table s1 single nucleotide mutations and deletions in...

TABLE S1 Single nucleotide mutations and deletions in pilus-deficient strainsMutation(+ strand)

Strain Nbr Positionin Lr GGgenome

From To Gene Codonchange

Aa change Strand

PB11 1 17025 C T LGG_00019, putative protein GTA → ATA Val → Ile -PB11 2 29051 C T LGG_00030, mono-oxygenase GTC → GTT Silent +PB11 3 32531 C T LGG_00032, ABC-transporter permease ATG → ATA Met → Ile -PB11 4 153222 G A LGG_00138, nrdD, anaerobic ribonucleoside

triphosphate reductaseCGC → CAC Arg → His +

PB11 5 220227 G A LGG_00207, phosphohydrolase, MutT/nudixfamily

GTC → ATC Val → Ile +

PB11 6 220666 G A LGG_00208, conserved protein GAT → AAT Asp → Asn +PB11 7 257316 G A Intergenic, after LGG_00255 (-), after

LGG_00254 (+)PB11 8 283205 G A LGG_00278, conserved protein GGC → GAC Gly → Asp +PB11 9 288659 G A LGG_00283, eps2 GGG → GGA Silent +PB11 10 320739 G A LGG_00319, α/β hydrolase superfamily protein CGC → TGC Arg → Cys -PB11 11 338773 G A LGG-00333, agaS, tagatose-6-phosphate

ketose/aldose isomeraseCGC → CAC Arg → His +

PB11 12 365382 C T LGG_00358, pepT, peptidase T GAT → AAT Asp → Asn -PB11 13 390606 C T LGG_00382, penicillin-binding protein 3 CCG → CCA Silent -PB11 14 403186 C T LGG_00398, transaldolase ATC → ATT Silent +PB11 15 443188 C T LGG_00441, srtC1 TGG → TAG Trp → STOP -PB11 16 554293 C T Intergenic, after LGG_00547 (ABS-transp.

ATP-binding), before LGG_548 (resD, two-component response regulator) (+)

PB11 17 564835 C T LGG_00557, xylP, transporter major facilitatorsuperfamily MFS_1, Na/xyloside symporter

CTG → CTA Silent -

PB11 18 579146 C T LGG_00573, yecS, amino acid ABC transporterpermease

ATG → ATA Met → Ile -

PB11 19 648935 G A LGG_00636, endA, DNA-entry nuclease GTC → GTT Silent -PB11 20 732466 C T LGG_00722, fthC, 5-formyltetrahydrofolate

cyclo-ligaseGAG → GAA Silent -

PB11 21 789704 G A LGG_00777, dltA, D-alanine--poly(phosphoribitol) ligase subunit 1

AAG → AAA Silent +

PB11 22 880842 C T LGG_00874, guaC, GMP reductase ATG → ATA Met → Ile -PB11 23 917809 C T Intergenic, before LGG_00914 (+, conserved),

before is34 (-)PB11 24 987489 G A LGG_00976, pacL, cation transporting ATPase AAC → AAT Silent -PB11 25 1117746 G A Intergenic, after LGG_01116 (+)PB11 26 1144533 C T LGG_01146, putative without homology GCC → ACC Ala → Thr -PB11 27 1171695 G A Intergenic, after LGG_001173 (+, sua), before

LGG_01174 (glyA)PB11 28 1192855 G A LGG_01200, sufD, Fe-S cluster assembly ABC

transporter permeaseGTC → ATC Val → Ile +

PB11 29 1200610 G A LGG_01208, usp, universal stress proteinfamily

CTC → TTC Leu → Phe -

PB11 30 1225557 C T LGG_01236, conserved GGT → GAT Gly → Asp -PB11 31 1238116 G A LGG_01246, putative without homology CGC → TGC Arg → Cys -PB11 32 1284491 G A LGG_1285, ftsA, cell division protein GGG → AGG Gly → Arg +PB11 33 1329432 G A LGG_1329, pyc, pyruvate carboxylase GAC → AAC Asp → Asn +PB11 34 1441024 G A LGG_01434, hpaG, fumarylacetoacetate

hydrolase family proteinCCT → TCT Pro → Ser -

PB11 35 1592837 C T LGG_01579, NADPH-quinone reductase GGT → GAT Gly → Asp -PB11 36 1923356 T C LGG_02981, tRNA-Thr +PB11 37 2034908 C T LGG_1988, diacylglycerol kinase family protein ACG → ATG Thr → Met +PB11 38 2043966 C T LGG_1996, rmlD, dTDP-4-dehydrorhamnose

reductaseCGG → CGA Silent -

PB11 39 2087697 C T LGG_2035, clpL, ATP-dependent Clp proteaseATP-binding subunit

GCG → GCA Silent -

PB11 40 2467768 C T Intergenic, far away from adjacent genesPB11 41 2663257 C T LGG_2603, SAM-dependent methyltransferase CAC → TAC His → Tyr +PB11 42 2745699 G A LGG_2683, ywtG, transporter major facilitator

superfamily MFS_1, Galactose/D-Xylose-protonsymporter

TAC → TAT Silent -

PB11 43 2770418 G A Intergenic, after LGG_02706 (+, putative), afterLGG_2707 (-)

PB11 44 2774572 G A LGG_02711, conserved membrane protein CTC → CTT Silent -PB11 45 2782691 G A LGG_02721, sorbitol operon transcription

regulatorGCT → GTT Ala → Val -

PB11 46 2841875 G A LGG_02773, β-lactamase class A ATC → ATT Silent -PB11 47 2846878 G A LGG_02779, levF, PTS system

mannose/fructose/N-acetylgalactosamine-specific transporter subunit IIC

CCG → TCG Pro → Ser -

PB11 48 2849497 G A LGG_02782, ytgI, phosphoesterase, DHHfamily protein

GGA → AGA Gly → Arg +

PB11 49 2868480 G A LGG_02803, cadA, heavy metal translocatingP-type ATPase

CGT → TGT Arg → Cys -

PB11 50 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB11 51 2893773 C T LGG_02831, ydiC, transporter major facilitator

superfamily MFS_1, EmrB/QacA family proteinCCG → TCG Pro → Ser +

PB11 52 2896965 C T LGG_02833, iolS, aldo/keto reductase CAT → TAT His → Tyr +PB11 53 2917935 C T LGG_02857, conserved CCG → TCG Pro → Ser +PB11 54 2923065 C T LGG_02862, glnH, ABC transporter glutamine-

binding periplasmic proteinAGC → AAC Ser → Asn -

PB11 55 2949133 C T LGG_02885, xerC, phage-related integrase GAT → AAT Asp → Asn -PB11 56 2963889 C T LGG_02906, prs, ribose-phosphate

pyrophosphokinaseCGG → CAG Arg → Gln -

PB12 1 1188 G A LGG_00002, dnaN, DNA polymerase III subunit GAG → GAA Silent +

betaPB12 2 172732 C T LGG_00159, celB, PTS system cellobiose-

specific transporter subunit IIBCTC → CTT Silent +

PB12 3 307575 C T Intergenic, before 16S rRNA (+) andLGG_00301 (-, methylase forubiquinone/menaquinone biosynthesis)

PB12 4 412942 G A LGG_00411, frwC2, PTS system fructose-specific transporter subunit IIC


PB12 5 443038 C T LGG_00441, srtC1 CGA → CAA Arg → Gln -PB12 6 443187 C T LGG_00441, srtC1 TGG → TGA Trp → STOP -PB12 7 593974 G A LGG_00588, yicL, carboxylate/amino

acid/amine transporterACT → ATT Thr → Ile -

PB12 8 874204 G A LGG_00867, rluD, pseudouridine synthase GTT → ATT Val → Ile +PB12 9 924432 C T Intergenic, between LGG_00920 (trxB) &

