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2,210,000bp 2,220,000bp 2,230,000bp 2,240,000bp
yopS yonP yonO yonN yonK yonJ yonH yonG yonF yonE yonD yonC yonB yonAyomZ
yomYyomX
yomWyomV
yomU yomTyomS
yomR yomQyomP
yomOyomN
yomM yomK yomJ yomI
yoqByoqA
yopZ
yopY
yopX
yopWyopV
yopU
yopT yopR yopQ yopP yopOyopN
yopMyopL
yopK yopJyopI
yopHyopG
yopF
yopE
yopD yopC yopB yopA yonX yonV yonU yonTyonS
yonR yonI yozP yomL
2,260,000bp 2,270,000bp 2,280,000bp 2,290,000bp
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
yomI yomH yomG yomF yomE yomD blyA bhlA bhlB yolC yokF yokE yokD yokA ypqP ypoP yplP yplQ
bdbB yolJ bdbA sunT sunA yolF uvrX yolD yolByolA
yokLyokK
yokJ yokI yokH yokG yokC yokB yppQ msrA ypnP ypmTypmS
ypmR ypmQypmP
ilvA ypkP dfrA thyB ypjQ ypjP ypiP yphP
Fig. S5-23
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
2,310,000bp 2,320,000bp 2,330,000bp 2,340,000bp
metA ugtP cspD ypzA ypdP ypdQsspL
kduI kduD ypqA yppF sspM recU ponA
ilvD ypgR ypgQ bsaA degRypeQ
ypeP ypcP ypbS ypbR ypbQ bcsA pbuX xpt ypwA kdgT kdgA kdgK kdgR ypvA yptA ypsC ypsBypsA
cotD yprB yprA ypqE yppG yppEyppD
yppC ypoC nth dnaD asnS aspB ypmBypmA
dinG
2,360,000bp 2,370,000bp 2,380,000bp 2,390,000bp
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
ypjC
dinG panD panC panB birA cca ypjH ypjGmgsA
dapB ypjD ypjB ypjA qcrC qcrB qcrA ypiF ypiB ypiA aroE tyrA hisC trpA trpB trpF trpC trpD trpE aroH aroB aroF cheR ndk hepT menH hepS mtrBmtrA
hbs spoIVA yphFyphE
gpsA yphC seaA yphA ypgA ypfD cmk ypfBypfA
ypeB sleB ypdC
Fig. S5-24
2,410,000bp 2,420,000bp 2,430,000bp 2,440,000bp
2,460,000bp 2,470,000bp 2,480,000bp 2,490,000bp
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
fer serA ypuF ypzC ypzD ypuA
ypdA gudB ypbH ypbGypbF
ypbE ypbD recQ ypbB ypaA ypzE aroC rsiX sigX resE resD resC resB resA rluB spmBspmA
dacB ypuI ypuH ypuG ribT ribH ribA ribE ribD ypuE ypuD sipSypuC
ypuB ppiB lysA spoVAF spoVAEspoVAD
spoVACspoVAB
spoVAA
sigF spoIIABspoIIAA
dacF punA drm ripX furspoIIM
ansR yqkF yqkD yqzH yqjV yqjU proI yqjM yqjL zwf yqzJ yqjG yqjF bmrU bmr bmrR
spoIIMyqkK mleA mleN ansB ansA yqxK nudF yqkE yqkC
yqkByqkA yqjZ
yqjYyqjX yqjW yqjT coaA dsdA yqjQ yqjP yqjN yqjK yqjI yqjH yqjE yqjD yqjC yqjB yqjA yqiZ yqiY yqiX yqiW bkdB bkdAB bkdAA lpdV
Fig. S5-25
2,510,000bp 2,520,000bp 2,530,000bp 2,540,000bp
yqzF yqiG yqhQ yqhP yqhL yqhH
lpdV buk bcd ptb bkdR yqiQ mmgE mmgD mmgC mmgB mmgA yqiK yqiI yqiH spo0A spoIVB recN ahrC yqxC dxs yqiD yqiC yqiB folD nusB yqhY accC accB spoIIIAHspoIIIAG
