Around the dynamics of bacterial genomes

Transcription

1 Around the dynamics of bacterial genomes Eduardo P. C. Rocha Unité Génétique des Génomes Bactériens, CNRS URA2171,Institut Pasteur Atelier de BioInformatique, Université Pierre et Marie Curie

2 L ADN

3

4

5 ORFs, CDS, etc. ORF : Open Reading Frame CDS : CoDing Sequence 5' -35 signal -10 signal RBS 3' ORF CDS ORF Start : Pattern (ATG,GTG,TTG) RBS : Pattern (AGGAGGT) Début de la transcription Stop : Pattern (TAA,TGA,TAG) Début de la traduction Fin de la traduction Fin de la transcription rho indépendante -35 signal : Pattern (TTGACA) -10 signal : Pattern (TATAAT) } Consensus "classique" : TTGACA (15 à 19 bp) TATAAT Terminateur de la transcription -> structure en tige-boucle suivie d'un poly T + gènes de trna et gènes de rrna

6

7 ATCTTTTTCGGCTTTTTTTAGTATCCACAGAGGTTATCGACAACATTTTCACATTACCAACCCCTGTGGACAAGGTTTTTTCAACAGGTT GTCCGCTTTGTGGATAAGATTGTGACAACCATTGCAAGCTCTCGTTTATTTTGGTATTATATTTGTGTTTTAACTCTTGATTACTAATCC TACCTTTCCTCTTTATCCACAAAGTGTGGATAAGTTGTGGATTGATTTCACACAGCTTGTGTAGAAGGTTGTCCACAAGTTGTGAAATTT GTCGAAAAGCTATTTATCTACTATATTATATGTTTTCAACATTTAATGTGTACGAATGGTAAGCGCCATTTGCTCTTTTTTTGTGTTCTA TAACAGAGAAAGACGCCATTTTCTAAGAAAAGGAGGGACGTGCCGGAAGATGGAAAATATATTAGACCTGTGGAACCAAGCCCTTGCTCA AATCGAAAAAAAGTTGAGCAAACCGAGTTTTGAGACTTGGATGAAGTCAACCAAAGCCCACTCACTGCAAGGCGATACATTAACAATCAC GGCTCCCAATGAATTTGCCAGAGACTGGCTGGAGTCCAGATACTTGCATCTGATTGCAGATACTATATATGAATTAACCGGGGAAGAATT GAGCATTAAGTTTGTCATTCCTCAAAATCAAGATGTTGAGGACTTTATGCCGAAACCGCAAGTCAAAAAAGCGGTCAAAGAAGATACATC TGATTTTCCTCAAAATATGCTCAATCCAAAATATACTTTTGATACTTTTGTCATCGGATCTGGAAACCGATTTGCACATGCTGCTTCCCT CGCAGTAGCGGAAGCGCCCGCGAAAGCTTACAACCCTTTATTTATCTATGGGGGCGTCGGCTTAGGGAAAACACACTTAATGCATGCGAT CGGCCATTATGTAATAGATCATAATCCTTCTGCCAAAGTGGTTTATCTGTCTTCTGAGAAATTTACAAACGAATTCATCAACTCTATCCG AGATAATAAAGCCGTCGACTTCCGCAATCGCTATCGAAATGTTGATGTGCTTTTGATAGATGATATTCAATTTTTAGCGGGGAAAGAACA AACCCAGGAAGAATTTTTCCATACATTTAACACATTACACGAAGAAAGCAAACAAATCGTCATTTCAAGTGACCGGCCGCCAAAGGAAAT TCCGACACTTGAAGACAGATTGCGCTCACGTTTTGAATGGGGACTTATTACAGATATCACACCGCCTGATCTAGAAACGAGAATTGCAAT TTTAAGAAAAAAGGCCAAAGCAGAGGGCCTCGATATTCCGAACGAGGTTATGCTTTACATCGCGAATCAAATCGACAGCAATATTCGGGA ACTCGAAGGAGCATTAATCAGAGTTGTCGCTTATTCATCTTTAATTAATAAAGATATTAATGCTGATCTGGCCGCTGAGGCGTTGAAAGA TATTATTCCTTCCTCAAAACCGAAAGTCATTACGATAAAAGAAATTCAGAGGGTAGTAGGCCAGCAATTTAATATTAAACTCGAGGATTT CAAAGCAAAAAAACGGACAAAGTCAGTAGCTTTTCCGCGTCAAATCGCCATGTACTTATCAAGGGAAATGACTGATTCCTCTCTTCCTAA AATCGGTGAAGAGTTTGGAGGACGTGATCATACGACCGTTATTCATGCGCATGAAAAAATTTCAAAACTGCTGGCAGATGATGAACAGCT TCAGCAGCATGTAAAAGAAATTAAAGAACAGCTTAAATAGCAGGACCGGGGATCAATCGGGGAAAGTGTGAATAACTTTTCGGAAGTCAT ACACAGTCTGTCCACATGTGGATAGGCTGTGTTTCCTGTCTTTTTCACAACTTATCCACAAATCCACAGGCCCTACTATTACTTCTACTA TTTTTTATAAATATATATATTAATACATTATCCGTTAGGAGGATAAAAATGAAATTCACGATTCAAAAAGATCGTCTTGTTGAAAGTGTC CAAGATGTATTAAAAGCAGTTTCATCCAGAACCACGATTCCCATTCTGACTGGTATTAAAATTGTTGCATCAGATGATGGAGTATCCTTT ACAGGGAGTGACTCAGATATTTCTATTGAATCCTTCATTCCAAAAGAAGAAGGAGATAAAGAAATCGTCACTATTGAACAGCCCGGAAGC ATCGTTTTACAGGCTCGCTTTTTTAGTGAAATTGTAAAAAAATTGCCGATGGCAACTGTA