LGG_00921 (pgm) (+)PB12 10 948499 G A Intergenic, between LGG_00940 (secG) &

LGG_00941 (yvaK) (+)PB12 11 1011850 G A LGG_01001, galA, alpha-galactosidase (GH36) GCA → ACA Ala → Thr +PB12 12 1042996 G A Intergenic, between LGG_01027 (res) &

LGG_01028 (+) (next gene is37)PB12 13 1048017 G A LGG_01032, murQ AAC → AAT Silent -PB12 14 1076969 G A LGG_01064, bglA TAC → TAT Silent -PB12 15 1160386 G A LGG_01163, ycfI, multidrug ABC transporter

ATPase/permeaseATG → ATA Met → Ile +

PB12 16 1325963 C T Intergenic, between LGG_01327 (typA) &LGG_01328 (ftsW, cell div) (+)

PB12 17 1501949 G A LGG_01496, rexA, ATP-dependent nucleasesubunit A

CCC → CTC Pro → Leu -

PB12 18 1525769 G A LGG_01513, glyS, glycyl-tRNA synthetasesubunit beta

CTT → TTT Leu → Phe -

PB12 19 1576507 C T LGG_01561, aspS, aspartyl-tRNA synthetase GCC → ACC Ala → Thr -

PB12 20 1736782 G A Intergenic, after LGG_01709, yneR, (-)PB12 21 1935675 G A LGG_01895, transcriptional regulator GCG → GCA Silent +PB12 22 2111509 C T LGG_02058, fabG, 3-oxoacyl-ACP reductase

(fatty acid biosynthesis)ATG → ATA Met → Ile -

PB12 23 2478832 C * LGG_02404, yqiG, NADH-dependent flavinoxidoreductase

+

PB12 24 2680828 C T LGG_02621, ydiA, tellurite resistance protein-like permease

GAG → GAA Silent -

PB12 25 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB13 1 26819 C T LGG_00028, ABC-transporter, ATP-binding

proteinATG → ATA Met → Ile -

PB13 2 45766 C T LGG_00045, putative protein CAG→ CAA Silent -PB13 3 55544 C T LGG_00051, galC, glycoside hydrolase CCA → TCA Pro → Ser +PB13 4 66077 C T LGG_00060, kdfK, 2-dehydro-3-

deoxygluconokinaseACC → ATC Thr → Ile +

PB13 5 72334 C T LGG_00065, aes, alpha/beta hydrolase fold-3 GAG → AAG Glu→ Lys -PB13 6 82758 C T LGG_00074, conserved protein GGG → AGG Gly → Arg -PB13 7 93735 C T LGG_00089, metal-dependent membrane

proteaseGGA → AGA Gly → Arg -

PB13 8 143827 G A Intergenic, between ileS & LGG_00132 (+)PB13 9 147576 G A LGG_00135, cadA, heavy metal-transporting

ATPaseGTG → ATG Val → Met +

PB13 10 152252 G A LGG_00138, nrdD, anaerobic ribonucleosidetriphosphate reductase

GAT → AAT Asp → Asn +

PB13 11 160029 G A Intergenic, between is4 (+) & yveB (-)PB13 12 166584 G A LGG_00151, transporter major facilitator

superfamily MFS_1CAG → TAG Gln → STOP -

PB13 13 178691 G A LGG_00167, conserved protein GTC → GTT Silent -PB13 14 181768 G A Intergenic, between LGG_00171 (+) and tauB (-

)

PB13 15 199316 G A LGG_00188, conserved ACC → ATC Thr → Ile -PB13 16 205351 G A LGG_00193, fbaA, fructose-bisphosphate

aldolaseGAA → AAA Glu → Lys +

PB13 17 240643 G A LGG_00234, putative GGG → GGA Silent +PB13 18 249017 G A LGG_00247, ychF, GTP-binding protein ACG → ACA Silent +PB13 19 301449 G A LGG_00295, glycosyl transferase group 2 GCA → ACA Ala → Thr +PB13 20 331930 G A LGG_00328, srmB, ATP-dependent helicase CCT → TCT Pro → Ser -PB13 21 343093 G A LGG_00338, manC, PTS system mannose-

specific transporter subunit IICGGA → GAA Gly → Glu +

PB13 22 368865 G A Intergenic, between yhbS & LGG_00361 (-)PB13 23 369905 G A LGG_00362, nisT, ABC transporter, cobalt CTT → TTT Leu → Phe -PB13 24 443200 C T LGG_00441, srtC1, sortase family protein TGG → TAG Trp → STOP -PB13 25 500328 G A LGG_00490, iolD, ABC transporter ATP-binding

proteinGGG → AGG Gly → Arg +

PB13 26 536019 G A LGG_00527, putative protein CTC → CTT Silent -PB13 27 537710 G A LGG_00529, conserved protein GAA → AAA Glu → Lys +PB13 28 550536 G A Intergenic, between LGG_00544 (-) &

LGG_00545 (+)PB13 29 607010 G A LGG_00598, lmrC,ABC transporter ATP-

binding protein/permeaseCGG → CGA Silent +

PB13 30 607189 G A LGG_00598, lmrC, ABC transporter ATP-binding protein/permease

CGG → CAG Arg → Gln +

PB13 31 608374 G A LGG_00599, lmrD, ABC transporter ATP-binding protein/permease

CGA → CAA Arg → Gln +

PB13 32 624362 G A Intergenic, between LGG_00611 & lsa (-)PB13 33 656340 G A LGG_00643, glpD, alpha-glycerophosphate

oxidaseGAC → GAT Silent -

PB13 34 749679 G A Intergenic, between LGG_00737 & wecD (+)PB13 35 777150 G A LGG_00764, rheB, ATP-dependent RNA

helicaseCAG → CAA Silent +

PB13 36 816058 G A LGG_00804, yunD, 5-nucleotidase GAT → AAT Asp → Asn +PB13 37 835362 G A LGG_00825, rfaG, glycosyl transferase group 1 GAT → AAT Asp → Asn +PB13 38 894318 G A LGG_00889, recA, protein recA GTT → ATT Val → Ile +PB13 39 904001 G A LGG_00900, prfB, peptide chain release factor ATG → ATA Met → Ile +PB13 40 905267 A T LGG_00901, ftsE, cell division ATP-binding

proteinGAT → AAT Asp → Asn +

PB13 41 924647 G A LGG_00921, pgm, phosphoglucomutase GCG → GCA Silent +PB13 42 928685 G A LGG_00923, uvrB, excinuclease ABC, subunit

BACG → ACA Silent +

PB13 43 938081 G A LGG_00931, clpP, ATP-dependent Clpprotease proteolytic subunit

GGT- > AGT Gly → Ser +

PB13 44 985710 G A LGG_00976, pacL, cation-transporting ATPase TAC → TAT Silent -PB13 45 1059413 G A LGG_01047, conserved protein CGT → CAT Arg → His +PB13 46 1074157 C T LGG_01061, mvaK, phosphomevalonate

kinaseGCG → GTG Ala → Val +

PB13 47 1105971 G A Intergenic, between LGG_01090 (-) &LGG_01091 (+)

PB13 48 1260933 C T LGG_01261, valS, valyl-tRNA synthetase CCG → TCG Pro → Ser +PB13 49 1265714 C T LGG_01265, mreB, rod shape-determining

protein MreBCCG → TCG Pro → Ser +

PB13 50 1298117 G A LGG_01299, mtnN, 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase

GCA → ACA Ala → Thr +

PB13 51 1300492 G A LGG_01303, uvrA, excinuclease ABC, subunitA

GTG → GTA Silent +

PB13 52 1307526 C T LGG_01308, recD, helicase CGG → TGG Arg → Trp +PB13 53 1315462 C T Intergenic, between LGG_01318 & LGG_01319

(+)PB13 54 1316670 C T Intergenic, between LGG_01319 & pdhA (+)PB13 55 1324083 C T LGG_01327, typA, GTP-binding protein TypA CAC → CAT Silent +PB13 56 1339125 C T LGG_01339, conserved protein CAA → TAA Gln → STOP +

