The identification of response regulator specific binding sites reveals new roles of two-component systems of Bacillus cereus and closely related low-GC Gram-positives

Mark de Been1,2,3, Marieke J. Bart2, Tjakko Abee1,3, Roland J. Siezen1,2,4, Christof Francke1,2

 
(1) TI Food & Nutrition (TIFN), Wageningen, The Netherlands
(2) Centre for Molecular and Biomolecular Informatics (CMBI), NCMLS, Radboud University Medical Centre, Nijmegen, The Netherlands
(3) Laboratory of Food Microbiology, Wageningen University and Research Centre, Wageningen, The Netherlands
(4) NIZO food research BV, Ede, The Netherlands


Correspondence
Mark de Been
mdebeen@cmbi.ru.nl
tel: +31 (0)24 3619827
fax: +31 (0)24 3619395
CMBI, NCMLS, Radboud University Nijmegen Medical Centre, PO box 9101, 6500 HB Nijmegen, The Netherlands
 

Supplementary tables & figures

 
01 - species abbreviations
 
02 - TCS classification and DNA-binding RRs
 
03 - RR family specific NJ trees
       OmpR family tree
       NarL family tree
       LytTR family tree
       other family trees
 
04 - phylogenetic footprints (and related TCSs)
       OmpR footprint01 (TCS31, PhoPR)        NarL footprint11 (TCS61, LiaRS)
       OmpR footprint02 (TCS29, ResDE)        NarL footprint12 (TCS57, YfiJK)
       OmpR footprint03 (TCS22, 23, HssRS)        NarL footprint13 (non B. cereus)
       OmpR footprint04 (TCS30)        NarL footprint14 (TCS60, YdfHI)
       OmpR footprint05 (TCS18, 19, BacRS)        NarL footprint15 (TCS56, YvfTU, DesKR)
       OmpR footprint06 (TCS13, 14, SpaRK)        LytTR footprint16 (TCS68, AgrCA)
       OmpR footprint07 (non B. cereus)        LytTR footprint17 (non B. cereus)
       OmpR footprint08 (TCS05, 06, VanRS)        LytTR footprint18 (TCS65, LytSR)
       OmpR footprint09 (TCS36, 37, 38, BceRS)        CitB footprint19 (TCS55, YufLM)
       OmpR footprint10 (TCS25, YkoGH)        Spo0A footprint20 (RR72, Spo0A)
 
05 - TCS minimal regulon predictions (TMRP) 06 - Additional TMRPs (and related TCSs)
       TMRP01        TMRP11        TMRP21 (TCS02, VanRS)
       TMRP02        TMRP12        TMRP22 (TCS15, YvrHG)
       TMRP03        TMRP13        TMRP23 (TCS16)
       TMRP04        TMRP14        TMRP24 (TCS24)
       TMRP05        TMRP15        TMRP25 (TCS25)
       TMRP06        TMRP16        TMRP26 (TCS32, YycFG)
       TMRP07        TMRP17        TMRP27 (TCS33, GlnKL)
       TMRP08        TMRP18        TMRP28 (TCS53, DctSR, CitST)
       TMRP09        TMRP19
       TMRP10        TMRP20