spoIIIAFspoIIIAE
spoIIIADspoIIIAC
spoIIIAB
spoIIIAAyqhV
efp yqhT yqhS yqhR yqhO mntR yqhM gcvPB gcvPA gcvT
2,560,000bp 2,570,000bp 2,580,000bp 2,590,000bp
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
yqhHyqhG
sinIsinR yqzG yqhB yqgY yqgW yqzD yqzC yqgB yqfZ yqfY yqfW yqfT yqfQ yqfP
tasAsipW
yqxM yqzEcomGG
comGF
comGE
comGDcomGC
comGB
comGA yqxL yqhA yqgZ yqgXyqgV
yqgU yqgT yqgS glcK yqgQ yqgP yqgOyqgN
rpmGAyqgM
yqgL pstBB pstBA pstA pstC pstS pbpA yqgE sodA yqgC yqgA yqfX zur yqfU yqfS yqfR yqfO yqfN cccA sigA
Fig. S5-26
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
2,610,000bp 2,620,000bp 2,630,000bp 2,640,000bp
2,660,000bp 2,670,000bp 2,680,000bp 2,690,000bp
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
yqeB spoIVCB rapEphrE
yqzI yqcG yqcF yqdB yqaP yqaE
yqeC nucB spoIVCA arsC arsB yqcK arsR yqcI yqxJ yqxI cwlA yqxHyqxG
yqcEyqcD
yqcC yqcByqcA
yqbT yqbSyqbR
yqbQ yqbP yqbO yqbN yqbMyqbL
yqbK yqbJyqbI
yqbHyqbG
yqbFyqbE
yqbD yqbC yqbB yqbA yqaT yqaS yqaR yqaQ yqaOyqaN
yqaM yqaL yqaK yqaJ yqaIyqaHyqaG
yqdAyqaF yqaD
yqaC
Fig. S5-27
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
antE yqeW rpsT comER sda yqeD
sigA dnaG yqxD yqfL yqzB glyS glyQ recO era cdddgkA
yqfG yqfF phoH yqfD yqfC yqfA yqeZ yqeY rpsU yqeV yqeU yqeT dnaJ dnaK grpE hrcA hemN lepA yqxA spoIIP gpr yqeN comEC comEB comEA yqeM yqeLyqeK
yqeJyqeIaroD yqeH yqeG yqeF cwlH yqeC
2,710,000bp 2,720,000bp 2,730,000bp 2,740,000bp
yqaBspoIIIC yrkO yrkN yrkM blt bltD yrdQ gltR yrpB yrpC yrpD yrpG yraM
yraLyraK
yrkS yrkR yrkQ yrkP yrkL yrkK yrkJ yrkI yrkH yrkGyrkF
yrkE yrkD yrkCyrkB
bltR yrkA yrdR trkA czcD yrdN yrdK brnQ azlD azlC azlB yrdF cypA yrdD yrdC yrdB yrdA aadK yrpE sigZ yraO yraN csn
2,760,000bp 2,770,000bp 2,780,000bp 2,790,000bp
yraGyraF
adhByraE
yraD adhA yraA aapA yrhO sigV yrhM yrhL yrhK yrhE yrhD yrzA
yraJ yraI yraH yraB sacC levG levF levE levD levR yrhP yrhJ yrhI yrhH yrzI yrhG yrhF yrhC yrhB yrhA mtn yrrT yrrS yrrR greA udk yrrO yrrN yrrM yrrL yrzByrrK
yrzL alaS
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-28
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
2,810,000bp 2,820,000bp 2,830,000bp 2,840,000bp
glnQ glnH glnM glnP yrvN yrvJ spoVB yrzE yrzF yrzGyrzH
yrbD nifS
yrrI yrrD yrrC yrrB trmU yrvO yrzC yrvM aspS hisS yrzK yrvI relA apt yrvE yrvDyrvC
secDF yrzD yrbG yrbF tgt queA ruvB ruvA bofC csbX yrbE yrbC coxA safA nadA nadC nadB
2,860,000bp 2,870,000bp 2,880,000bp 2,890,000bp
yrxA ysxD ysnDysnE
ysnF