PB13 57 1343707 C T LGG_01343, conserved protein GAC → AAC Asp → Asn -PB13 58 1372134 C T LGG_01370, ycjM, 2',3'-cyclic-nucleotide 2'-

phosphodiesteraseGCC → GCT Silent +

PB13 59 1387631 G A LGG_01386, recQ, ATP-dependent DNAhelicase

GGG → AGG Gly → Arg +

PB13 60 1416463 C T LGG_01413, xerC, tyrosine recombinase ATC → ATT Silent +PB13 61 1457025 C T LGG_01452, pfoS/R,membrane protein, toxin

regulator-likeGGG → AGG Gly → Arg -

PB13 62 1468661 G A LGG_01463, rluD, ribosomal large subunitpseudouridine synthase D

CGC → CGT Silent -

PB13 63 1469124 G A LGG_01463, rluD, ribosomal large subunitpseudouridine synthase D

GCC → GTC Ala → Val -

PB13 64 1492214 C T LGG_01487, pbp1A, penicillin-binding protein1A

CCT → TCT Pro → Ser +

PB13 65 1537075 C T LGG_01524, phage-related tail component GAA → AAA Glu → Lys -PB13 66 1558421 G A Intergenic, between LGG_01543 & LGG_01544

(-)PB13 67 1566051 G A LGG_01548, conserved protein CGA → TGA Arg → STOP -PB13 68 1592590 G A LGG_01579, NADPH-quinone reductase TAC → TAT Silent -PB13 69 1610342 G A LGG_01592, putative protein GCC → GTC Ala → Val -PB13 70 1623906 G A Intergenic, between recJ (-) & LGG_01599 (+)PB13 71 1631191 G A LGG_01605, grpE, GrpE protein (HSP-70

Cofactor HSP20)GCC → GTC Ala → Val -

PB13 72 1714292 C T LGG_01692, conserved GCG → GCA Silent -PB13 73 1806657 G A LGG_01777, ecsA, ABC transporter ATP-

binding proteinCCG → TCG Pro → Ser -

PB13 74 1820010 G A LGG_01790, glycerophosphodiesterphosphodiesterase


PB13 75 1823663 A G LGG_01795, antimicrobial peptide ABCtransporter permease

AGT → AGC Silent -

PB13 76 1824942 C T LGG_01795, ABC transporter, antimicrobial GGG → GAG Gly → Glu -

peptide tPB13 77 1833559 C T LGG_01803, purD, phosphoribosylamine--

glycine ligaseGAG → AAG Glu → Lys -

PB13 78 1908409 C T LGG_01868, dtpT, transporter major facilitatorsuperfamily MFS_1, di/tripeptide transporter

GCG → GCA Silent -

PB13 79 1934972 G A Intergenic, between LGG_01894 (-) &LGG_01895 (+)

PB13 80 1956538 G A LGG_01915, citE, citrate lyase beta subunit CCA → TCA Pro → Ser -PB13 81 2231098 C T LGG_02164, aspC, aspartate/tyrosine/aromatic

aminotransferaseGGG → GAG Gly → Glu -

PB13 82 2266443 T A Intergenic, between LGG_02200 & LGG_02201(-)

PB13 83 2333210 G A LGG_02269, rsmC, 16S rRNA m(2)G 1207methyltransferase

ACC → ATC Thr → Ile -

PB13 84 2370094 C T LGG_02294, conserved membrane protein GTG → GTA Silent -PB13 85 2452279 C T LGG_02375, conserved protein CAG → TAG Gln → STOP +PB13 86 2471312 C T Intergenic, between LGG_02394 & LGG_02395

(-)PB13 87 2475301 C T LGG_02400, prebacteriocin GCG → GCA Silent -PB13 88 2543533 C T LGG_02484, rplB, LSU/50S ribosomal protein

L2PGTG → GTA Silent -

PB13 89 2571327 C T LGG_02508, lysS, lysyl-tRNA synthetase GGT → GAT Gly → Asp -PB13 90 2606944 G A LGG_02539, murF, UDP-N-acetylmuramoyl-

tripeptide--D-alanyl-D-alanine ligaseCCG → TCG Pro → Ser -

PB13 91 2627911 C T Intergenic, between glmU & LGG_02563 (-)PB13 92 2658446 C T LGG_02600, ppk, polyphosphate kinase GGG → GAG Gly → Glu -PB13 93 2687558 G A LGG_02627, yagB, HD domain protein TAC → TAT Silent -PB13 94 2713236 G A LGG_02652, alpha-L-fucosidase ATC → ATT Silent -PB13 95 2754790 G A LGG_02691, iolF, transporter major facilitator

superfamily MFS_1, sugar transporter/L-rhamnose-proton symport

CAT → TAT His → Tyr -

PB13 96 2760552 G A LGG_02696, treC, alpha-phosphotrehalase GAC → AAC Asp → Asn +PB13 97 2789338 C T LGG_02728, sgbH, hexulose-6-phosphate

synthaseGCT → ACT Ala → Thr -

PB13 98 2792332 C T LGG_2732, cmtB, PTS system ascorbate-specific transporter subunit IIA

GAT → AAT Asp → Asn -

PB13 99 2806718 C T LGG_02742, conserved protein GTT → ATT Val → Ile -PB13 100 2812435 C T LGG_02749, PTS system

mannose/fructose/sorbose-specific transportersubunit IIA


PB13 101 2818692 C T LGG_02753, gatC, pts system, galactitol-specific

GTT → ATT Val → Ile -

PB13 102 2877100 G A LGG_02811, conserved protein GTC → GTT Silent -PB13 103 2877919 G A LGG_02812, phoR4, two component sensor

transduction histidine kinaseCCG → TCG Pro → Ser -

PB13 104 2882753 G A LGG_02816, glnP, amino acid ABC transporterpermease

ACG → ACA Silent +

PB13 105 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB13 106 2927297 C T LGG_02866, moxR, ATPase GCA → GTA Ala → Val +PB13 107 2932711 C T LGG_02869, glycosyl transferase group I CTT → TTT Leu → Phe +PB13 108 2935085 C T LGG_02872, aspA, aspartate ammonia-lyase GCG → GCA Silent -PB13 109 2944875 C T Intergenic, between LGG_02880 & LGG_02881

(-)PB13 110 2966242 C T LGG_02908, esterase/lipase TGC → TAC Cys → Tyr -PB13 111 2976840 G A LGG_02918, transcriptional regulator GCC → ACC Ala → Thr +PB21 1 70617 C T LGG_00064, ypiB, transporter major facilitator

superfamily MFS_1GGA → GAA Gly → Glu -

PB21 2 82141 C T LGG_00073, conserved GAA → AAA Glu → Lys -PB21 3 115714 C T LGG_00110, hipO, M20/M25/M40 family

peptidaseGCA → ACA Ala → Thr -

PB21 4 129684 C T LGG_00121, yybT, phosphoesterase, DHHfamily protein

CCA → TCA Pro → Ser +

PB21 5 134002 C T LGG_00125, pts, PTS system sucrose-specifictransporter subunit IIABC


PB21 6 150544 C T LGG_00137, transporter major facilitatorsuperfamily MFS_1, tetracycline resistanceprotein

ACG → ATG Thr → Met +

PB21 7 170886 G A LGG_00157, ogt, methylated DNA-proteincysteine methyltransferase

GCG → GCA Silent +

PB21 8 217567 G A LGG_00203, conserved GTG → ATG Val → Met +PB21 9 459628 C T LGG_00454, is19 GGT → GAT Gly → Asp -PB21 10 544082 C T LGG_00538, metal-dependent hydrolase of the

