Table S7 Potential CtrA‐regulated genes in fully sequenced Wolbachia strains wOo locus name wBm locus name Total # CtrA binding sites 125 115 # genes adjacent to a CtrA 34 40 binding site wOo_01470 DNA polymerase III delta subunit Wbm0170 Preprotein translocase subunit SecG wOo_01880 50S ribosomal protein L25 Wbm0295 Protein chain release factor B wOo_02570 preprotein translocase subunit SecA Wbm0343 Translation elongation factor EF‐Tu, GTPase wOo_05860 protein chain release factor B Wbm0393 DNA‐directed RNA polymerase sigma 70 subunit, RpoD Translation/ Protein synthesis wOo_06100 methionyl‐tRNA synthetase Wbm0464 Seryl‐tRNA synthetase wOo_00730 cysteinyl‐tRNA synthetase (@start) Wbm0528 Transcription termination factor, rho wOo_01850 tRNA‐His wOo_08210 transcription termination factor Rho wOo_02540 small protein A tmRNA‐binding wOo_06430 DNA polymerase I Wbm0171 RadC‐like DNA repair protein wOo_05460 CtrA response regulator Wbm0305 Ribonuclease HI Wbm0596 CtrA response regulator DNA replication /repair

wOo_04550 bifunctional GMP synthaseglutamine amidotransferase protein Wbm0101 2‐methylthioadenine synthetase wOo_04050 aspartate carbamoyltransferase catalytic subunit (@start) Wbm0142 Predicted phosphatase wOo_07980 putative glycerol‐3‐phosphate acyltransferase Pls X (@start) Wbm0446 Dihydroorotase, PyrC wOo_04140 S‐adenosyl‐methyltransferase MraW Wbm0588 Acetyl‐CoA carboxylase, carboxyltransferase component wOo_00570 SAM‐dependent methyltransferase Wbm0017 NADH:ubiquinone oxidoreductase 17.2 kD subunit wOo_02300 NADH dehydrogenase I subunit F Wbm0517 Nitroreductase wOo_02550 ribonucleotide‐diphosphate reductase subunit beta Wbm0597 Glycerol‐3‐phosphate dehydrogenase wOo_03050 Signal peptidase I Wbm0735 Citrate synthase wOo_05030 dihydroorotate dehydrogenase 2 wOo_05450 glycerol‐3‐phosphate dehydrogenase Metabolism wOo_06790 phosphatidylglycerophosphate synthase wOo_06800 malic enzyme wOo_07780 UDP‐N‐acetylmuramyl pentapeptide synthase wOo_09340 citrate synthase

wOo_05870 MgCoNi transporter MgtE Wbm0447 Ankyrin repeat‐containing protein and possible domain WF‐3 wOo_01800 putative monovalent cationH+ antiporter subunit B (@start) Wbm0294 Mg/Co/Ni transporter MgtE wOo_06290 membrane protease subunit stomatinprohibitin‐like protein Wbm0670 Uncharacterized conserved protein, YebC family ABC‐type protease secretion system ATPase and permease component wOo_08410 Wbm0016 Multisubunit Na+/H+ antiporter, MnhD subunit AprD ABC‐type transport system involved in resistance to organic solvents wOo_09650 Wbm0175 ABC‐type Mn2+/Zn2+ transport system, permease component Membrane associated auxiliary component Wbm0293 ABC‐type phosphate transport system, periplasmic component Wbm0296 Ankyrin repeat‐containing protein Wbm0394 Ankyrin repeat‐containing protein Wbm0463 Predicted membrane‐associated or secreted protein Wbm0768 Membrane protease subunit, stomatin/prohibitin homolog Wbm0060 Predicted protein

Phage‐related

wOo_00580 hypothetical protein Wbm0109 Predicted protein wOo_06270 hypothetical protein Wbm0141 Predicted protein wOo_07770 hypothetical protein Wbm0274 Predicted protein wOo_10100 hypothetical protein Wbm0659 Predicted protein Wbm0085 Predicted protein Wbm0089 Predicted protein Unknown Function Wbm0484 Predicted protein Wbm0659 Predicted protein Wbm0712 Predicted protein Wbm0752 Predicted protein WF‐3 Wbm0767 Predicted protein Wbm0516 Uncharacterized conserved protein

Listed locus IDs identified as containing a CtrA‐binding site if either 8‐mer or 9‐mer consensus sequences found within ‐450bp upstream of the start of an annotated ORF, regardless of +/‐ strand orientation Blue entries indicate the 8‐mer consensus TTAACCAT Black entries indicate the 9‐mer consensus TTAA(N7)TTAAC (@start) = consensus site positioning corresponds with start of the ORF/locus indicated