pheA pheB obg spo0B rpmAysxB
rplUspoIVFB
spoIVFAminD
minC mreDmreC
mreB radC maf spoIIB comC folC valS ysxE spoVID hemL hemB hemD hemC hemX hemA ysxC lonA lonB clpX tig ysoA leuD leuC leuB leuA ilvC ilvH ilvB ysnBysnA
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-29
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
2,910,000bp 2,920,000bp 2,930,000bp 2,940,000bp
yslB rnhC sspI ysfB ysfC ysfD
ysnArph gerM racE ysmB
gerEysmA
sdhBsdhA sdhC lysC ask uvrC trxA xsa etfA etfB ysiB ysiA lcfA yshE mutSB yshC yshB yshA pheT pheS ysgA ysfE cstA abfA araQ araP araN araM araL araD araB araA abnA ysdC
2,960,000bp 2,970,000bp 2,980,000bp 2,990,000bp
ysdB yscA yscB ysaA ytbD ytbE ytvI ytrI ytpI
ysdC ysdArplT
rpmIinfC
ysbB ysbA lytT lytS thrS ytxC ytxB dnaI dnaB ytcG speD gapB ytcD ytaG ytaF mutM polA phoR phoP mdh icd citZ ytwI ytzA pyk pfkA accA accD ytsJ dnaE ytqI ytoI ytnM ytnL
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-30
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,010,000bp 3,020,000bp 3,030,000bp 3,040,000bp
ytlI ytdI braB hisJ ytsP rpsD acuA acuB acuC
ribR ytnJ ytnI ytmO ytmN ytmM ytmL ytmK ytmJ ytmI ytkL ytkK ytzD argH argG moaB ackA ytxK tpx ytfJ ytfI yteJ sppA ytcJ ytcI sspA ytbJ nifZ ezrA yttP ytrP tyrS acsA ytxE ytxD ccpA aroA ytxJytxH
ytxG murC ytpT
3,060,000bp 3,070,000bp 3,080,000bp 3,090,000bp
ytoQ ytzB ytzH ytkP ytiP ytzE ytfP opuD ytdP msmR msmE amyD amyC
ytpT ytpS ytpR ytpQ ytpP ytoP malS ytnP ytmQ ytmP amyX ytlR ytlQ ytlP ytjP ythQ ythP ytzFytzG
ytgP yteV yteU yteT yteS yteR yteQ yteP ytcQ ytcP ytbQ bioI bioB bioD bioF bioA bioW ytaP
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-31
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,110,000bp 3,120,000bp 3,130,000bp 3,140,000bp
melA ytvA yttA ytqA ytqB ytoA pckA ytlA ytlB ytlC ytlD ytjA ythA ythB ythC
ytwF leuS ytvB yttB ytsD ytsC ytsB ytsA ytrF ytrE ytrD ytrC ytrB ytrA ytzC ytpB ytpA ytnA asnB metK ytmB ytmA ytkD ytkC dps ytkA luxS ytiB ytiA mntD mntC mntB mntA menC menE menB ytxMmenD
3,160,000bp 3,170,000bp 3,180,000bp 3,190,000bp
yteA ytcA ytcB ytcC ytaA ytaB yuaJ yuaE yuaC yuaB yuaAyubG yubC yulF
menD menF ytdA ytxO cotS cotSA glgP glgA glgD glgC glgB yuaI yuaG yuaF yuaD gbsB gbsA yubF yubE yubD yubB yubA yulE yulD yulC
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-32
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,210,000bp 3,220,000bp 3,230,000bp 3,240,000bp
tgl yugO yuzA yugF patB kinB kapB yuxJ pbpD yuxK yufL yufM yufN yufO yufP yufQ maeN mrpA mrpB mrpCmrpD
