Life without Fur

1. Life without Fur

2. Life without FUR: evolutionary reconstruction of transcriptional regulation of iron homeostasis in alpha-proteobacteria Mikhail Gelfand Research and Training Center “Bioinformatics”, Institute for Information Transmission Problems, RAS Russian-German Systems Biology Workshop Moscow, February 27-29, 2008

3. Regulation of iron homeostasis (the Escherichia coli paradigm) Iron: • essential cofactor (limiting in many environments) • dangerous at large concentrations FUR (Ferric Uptake Regulator: responds to iron): • synthesis of siderophores • transport (siderophores, heme, Fe2+, Fe3+) • storage • iron-dependent enzymes • synthesis of heme • synthesis of Fe-S clusters Similar in Bacillus subtilis

4. [+Fe] [+Fe] [- Fe] [ Fe] - Irr Irr RirA RirA FeS heme degraded 2+ 3+ S i d e r o p h o r e F e / F e I r o n - r e q u i r i n g I r o n s t o r a g e F e S H e m e T r a n s c r i p t i o n u p t a k e u p t a k e e n z y m e s f e r r i t i n s s y n t h e s i s s y n t h e s i s f a c t o r s I r o n u p t a k [ i r o n c o f a c t o r ] e s y s t e m s FeS status IscR Fur Fur of cell Fe FeS [- Fe] [+Fe] Regulation of iron homeostasis in α-proteobacteria Experimental studies: • FUR/MUR: Bradyrhizobium, Rhizobium and Sinorhizobium • RirA (Rrf2 family): Rhizobium and Sinorhizobium • Irr (FUR family): Bradyrhizobium, Rhizobium and Brucella

5. Comparative genomics of regulatory systems • Standard methods of comparative genomics: • similarity search by BLAST • Construction of phylogenetic trees to identify orthologs • General functional annotation by similarity • Assigning genes to functional subsystems using co-localization scores and phylogenetic profiles • Analysis of regulation: • Phylogenetic footprinting at short evolutionary distances: conserved motifs upstream of orthologs are likely sites • Consistency filtering at longer distances: true sites occur upstream of orthologs; false positives scattered at random

6. Distribution of transcription factors in genomes

7. Fur in g- and b- proteobacteria Escherichia coli : P0A9A9 sp| ECOLI Fur Pseudomonas aeruginosa : sp|Q03456 PSEAE Fur in e- proteobacteria Neisseria meningitidis : sp|P0A0S7 NEIMA HELPY : sp|O25671 Helicobacter pylori Fur in Firmicutes BACSU Bacillus subtilis : P54574 sp| SM mur Sinorhizobium meliloti MBNC03003179 Mesorhizobium sp. BNC1 (I) BQ fur2 Bartonella quintana BMEI0375 Brucella melitensis EE36 12413 sp. EE-36 Sulfitobacter a MBNC03003593 sp. BNC1 (II) Mesorhizobium RB2654 19538 HTCC2654 Rhodobacterales bacterium AGR C 620 Agrobacterium tumefaciens RHE_CH00378 Rhizobium etli RL mur Rhizobium leguminosarum Nham 0990 Mur Nitrobacter hamburgensis X14 in a-proteobacteria Nwi 0013 Nitrobacter winogradskyi RPA0450 Rhodopseudomonas palustris Regulator of manganese uptake genes (sit, mntH) BJ fur Bradyrhizobium japonicum ROS217 18337 Roseovarius sp.217 Jann 1799 Jannaschia sp. CC51 SPO2477 Silicibacter pomeroyi STM1w01000993 Silicibacter sp. TM1040 MED193 22541 sp. MED193 Roseobacter OB2597 02997 HTCC2597 Oceanicola batsensis SKA53 03101 Loktanella vestfoldensis SKA53 Rsph03000505 Rhodobacter sphaeroides ISM 15430 Roseovarius nubinhibens ISM PU1002 04436 Pelagibacter ubique HTCC1002 GOX0771 Gluconobacter oxydans ZM01411 Zmomonas mobilis y Saro02001148 Novosphingobium aromaticivorans a Sala 1452 RB2256 Sphinopyxis alaskensis Fur ELI1325 in a-proteobacteria Erythrobacter litoralis OA2633 10204 Oceanicaulis alexandrii HTCC2633 PB2503 04877 Parvularcula bermudensis HTCC2503 Regulator of iron uptake and metabolism genes CC0057 Caulobacter crescentus Rrub02001143 Rhodospirillum rubrum Amb1009 (I) Magnetospirillum magneticum a Amb4460 Magnetospirillum magneticum (II) Irr a-proteobacteria FUR/MUR branch of the FUR family

