S2 Table. - PLOS

Table S2 – Primers used in this study Primer Primer Sequence (5’à3’) Name Primers for SOE Deletions ABD 796 ABD 797 ABD 798 ABD 799 CAH 009 CAH 010 CAH 011 CAH 012 ABD 767 ABD 768 ABD 769 ABD 770 ABD 927 ABD 928 ABD 929 ABD 930 BBC 081 BBC 082 BBC 083 BBC 084 BBC 285 BBC 286 BBC 287 BBC 288 CAH 050 CAH 051 CAH 052 CAH 053 CAH 095 CAH 096 CAH 097 CAH 098 CAH 100 CAH 101 CAH 102 CAH 103 CAH 105 CAH 106 CAH 107 CAH 108 BBC 717 ABD 340

TTAGAATCTGCGCCAGAAGCG gtcgacggatccccggaatCATAGCTGTTCCTTACTAGTTGC gaagcagctccagcctacaGTACTGGATCTGAAACCAGTTAAG GTATTGCGGAATGACCAGCATG TGATGTTCATGCTCTGCACC gtcgacggatccccggaatCATGCCCCGTTTTTCCTTTTG gaagcagctccagcctacaATTAAGTGAGTACAATGAGTCAAG GAAGGCATCGTTGTTAGATTGA TTAATTTGGATCCCTGCGACACTC gtcgacggatccccggaatCAAAAAACGTGAGGAGAATGCC gaagcagctccagcctacaTTCTTGAGCATTGCAAAGAAGC CTGGAACGAATGAAGAAGTCCAG GCAGAGAAAGGGTATCATTACTGG GcTAATTCAGTTTAAGCGGCCATCTTAAGTTCCCCCTATAG GATTTTTG ATGGCCGCTTAAACTGAATTAgCACATCAGGTGCTTTAGGC CAATTTG TACTCTCGTTTTTCGGCTTACTC AAGCAAGTTCACGTTTGCCG gtcgacggatccccggaatCATAACTTACACCTTACTCACCCAG gaagcagctccagcctacaGGAGATAAATAATCATGACTACGCC TAAAGTTCGCAACACGCC TCACTCTGCGTTTCTCATTGG gtcgacggatccccggaatCATAGCGGCCTCCCCCTGG gaagcagctccagcctacaTAATTTTTCCAGACTCATCCAAAAC AAAACCCAGACATTCTGCTG CTCTAATTCCGGAGAATCATCAG gtcgacggatccccggaatCATGCAGTAATGGATGCCTTG gaagcagctccagcctacaCTATAGGCCTAAACTAGAGAAGG GAGAGTCGCTTCAAACATGTTC CTGCACGTATTGTTGAACAAGAG gtcgacggatccccggaatCATTCAATTCCTCATCATTCTCTG gaagcagctccagcctacaTGATTTCACATTGCGTAACAGC GATCAGGAGCAGTACTATGAC CGATATTCGCACCATAGTGC gtcgacggatccccggaatGTATTGATCGTATGTAAGCGC gaagcagctccagcctacaCGGAATGACTAAATATCACTGATC CCATGGTAGAGTCAATATCGATC GAGATGCGTGAGCATCAGTTC gtcgacggatccccggaatCATTCGAGCGGTCACTCCTATTG gaagcagctccagcctacaCTTCTGTAACGCAAATTCCG GAGCAACGCACAGCATCAATC AAATAGATTTGGTGACTTTACCTCC gtcgacggatccccggaatACGTTTCATTAGTCACCTCTATTGTT AACTTGTTC

Description ∆CBP F1 ∆CBP R1 ∆CBP F2 ∆CBP R2 ∆SlmA F1 ∆SlmA R1 ∆SlmA F2 ∆SlmA R2 ∆ChiS F1 ∆ChiS R1 ∆ChiS F2 ∆ChiS R2 ∆VC0995 F1 ∆VC0995 R1 ∆VC0995 F2 ∆VC0995 R2 ∆VC0618-19 F1 ∆VC0618-19 R1 ∆VC0618-19 F2 ∆VC0618-19 R2 ∆rpoS F1 ∆rpoS R1 ∆rpoS F2 ∆rpoS R2 ∆rpoN F1 ∆rpoN R1 ∆rpoN F2 ∆rpoN R2 ∆rpoF F1 ∆rpoF R1 ∆rpoF F2 ∆rpoF R2 ∆rpoH F1 ∆rpoH R1 ∆rpoH F2 ∆rpoH R2 ∆rpoE F1 ∆rpoE R1 ∆rpoE F2 ∆rpoE R2 ∆VC1807 F1 ∆VC1807 R1

