Comparative%20genomic%20analysis%20of%20T-box%20regulation:%20identification%20of%20new%20structural%20classes%20and%20reconstruction%20of%20evolution

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Comparative genomic analysis of T-box
regulation identification of new structural
classes and reconstruction of evolution

• Mikhail Gelfand
• Research and Training Center Bioinformatics
• Institute for Information Transmission Problems
• Moscow, Russia

Burnham Institute, October 2008 To Andrei
Osterman on the occasioin of his Nth birthday
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T-boxes the mechanism (Grundy Henkin Putzer
Grunberg-Manago)
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Partial alignment of predicted T-boxes
TGG T-box
Aminoacyl-tRNA synthetases
Amino acid biosynthetic genes
Amino acid transporters
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continued (in the 5 direction)
anti-anti (specifier) codon
Aminoacyl-tRNA synthetases
Amino acid biosynthetic genes
Amino acid transporters
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Why T-boxes?

• May be easily identified
• In most cases functional specificity may be
  reliably predicted by the analysis of the
  specifier codons (anti-anti-codons)
• Sufficiently long to retain phylogenetic signal
• gt T-boxes are a good model of regulatory
  evolution

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805 T-boxes in 96 bacteria

• Firmicutes
• aa-tRNA synthetases
• enzymes
• transporters
• all amino acids excluding glutamate
• Actinobacteria (regulation of translation
  predicted)
• branched chain (ileS)
• aromatic (Atopobium minutum)
• Delta-proteobacteria
• branched chain (leu enzymes)
• Thermus/Deinococcus group (aa-tRNA synthases)
• branched chain (ileS, valS)
• glycine
• Chloroflexi, Dictyoglomi
• aromatic (trp enzymes)
• branched chain (ileS)
• threonine

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Double and partially double T-boxes

• TRP trp operon (Bacillales, C. beijerincki, D.
  hafniense)
• TYR pah (B. cereus)
• THR thrZ (Bacillales) hom (C. difficile)
• ILE ilv operon (B. cereus)
• LEU leuA (C. thermocellum)
• ILE-LEU ilvDBNCB-leuACDBA (Desulfotomaculum
  reducens)

• TRP trp operon (T. tengcongensis)
• PHE arpLA-pheA (D. reducens, S. wolfei)
• PHE trpXY2 (D. reducens)
• PHE yngI (D. reducens)
• TYR yheL (B. cereus)
• SER serCA (D. hafniense)
• THR thrZ (S. uberis)
• THR brnQ-braB1 (C. thermocellum)
• HIS hisXYZ (Lactobacillales)
• ARG yqiXYZ (C. difficile)

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Predicted regulation of translationileS in many
Actinobacteria

• Instead of the terminator, the sequester hairpin
  (hides the translation initiation site)
• Same mechanism regulates different processes
  cf. riboswitches

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A new type of translational T-boxes in
Actinobacteria

• Shorter specifier hairpin
• Anti-anti-codon in the head loop, not a bulge
  loop
• A majority of cases (all except Streptomyces spp.)

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Same enzymes different regulators (common part
of the aromatic amino acids biosynthesis pathway)
cf. E.coli aroF,G,H feedback inhibition by TRP,
TYR, PHE transcriptional regulation by TrpR,
TyrR
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Recent duplications and bursts ARG-T-box in
Clostridium difficile
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caused by loss of transcription factor AhrC
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Duplications and changes in specificity
ASN/ASP/HIS T-boxes
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Blow-up 1
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Blow-up 2. Prediction

• Regulators lost in lineages with expanded
  HIS-T-box regulon??

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and validation

• conserved motifs upstream of HIS biosynthesis
  genes
• candidate transcription factor yerC co-localized
  with the his genes
• present only in genomes with the motifs upstream
  of the his genes
• genomes with neither YerC motif nor HIS-T-boxes
  attenuators

Bacillales (his operon)
Clostridiales Thermoanaerobacteriales Halanaerobia
les Bacillales
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New histidine transporters

• hisXYZ (The ATP-binding Cassette (ABC)
  Superfamily)Firmicutes
• yuiF (Na/H antiporter, NahC
  family)Bacillales, some Clostridiales(regulated
  by his-attenuator in Haemophilus inlfuenzae)
• Cphy_3090 (SSS sodium solute transporter
  superfamily)Clostridiales, Thermoanaerobacteriale
  s, Halanaerobiales

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The evolutionary history of the his genes
regulation in the Firmicutes
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More duplications THR-T-box in C. difficile and
B. cereus
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Duplications and changes in specificity
branched-chain amino acids
ATC
CTC
ATC
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Blow-up
transporter
ATC
GTC
dual regulation of common enzymes
ATC
CTC
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Three regulatory systems for the methionine
bio-synthesis

• SAM-dependent riboswitch
• Met-T-box
• C. MtaR repressor of transcription

MtaR
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Methionine regulatory systems loss of S-box
regulons

• S-boxes (SAM-1 riboswitch)
• Bacillales
• Clostridiales
• the Zoo
• Petrotoga
• actinobacteria (Streptomyces, Thermobifida)
• Chlorobium, Chloroflexus, Cytophaga
• Fusobacterium
• Deinococcus
• proteobacteria (Xanthomonas, Geobacter)
• Met-T-boxes (Met-tRNA-dependent attenuator)
  SAM-2 riboswitch for metK
• Lactobacillales
• candidate TF-binding motif MtaR
• Streptococcales

ZOO
Lact.
Strep.
Bac.
Clostr.
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Summary / History
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Acknowledgements

• Alexei Vitreschak
• Andrei Mironov (software)
• Galina Kovaleva (methionine)
• Dmitry Rodionov, Burnham (early work on
  methionine and S-boxes)

• HHMI
• RFBR
• RAS (program Molecular and Cellular Biology)

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