TIM-barrel fold proteinACC → ACT Silent +

PB21 11 550854 C T LGG_00545, ABC transporter permease ACG → ATG Thr → Met +PB21 12 556890 C T LGG_00550, mppX, ABC transporter ATP-

binding proteinGCG → GTG Ala → Val +

PB21 13 560825 C T LGG_00554, pepN, aminopeptidase N CCG → TCG Pro → Ser +PB21 14 612425 G A LGG_00601, treR, trehalose operon repressor GAC → AAC Asp → Asn +PB21 15 655574 C T LGG_00643, glpD, alpha-glycerophosphate

oxidaseGAT → AAT Asp → Asn -

PB21 16 822364 C T LGG_00812, yugI, general stress protein 13 CCG → TCG Pro → Ser +PB21 17 855997 C T LGG_00847, membrane-associated

phospholipid phosphataseATG → ATA Met → Ile -

PB21 18 861601 C T LGG_00852, rsuA, pseudouridine synthase A GCA → GTA Ala → Val +PB21 19 881838 G A LGG_00875, corA, magnesium transporter

CorA familyATC → ATT Silent -

PB21 20 1036402 G A LGG_01022, rumA, tRNA (uracil-5-)-methyltransferase

CAG → CAA Silent +

PB21 21 1057928 G A LGG_01044, rhe, ATP-dependent RNAhelicase


PB21 22 1091917 C T LGG_01077, pbuX, xanthine permease TCG → TTG Ser → Leu +PB21 23 1117833 A T Intergenic, between LGG_01116 (putative) &

LGG_01117 (phage related protein) (+)

PB21 24 1221189 C T LGG_01231, pcaC, carboxymuconolactonedecarboxylase

CCG → CTG Pro → Leu +

PB21 25 1435202 C T LGG_01427, vraD, ABC transporter, ATP-binding protein

GAC → AAC Asp → Asn -

PB21 26 1464437 G A LGG_01458, pyrC, dihydroorotase TCG → TTG Ser → Leu -PB21 27 1610873 G A LGG_01592, putative GCC → GTC Ala → Val -PB21 28 1891089 C T LGG_01860, pncB, nicotinate

phosphoribosyltransferaseGTT → ATT Val → Ile -

PB21 29 2138907 G A LGG_02085, conserved ACG → ACA Silent +PB21 30 2139584 C T Intergenic, after LGG_02085 (+) & LGG_02086

(sugar kinase, (-))PB21 31 2142652 C T LGG_02087, N-acetylmuramoyl-L-alanine

amidaseGAT → AAT Asp → Asn -

PB21 32 2293004 C T Intergenic, between LGG_02225 (putative) &LGG_02226 (GMP synthase) (-)

PB21 33 2306253 C T LGG_02236, yda0, amino acid transporter GAA → AAA Glu → Lys -PB21 34 2371134 C T LGG_02296, rtpR, adenosylcobalamin-

dependent ribonucleoside-triphosphatereductase


PB21 35 2459202 C T LGG_02383, conserved ATG → ATA Met → Ile -PB21 36 2483689 C T LGG_02411, mntH, NRAMP family Mn2/Fe2

transporterGAT → AAT Asp → Asn -

PB21 37 2483865 C T Intergenic, before LGG_02411 (mntH, (-))PB21 38 2550392 C T LGG_02493, fusA, translation elongation factor GAA → AAA Glu → Lys -PB21 39 2561836 T A LGG_02499, clpC, ATP-dependent Clp

protease ATP-binding subunitATG → TTG Met → Leu -

PB21 40 2611900 G A LGG_02545, murA, UDP-N-acetylglucosamine1-carboxyvinyltransferase


PB21 41 2631095 G A LGG_02566, ybbM, ABC transporter permease GAT → AAT Asp → Asn +PB21 42 2656274 G A LGG_02598, conserved secreted TCC → TTC Ser → Phe -PB21 43 2681961 C T Intergenic, between nodJ & ydiA (-)

PB21 44 2706913 C T LGG_02647, tagT, PTS system fructose-specific transporter subunit IIABC

GGA → GAA Gly → Glu -

PB21 45 2714270 T C LGG_02653, pts, PTS system transportersubunit IIAB

GTT → GTC Silent +

PB21 46 2742359 C T LGG_02680, fcsR, fucose operon repressor,DeoR family

GGT → GAT Gly → Asp -

PB21 47 2756337 C T LGG_02693, xylB, alcohol dehydrogenase GTC → GTT Silent +PB21 48 2765233 C T LGG_02701, glvA, maltose-6'-phosphate

glucosidaseGTT → ATT Val → Ile -

PB21 49 2804805 G A LGG_02740, transporter major facilitatorsuperfamily MFS_1

GCC → ACC Ala → Thr +

PB21 50 2866503 G A Intergenic, before LGG_02802 (+) & oppA (-)PB21 51 2874802 G A LGG_02809, vicX, metallo-beta-lactamase

family proteinACT → ATT Thr → Ile -

PB21 52 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB22 1 82141 C T LGG_00073, conserved GAA → AAA Glu → Lys -PB22 2 115714 C T LGG_00110, hipO, M20/M25/M40 family

peptidaseGCA → ACA Ala → Thr -

PB22 3 129684 C T LGG_00121, yybT, phosphoesterase, DHHfamily protein

CCA → TCA Pro → Ser +

PB22 4 134002 C T LGG_00125, pts, PTS system sucrose-specifictransporter subunit IIABC


PB22 5 150544 C T LGG_00137, transporter major facilitatorsuperfamily MFS_1, tetracycline resistanceprotein

ACG → ATG Thr → Met +

PB22 6 170886 G A LGG_00157, ogt, methylated DNA-proteincysteine methyltransferase

GCG → GCA Silent +

PB22 7 217567 G A LGG_00203, conserved GTG → ATG Val → Met +PB22 8 459628 C T LGG_00454, is19 GGT → GAT Gly → Asp -PB22 9 544082 C T LGG_00538, metal-dependent hydrolase of the

TIM-barrel fold proteinACC → ACT Silent +

PB22 10 550854 C T LGG_00545, ABC transporter permease ACG → ATG Thr → Met +PB22 11 556890 C T LGG_00550, mppX, ABC transporter ATP-

binding proteinGCG → GTG Ala → Val +

PB22 12 560825 C T LGG_00554, pepN, aminopeptidase N CCG → TCG Pro → Ser +PB22 13 612425 G A LGG_00601, treR, trehalose operon repressor GAC → AAC Asp → Asn +PB22 14 655574 C T LGG_00643, glpD, alpha-glycerophosphate

oxidaseGAT → AAT Asp → Asn -

PB22 15 822364 C T LGG_00812, yugI, general stress protein 13 CCG → TCG Pro → Ser +PB22 16 855997 C T LGG_00847, membrane-associated

phospholipid phosphataseATG → ATA Met → Ile -

PB22 17 861601 C T LGG_00852, rsuA, pseudouridine synthase A GCA → GTA Ala → Val +PB22 18 881838 G A LGG_00875, corA, magnesium transporter

CorA familyATC → ATT Silent -

PB22 19 1036402 G A LGG_01022, rumA, tRNA (uracil-5-)-methyltransferase

CAG → CAA Silent +

PB22 20 1091917 C T LGG_01077, pbuX, xanthine permease TCG → TTG Ser → Leu +PB22 21 1117833 A T Intergenic, between LGG_01116 (putative) &

LGG_01117 (phage related protein) (+)PB22 22 1221189 C T LGG_01231, pcaC, carboxymuconolactone

decarboxylaseCCG → CTG Pro → Leu +

PB22 23 1435202 C T LGG_01427, vraD, ABC transporter, ATP-binding protein

GAC → AAC Asp → Asn -

PB22 24 1464437 G A LGG_01458, pyrC, dihydroorotase TCG → TTG Ser → Leu -PB22 25 1610873 G A LGG_01592, putative GCC → GTC Ala → Val -PB22 26 1891089 C T LGG_01860, pncB, nicotinate

phosphoribosyltransferaseGTT → ATT Val → Ile -

PB22 27 2138907 G A LGG_02085, conserved ACG → ACA Silent +PB22 28 2139584 C T Intergenic, after LGG_02085 (+) & LGG_02086