ABD 341 BBC 718 ABD 123 ABD 124

gaagcagctccagcctacaTAGTCGAAAATAAAAAAAAGAGGCTC GCCTC CTTTACGCCTGATTGTCTACAC ATTCCGGGGATCCGTCGAC TGTAGGCTGGAGCTGCTTC

∆VC1807 F2 ∆VC1807 R2 R R R R Kan , Spec , Amp , or Tm cassette F R R R R Kan , Spec , Amp , or Tm cassette R

Primers for Colony PCR ABD 725 CAH 023 BBC 085 BBC 289 CAH 054 CAH 099 CAH 104 CAH 109

GAAGCAGCTCCAGCCTACA GGTGATTTCCAGATTGAGTGC AACTTCCCAACCCTTTGG CAGCTGAGCTTAATTCCTG GTCGAACCAATTTATCCACC CGCTAGAGTCAAACTACTTAGAG CAGGTGCTTCAGTTCTTCGTC GCTTCCAGCAAGAGGAATGG

CKP 043

TCACTTAATCTGTGCACTTAGCAG

CKP 045 CKP 097 CKP 119 CKP 042 CKP 044 BBC 895 ABD 769

GAAGGGGCTTCACGCATtg AAGCAAGTTGGCGTGTCCac CGCTAAGCAAGTTGGCGTGTCta TTTGAAGGCTTAATTGAGgcg GAAGAATCCTTGATGTCGga TTGAATCGCTTTGTGgaa gaagcagctccagcctacaTTCTTGAGCATTGCAAAGAAGC

CKP 053 CKP 054 ABD 797 CKP 052

GTTTAGCTAGGTTtaaTAGTGTTTctg GGTACGGTTTAGCTAGGTTtaa gtcgacggatccccggaatCATAGCTGTTCCTTACTAGTTGC AGCCATTATCAAACAAGTAGCTAAACCGTA

F oligo to detect all SOE mutants ∆slmA detect R (401 bp) ∆VC0618-19 detect R (780 bp) ∆rpoS detect R (225 bp) ∆rpoN detect R (254 bp) ∆rpoF detect R (176 bp) ∆rpoH detect R (240 bp) ∆rpoE detect R (447 bp) R oligo to detect all SlmA point mutants SlmA T31A F (520 bp) SlmA E43A F (487 bp) SlmA E43K F (487 bp) SlmA F63A F (420 bp) SlmA R71D F (400 bp) SlmA R173E F (90 bp) Scrambled SBS detect F st 1 conserved SBS site scrambled R nd 2 conserved SBS site scrambled R ∆SBS detect R ∆SBS detect F

Primers for Transcriptional Reporter Constructs ABD332 BBC219 BBC218 BBC262 BBC266 BBC267 BBC252 BBC254 ABD255 ABD256 BBC817 BBC821 CKP210

GGCTGAACGTGGTTGTCGAAAATGAC GTTTATTTTTGTCGACTGTACAGCGTTTAAATAGAGGTCG ATATTGACCC CGCTGTACAGTCGACAAAAATAAAC TACCGAGGACGCGAAGCTG CAGCTTCGCGTCCTCGGTAGAATAAAGCAATCCGCAAGCG CCCGGGATCCTGTGTGAAATTGAGTTGCTTTCATTTCACTA ATGG CAATTTCACACAGGATCCCGGGAGGAGGTAACGTAATGCG TAAAGGAGAAGAAC tgtaggctggagctgcttcTTAGTTGTATAGTTCATCCATGCC gaagcagctccagcctacaCCACAATAAGCCAGAGAGCCTTAAG CCCAAATACGGCAACTTGGCG ttgagtaagtgagcgctcacttactataatgtgtggAATTGTGAGCGGAT AACAATTTCA ccacacattatagtaagtgagcgctcacttactcaaCTCATTAGGCACCC CAGGC TGACCATTTAGAGATGCTAGGTTTGTTAGTGTTTACTTAC