8 Des données à l information ORIGIN - origine de réplication; TCGA - restriction (défense?); TGTGGATAA - promoteur (transcription); souligné - DnaA Box (réplication); ATG/TAA/RBS - codon start/stop /RBS (traduction); séquence codante (traduction). ATCTTTTTCGGCTTTTTTTAGTATCCACAGAGGTTATCGACAACATTTTCACATTACCAACCCCTGTGGACAAGGTTTTTTCAACAGGTT GTCCGCTTTGTGGATAAGATTGTGACAACCATTGCAAGCTCTCGTTTATTTTGGTATTATATTTGTGTTTTAACTCTTGATTACTAATCC TACCTTTCCTCTTTATCCACAAAGTGTGGATAAGTTGTGGATTGATTTCACACAGCTTGTGTAGAAGGTTGTCCACAAGTTGTGAAATTT GTCGAAAAGCTATTTATCTACTATATTATATGTTTTCAACATTTAATGTGTACGAATGGTAAGCGCCATTTGCTCTTTTTTTGTGTTCTA TAACAGAGAAAGACGCCATTTTCTAAGAAAAGGAGGGACGTGCCGGAAGATGGAAAATATATTAGACCTGTGGAACCAAGCCCTTGCTCA AATCGAAAAAAAGTTGAGCAAACCGAGTTTTGAGACTTGGATGAAGTCAACCAAAGCCCACTCACTGCAAGGCGATACATTAACAATCAC GGCTCCCAATGAATTTGCCAGAGACTGGCTGGAGTCCAGATACTTGCATCTGATTGCAGATACTATATATGAATTAACCGGGGAAGAATT GAGCATTAAGTTTGTCATTCCTCAAAATCAAGATGTTGAGGACTTTATGCCGAAACCGCAAGTCAAAAAAGCGGTCAAAGAAGATACATC TGATTTTCCTCAAAATATGCTCAATCCAAAATATACTTTTGATACTTTTGTCATCGGATCTGGAAACCGATTTGCACATGCTGCTTCCCT CGCAGTAGCGGAAGCGCCCGCGAAAGCTTACAACCCTTTATTTATCTATGGGGGCGTCGGCTTAGGGAAAACACACTTAATGCATGCGAT CGGCCATTATGTAATAGATCATAATCCTTCTGCCAAAGTGGTTTATCTGTCTTCTGAGAAATTTACAAACGAATTCATCAACTCTATCCG AGATAATAAAGCCGTCGACTTCCGCAATCGCTATCGAAATGTTGATGTGCTTTTGATAGATGATATTCAATTTTTAGCGGGGAAAGAACA AACCCAGGAAGAATTTTTCCATACATTTAACACATTACACGAAGAAAGCAAACAAATCGTCATTTCAAGTGACCGGCCGCCAAAGGAAAT TCCGACACTTGAAGACAGATTGCGCTCACGTTTTGAATGGGGACTTATTACAGATATCACACCGCCTGATCTAGAAACGAGAATTGCAAT TTTAAGAAAAAAGGCCAAAGCAGAGGGCCTCGATATTCCGAACGAGGTTATGCTTTACATCGCGAATCAAATCGACAGCAATATTCGGGA ACTCGAAGGAGCATTAATCAGAGTTGTCGCTTATTCATCTTTAATTAATAAAGATATTAATGCTGATCTGGCCGCTGAGGCGTTGAAAGA TATTATTCCTTCCTCAAAACCGAAAGTCATTACGATAAAAGAAATTCAGAGGGTAGTAGGCCAGCAATTTAATATTAAACTCGAGGATTT CAAAGCAAAAAAACGGACAAAGTCAGTAGCTTTTCCGCGTCAAATCGCCATGTACTTATCAAGGGAAATGACTGATTCCTCTCTTCCTAA AATCGGTGAAGAGTTTGGAGGACGTGATCATACGACCGTTATTCATGCGCATGAAAAAATTTCAAAACTGCTGGCAGATGATGAACAGCT TCAGCAGCATGTAAAAGAAATTAAAGAACAGCTTAAATAGCAGGACCGGGGATCAATCGGGGAAAGTGTGAATAACTTTTCGGAAGTCAT ACACAGTCTGTCCACATGTGGATAGGCTGTGTTTCCTGTCTTTTTCACAACTTATCCACAAATCCACAGGCCCTACTATTACTTCTACTA TTTTTTATAAATATATATATTAATACATTATCCGTTAGGAGGATAAAAATGAAATTCACGATTCAAAAAGATCGTCTTGTTGAAAGTGTC CAAGATGTATTAAAAGCAGTTTCATCCAGAACCACGATTCCCATTCTGACTGGTATTAAAATTGTTGCATCAGATGATGGAGTATCCTTT ACAGGGAGTGACTCAGATATTTCTATTGAATCCTTCATTCCAAAAGAAGAAGGAGATAAAGAAATCGTCACTATTGAACAGCCCGGAAGC ATCGTTTTACAGGCTCGCTTTTTTAGTGAAATTGTAAAAAAATTGCCGATGGCAACTGTA

