data and in silico
predictions, that are tested using expression profiling
(transcriptome and proteome) as well as many other
« neighborhoods », such as amino acid composition,
isolectric point in proteins or codon usage biases in
genes
One notes that regulation evolves much faster than any
other process: in the long run the structural genes are the
most important ones
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Ecological
neighbourhood:
growth in the cold
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Challenges posed by cold
Protein folding
RNA folding
Membrane fluidity
Sensitivity towards oxygen and radicals
Distribution of aminoacids in proteins...
=> A series of unexpected answers
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
folding
Genome
Organisation
P. haloplanktis
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
origins
[email protected]
Bias in amino acid distribution
Neighbourhood:
distribution of
aminoacids in the
proteome
G. Pascal
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Universal biases in protein
amino acid composition
First axis: separates Integral Inner Membrane Proteins
(IIMP) from the rest; driven by opposition between charged
and large hydrophobic residues
Second axis: separates proteins according to an
opposition driven by the G+C content of the first codon
base
Third axis: separates proteins by their content in
aromatic amino acids; enriched in orphan proteins
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Temperature-dependent
biases in protein amino acid
composition
• The general trend of amino acid composition bias
is to avoid some aminoacids at higher
temperatures (associated to aging processes)
• Mesophilic bacteria belong to at least two
different classes (in a 5-clusters analysis)
• Biases are always dominated by the IIMP
clustering
C Médigue, E Krin, G Pascal, V Barbe, A Bernsel, PN Bertin, F Cheung, S Cruveiller, S D'Amico, A Duilio, G Fang, G Feller, C Ho, S Mangenot, G
Marino, J Nilsson, E Parrilli, EPC Rocha, Z Rouy, A Sekowska, ML Tutino, D Vallenet, G von Heijne, A Danchin
Coping with cold: the genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
Genome Research (2005) 15: 1325-1335
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Biases correlated with temperature
An asparagine bias is specific to psychrophiles
IIMPs
Motility
Envelope,
outer
membrane
Transport
(TonB),
secretion
Adaptation to
stress
DNA and
RAN
metabolism
53%
mesophiles
55%
psychrophiles
62%
thermophiles
G. Pascal
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
isoaspartate
Underlying chemistry
Asparagine deamidation: major contribution to protein aging
Major post-translational modificationAsparagine (N)
Poorly understood reaction
Targeted reaction (?)
Degradation:
succinimide
Affect both structure (and function) of the protein
Intermediary:
succinimide
Interferes with folding
Signal for protein degradation
Isoaspartate
Aspartate
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Orphans: the gluons
A remarkable role of aromatic amino acids creates
a universal bias. Expressed orphan proteins are
enriched in these residues, suggesting that they
might participate in a process of gain of function
during evolution. We postulate that the majority is
made of proteins — gluons — involved in
stabilising complexes, thus defining the "self" of
the species.
G Pascal, C Médigue, A Danchin
Universal biases in protein composition of model prokaryotes
Proteins (2005) 60: 27-35
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Why aromatic residues in orphan proteins?
From orphans « Gluons »
G. Pascal
Orphan loose their status in the course of evolution: Rocha. 2002.
Pedulla. 2003
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Resistance to oxygen
A remarkable way to cope with increased oxygen
solubility at loz temperature is concerted deletion
of the whole molybdopterin metabolic pathway.
Also many dioxygenase scavenge dioxygen, and
desaturation of proteins uses dioxygen, permitting
the cell to increase membrane fluidity while
destroying dioxygen....
G Pascal, C Médigue, A Danchin
Universal biases in protein composition of model prokaryotes
Proteins (2005) 60: 27-35
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]
Thank you
In portuguese:
O ovo et a Galinha
Uma Aurora da Pedras
Génétique des Génomes Bactériens
http://www.pasteur.fr/recherche/unites/REG/
[email protected]