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Life without Fur. Life without FUR: evolutionary reconstruction of transcriptional regulation of iron homeostasis in alpha-proteobacteria. Mikhail Gelfand Research and Training Center of Bioinformatics, Institute for Information Transmission Problems, RAS - PowerPoint PPT Presentation
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Life without
Fur
Mikhail Gelfand
Research and Training Center of Bioinformatics, Institute for Information Transmission Problems, RAS
Genome Dynamics: From Replication to Post-Translation and Turnover
HHMI, 11-14 March 2007
Life without FUR: evolutionary reconstruction of transcriptional regulation of iron homeostasis in
alpha-proteobacteria
Regulation of iron homeostasis (the Escherichia coli paradigm)
Iron:• essential cofactor (limiting in many environments)• dangerous at large concentrations
FUR (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
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
RirA IrrFeS heme
RirA
degraded
FurFe
Fur
Iron uptake systems
Siderophoreuptake
Fe / Feuptake Transcription
factors
2+ 3+
Iron storage ferritins
FeS synthesis
Heme synthesis
Iron-requiring enzymes
[iron cofactor]
IscR
Irr
[- Fe] [+Fe]
[+Fe][- Fe]
[+Fe][ Fe]-
FeS
FeS statusof cell
Comparative genomics of regulatory systems
• Standard methods:– BLAST– Construction of phylogenetic trees to identify orthologs– Functional annotation by similarity– Co-localization patterns
• Analysis of regulation:– Phylogenetic footprinting
(Conserved motifs upstream of orthologs)– Consistency filtering
(true sites upstream of orthologs; false positives scattered at random)
Distribution of transcription
factors in genomes
FUR/MUR branch of the FUR familyFur in - and - proteobacteria
Fur in - proteobacteria Fur in Firmicutes
in proteobacteria
Fur
MBNC03003593RB2654 19538
AGR C 620
RL mur
Nwi 0013RPA0450
BJ furROS217 18337
Jann 1799SPO2477
STM1w01000993MED193 22541
OB2597 02997SKA53 03101Rsph03000505ISM 15430
GOX0771ZM01411
Saro02001148Sala 1452
ELI1325OA2633 10204
PB2503 04877CC0057
Rrub02001143Amb1009Amb4460
SM murMBNC03003179
BQ fur2BMEI0375
Mesorhizobium sp. BNC1 (I)
Sinorhizobium meliloti
Bartonella quintana
Rhodopseudomonas palustris
Bradyrhizobium japonicum
Caulobacter crescentus
Zmomonas mobilisy
Rhodobacter sphaeroides
Silicibacter sp. TM1040Silicibacter pomeroyi
Agrobacterium tumefaciens
Rhizobium leguminosarum
Brucella melitensis
Mesorhizobium sp. BNC1 (II)
Rhodobacterales bacterium HTCC2654
Nitrobacter winogradskyiNham 0990 Nitrobacter hamburgensis X14
Jannaschia sp. CC51Roseovarius sp.217
Roseobacter sp. MED193Oceanicola batsensis HTCC2597
Loktanella vestfoldensis SKA53
Roseovarius nubinhibens ISM
Gluconobacter oxydans
Erythrobacter litoralis
Novosphingobium aromaticivoransSphinopyxis alaskensis RB2256
Oceanicaulis alexandrii HTCC2633
Rhodospirillum rubrum
Parvularcula bermudensis HTCC2503
Magnetospirillum magneticum (I)
EE36 12413 Sulfitobacter sp. EE-36
ECOLIPSEAE
NEIMAHELPY
BACSUHelicobacter pylori : sp|O25671
Bacillus subtilis : P54574sp|
Neisseria meningitidis : sp|P0A0S7Pseudomonas aeruginosa : sp|Q03456
Escherichia coli: P0A9A9sp|
Mur
Fur
Magnetospirillum magneticum (II)
RHE_CH00378Rhizobium etli
PU1002 04436Pelagibacter ubique HTCC1002
Irr
in proteobacteria
proteobacteria
Regulator of manganese uptake genes (sit, mntH)
Regulator of iron uptake and metabolism genes
of - proteobacteria - Mur
Caulobacter crescentus
Zymomonas mobilis
Gluconobacter oxydans
Erythrobacter litoralis
Novosphingobium aromaticivorans
Rhodospirillum rubrum
Magnetospirillum magneticum
Escherichia coli
Sphinopyxis alaskensis
Parvularcula bermudensis -
Oceanicaulis alexandrii
Bacillus subtilis
Sequence logos for the known Fur-binding sites in Escherichia coli and Bacillus subtilis
Identified Mur-binding sites
FUR and MUR
boxes
Fur in - and - proteobacteria
Fur in - proteobacteria Fur in Firmicutes
Irr in proteo-bacteria regulator of ironhomeostasis
proteobacteria Fur
ECOLIPSEAE
NEIMAHELPY
BACSUHelicobacter pylori : sp|O25671
Bacillus subtilis : P54574sp|
Neisseria meningitidis : sp|P0A0S7
Pseudomonas aeruginosa : sp|Q03456Escherichia coli : P0A9A9sp|
Mur /
Fur
Irr-
AGR C 249SM irr
RL irr1RL irr2
MLr5570MBNC03003186
BQ fur1BMEI1955BMEI1563BJ blr1216
RB2654 182SKA53 01126
ROS217 15500ISM 00785
OB2597 14726Jann 1652
Rsph03001693EE36 03493
STM1w01001534MED193 17849
SPOA0445RC irr
RPA2339RPA0424*
BJ irr*Nwi 0035*Nham 1013* Nitrobacter hamburgensis X14
Nitrobacter winogradskyi
Bradyrhizobium japonicum (I)
Agrobacterium tumefaciens
Rhizobium leguminosarum (I)
Mesorhizobium sp. BNC1
Sinorhizobium meliloti
Mesorhizobium loti
Bartonella quintanaBrucella melitensis (I)
Bradyrhizobium japonicum (II)
Rhodobacter sphaeroides
Rhodobacter capsulatusSilicibacter pomeroyi
Silicibacter sp. TM1040Roseobacter sp. MED193
Sulfitobacter sp. EE-36
Jannaschia sp. CC51Oceanicola batsensis HTCC2597Roseovarius nubinhibens ISMRoseovarius sp.217Loktanella vestfoldensis SKA53
Rhodobacterales bacterium HTCC2654
Rhizobium etliRHE CH00106
Rhizobium leguminosarum (II)
Brucella melitensis (II)
Rhodopseudomonas palustris (II)Rhodopseudomonas palustris (I)
PU1002 04361 Pelagibacter ubique HTCC1002
Irr branch of the FUR family
Irr boxes
Rhizobiaceae plus
Bradyrhizobiaceae
Rhodobacteriaceae
Rhodospirillales
RirA/NsrR family (Rhizobiales)
IscR family
Summary: regulation of genes in functional
subsystems
Rhizobiales
Bradyrhizobiaceae
Rhodobacteriales
The Zoo (likely ancestral state)
Reconstruction of history
Appearance of theiron-Rhodo motif
Frequent co-regulation
with Irr
Strict division of function
with Irr
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)
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
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)
Acknowledgements
• 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”