19 SI S. Christensen and L.R. Serbus Table S7 continued wPip Pel locus name wHa locus name 109 98 49 53 WPa_0077 cysteinyl‐tRNA synthetase (@start) wHa_03030 lepA, Elongation factor 4 WPa_0671 rpmE, ribosomal protein L31 wHa_04750 prfB, Peptide chain release factor 2 WPa_0561 tuf, translation elongation factor Tu wHa_00240 serS, Seryl‐tRNA synthetase WPa_0829 truB, trna pseudouridine synthase b wHa_06730 rho, Transcription termination factor Rho

WPa_0215 transposase wHa_10010 priA, Primosomal protein N', superfamily II helicase WPa_0585 two component transcriptional regulator (ctrA) wHa_07740 uvrA, Excinuclease ABC, subunit A WPa_0766 primosomal protein N wHa_00600 ruvC, Crossover junction endodeoxyribonuclease RuvC WPa_0769 recR, recombination protein RecR wHa_06210 ctrA, Two component transcriptional regulator WPa_1146 ruvC, crossover junction endodeoxyribonuclease

WPa_0151 Antioxidant, AhpC/Tsa family wHa_01350 Ferredoxin, 4Fe‐4S WPa_0211 haloacid dehalogenase‐like hydrolase wHa_05350 coxB, Cytochrome c oxidase subunit 2 WPa_0721 asd, aspartate‐semialdehyde dehydrogenase wHa_06300 era, GTP‐binding protein Era (@start)

WPa_0801 purC, phosphoribosylaminoimidazole‐succinocarboxamide synthase wHa_06810 Cytochrome c family protein

WPa_0942 O‐methyltransferase family protein wHa_08560 purC, Phosphoribosylaminoimidazole‐succinocarboxamide synthase

WPa_1060 multiple resistance and ph regulation protein f wHa_09740 pgk, Phosphoglycerate kinase WPa_0431 Putative virulence factor RhuM protein wHa_10900 sucA, 2‐oxoglutarate dehydrogenase E1 component WPa_0526 peptidyl‐prolyl cis‐trans isomerse D, putative wHa_02160 UDP‐N‐acetylglucosamine pyrophosphorylase‐related protein WPa_0570 clpP, ATP‐dependent Clp protease, proteolytic subunit ClpP wHa_02630 Putative siRNA binding protein (contains 2PAZ domains)

murG, UDP‐N‐acetylglucosamine‐‐N‐acetylmuramyl‐(pentapeptide) WPa_0574 polysaccharide deacetylase, putative wHa_05250 pyrophosphoryl‐undecaprenol N‐acetylglucosamine transferas

WPa_0575 Mg chelatase‐related protein wHa_05350 coxB, Cytochrome c oxidase subunit 2 WPa_0584 glycerol‐3‐phosphate dehydrogenase (NAD+) wHa_06110 Polysaccharide deacetylase, putative WPa_0634 cytochrome b561 wHa_06120 Mg chelatase‐related protein

murG, UDP‐N‐acetylglucosamine‐‐N‐acetylmuramyl‐(pentapeptide) WPa_0898 wHa_06200 gpsA, Glycerol‐3‐phosphate dehydrogenase pyrophosphoryl‐undecaprenol N‐acetylglucosamine transferase

WPa_0983 gltA, citrate synthase wHa_06750 Peptidyl‐prolyl cis‐trans isomerase D, putative WPa_1017 nadh dehydrogenase (quinone) wHa_08170 nuoF, NADH:ubiquinone oxidoreductase subunit F WPa_1018 NADH:ubiquinone oxidoreductase wHa_08570 purM, Phosphoribosylformylglycinamidine cyclo‐ligase wHa_09250 Putative NADH:ubiquinone oxidoreductase subunit wHa_09260 NADH‐ubiquinone oxidoreductase family protein wHa_09630 gltA, citrate synthase WPa_0296 Ankyrin repeat domain protein wHa_02680 Ankyrin repeat domain protein WPa_0801 putative membrane protein (@start) wHa_03370 Ankyrin repeat domain protein WPa_1264 major facilitator family transporter wHa_04740 Magnesium transporter MgtE WPa_1376 mgtE, magnesium transporter wHa_08650 Permease, putative WPa_0296 Ankyrin repeat domain protein wHa_04820 Cation ABC transporter, permease protein, putative WPa_0765 putative membrane protein wHa_08640 Permease, putative wHa_08650 Permease, putative

WPa_0430 putative phage related protein wHa_08510 Putative phage terminase WPa_1313 Putative phage related protein wHa_09480 Putative phage terminase WPa_1355 Putative outer membrane protein (porin superfamily)