yulB yuxG tlpB mcpA tlpA mcpB yugU yugT yugS yugP yugNyugM
pgi yugK yugJ yugI alaT alaR yugE kapD yufK yufS
3,260,000bp 3,270,000bp 3,280,000bp 3,290,000bp
mrpDmrpE
mrpF
mrpG yuzC yuzE yukF ald yuxI yukJ yuiG yuiD
yuxOcomA
comPcomX
comQ degQ yuxH yueK yueJ yueIyueH
yueG yueF yuzF yueE yueD yueC yueB yukA yukB yukC yukD yukE dhbF dhbB dhbE dhbC dhbA yuiI yuiH yuiF yuiE yuiCyuiB
yuiAyumB
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-33
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,310,000bp 3,320,000bp 3,330,000bp 3,340,000bp
yumC guaC yutJ yutI yutG yutC yunA pucR pucJ pucK pucL pucM yurI yurK
yumB yuzG paiB paiA yutM dapF yutK yuzB yuzD yuxL thrB thrC hom yutH yutF yutE yutD lipA yunB yunC yunD yunE yunF yunG pucH pucE pucD pucC pucB pucA yurG yurH yurJ yurL yurM yurN yurO
3,360,000bp 3,370,000bp 3,380,000bp 3,390,000bp
sspGyurS
yusN yusO yusP yusT yusZ mrgA cssR cssS yuxN gerAA gerAB gerAC
yurP yurQ yurR yurT yurU yurV csd yurX yurY yurZ yusA yusB yusC yusDyusE
yusFyusG
gcvHyusI
yusJ yusK yusL yusM yusQyusR
yusS yusU yusV yusW yusX yusY yvtA citG yvqC yvqE yvqF yvqG yvqH yvqI yvqJ yvqK
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-34
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,410,000bp 3,420,000bp 3,430,000bp 3,440,000bp
yvrD oxdC yvrL fhuD yvsG yvgJ yvgL yvgM yvgO yvaA
yvrA yvrB yvrC yvrE yvrG yvrH yvrI yvrN yvrO yvrP fhuC fhuG fhuB yvsH sspJ yvgK yvgN yvgP yvgQ yvgR yvgS yvgTbdbC
bdbD yvgW yvgX yvgY yvgZ yvaB yvaC yvaDyvaE
yvaF yvaG
3,460,000bp 3,470,000bp 3,480,000bp 3,490,000bp
yvaM yvaNyvaO
yvaP yvaQ yvaV yvaW yvaX yvaY yvbF yvbH yvbI yvbK araR yvbV rsbQ rsbP
smpB rnr yvaK secG yvzC opuBD opuBC opuBB opuBA yvaZyvbA
opuCDopuCC
opuCB opuCA yvbG yvbJ eno pgm tpiA pgk gapA cggR araE yvbT yvbU yvbW yvbX yvbY yvfW yvfV yvfU yvfT yvfS yvfR
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-35
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,510,000bp 3,520,000bp 3,530,000bp 3,540,000bp
rsbP yvfH yvfG slr pnbA sacB yveB yveA yvdTyvdS
yvdR yvdO clpP
yvfO lacA yvfM yvfL yvfK lacR yvfI sigL yvfF yvfE yvfD yvfC yvfB yvfA yveT yveS yveR yveQ yveP yveO yveN yveM yveL yveK padCyveG
yveFracX
pbpE yvdQ yvdP pgcM malL yvdK
3,560,000bp 3,570,000bp 3,580,000bp 3,590,000bp
yvdC yvcT yvpB yvpA nagA nagB yvoA
yvdK yvdJ yvdI yvdH yvdG yvdF yvdE yvdD yvdB yvdA yvcS yvcR yvcQ yvcP yvcN crh yvcL yvcK yvcJ yvcI trxB yvcE yvcD yvcC yvzA yvcB yvcA hisI hisF hisA hisH hisB hisD hisG hisZ yvoF hprP yvoD lgt hprK yvnB