(sugar kinase, (-))PB22 29 2142140 C T LGG_02087, N-acetylmuramoyl-L-alanine

amidaseAAG → AAA Silent -

PB22 30 2142652 C T LGG_02087, N-acetylmuramoyl-L-alanineamidase


PB22 31 2293004 C T Intergenic, between LGG_02225 (putative) &LGG_02226 (GMP synthase) (-)

PB22 32 2306253 C T LGG_02236, yda0, amino acid transporter GAA → AAA Glu → Lys -PB22 33 2371134 C T LGG_02296, rtpR, adenosylcobalamin-

dependent ribonucleoside-triphosphatereductase


PB22 34 2459202 C T LGG_02383, conserved ATG → ATA Met → Ile -PB22 35 2483689 C T LGG_02411, mntH, NRAMP family Mn2/Fe2

transporterGAT → AAT Asp → Asn -

PB22 36 2483865 C T Intergenic, before LGG_02411 (mntH, (-))PB22 37 2550392 C T LGG_02493, fusA, translation elongation factor GAA → AAA Glu → Lys -PB22 38 2561836 T A LGG_02499, clpC, ATP-dependent Clp

protease ATP-binding subunitATG → TTG Met → Leu -

PB22 39 2611900 G A LGG_02545, murA, UDP-N-acetylglucosamine1-carboxyvinyltransferase


PB22 40 2631095 G A LGG_02566, ybbM, ABC transporter permease GAT → AAT Asp → Asn +PB22 41 2681961 C T Intergenic, between nodJ & ydiA (-)PB22 42 2706913 C T LGG_02647, tagT, PTS system fructose-

specific transporter subunit IIABCGGA → GAA Gly → Glu -

PB22 43 2714270 T C LGG_02653, pts, PTS system transportersubunit IIAB

GTT → GTC Silent +

PB22 44 2742359 C T LGG_02680, fcsR, fucose operon repressor,DeoR family

GGT → GAT Gly → Asp -

PB22 45 2756337 C T LGG_02693, xylB, alcohol dehydrogenase GTC → GTT Silent +PB22 46 2765233 C T LGG_02701, glvA, maltose-6'-phosphate

glucosidaseGTT → ATT Val → Ile -

PB22 47 2801528 G A LGG_02738, dipeptidase, M20 family CGC → TGC Arg → Cys -PB22 48 2804805 G A LGG_02740, transporter major facilitator

superfamily MFS_1GCC → ACC Ala → Thr +

PB22 49 2866503 G A Intergenic, before LGG_02802 (+) & oppA (-)PB22 50 2874802 G A LGG_02809, vicX, metallo-beta-lactamase

family proteinACT → ATT Thr → Ile -

PB22 51 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB23 1 96111 G A LGG_00091, putative CTG → CTA Silent +PB23 2 214854 G A LGG_00201, oppA, ABC transporter

oligopeptide-binding proteinACG → ACA Silent +

PB23 3 567669 G A LGG_00561, sugar phosphateisomerase/epimerase


PB23 4 571530 G A LGG_00565, yfkL, transporter major facilitatorsuperfamily MFS_1

CGG → CGA Silent +

PB23 5 610867 T A LGG_00600, oxlT, transporter major facilitatorsuperfamily MFS_1

AGT → AGA Ser → Arg +

PB23 6 622045 C T LGG_00607, gdhA, glutamate dehydrogenase GGC → GGT Silent +PB23 7 830569 G A Intergenic, after LGG_02970, transfer-RNA Leu +PB23 8 889796 G A LGG_00884, ymfH, Zn-dependent M16 family

peptidaseGAA → AAA Glu → Lys +

PB23 9 1219347 C T LGG_01228, conserved ACC → ATC Thr → Ile +PB23 10 1321490 G A LGG_01323, pdhD, dihydrolipoamide

dehydrogenase (Artemis: pyruvatedehydrogenase complex)

GAA → AAA Glu → Lys +

PB23 11 1421951 G A LGG_01419, parE, DNA topoisomerase IVsubunit B


PB23 12 1455735 G A Intergenic, between, fbp & LGG_01415(pyrophosphatase) (+)

PB23 13 1748619 G A LGG_01721, spoU, rRNA methyltransferase CTT → TTT Leu → Phe -PB23 14 2447729 C T LGG_02372, spaF, pilus specific adhesion

proteinGAT → AAT Asp → Asn -

PB23 15 2455413 C T LGG_02378, conserved TCC → TTC Ser → Phe +PB23 16 2459759 C T LGG_02384, conserved ACG → ACA Silent -PB23 17 2509945 C T LGG_02436, 4cll, acyl-CoA synthetase family CGG → CGA Silent -

proteinPB23 18 2647786 C T LGG_02584, metG, methionyl-tRNA

synthetase/protein secretion chaperonin, CsaAGTC → ATC Val → Ile -

PB23 19 2669934 C T LGG_02610, conserved CGA → TGA Arg → STOP +PB23 20 2688709 G C Intergenic, between LGG_02628 (MarR family

transcriptional regulator) & uvrA (+)PB23 21 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB24 1 5594 C T LGG_00006, gyrA, DNA gyrase subunit A TCG → TTG Ser → Leu +PB24 2 51831 C T Intergenic, between uidA & galC (+)PB24 3 221504 G A LGG_00208, conserved protein AGT → AAT Ser → Asn +PB24 4 324677 C T Intergenic, between deoB & deoD (+)PB24 5 1063979 C T LGG_01050, ampS, aminopeptidase S GCG → ACG Ala → Thr -PB24 6 1235382 C T LGG_01244, putative protein TCG → TTG Ser → Leu +PB24 7 1510830 G A LGG_01499, mvaD, diphosphomevalonate

decarboxylaseACG → ACA Silent +

PB24 8 1537098 C T LGG_01524, phage-related tail component GGA → GAA Gly → Glu -PB24 9 1833405 G A LGG_01803, purD, phosphoribosylamine--

glycine ligaseCCG → CTG Pro → Leu -

PB24 10 1903414 C A LGG_1865, conserved extracellular matrixbinding protein

GCG → GCT Silent -

PB24 11 2103347 G A Intergenic, between wzx & glf (-)PB24 12 2266443 T A Intergenic, between LGG_02200 & LGG_02201

(-)PB24 13 2352557 A * LGG_02282, putative protein codon 1097 -PB24 14 2422358 C T LGG_02348, conserved protein ACT → ATT Thr → Ile +PB24 15 2426897 C T LGG_02351, ppdK, pyruvate phosphate

dikinaseGGG → GGA Silent -

PB24 16 2525676 C T Intergenic, between lhv (+) & LGG_02453 (-)PB24 17 2531154 C T Intergenic, between LGG_02459 & rplQ (-)

PB24 18 2661932 C T Intergenic, between ppx (-) & aRA12 (+)PB24 19 2734977 C T LGG_02674, ypdC, conserved protein GAT → AAT Asp → Asn -PB24 20 2856717 G A LGG_02792, acetyltransferase, GNAT family ACG → ATG Thr → Met -PB24 21 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB24 22 2891002 C T Intergenic, between wecC (-) & LGG_02826 (+)PB24 23 2946022 C T Intergenic, between LGG_02881 & LGG_02882

(-)PB25 1 12622 C T LGG_00013, rpsR, SSU/30S, ribosomal protein

S18PATC → ATT Silent +

PB25 2 116881 G A LGG_00111, dapD, 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase

