1. Evolution of bacterial regulatory systems Mikhail Gelfand Institute for Information Transmission Problems, RAS BGRS-2004, Novosibirsk

2. Early analyses (BGRS’98, 00, 02) “Making good predictions with bad rules” Basic assumption: regulons are conserved => Consistency check: sites upstream of orthologous genes are correct; false positives are scattered at random Validation of individual sites Validation of signals: candidate signals for orthologous factors are correct if similar

3. Multiple genomes: taxon-specific regulation; multiple interacting systems; evolution of regulation Evolution of orthologous regulatory sites Co-evolution of transcription factors and their binding signals Evolution of regulons (sets of co-regulated genes) Evolution of regulatory systems

4. Это – ряд наблюдений. В углу – тепло. Взгляд оставляет на вещи след. Вода представляет собой стекло. Человек страшней, чем его скелет. Иосиф Бродский A list of some observations. In a corner, it’s warm. A glance leaves an imprint on anything it’s dwelt on. Water is glass’s most public form. Man is more frightening than its skeleton. Joseph Brodsky

5. Conservation of non-consensus positions in orthologous sites regulatory site LexA  lexA consensus nucleotides are in caps wrong consensus?

6. PurR  purL PurR  purM

7. Non-consensus positions are more conserved than synonymous codon positions

8. Non-consensus positions may be more conserved than consensus positions

9. Regulators and their signals Subtle changes at close evolutionary distances Changes in spacing / geometry of dimers Correlation between contacting nucleotides and amino acid residues Cases of conservation at surprisingly large distances

10. Zinc repressors nZUR-  nZUR-  AdcRpZUR TTAACYRGTTAA GATATGTTATAACATATC GAAATGTTATANTATAACATTTC GTAATGTAATAACATTAC TAAATCGTAATNATTACGATTTA

11. Alignment of nZUR binding signals GTAATGTAA TAACATTAC (alpha – most genera) GATATGTTA TAACATATC (alpha – Rhodobacter) GAAATGTTATANTATAACATTTC (gamma) GaaATGTtA-----TAACATttC (consensus of consensi)

12. CRP/FNR family of regulators

13. Correlation between contacting nucleotides and amino acid residues CooA in Desulfovibrio spp. CRP in Gamma-proteobacteria HcpR in Desulfovibrio spp. FNR in Gamma-proteobacteria DD COOA ALTTEQLSLHMGATRQTVSTLLNNLVR DV COOA ELTMEQLAGLVGTTRQTASTLLNDMIR EC CRP KITRQEIGQIVGCSRETVGRILKMLED YP CRP KXTRQEIGQIVGCSRETVGRILKMLED VC CRP KITRQEIGQIVGCSRETVGRILKMLEE DD HCPR DVSKSLLAGVLGTARETLSRALAKLVE DV HCPR DVTKGLLAGLLGTARETLSRCLSRMVE EC FNR TMTRGDIGNYLGLTVETISRLLGRFQK YP FNR TMTRGDIGNYLGLTVETISRLLGRFQK VC FNR TMTRGDIGNYLGLTVETISRLLGRFQK TGTCGGCnnGCCGACA TTGTgAnnnnnnTcACAA TTGTGAnnnnnnTCACAA TTGATnnnnATCAA Contacting residues: REnnnR TG: 1 st arginine GA: glutamate and 2 nd arginine

14. The correlation holds for other factors in the family

15. The LacI family of transcrip- tional regulators (each branch represents a subfamily)

16. … and their signals

17. BirA: regulator of biotin biosynthesis and transport in eubacteria and archaea Profile 2: Gram-negative bacteriaProfile 1: Gram-positive bacteria, Archaea

18. Evolution of regulons and regulatory systems conserved cores taxon-specific marginal members migration of genes between interacting regulatory systems taxon-specific cross-regulation genome-specific operons and genomic loci complete change of regulatory mechanisms

19. Genome loci for hyaluronate utilization in invasive Streptococcus spp. S. pyogenes, S. agalactiae S. equi S. pneumoniae TIGR4 S. suis S. pneumoniae R6