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-36
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,610,000bp 3,620,000bp 3,630,000bp 3,640,000bp
yvnA yvmB yvmA yvkN yvkC yvkB yvkA yvyE yvhJ
yvnB cypX yvmC yvlDyvlC
yvlB yvlA yvzB uvrA uvrB csbA yvjD yvzD yvjB ftsX ftsE cccB yvjA prfB secA yvyD fliTfliS fliD yvyC hagcsrA
yviF yviE flgL flgK yvyGflgM
yvyFcomFC
comFBcomFA
yviA degU degS tagO tuaH
3,660,000bp 3,670,000bp 3,680,000bp 3,690,000bp
lytR gtaB tagA tagB tagC gerBA gerBB gerBC ywtF ywtE
tuaG tuaF tuaE tuaD tuaC tuaB tuaA lytC lytB lytA yvyH ggaB ggaA tagH tagG tagF tagE tagD lytD pmi ywtG ywtD ywtC ywtB ywtA ywsC
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-37
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,710,000bp 3,720,000bp 3,730,000bp 3,740,000bp
rbsR rbsK rbsD rbsA rbsC rbsB ywsB ywsA alsR ywrK cotG ywrF ywrE ywrC ywrB ywrA ywqM ywqB ywqA ywpF ywpD rapD ywoH ywoG
ywrO alsD alsS ywrJ cotB cotH ywrDywqO
ywqN ywqL ywqK ywqJywqI
ywqH ywqG ywqF ywqE ywqD ywqC ywpJ glcRywpH
ywpG ywpE mscL ywpB flhP flhO mblspoIIID
usd ywoF
3,760,000bp 3,770,000bp 3,780,000bp 3,790,000bp
nrgA nrgB ywoA ywnH ywnG ywnE ywnC ywmA ywlA ywkD ywkC
ywoF ywoE ywoD ywoC ywoB ywnJ spoIIQ ywnF mta ywnBywnA
ureC ureB ureA csbDywmF
rapB moaA fdhDywmE
ywmD ywmC spoIID murAA ywmB ywzB atpC atpD atpG atpA atpH atpF atpEatpB
atpI upp glyA ywlGywlF
ywlEywlD
ywlC ywlB spoIIRywkF
ywkE prfA ywkB ywkA
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-38
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,810,000bp 3,820,000bp 3,830,000bp 3,840,000bp
ywjG ywjE ywjD ywjC ywiC sboAsboX
albAalbB
albC albD albE albF albG rapFphrF
ywhH ywhE
ywkA tdkrpmE
rho ywjI murAB ywjH fbaA spo0F pyrG rpoE acdA ywjF ywjB ywjA ywiE narI narJnarH narG arfM fnr narK argS ywiB ywhL ywhK speB speE
3,860,000bp 3,870,000bp 3,880,000bp 3,890,000bp
ywhE ywhB rsfA ywfI ywfH ywdL ywdH ywdC
ywhD ywhC ywhA thrZ mmr ywgBywgA
ywfO ywzC ywfM ywfL ywfK pta ywfG ywfF ywfE ywfD ywfC ywfB ywfA rocC rocB rocA rocG yweAspsL
spsK spsJ spsI spsG spsF spsE spsD spsC spsB spsA ywdK ywdJ ywdI ung ywdF ywdE ywdD
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-39
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
3,910,000bp 3,920,000bp 3,930,000bp 3,940,000bp
thiD ywcJ vpr ywcE ywzA ywcB ywcA ywbH ywbG ywbF ywbE ywbC epr sacX sacY ywaE tyrZ ywaD
ywdA sacA sacP sacT ywcI ywcH nfrA rodA qoxDqoxC
qoxB qoxA galT galK ywcD ywcC ywbO ywbN ywbM ywbL thiE thiM ywbI ywbD ywbB ywbA gspA ywaF ywaCmenA