9 (Himmelreich et al, NAR, 96)

10 Mutation & Recombination

11 Fading homologies (Clarck, TREE, 06)

12 Bioinformatics beyond model organisms ripr chtr pyho aqae trpa mytu arfu bobu meth basu hepy esco mypn sysp meja myge hain ,190 14,357 11,082 Nombre de papiers citant chaque espèce 167, Nombre de gènes classés fonctionnellement

13

14 Production d hypothèses Données Théorie Tests d hypothèses

15 Summary i- Genome stability ii- Genome organization iii -Conflicts

16 Gene order conservation Data Model A α i β j B GOC is derived from the order of pairs of orthologues : α i α i+1 β j β j+k GOC i =1 iff k =1, GOC = i genes GOC i N (method adapted from Huynen, PNAS, 98) If all pairs are conserved with equal probability (p) per unit of time : GOC α p t If there are 2 classes of conservation : GOC = p fast t + p slow t

17 Gene order conservation (GOC) GOC = p t GOC= p fastt +p slow t A B Δ<k p - probability that two contiguous genes have contiguous orthologs p fast and p fast allow for pairs of genes with different rearrangement rates. Data: 126 genomes of 6 clades with more than 8 genomes, 16S rdna distances (HKY+Γ) (Rocha, Mol Biol Evol, 06)

18 Genome backbones are stable ~100 million years ~500 million years : ~50% of contiguity is conserved (Rocha, Mol Biol Evol, 06)

19 What is the E. coli genome? Core genome evolution 1 2 Pan genome evolution ~18000 number of genes number of genes ~ ~1800 ~4600 number of genomes number of genomes

20 Genome backbones are stable ~100 million years ~500 million years : ~50% of contiguity is conserved (Fischer, PlosG, 06)

21 Different constraints GOC = p fastt +p slow t pairs slowly separating pairs quickly separating

22 Détection d opérons

23 Détection d opérons 1. Co-orientation : un opéron est une séquence de gènes coorientés contigus.

24 Détection d opérons 1. Co-orientation : un opéron est une séquence de gènes coorientés contigus. 2. Dans la plupart des génomes la majorité des opérons a un signal de terminaison de transcription rho-indépendant.