WPa_0212 Hypothetical protein wHa_04520 hypothetical protein WPa_0224 Hypothetical protein wHa_08410 hypothetical protein WPa_0528 conserved hypothetical protein wHa_00230 hypothetical protein WPa_0641 Hypothetical protein wHa_00330 hypothetical protein WPa_0943 Hypothetical protein wHa_01090 hypothetical protein WPa_0275 (conserved hypothetical protein @start) wHa_02430 hypothetical protein WPa_0686 conserved hypothetical protein wHa_04610 hypothetical protein WPa_0198 hypothetical protein wHa_05260 hypothetical protein WPa_0685 hypothetical protein wHa_06070 hypothetical protein WPa_0828 hypothetical protein wHa_06080 hypothetical protein WPa_0838 hypothetical protein wHa_06130 hypothetical protein WPa_0839 hypothetical protein wHa_06740 hypothetical protein WPa_0897 hypothetical protein wHa_08580 hypothetical protein WPa_1266 hypothetical protein wHa_08630 hypothetical protein wHa_09590 hypothetical protein wHa_09770 hypothetical protein

20 SI S. Christensen and L.R. Serbus Table S7 continued wNo locus name wRi locus name 109 120 48 55 wNo_02380 rpmE, 50S ribosomal protein L31 wRi_001440 dnaQ, DNA polymerase III, epsilon subunit wNo_10050 pvfB, Peptide chain release factor 2 wRi_004150 Protein chain release factor B wNo_02650 tuf1,Elongation factor Tu 1 wRi_002950 GTP‐binding protein LepA wNo_04870 truB, tRNA pseudouridine synthase B wRi_008350 rpmE, ribosomal protein L31 wRi_009070 ribosomal slippage (transopase IS5 family) wRi_00260 seryl‐tRNA synthetase wRi_006360 rho, Transcription termination factor Rho wRi_006380 peptidyl‐prolyl cis‐trans isomerse D, putative

wNo_02120 RNA‐directed DNA polymerase wRi_011780 priA, Primosomal protein N', superfamily II helicase wNo_10780 topA, DNA topoisomerase wRi_008740 uvrA, excinuclease ABC, A subunit wNo_01920 putative transposase wRi_001110 ruvC, crossover junction endodeoxyribonuclease RuvC wNo_02870 ctrA, transcriptional regulator wRi_007780 transposase wNo_03500 dnaE, DNA polymerase III, alpha subunit wRi_009640 transposase wNo_08060 ruvC, crossover junction endodeoxyribonuclease RuvC wRi_006620 radC, DNA repair protein wRi_007440 ctrA, cell cycle transcriptional regulator wNo_00590 NUDIX hydrolase wRi_001570 ferredoxin, 4Fe‐4S wNo_03830 asd, Aspartate‐semialdehyde dehydrogenase wRi_004830 coxB, cytochrome c oxidase, subunit II wNo_03880 surE, 5'‐nucleotidase surE wRi_007720 cytochrome c family protein

wNo_05400 purC, Phosphoribosylaminoimidazole‐succinocarboxamide synthase wRi_010490 purC, Phosphoribosylaminoimidazole‐succinocarboxamide synthase

murG,UDP‐N‐acetylglucosamine‐‐N‐acetylmuramyl‐(pentape ptide) wNo_05810 Toluene tolerance family protein wRi_004740 pyrophosphoryl‐undecaprenol N‐acetylglucosamine

wNo_05820 Putative polyketide cyclase/dehydrase and lipid transport family protein wRi_005730 UDP‐N‐acetylglucosamine pyrophosphorylase‐related protein

wNo_05850 O‐methyltransferase family protein wRi_006610 polysaccharide deacetylase, putative wNo_06180 Multiple resistance and pH regulation protein F wRi_007450 gpsA, glycerol‐3‐phosphate dehydrogenase (NAD+) wNo_06790 Citrate synthase wRi_009240 nuoF, NADH dehydrogenase I, F subunit

wNo_01910 Peptidyl‐prolyl cis‐trans isomerase D, putative wRi_009870 gltA, citrate synthase

wNo_02100 UDP‐N‐acetylglucosamine pyrophosphorylase‐related protein wRi_010390 UDP‐N‐acetylglucosamine pyrophosphorylase‐related protein wNo_02860 gpsA, Glycerol‐3‐phosphate dehydrogenase wNo_04550 ftsH, ATP‐dependent zinc metalloprotease FtsH wNo_05030 NADH:ubiquinone oxidoreductase wNo_05040 Nadh dehydrogenase (Quinone) wNo_06790 Citrate synthase wNo_07810 psd, Phosphatidylserine decarboxylase proenzyme