3,960,000bp 3,970,000bp 3,980,000bp 3,990,000bp
dltA dltB dltC dltD dltE ywaA katX yxlH yxlA yxkJ yxkI yxzE aldY yxkC yxjO yxjN yxjM yxjL pepT yxjJ yxjI yxjH yxjG
menA licH licA licC licB licR yxzF yxlJ yxlG yxlFyxlE
yxlDyxlC
sigY yxkO cydD cydC cydB cydA yxkH msmX yxkF yxkD galE yxkA yxjF
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-40
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
4,010,000bp 4,020,000bp 4,030,000bp 4,040,000bp
yxjA citH yxiO hutP hutH hutU hutI hutG hutM
yxjFscoB scoA yxjC yxjB yxiT yxiS katE bglS licT yxiP deaD yxiM yxiL
yxiKyxiJ
yxiIyxzG
yxiHyxiG
yxzCyxiF yxxG wapA yxxF yxiE bglH bglP yxxE
yxxDyxiD yxiC
yxiByxiA pdp nupC
4,060,000bp 4,070,000bp 4,080,000bp 4,090,000bp
yxeE yxeD yxeB iolR iolS yxcEyxcD
csbC yxbG aldX yxbB yxbAyxnB
asnH
nupCdra deoR yxxB yxeR yxeQ yxeP yxeO yxeN yxeM yxeL yxeK yxeJ yxeI yxeH yxeG yxeF yxeC yxeA yxdM yxdL yxdK yxdJ fbaB iolI iolH idh iolF iolE iolD iolC iolB mmsA htpG yxcA yxbF yxbD yxbC
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-41
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
4,110,000bp 4,120,000bp 4,130,000bp 4,140,000bp
yxaM yxaI yxnA yxaC gntR gntK gntP gntZ ahpC ahpF yydK fbp yycS rapG phrG rocR
yxaL yxaJ yxaH yxaG yxaF yxaD yxaB yxaA bglA yyzE yydJ yydI yydH yydG yydF yydD yydC yydB yydAyydA-1
yydA-2 yycR yycQyycP
yycO yycN rocF rocE rocD yyxA yycJ yycI yycH
4,160,000bp 4,170,000bp 4,180,000bp 4,190,000bp
yycDyycC
yycB yycA cotF ppaC yybO yybN yybM yybL yybK yybJ yybG yybE yybD yybC yyaT yyaS yyaQ yyaP yyaOyyaN
yyaM yyaL yyaJ
yycH yycG yycF purA yycE dnaC yyzB rplI yybT yybS yybR yybP yybI yybH yybF yybB yybA yyaR tetB tetL yyaK maayyaH
ccpB exoA rpsRssb
rpsF yyaF
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-42
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
4,210,000bp
yyaC yyaB
yyaE yyaD spo0J soj yyaA gidB gidA thdF jag spoIIIJ rnpArpmH
∆greA
Gre
A-D
44A
RN
AP
exp.
1ex
p. 2
exp.
1ex
p. 2
exp.
1ex
p. 2
wild
Fig. S5-43
10.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.0010.00
0.00
Fig. S5. Whole-genome profiles of RNAP (β′) binding signals in wild -type, ∆greA, and GreA-D44A cells.Distribution of core RNAP binding signals (β′ binding signals) in wild-type, ∆greA, and GreA-D44A cells are shown above the schematic representation of gene arrangement. Pink (∆greA), blue (GreA-D44A), green (both) arrows below the binding profiles indicate the genes in which RNAP accumulate at promoter or promoter proximal regions.