CCA → TCA Pro → Ser -

PB25 3 147287 G A LGG_00135, cadA, heavy metal-transportingATPase

GAG → GAA Silent +

PB25 4 188858 A G Intergenic, between LGG_00177 (+) & mhqA (-)PB25 5 273769 G A LGG_00269, iolJ, fructose-bisphosphate

aldolaseGGC → AGC Gly → Ser +

PB25 6 544911 G A LGG_00539, amino acid transporter GAA → AAA Glu → Lys +PB25 7 601998 C T LGG_00595, pdxK,

pyridoxal/pyridoxine/pyridoxamineAAG → AAA Silent -

PB25 8 665043 G A LGG_00651, lacG2, 6-phospho-beta-galactosidase


PB25 9 734367 C T LGG_00725, mleR, malolactic regulator, LysRfamily


PB25 10 768015 G A LGG_00757, adhE, aldehyde-alcoholdehydrogenase

GGT → GAT Gly → Asp +

PB25 11 771445 C T LGG_00760, zwf, glucose-6-phosphate 1-dehydrogenase

TAC → TAT Silent +

PB25 12 1079283 G A LGG_01065, bglH, PTS system beta-glucoside-specific transporter subunit IIABC

CTC → TTC Leu → Phe -

PB25 13 1541316 G A LGG_01525, phage-related minor tail protein ACA → ATA Thr → Ile -PB25 14 2015110 C T LGG_01971, conserved protein CGT → TGT Arg → Cys +

PB25 15 2711650 C T LGG_02651, transcriptional regulator, GntRfamily

CGA → CAA Arg → Gln -

PB25 16 2791676 C T ulaA, LGG_02731, PTS system ascorbate-specific transporter subunit IIC

CGG → CAG Arg → Gln -

PB25 17 2799330 C A Intergenic, between LGG_02735 (+) &LGG_02736 (-)

PB25 18 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB25 19 2918502 G A LGG_02858, conserved membrane protein GGG → GGA Silent +PB25 20 2958234 C T LGG_02898, terL, phage-related terminase

large subunitGCA → GTA Ala → Val +

PB25 21 2972252 C T Intergenic, between mtlA (-) & nagB (+)PB25 22 2974923 C T LGG_02915, conserved protein CTC → CTT Silent +PB25 23 2975836 C T LGG_02917, conserved protein CTT → TTT Leu → Phe +PB31 1 19946 G A LGG_00021, abortive infection protein TCG → TCA Silent +PB31 2 86489 C T LGG_00078, opuCa, glycine/betaine/L-proline

ABC transporter ATP-binding proteinGGG→ GGA Silent -

PB31 3 241654 G A LGG_00237, putative protein without homology GAA → AAA Glu → Lys -PB31 4 252031 G A LGG_00249, guaB, inosine-5'-monophosphate

dehydrogenaseACG → ACA Silent +

PB31 5 269559 G A LGG_00265, iolD, myo-inositol catabolismprotein


PB31 6 326384 C T LGG_00324, p75, cell wall-associatedglycoside hydrolase (NLP/P60 protein)

GCC → GTC Ala → Val +

PB31 7 338021 G A LGG_00333, agaS, tagatose-6-phosphateketose/aldose isomerase


PB31 8 346108 G A Intergenic, between lacC LGG_00341 & srlDLGG_00342 (-)

PB31 9 365175 G A LGG_00358, pepT, peptidase T CGC → TGC Arg → Cys -PB31 10 419850 G A LGG_00417, manZ, PTS system mannose-

specific transporter subunit IICDCTC → CTT Silent -

PB31 11 445030 C T LGG_00442, spaA, pilus specific protein ATG → ATA Met → Ile -

PB31 12 458773 C T Intergenic, between is18 & is19PB31 13 497620 C T LGG_00487, putative protein without homology GGA → GAA Gly → Glu -PB31 14 609160 C T LGG_00599, lmrD, ABC transporter ATP-

binding protein/permeaseTCT → TTT Ser → Phe +

PB31 15 678043 C T Intergenic, between lacC LGG_00664 & lacDLGG_00665

PB31 16 819843 C T LGG_00809, ltrC,phosphatidylglycerophosphatase A

AAG → AAA Silent -

PB31 17 835115 G A LGG_00825, rfaG, glycosyl transferase group 1 CAG → CAA Silent +PB31 18 953450 G A LGG_00944, nplT, neopullulanase GH13 TGG → TGA Trp → STOP +PB31 19 1020550 G A LGG_01009, acetyl-CoA carboxylase

carboxyltransferase subunitCTC →TTC Leu → Phe -

PB31 20 1135106 G A LGG_01137, putative protein without homology TTG → TTA Silent +PB31 21 1173674 G A LGG_01175, upp, uracil

phosphoribosyltransferaseCTG → CTA Silent +

PB31 22 1335294 G A LGG_01335, comEc, metallo-beta-lactamasesuperfamily hydrolase protein

GGC → GAC Gly → Asp +

PB31 23 1909315 G A LGG_01869, salX, ABC transporter ATP-binding protein

CTC → CTT Silent -

PB31 24 2158023 C T LGG_02094, conserved protein, pglZ domain CCG → CCA Silent -PB31 25 2161286 C T LGG_02096, xerC, phage-related integrase CGC → TGC Arg → Cys +PB31 26 2259770 G A Intergenic, between blgG LGG_02194 & cydC

LGG_02195 (-)PB31 27 2377551 C T ubiA, LGG_02303, 1,4-Dihydroxy-2-naphtoate

prenyltransferaseGTT → ATT Val → Ile -

PB31 28 2534557 C T LGG_02466, adk, adenylate kinase GTT → ATT Val → Ile -PB31 29 2605128 C T LGG_02538, deaD, ATP-dependent ATP-

helicaseCGT→CAT Arg → His -

PB31 30 2645815 G A LGG_02583, conserved protein GGA → AGA Gly → Arg +PB31 31 2697771 G A LGG_02637, rnhA, ribonuclease H1 GAG → AAG Glu → Lys +

PB31 32 2698808 G A Intergenic, between yoaU2 LGG_02638 (-) &avtA LGG_02639 (+)

PB31 33 2711797 C T LGG_02651, transcriptional regulator, GntRfamily

AGC → AAC Ser- > Asn -

PB31 34 2727869 G A LGG_02668, kdgA, 2-dehydro-3-deoxyphosphogluconate aldolase

ATC → ATT Silent -

PB31 35 2750899 C T LGG_02688, rhaA, L-rhamnose isomerase AGT → AAT Ser- > Asn -PB31 36 2763239 C T LGG_02699, rpiA, ribose-5-phosphate

isomerase AGTG → ATG Val → Met -

PB31 37 2774608 G A LGG_02711, conserved membrane protein CTC → CTT Silent -PB31 38 2864132 C T LGG_02800, dapE, peptidase M 20 GAG → AAG Glu → Lys -PB31 39 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +PB31 40 2923253 G A LGG_02862, glnH, glutamine ABC transporter

substrate-binding proteinACC → ACT Silent -

PB32 1 272064 G A LGG_00267, iolG2, myo-inositol 2-dehydrogenase

GTG → GTA Silent +

PB32 2 328041 G A LGG_00325, nox, NADH oxidase ACC → ATC Thr → Ile -PB32 3 355654 G A LGG_00349, yohH, poly(Glycerol-phosphate)

alpha-glucosyltransferaseGAT → AAT Asp → Asn +

PB32 4 435792 C T Intergenic, between LGG_00433 menC (-) &LGG_00434 nagZ (+)

PB32 5 436177 C T Intergenic, between LGG_00433 menC (-) &LGG_00434 nagZ (+)

PB32 6 444293 G A LGG_00442, spaA, pilus specific protein TCT → TTT Ser → Phe -PB32 7 660116 C T Intergenic, between LGG_00645 (-) &

LGG_00646 (+)PB32 8 829869 C T LGG_02963, transfer RNA-AspPB32 9 839639 G A Intergenic, between ykuJ & ltaS (+)PB32 10 987499 G C LGG_00976, pacL, cation-transporting ATPase GCC → GGC Ala → Gly -PB32 11 1229814 G A Intergenic, between LGG_01241 (+) & yvfR (-)

PB32 12 1372823 C T LGG_01371, conserved protein CCG → TCG Pro → Ser +PB32 13 1888062 G A LGG_01857, pbpx, beta-lactamase class C-like

penicillin binding proteinCAA → TAA Gln → STOP -

PB32 14 2504834 C T Intergenic, between LGG_02432 (-) &LGG_02433 (+)