20. Respiration in gamma-proteobacteria 1. Three regulators, different regulatory cascades Haemophilus ducreyi, Vibrio spp. Haemophilus influenzae, Pasteurella multocida, A. actinomycetemcomitans Escherichia coli (experimental data)

21. Respiration in gamma-proteobacteria 2. New genome/taxon-specific regulon members Escherichia coli (known)New, non-homologous regulon member FnrArcA — Yersinia pestisFnrArcA — Fnr — — Yersinia entercoliticaFnr — — FnrArcANarP Pasteurella multocidaFnrArcANarP —ArcANarP Actinobacillus actinomycetemcomitans — ArcANarP FnrArcA — Haemophilus influenzae FnrArcA — FnrArcA NarP Haemophilus ducreyiFnrArcA NarP —ArcA — Vibrio vulnificus —ArcA — —ArcA — Vibrio parahaemolyticus —ArcA — FnrArcA — Vibrio choleraeFnrArcA — —ArcA — Vibrio fischeri — ArcA —

22. Respiration in gamma-proteobacteria 3. New genome/taxon-specific regulon members, cont’d Synthesis of molybdate cofactor Fnr — — Yersinia pestisFnr — — FnrArcA — Yersinia entercoliticaFnrArcA — FnrArcA — Pasteurella multocidaFnrArcA — Fnr — NarP Actinobacillus actinomycetemcomitansFnr — NarP Fnr — NarP Haemophilus influenzae Fnr — NarP FnrArcANarP Haemophilus ducreyiFnrArcANarP — — NarP Vibrio vulnificus — — NarP — — NarP Vibrio parahaemolyticus — — NarP — — NarP Vibrio cholerae — — NarP —ArcANarP Vibrio fischeri — ArcANarP

23. Zinc repressors - recapitulation nZUR-  nZUR-  AdcRpZUR TTAACYRGTTAA GATATGTTATAACATATC GAAATGTTATANTATAACATTTC GTAATGTAATAACATTAC TAAATCGTAATNATTACGATTTA

24. Five regulatory systems for methionine biosynthesis A.SAM- dependent RNA riboswitch B.Met-tRNA- dependent T-box (RNA) C,D,E. repressors of transcription

25. Three methionine regulatory systems in Gram- positive bacteria: loss of S-box regulons S-boxes (riboswitch) –Bacillales –Clostridiales –the Zoo: Petrotoga actinobacteria (Streptomyces, Thermobifida) Chlorobium, Chloroflexus, Cytophaga Fusobacterium Deinococcus proteobacteria (Xanthomonas, Geobacter) Met-T-boxes (Met-tRNA-dependent attenuator) –Lactobacillales MET-boxes (candidate transcription signal) –Streptococcales Lact. Strep. Bac. Clostr. ZOO

26. Catabolism of gluconate in proteobacteria

27. Three regulatory systems one global (FruR), two taxon-specific (GntR, PtxS) β γ1γ1 Pseudomonas spp.

28. Instead of conclusions… Andrei A. Mironov (BGRS’98,00,02,04) Anna Gerasimova (BGRS’02,04) Olga Kalinina (BGRS’02,04) Alexei Kazakov (BGRS’02,04) Ekaterina Kotelnikova (BGRS’02,04) Galina Kovaleva (BGRS’04) Pavel Novichkov (BGRS’00,02,04) Olga Laikova (BGRS’02,04) Ekaterina Panina (BGRS’00) (now at UCLA, USA) Elizabeth Permina (BGRS’02,04) Dmitry Ravcheev (BGRS’02,04) Alexandra B. Rakhmaninova (BGRS’00) Dmitry Rodionov (BGRS’00) Alexey Vitreschak (BGRS’00,04) (visiting LORIA, France) Howard Hughes Medical Institute Ludwig Institute of Cancer Research Russian Fund of Basic Research Programs “Origin and Evolution of the Biosphere” and “Molecular and Cellular Biology”, Russian Academy of Sciences