25 Détection d opérons 1. Co-orientation : un opéron est une séquence de gènes coorientés contigus. 2. Dans la plupart des génomes la majorité des opérons a un signal de terminaison de transcription rho-indépendant. 3. Si la distance entre deux gènes est très grande (>~150 nt) ils ont une forte probabilité d être dans des opérons diférents

26 Détection d opérons 1. Co-orientation : un opéron est une séquence de gènes co-orientés contigus. 2. Dans la plupart des génomes la majorité des opérons a un signal de terminaison de transcription rho-indépendant. 3. Si la distance entre deux gènes est très grande (>~150 nt) ils ont une forte probabilité d être dans des opérons différents. 4. Naturellement d autres données peuvent améliorer les prédictions

27 Operons organize genomes locally observed fit vs expected fit operons inter-operons Genes contiguous in the same operon Genes contiguous in different operons (Rocha, Mol Biol Evol, 06)

28 Defining genome stability + stable Obs>Expected - stable Obs<Expected Genome stability can be defined as the average of the residuals for the comparisons in which the genome participates.

29 Repeats decrease stability Stability density of repeats (Rocha, Trends Genetics, 03)

30 Why repeats? Creation mechanisms : Molecular parasites (e.g. transposases) Intra-chromosomal recombination Horizontal transfer Fixation in populations: For dosage effects (e.g. ARNr) To generate variability by recombination (e.g. antigenic variation in pathogens) In the way for sub- or neo-functionalization

31 Summary i- Genome stability Bacterial genomes are stable Some genomes are more stable than others depending on mutational events At a local level, transcription constrains genome rearrangements. ii- Genome organization iii -Conflicts

32 Replication-associated gene dosage Time replication round Ori R = replication time/doubling time # replication forks = 2x(2 R -1) # origins / # termini = 2 R R can be up to 4! -> 30 replication forks and 16 ori/ter. Θ Ter (Couturier, Mol Microbiol, 06)

33 Replication-associated gene dosage fast growing slow growing Ori Θ Highly expressed genes group near the origin of replication in fast growing bacteria The regulatory cascade is imprinted in the organization of the genome: RNAP>RDNA>RP Ter (Couturier, Mol Microbiol, 06)

34 In short

35 Not all rearrangements are alike ter A ter B before before A C before B no change ter before C after ter Op- operons Gi- genomic islands Sb- strand bias Gd- gene dosage Rs- segregation Cs- symmetry after after

36 . Keeping order at a global scale Buchnera Bp Chlamydia muridarum 16S:.076 nt-1 Buchnera Ap Chlamydia pneumoniae 16S:.071 nt -1 Escherichia coli origin terminus Bacillus subtilis 16S:.063 nt -1 Yersinia pestis Bacillus halodurans 16S:.051 nt -1

37 Summary i- Genome stability Bacterial genomes are stable Some genomes are more stable than others depending on mutational events At a local level, transcription constrains genome rearrangements. ii- Genome organization Genomes are organized at local and global scales Replication structures the chromosome at a large-scale The organization depends on cell machinery and cell structure iii -Conflicts

38 Taming disorder I regionalization Unstable Streptomyces coelicolor Stable (Bentley, Nature, 02)

39 (Himmelreich et al, NAR, 96)

40 Rearrangements in Mycoplasma genome M. genitalium M. pneumoniae D/I M. pneumoniae M. genitalium (Rocha, NAR, 02)

41 Taming disorder III delocalizing repeats Borrelia burgdorferi Plasmids (600 kb) : 1256 repeats Chromosome (900 kb) : 21 repeats (Fraser, Nature, 97)

42 Genome organization Genome organization is driven by the cellular processes interacting with the chromosome. But is constantly challenged by the fluidity of the chromosome. Thus, only organizational elements under strong selection endure. The genome allows inferring cellular mechanisms and phenotypic characteristics underlying its organisation. (Rocha, Curr Op Microb, 04)

43 All things have varying capacities. Consequently he who wants to have right without wrong, order without disorder, does not understand [ ] how things hang together. Chuang-Tzu (300 BC) «Forgetting about preferences»