Coping with cold and aging: the genome of Pseudoalteromonas haloplanktis 1 August 2006

1. Coping with cold and aging: the genome of Pseudoalteromonas haloplanktis1 August 2006

2. 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 Authors 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

3. 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)

4. 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)

5. 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

6. Ecological neighbourhood: growth in the cold

7. 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 folding

8. Genome OrganisationP. haloplanktis origins

9. Bias in amino acid distribution Neighbourhood: distribution of aminoacids in the proteome G. Pascal

10. 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

11. 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

12. 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 isoaspartate

13. Asparagine (N) Degradation:succinimide Intermediary:succinimide Isoaspartate Aspartate Underlying chemistry Asparagine deamidation: major contribution to protein aging Major post-translational modification Poorly understood reaction Targeted reaction (?) Affect both structure (and function) of the protein Interferes with folding Signal for protein degradation

14. 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

15. Why aromatic residues in orphan proteins? From orphans « Gluons » G. Pascal Orphan loose their status in the course of evolution: Rocha. 2002. Pedulla. 2003

16. 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

17. Thank you In portuguese: O ovo et a Galinha Uma Aurora da Pedras