wNo_03920 Ankyrin repeat domain protein wRi_010690 permease, putative wNo_04240 Ankyrin repeat domain protein wRi_003070 ankyrin repeat domain protein wNo_04610 Putative membrane protein (@start) wRi_006090 ankyrin repeat domain protein wNo_10040 mgtE, magnesium transporter wRi_004140 Mg/Co/Ni transporter MgtE wNo_10640 Ankyrin repeat domain protein wRi_004240 cation ABC transporter, permease protein

wNo_11300 Ankyrin repeat domain and putative OTU‐like cysteine protease wRi_004830 coxB, cytochrome c oxidase, subunit II

wNo_07820 Ankyrin repeat domain protein wRi_010690 permease, putative wNo_10490 Putative outer membrane protein wRi_012820 putative monovalent cation/H+ antiporter subunit D

wRi_006590 phage uncharacterized protein wRi_009740 phage uncharacterized protein wRi_005470 baseplate assembly protein J, putative wRi_010130 baseplate assembly protein J, putative wNo_01610 hypothetical protein wRi_001450 hypothetical protein wNo_01930 hypothetical protein wRi_002970 hypothetical protein wNo_10480 hypothetical protein wRi_003850 hypothetical protein wNo_02910 hypothetical protein (@start) wRi_003900 hypothetical protein wNo_03370 hypothetical protein wRi_005830 hypothetical protein wNo_03840 hypothetical protein wRi_006370 hypothetical protein wNo_05840 hypothetical protein wRi_00250 hypothetical protein wNo_08880 hypothetical protein (@start) wRi_00360 hypothetical protein wNo_00230 hypothetical protein wRi_001260 hypothetical protein wNo_04860 hypothetical protein wRi_003990 hypothetical protein wNo_04960 hypothetical protein wRi_004750 hypothetical protein wNo_07950 hypothetical protein wRi_006370 hypothetical protein wNo_09620 hypothetical protein wRi_007530 hypothetical protein wRi_009810 hypothetical protein wRi_009910 hypothetical protein wRi_011460 hypothetical protein wRi_012810 hypothetical protein

21 SI S. Christensen and L.R. Serbus Table S7 continued wMel locus name 111 53 WD_0477 lepA, GTP‐binding protein WD_0870 ribosomal protein L31, putative WD_0464 valS, valyl‐tRNA synthetase WD_0794 rho, Transcription termination factor Rho

WD_0916 uvrA, excinuclease ABC, A subunit WD_0732 ctrA, cell cycle transcriptional regulator

WD_0093 ferredoxin, 4Fe‐4S WD_0301 coxB, cytochrome c oxidase, subunit II WD_0740 cydA, cytochrome d ubiquinol oxidase, subunit I WD_0803 cytochrome c family protein murG, UDP‐N‐acetylglucosamine‐‐N‐acetylmuramyl‐(pentapeptide) WD_0323 pyrophosphoryl‐undecaprenol N‐acetylglucosamine transferase WD_0611 UDP‐N‐acetylglucosamine pyrophosphorylase‐related protein WD_0720 polysaccharide deacetylase, putative WD_0721 Mg chelatase‐related protein WD_0731 gpsA, glycerol‐3‐phosphate dehydrogenase (NAD+)

WD_1151 gltA, citrate synthase

WD_0375 mgtE, magnesium transporter WD_0438 ankyrin repeat domain protein WD_0621 membrane protein, putative WD_1033 permease, putative WD_1034 membrane protein, putative WD_1033 permease, putative WD_1107 Na+/H+ antiporter subunit, putative

WD_0644 prophage LambdaW5, minor tail protein Z, putative WD_1016 phage uncharacterized protein WD_0283 prophage LambdaW1, baseplate assembly protein J, putative

WD_0299 hypothetical protein WD_0484 conserved hypothetical protein WD_0736 hypothetical (@start) WD_0742 hypothetical (@start) WD_0808 hypothetical protein WD_0810 hypothetical protein WD_1307 hypothetical protein WD_1308 hypothetical protein WD_0041 hypothetical protein WD_0127 hypothetical protein WD_0268 hypothetical protein WD_0289 hypothetical protein WD_0324 hypothetical protein WD_0390 conserved domain protein WD_0465 hypothetical protein WD_0716 hypothetical protein WD_0717 conserved hypothetical protein WD_0722 hypothetical protein WD_0811 hypothetical protein WD_1025 conserved domain protein WD_1030 hypothetical protein WD_1031 hypothetical protein WD_1092 hypothetical protein WD_1106 conserved hypothetical protein WD_1147 hypothetical protein WD_1161 hypothetical protein WD_1171 hypothetical protein

22 SI S. Christensen and L.R. Serbus