∆lacZ F1 (Up Arm) ∆lacZ R1 (Up Arm) R

Kan F (Middle Arm) R Kan R (Middle Arm) Pchb F (Middle Arm) Pchb R (Middle Arm) GFP F (Middle Arm) GFP R (Middle Arm) ∆lacZ F2 (Down Arm) ∆lacZ R2 (Down Arm) Synthetic SBS-GFP DNA biding reporter F2 Synthetic SBS-GFP DNA biding reporter R1 Pchb 612-724 lacZ swap R1

CKP212 CKP213 CKP215

ACATTCCTGTACCGAACGGGAATTGCAATTGATAAATTTC ACTAACAAACCTAGCATCTCTAAATGGTCAGTGGCG AATTGCAATTCCCGTTCGGTACAGGAATGTGCGCCCAAG

Pchb 612-724 lacZ swap F2 112 bp lacZ intergenic F 112 bp lacZ intergenic R

Primers for SlmA Mutants CKP 040 CKP 041 CKP 095 CKP 096 CKP 117 CKP 118 CKP 036 CKP 037 CKP 038 CKP 039 BBC 894 BBC 893 CAH0009 BBC768 BBC770 BBC771 BBC769 CAH0012

GAAGGGGCTTCACGCATCgCgACCGCAAAACTCGCTAAGCA AG GCGAGTTTTGCGGTcGcGATGCGTGAAGCCCCTTCATTG TGGCGTGTCCGcAGCCGCGCTGTATCGCCATTTCCCGAGC TGGCGATACAGCGCGGCTgCGGACACGCCAACTTGCTTAG TGGCGTGTCCaAAGCCGCGCTGTATCGCCATTTCCCGAGC TGGCGATACAGCGCGGCTTtGGACACGCCAACTTGCTTAG TGAAGGCTTAATTGAGgcgATTGAAGAATCCTTGATGTCG AGGATTCTTCAATcgcCTCAATTAAGCCTTCAAACATACG GAATCCTTGATGTCGgaTATCAACCGCATCTTTGATGAAG GATGCGGTTGATAtcCGACATCAAGGATTCTTCAAT GGCAGTTTGAATCGCTTTGTGgaaTCTGATTTCAAATATCT GCC GGCAGATATTTGAAATCAGAttcCACAAAGCGATTCAAACT GCC TGATGTTCATGCTCTGCACC GCCCCGTTTTTCCTTTTGG ccaaaaggaaaaacggggcATGGCAGAAAAACAAACTGC gctgtatttatcttgactcattgtacTTcAtTGtAACTGTGCCGCAATTA G GTACAATGAGTCAAGATAAATACAGC GAAGGCATCGTTGTTAGATTGA

SlmA T31A F2 SlmA T31A R1 SlmA E43A F2 SlmA E43A R1 SlmA E43K F2 SlmA E43K R1 SlmA F63A F2 SlmA F63A R1 SlmA R71D F2 SlmA R71D R1 SlmA R173E F2 SlmA R173E R1 Replace Vc slmA with Ec slmA F1 Replace Vc slmA with Ec slmA R1 Replace Vc slmA with Ec slmA (middle) F Replace Vc slmA with Ec slmA (middle) R Replace Vc slmA with Ec slmA F2 Replace Vc slmA with Ec slmA R2

Primers for Pchb Modifications CKP 102 CKP 101 CKP 049 CKP 048 BBC 266 BBC 609 BBC 608

gtaagtgagcgctcacttacCTAGCTAAACCGTACCCGTTTTG gtaagtgagcgctcacttacTTATTTGGCCTTGTTTGATAATGG ATTATCAAACAAGGCCAAATAAGTAcagAAACACTAttaAAC CTAGCTAAACCGTACCCG GGGTACGGTTTAGCTAGGTTtaaTAGTGTTTctgTACTTATT TGGCCTTGTTTGATAATG CAGCTTCGCGTCCTCGGTAGAATAAAGCAATCCGCAAGCG cccgggatcctgtgtgaaattgCCTAGCGGCAATTCAAGTTGC cccgggatcctgtgtgaaattgCTGAGTTATATTTGCGAGATCTCG C

BBC 606 CKP 001 CKP 071 CKP 072 BBC 267 CKP 073 BBC 607 CKP 084

cagcttcgcgtcctcggtaGAGATTGCGAAGGGAGTCAC cccgggatcctgtgtgaaattgCTTATTTGGCCTTGTTTGATAATG cccgggatcctgtgtgaaattgGTGATTCAACTCGCAAAACGGG cccgggatcctgtgtgaaattgCTTTGGCAGGAGTAAGAAAACACC TAG CCCGGGATCCTGTGTGAAATTGAGTTGCTTTCATTTCACTA ATGG cagcttcgcgtcctcggtaCAGGCTAGTGAGCGAGATCT cagcttcgcgtcctcggtaTACAGGCCACTCATGACTCC cccgggatcctgtgtgaaattgGACCTACCTCATCACTTTTACCC