PB32 15 2504932 C T Intergenic, between LGG_02432 (-) &LGG_02433 (+)

PB32 16 2720343 C T LGG_02659, transcriptional regulator LysR GAG → GAA Silent -PB32 17 2805123 C T LGG_02741, alpha-L-fucosidase GH29 GTC → GTT Silent +PB32 18 2823199 C T LGG_02759, yjhB, phosphohydrolase,

mutT/nudix familyGCG → ACG Ala → Thr -

PB32 19 2828153 C T LGG_02762, alpha-glucosidase AAG → AAA Silent -PB32 20 2871512 G A LGG_02805, conserved protein TTC → TTT Silent -PB32 21 2883065 C T LGG_02817, argG, argininosuccinate synthase GCC → GCT Silent +*: deletion

TABLE S2 Deletions in Class II mutantsPosition Deleted genes in Class II

strainsGenomic islands

GeneNbr

Gene nameor locus tag

Start End Product PB21 PB22 PB23 PB24 PB25 LGGISL1 LGGISL2

342 srlD 346166 346969 Sorbitol-6-phosphate 2-dehydrogenase

x x x x x

343 gatC 347024 348373 PTS system, galactitol-specific IIC component

x x x x x

344 is9 348729 350144 Transposase, IS5 familyprotein

x x x - -

345 gatA 350258 350764 PTS system, galactitol-specific IIA component

x x x - -

346 gatB 350761 351060 PTS system, galactitol-specific IIB component

x x x - -

347 LGG_00347 351291 352151 Conserved protein x x x - -348 yohJ 352522 354048 Lipopolysaccharide

biosynthesis proteinx x x - -

349 yohH 354064 355677 Poly(Glycerol-phosphate)alpha-glucosyltransferase

x x x - -

350 LGG_00350 355828 357099 Conserved protein x x x - -351 patB 357239 358435 Aminotransferase x x x - -352 ypdF 358422 359501 Aminopeptidase YpdF x x x - -353 pts 359609 360934 PTS system, IIC component x x x - -354 celA 360969 361307 PTS system,

lactose/cellobiose-specificIIB component

x x x - -

355 chbA 361374 361691 PTS system,lactose/cellobiose-specificIIA component

x x x - -

356 ypdE 361776 362816 Aminopeptidase x x x - -

357 LGG_00357 362801 364594 Transcription antiterminator x x x - -358 pepT 364999 366228 Peptidase T x x x - -359 oppA 366359 367999 ABC transporter,

oligopeptide-binding proteinx x x - -

360 yhbS 368086 368730 Acetyltransferase x x x - -361 LGG_00361 368896 369108 Conserved protein x x x - -362 nisT 369738 371543 ABC transporter, cobalt

transporter ATPase andpermease components

x x x - -

363 LGG_00363 371961 372527 ABC transporter, cobalttransporter permeasecomponent

x x x - -

364 cbiO 372534 373877 ABC transporter, cobalttransporter ATP-bindingprotein

x x x - -

365 cbiQ 373882 374529 ABC transporter, cobalttransporter permeasecomponent

x x x - -

366 tenA 374644 375336 Transcriptional activatorTenA

x x x - -

367 thiW 375317 375817 Hydroxyethylthiazolepermease

x x x - -

368 thiM 375868 376707 Hydroxyethylthiazole kinase x x x - -369 thiE 376704 377333 Thiamine-phosphate

pyrophosphorylasex x x - -

370 thiD 377335 378186 Phosphomethylpyrimidinekinase

x x x - -

371 ycaM 378576 380024 Amino acid transporter x x x - -372 rbsR 380438 381457 Transcriptional regulator,

LacI familyx x x - -

373 rbsK 381723 382664 Ribokinase x x x - -

374 LGG_00374 382770 383072 Transcriptional regulator x x x - -375 LGG_00375 383237 383482 Putative protein without

homologyx x x - -


- - - - -

377 LGG_00377 386245 386430 Putative protein withouthomology

- - - - -


- - - - -


- - - - -

380 LGG_00380 387901 388716 Conserved protein - - - - -381 LGG_00381 389385 389696 Conserved protein - - - - -382 pbp 390000 391955 Penicillin-binding protein 3 - - - - -383 is11 392315 393730 Transposase, IS5 family

protein- - - - -


- - - - -


- - - - -

386 LGG_00386 394391 395779 Transporter, major facilitatorsuperfamily MFS_1

- - - - -

387 slyA 395755 396189 Transcriptional regulator,MarR family

- - - - -

388 LGG_00388 396186 396746 Conserved protein - - - - -389 LGG_00389 396929 397144 Putative protein without

homology- - - - -

390 aroE 397288 397575 Conserved protein - - - - -391 LGG_00391 397793 398128 Putative protein without

homology- - - - -


- - - - -

393 manR 399211 400695 Transcription antiterminatorBglG family protein

- - - - - o

394 LGG_00394 400685 401113 PTS system, IIA component - - - - - o395 frwA1 401179 401628 PTS system, fructose-

specific IIA component- - - - - o

396 frwB1 401644 401961 PTS system, fructose-specific IIB component

- - - - - o

397 frwC1 401995 403095 PTS system, fructose-specific IIC component

- - - - - o

398 tal 403139 403807 Transaldolase - - - - - o399 rpe 403800 404489 Ribulose-phosphate 3-

epimerase- - - - - o

400 ulaA 404798 405247 PTS system,lactose/cellobiose-specificIIA component

- - - - - o

401 ulaB 405249 405530 PTS system,lactose/cellobiose-specificIIB subunit

- - - - - o

402 pts 405558 405971 PTS system, IIC component - - - - - o403 is12 405976 406992 Transposase, IS30 family

protein- - - - - o

404 ulaC 407068 408117 PTS system, ascorbate-specific IIC component

- - - - - o

405 tktN 408138 408995 Transketolase - - - - - o406 tktC 408988 410004 Transketolase - - - - - o407 scrK 410196 411050 Fructokinase - - - - - o408 lacR 411100 411858 Lactose phosphotransferase

system repressor- - - - - o

409 frwA2 412099 412572 PTS system, fructose-specific IIA component

- - - - - o

410 frwB2 412577 412906 PTS system, fructose-specific IIB component

- - - - - o

411 frwC2 412931 414037 PTS system, fructose-specific IIC component

- - - - - o


- - - - - o

413 fba 415271 416113 Fructose-bisphosphatealdolase

- - - - - o

414 gatY 416135 417028 Fructose-bisphosphatealdolase

- - - - - o

415 pts 417573 418049 PTS system, mannose-specific IIB component

- - - - - o

416 pts 418021 418449 PTS system, mannose-specific IIA component

- - - - - o

417 manZ 418467 420155 PTS system, mannose-specific IICD component

- - - - - o

418 tal 420195 420905 Transaldolase - - - - - o419 LGG_00419 421109 422140 Transcriptional regulator,

LacI family- - - - - o

420 yhfZ 422379 423293 Transcriptional regulator,GntR family

- - - - - o

421 LGG_00421 423326 423676 Conserved protein - - - - - o422 LGG_00422 423678 424040 Conserved protein - - - - - o423 LGG_00423 424101 425396 Conserved membrane

protein- - - - - o

424 php 425426 426310 Hydrolase - - - - - o425 yhfS 426303 427409 Pyridoxal phosphate-

dependent transferase- - - - - o

426 yhfX 427400 428572 Amino acid racemase - - - - - o427 YHFW 428574 429803 Phosphopentomutase - - - - - o428 ilvH 430131 430967 DNA-directed RNA

polymerase subunit delta- - - - -

429 LGG_00429 431050 431610 Cobalt transport protein cbiQ - - - - -

430 cbiO 431612 433312 ABC transporter, cobalttransporter eATP-bindingprotein cbiO