8. FUR and MUR boxes Erythrobacter litoralis Caulobacter crescentus Novosphingobium aromaticivorans Zymomonas mobilis Oceanicaulis alexandrii Sphinopyxis alaskensis Rhodospirillum rubrum Gluconobacter oxydans Parvularcula bermudensis - Magnetospirillum magneticum Identified Mur-binding sites Bacillus subtilis Sequence logos for known Fur-binding sites in Escherichia coli and Bacillus subtilis Mur a of - proteobacteria - Escherichia coli

9. Irr branch of the FUR family Fur in g- and b- proteobacteria Escherichia coli ECOLI : P0A9A9 sp| Fur Pseudomonas aeruginosa : sp|Q03456 PSEAE Neisseria meningitidis : sp|P0A0S7 NEIMA Fur in e- proteobacteria HELPY Helicobacter pylori : sp|O25671 Fur in Firmicutes BACSU Bacillus subtilis : P54574 sp| a a-proteobacteria Mur / Fur AGR C 249 Agrobacterium tumefaciens SM irr Sinorhizobium meliloti RHE CH00106 Rhizobium etli RL irr1 Rhizobium leguminosarum (I) RL irr2 Rhizobium leguminosarum (II) MLr5570 Mesorhizobium loti MBNC03003186 sp. BNC1 Mesorhizobium BQ fur1 Bartonella quintana BMEI1955 Irrin a-proteo- bacteria regulator of iron homeostasis Brucella melitensis (I) BMEI1563 Brucella melitensis (II) BJ blr1216 (II) Bradyrhizobium japonicum RB2654 182 Rhodobacterales bacterium HTCC2654 SKA53 01126 Loktanella vestfoldensis SKA53 ROS217 15500 Roseovarius sp.217 ISM 00785 ISM Roseovarius nubinhibens OB2597 14726 Oceanicola batsensis HTCC2597 Jann 1652 sp. CC51 Jannaschia a I r r - Rsph03001693 Rhodobacter sphaeroides EE36 03493 Sulfitobacter sp. EE-36 STM1w01001534 sp. TM1040 Silicibacter MED193 17849 Roseobacter sp. MED193 SPOA0445 Silicibacter pomeroyi RC irr Rhodobacter capsulatus RPA2339 (I) Rhodopseudomonas palustris RPA0424* Rhodopseudomonas palustris (II) BJ irr* (I) Bradyrhizobium japonicum Nwi 0035* Nitrobacter winogradskyi Nham 1013* Nitrobacter hamburgensis X14 PU1002 04361 Pelagibacter ubique HTCC1002

10. Irr boxes Rhizobiaceae plus Bradyrhizobiaceae Rhodobacteriaceae Rhodospirillales

11. RirA/NsrR family (Rhizobiales)

12. IscR family

13. Summary: regulation of genes in functional subsystems Rhizobiales Bradyrhizobiaceae Rhodobacteriales The Zoo (likely ancestral state)

14. Reconstruction of history Frequent co-regulation with Irr Strict division of function with Irr Appearance of theiron-Rhodo motif

15. Experimental validation • RirA: sites and binding motifin Rhisobium legumisaurum(site-directed mutagenesis).Andy Johnston lab (University of East Anglia) • Microarray study if the Bradyrhizobium japonicum FUR– mutant: regulatory cascade FUR  irr:Mark O’Brian group (SUNY, Buffalo)

16. 2 All logos and Some Very Tempting Hypotheses: • Cross-recognition of FUR and IscR motifs in the ancestor. • When FUR had become MUR, and IscR had been lost in Rhizobiales, emerging RirA (from the Rrf2 family, with a rather different general consensus) took over their sites. • Iron-Rhodo boxes are recognized by IscR: directly testable 1 3

17. More stories • Regulation of methionine metabolism in Firmicutes (from S-boxes to T-boxes and transcriptional factors) • T-box regulon in Firmicutes (duplications, bursts, changes of specificity) • Regulation of respiration in gamma-proteobacteria (rewiring of regulatory cascades and shuffling of regulons) • Emerging global regulators in Enterobacteriaceae (how FruR has become CRA, and how duplicated RbsR has become PurR)

18. Open problems • Regulatory systems are very flexible • easily lost • easily expanded (in particular, by duplication) • may change specificity • rapid turnover of regulatory sites • With more stories like these, we can start thinking about a general theory • catalog of elementary events; how frequent? • mechanisms (duplication, birth e.g. from enzymes, horizontal transfer) • conserved (regulon cores) and non-conserved (marginal regulon members) genes in relation to metabolic and functional subsystems/roles • (TF family-specific) protein-DNA recognition code • distribution of TF families in genomes; distribution of regulon sizes; etc.

19. Dmitry Rodionov (IITP, now at Burnham Institute, La Jolla, CA) Andrew Johnston and Jonathan Todd(University of East Anglia, UK) Howard Hughes Medical Institute Russian Academy of Sciencesprogram “Molecular and Cellular Biology” Acknowledgements