Pchb E. coli SBS F Pchb E. coli SBS R Pchb Scrambled SBS F Pchb Scrambled SBS R Pchb P1 only and P1+P2 F Pchb P1 only R Pchb P1+P2 R Pchb P2 only, P2+SBS, P2+SBS more space, P2+P3, P3 only more space, ∆hairpin F Pchb P2 only R Pchb P2+SBS R Pchb P2+SBS more space and P2+P3 internal region R Pchb P2+P3 and P3 only R Pchb P2+P3 internal region and P3 only more space F Pchb P3 only F Pchb ∆hairpin R

CKP 106 CKP 105 CKP 108 CKP 107 CKP 104 CKP 103 CKP 110 CKP 109 CKP 136 CKP 135 CKP 138 CKP 137 CKP 132 CKP 131 CKP 134 CKP 133 BBC 968 BBC 967 BBC 966 BBC 965 CKP 128 CKP 127 CKP 130 CKP 129 CKP 124 CKP 123 CKP 126

AACAAGGCCAAAGTAAGTAAACACTAACAAACtaaCTAGCT AAACCGTACCCG ttagtttgttagtgtttacttacTTTGGCCTTGTTTGATAATGGC GCCAAATAActaGTAAGTAAACACTAACAAACGCTAAACCG TACCCGTTTTG AGCGTTTGTTAGTGTTTACTTACtagTTATTTGGCCTTGTT TGATAATGG GGCCAGTAAGTAAACACTAACAAACaataaCTAGCTAAACCG TACCCGTTTTG GCTAGttattGTTTGTTAGTGTTTACTTACTGGCCTTGTTTGA TAATGGC GGCCAAATAActagcGTAAGTAAACACTAACAAACTAAACCG TACCCGTTTTGCG GGTTTAGTTTGTTAGTGTTTACTTACgctagTTATTTGGCCT TGTTTGATAATGG GTAAGTAAACACTAACAAACccaaataaCTAGCTAAACCGTA CCCG ttatttggGTTTGTTAGTGTTTACTTACCCTTGTTTGATAATG GCTCTTTGCC ctagctaaGTAAGTAAACACTAACAAACACCGTACCCGTTTTG CGAGTTGAATC GTTTGTTAGTGTTTACTTACttagctagTTATTTGGCCTTGTT TGATAATGGC GTAAGTAAACACTAACAAACgccaaataaCTAGCTAAACCGT ACCCG ttatttggcGTTTGTTAGTGTTTACTTACCTTGTTTGATAATG GCTCTTTGCC ctagctaaaGTAAGTAAACACTAACAAACCCGTACCCGTTTTG CGAGTTGAATC GTTTGTTAGTGTTTACTTACtttagctagTTATTTGGCCTTGT TTGATAATGGC ATTATCAAACAAGTAAGTAAACACTAACAAACggccaaataa CTAGCTAAACCGTACCCG TTAGCTAGttatttggccGTTTGTTAGTGTTTACTTACTTGTTT GATAATGGCTCTTTGC GCCAAATAActagctaaacGTAAGTAAACACTAACAAACCGTA CCCGTTTTGCGAGTTG GGGTACGGTTTGTTAGTGTTTACTTACgtttagctagTTATTT GGCCTTGTTTGATAATG GTAAGTAAACACTAACAAACaggccaaataaCTAGCTAAACCG TACCCG ttatttggcctGTTTGTTAGTGTTTACTTACTGTTTGATAATGG CTCTTTGCC ctagctaaaccGTAAGTAAACACTAACAAACGTACCCGTTTTG CGAGTTGAATC GTTTGTTAGTGTTTACTTACggtttagctagTTATTTGGCCTTG TTTGATAATGGC GTAAGTAAACACTAACAAACaaggccaaataaCTAGCTAAACC GTACCCG ttatttggccttGTTTGTTAGTGTTTACTTACGTTTGATAATGGC TCTTTGCC ctagctaaaccgGTAAGTAAACACTAACAAACTACCCGTTTTGC GAGTTGAATC