- - - - -

431 cbiQ 433309 434136 Cobalt transport protein cbiQ - - - - -432 LGG_00432 434102 434266 Putative protein without

homology- - - - -

433 menC 434488 435621 N-acylamino acid racemase - - - - - o434 nagZ 436451 438265 Beta-N-

acetylhexosaminidase (GH3)- - - - - o


- - - - - o

436 tnpR 439988 440638 Resolvase - - - - - o437 LGG_00437 440644 440928 Conserved cytosolic protein - - - - - o438 LGG_00438 440992 441147 Putative protein without

homology- - - - - o


- - - - - o


- - - - - o

441 srtC1* 442875 443954 Sortase family protein - - - - - o442 spaA* 444028 445032 Pilus specific protein, major

backbone protein- - - - - o

443 spaB* 445035 445760 Pilus specific protein, minorbackbone protein

- - - - - o

444 spaC* 445753 448440 Pilus specific protein,ancillary protein involved inmucus-adhesion, containsvon Willebrand factor (VWF)domain

- - - - - o


- - - - - o

446 LGG_00446 450276 450833 Conserved protein - - - - - o

447 LGG_00447 450928 451500 Conserved protein - - - - - o448 LGG_00448 451522 451797 Putative protein without

homology- - - - - o

449 LGG_00449 451872 453659 UvrD/REP helicase - - - - - o450 ybjD 453656 455746 Putative protein without

homology- - - - - o


- - - - -

452 is17 457654 457905 Transposase, IS3/IS911family protein

x x - - -


x x - - -


x x - - -

455 LGG_00455 460536 460799 Conserved protein x x - - -456 pacL 460859 463681 Cation-transporting ATPase x x - - -457 is20 463990 464310 Transposase x x - - -458 is21 464307 464777 Transposase, IS4 family

proteinx x - - -

459 napA 464786 465940 Na /H antiporter x x - - -460 is22 466447 466917 Transposase, IS4 family

proteinx x - - -

461 is23 466914 467234 Transposase x x - - -462 is24 467284 467958 Transposase x x - - -463 eriC 468801 470366 Chloride channel protein x x - - -464 is25 470708 471628 Transposase, IS30 family

proteinx x - - -


x x - - -


x x - - -

467 LGG_00467 474513 475835 Peptidase M20 x x - x x468 LGG_00468 475951 476394 Transcriptional regulator,

LysR familyx x - x x


x x - x x

470 ebgA 477195 480173 Beta-galactosidase (GH42) x x - x x471 ygjI 480206 481687 Amino acid permease family

proteinx x - x x

472 lysP 481835 483292 Lysine-specific permease x x - x x473 araC 483560 484414 Transcriptional regulator,

AraC familyx x - x x


x x - x x


x x - x x

476 abgB 488248 489678 Aminobenzoyl-glutamateutilization protein B

x x - x x

477 LGG_00477 489764 490825 Opine/octopinedehydrogenase

x x - x x

478 yecC 490822 491568 ABC transporter, amino acidtransporter ATP-bindingprotein

x x - x x

479 LGG_00479 491584 492462 ABC transporter, amino acidbinding protein

x x - x x

480 LGG_00480 492476 493144 ABC transporter, amino acidtransporter permease protein

x x - x x

481 LGG_00481 493141 493827 ABC transporter, amino acidtransporter permease protein

x x - x x

482 LGG_00482 494296 495033 Conserved protein x x - x x483 LGG_00483 495269 495670 Putative protein without

homologyx x - x x

484 LGG_00484 495808 496305 DNA-directed RNA x x - x x

polymerase specializedsigma subunit, sigma24-likeprotein

485 LGG_00485 496422 496574 Conserved protein x x - x x486 LGG_00486 496586 497350 Lyzozyme M1 (1,4-beta-N-

acetylmuramidase) (GH25)x x - x x


x x - x x

488 LGG_00488 498619 499122 Transcriptional regulator,TetR family

x x - x x

489 LGG_00489 499130 500191 ABC transporter,antimicrobial peptidetransporter permeasecomponent

x x - x x

490 lolD 500196 500885 ABC transporter, ATP-binding protein

x x - x x

491 npr 501174 502544 NADH peroxidase x x - x x492 LGG_00492 502791 503609 Hydrolase of the HAD

superfamilyx x - x x

493 LGG_00493 503732 504004 Conserved protein x x - x x494 LGG_00494 504153 504917 Nucleotidyltransferase x x - x x495 LGG_00495 505327 505755 Putative protein without

homologyx x - x x


x x - x x


x x - x x


x x - x x


x x - x x

500 metQ 509532 510389 ABC transporter, metal ion x x - x x

transporter periplasmiccomponent/surface antigen

501 LGG_00501 510599 511615 Choloylglycine hydrolase x x - x x502 LGG_00502 511795 512760 Conserved protein x x - x x503 LGG_00503 513031 514725 Oxidoreductase; Myosin-

crossreactive antigenortholog

x x - x x

504 LGG_00504 514737 514868 Conserved protein x x - x x505 LGG_00505 514954 515520 Transcriptional regulator x x - x x506 LGG_00506 515610 515978 Dihydroxyacetone kinase,

phosphotransfer subunitx x - x x


x x - x x

508 dhaL 516254 516835 Dihydroxyacetone kinase x x - x x509 dhaK 516822 517841 Dihydroxyacetone kinase x x - x x510 LGG_00510 518035 518463 Redox protein, regulator of

disulfide bond formationx x - x x

511 LGG_00511 518922 519605 ABC transporter, ATP-binding protein

x x - x x

512 LGG_00512 519612 520784 ABC transporter x x - x x513 is28 521184 522599 Transposase, IS5 family

proteinx x - x x


x x - x x


x x - x x

516 LGG_00516 524051 524887 Transcriptional activator x x - x x517 is29 524935 526350 Transposase, IS5 family

proteinx x - x x

518 LGG_00518 527101 528510 DNA polymerase III, alphasubunit (Gram-positive type)

x x x x x

519 LGG_00519 528947 529219 Conserved protein x x x x xx: gene present, -: gene deleted, o: genomic island, * : spaCBA-srtC

gene cluster

FIG S3. Western analysis of cytosolic and secreted proteins detected using SpaA and SpaC antibodies. Above are the blots

prepared with the cell-free extracts and below the blots prepared with the growth medium samples. The different mutant classes are

depicted above the blots. In the SpaC Western blots the amount of protein extract in each lane is 1.5 times more than in the SpaA blots.

Positions of monomeric pilins are indicated with black arrows. White arrow indicates cross-reacting SpaA monomer in the SpaC blot.

Molecular masses (kDa) of the standard proteins are depicted on the left side of the blots. HMW: High molecular weight fraction.

TABLE S4 Collateral mutations in strain PB12 excluding silent and intergenic mutations

Gene Product Protein existence (UniProt)Total

size (aa)Mutatedresidue Nt change Aa change

yicL Carboxylate/amino acid/amine transporter Predicted 316 182 ACT → ATT Thr → IlerluD Pseudouridine synthase Inferred from homology 300 70 GTT → ATT Val → IlegalA Alpha-galactosidase (GH36) Predicted 764 68 GCA → ACA Ala → ThrycfI Multidrug ABC transporter ATPase/permease Inferred from homology 576 286 ATG → ATA Met → IlerexA ATP-dependent nuclease subunit A Inferred from homology 1236 1154 CCC → CTC Pro → LeuglyS Glycyl-tRNA synthetase subunit beta Inferred from homology 689 519 CTT → TTT Leu → PheaspS Aspartyl-tRNA synthetase Inferred from homology 601 209 GCC → ACC Ala → ThrfabG 3-oxoacyl-ACP reductase (fatty acid

biosynthesis)Predicted 237 43 ATG → ATA Met → Ile

yqiG NADH-dependent flavin oxidoreductase Predicted 381 323(deletion)

CGC → CG*(G)

*: deleted base, (G): next base in sequence

table s1 single nucleotide mutations and deletions in...

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