Pchb -3 SBS F Pchb -3 SBS R Pchb +3 SBS F Pchb +3 SBS R Pchb -5 SBS F Pchb -5 SBS R Pchb +5 SBS F Pchb +5 SBS R Pchb -8 SBS F Pchb -8 SBS R Pchb +8 SBS F Pchb +8 SBS R Pchb -9 SBS F Pchb -9 SBS R Pchb +9 SBS F Pchb +9 SBS R Pchb -10 SBS F Pchb -10 SBS R Pchb +10 SBS F Pchb +10 SBS R Pchb -11 SBS F Pchb -11 SBS R Pchb +11 SBS F Pchb +11 SBS R Pchb -12 SBS F Pchb -12 SBS R Pchb +12 SBS F

CKP 125

GTTTGTTAGTGTTTACTTACcggtttagctagTTATTTGGCCTT GTTTGATAATGGC

Pchb +12 SBS R

Primers for Overexpression Constructs BBC 772 BBC 773 BBC 1236 BBC 577 CKP 224 CKP 225

caatttcacacaggatcccgggAGGAGGTaacgtaATGGCCGGCAAT AAAAAAATC tgtaggctggagctgcttcTCACTTAATCTGTGCACTTAGC caatttcacacaggatcccgggAGGAGGTaacgtaATGTTTAGGTTC TATCGAAAACAA tgtaggctggagctgcttcTTATTCACTGGTCAGGAGTTTTTGC tgtaggctggagctgcttcTTAtttgtcatcgtcatccttataatc tgtaggctggagctgcttcTCACTTtttgtcatcgtcatc

Ptac-SlmA F Ptac-SlmA R Ptac-ChiS F Ptac-ChiS R Ptac ChiS FLAG tag R Ptac SlmA FLAG tag R

Primers for Vector Cloning CKP 046 CKP 047 CKP 076

tatatatacatATGGCCGGCAATAAAAAAAT tatatataggatccTCACTTAATCTGTGCA tatatagaattcaggaggtaacgtaATGGCCGGCAATAAAAAAATC

SlmA NdeI F SlmA BamHI R SlmA EcoRI F

Primers for EMSA Probes BBC 744 CKP 072 BBC 928 BBC 929 ABD 009 ABD 010

cagcttcgcgtcctcggtaCGCAAATATAACTCAGGCAAAG cccgggatcctgtgtgaaattgCTTTGGCAGGAGTAAGAAAACACC TAG CAAATATATCCTCCTCACTATTTTG AACATCACCATCTAATTCAACAAG TATATGCCTTTAGGCATTAACTGTACTTCCGTC TGAAGTCATCTTGATTGACAAGTCTCCATCGAATG

Pchb SBS F Pchb SBS R Ec SBS Repression Reporter F Ec SBS Repression Reporter R PnanH F PnanH R

Primers for qRT PCR BBC 989 BBC 990 BBC 918 BBC 919 ABD 132 ABD 133

GCATCTAGGTTTTGACGTTTTTAACG AACACTCTCCAAGACCTACCTC AGTAATCGCAGCAGCAACCAG GGTTCATAGATAAAGTCGGTGGTTG CTGTCTCAAGCCGGTTACAA TTTCTACCAGTGCAGAGATGC

Uninduced transcript F Uninduced transcript R Induced transcript F Induced transcript R rpoB F rpoB R

Primers for 5’ RACE BBC969 BBC970

GATTACGCCAAGCTTCTGGTAACCCACTTGTTGATACCACG GATTACGCCAAGCTTAGCAGGCCGAAAGAGTAAACCACG

GSP1 – for Pchb 5’ RACE NGSP1 – for Pchb 5’ RACE

Primers for FLAG Tag Fusions CKP 220 CKP 221 CKP 237 CKP 238



ggtgactacaaggatcacgacattgattataaggatgacgatgacaaaAAGT GAGTACAATGAGTCAAGATAAATACA ataatcaatgtcgtgatccttgtagtcaccatcatggtctttataatcAATCTGT GCACTTAGCAGCG GTGAAgattataaggatgacgatgacaaaTAAAGCAATCCGCAAGC GAG CTTTAtttgtcatcgtcatccttataatcTTCACTGGTCAGGAGTTTT TG

SlmA-3x FLAG F SlmA-3x FLAG R ChiS-1x FLAG F ChiS-1x FLAG R