Article Figures & Data
Figures
- FIG. 1.
Distributions of genes (A) and reactions (B) over subsystems. The reactions of each subsystem in panel B are additionally subcategorized into gene-associated and non-gene-associated reactions. w/o, without.
- FIG. 2.
Schematic representation of biotin biosynthesis. The dotted line represents the hypothetical downstream conversion of S-adenosyl-4-methylthio-2-oxobutanoate (amob) (43). Metabolites a and b represent 2-oxobut-3-enoate and 5′-methylthioadenosine, respectively. Reaction and metabolite abbreviations used here can be found in Table S2 in the supplemental data.
- FIG. 3.
Results of the in silico single-deletion studies. The growth rate percentages of lethal and nonlethal deletions are shown for each medium. The reduced-growth section indicates the percentage of mutants displaying reduced growth compared to that of the wild type in the same medium. See Table 1, footnote a, for medium abbreviations.
- FIG. 4.
Distributions of essential genes (A) and conditionally essential genes (B) over subsystems. The number of essential or conditionally essential genes per subsystem is shown in parentheses.
- FIG. 5.
Variation in growth rate observed in single knockouts of nonessential genes. The percentage growth rate was calculated relative to that of the wild type under the same medium conditions. The reaction abbreviations used here can be found in Table S2 of the supplemental data at http://gcrg.ucsd.edu/organisms/hpylori.html ). See Table 1, footnote a, for medium abbreviations.
Tables
- TABLE 1.
Compositions of in silico mediaa
Component Min I Min II Min III Min IV Rich mediuma Medium basis Min I Min II Min III Min IV Amino acids l-Alanine, d-alanine, l-arginine, l-histidine, l-isoleucine, l-leucine, l-methionine, l-valine l-Asparagine, l-aspartate, l-glutamine, l-glutamate, l-serine, d-serine l-Cysteine, l-lysine, l-phenylalanine, l-proline, l-threonine, l-tryptophane, l-tyrosine Glycine, ornithine Carbon sources d-Glucose Pyruvate, lactate, malate, fumarate, succinate, α-ketoglutarate adenosine, guanosine Nucleotides and/or nucleosides Adenine, cytidine, deoxyadenosine, deoxycytidine, deoxyuridine, guanine, hypoxanthine, nicotinamide d-ribonucleotide, orotate, thymidine, uracil, uridine, xanthine Others Phosphate, sulfate, iron (II), iron (III), pimelate, thiamine, water, oxygen, protons Acrylamide, acetate, acetoacetate, acetaldehyde, acetamide, citrate ethanol, formate, d-galactose, H2, carbonic acid, sodium, ammonium, Ni2+, nitric oxide, nitrite, nitrate, protoheme, urea ↵ a Min I, minimal medium; min II, minimal medium plus d-glucose; min III, minimal medium plus d-glucose plus alternative carbon sources; min IV, minimal medium plus d-glucose plus alternative carbon sources plus amino acids; rich medium, medium containing all compounds for which a transport system has been defined based on the work of Schilling et al. (39).
- TABLE 2.
Comparison of iCS291 and iIT341 GSM/GPR
Parameter iCS291 iIT341 GSM/GPR % Similarity No. of genes included 291 341 83 No. of gene-associated reactions 272 354 68 No. of other reactions 116 113 61 No. of total reactions 388 476 66 No. of metabolites (internal/external) 339/64 411/74 70/80 No. of exchange fluxesa 115 74 S matrix (no. of reactions × no. of metabolites)a 649 × 403 554 × 485 ↵ a Influxes and effluxes for each metabolite were written as separate unidirectional reactions in iCS291 but were represented as reversible reactions in iIT341 GSM/GPR.
- TABLE 3.
Comparison of in silico predictions of single knockouts with experimental data
Gene locus Gene name Reaction name Exptl dataa Reference Medium compound that induces growth phenotype switch Min I Min II Min III Min IV Rich Exp HP0002, HP1574 ribD, ribG DB4PS − − − − − − 50 HP0004, HP1186 cynT, icfA H2CO3D + + + + + + 5 HP0055 putP PROt4r + + + + + + 18 HP0067 to HP0070, HP0072 to HP0073 ureH, ureG, ureF, ureE, ureB, ureA UREA + + + + + + 41 HP0071 ureI UREAt + + + + + + 18 HP0075 glmM, ureC PGAMT − − − − − − 7 HP0086 mqo MDH4 − − + + + − 3 l-Asparagine, l-aspartate, l-threonine HP0112 fucA FCLPA + + + + + + 18 HP0121 ppsA PPS − + + + + + 18 d-Glucose HP0191 to HP0193 frdB, frdA, frdC FRD5 + + + + + + 12, 18 HP0197 metK, metX METAT − − − − − + 18 HP0212 dapE SDPDS − − − − − − 21 HP0215 cdsA DASYN_HP − − − − − + 18 HP0255 purA ADSS − − + + + + 18 Adenine, adenosine HP0293 pabB PABB − − − − − + 18 HP0329 nadE NADS1 − − − − + + 18 Nicotinamide d-ribonucleotide HP0360 galE UDPG4E − − − − + + 24 l-Galactose HP0372 dcd DCTPD, DCTPD2 + + + + + + 3 HP0380 gdhA GLUDy + + + + + + 18 HP0381 hemG, hemK PPPGO − − − − + + 18 (Proto-) Heme HP0389 sodB, sodF SPODM + + + + + + 40 HP0476 gltX, gltX_1, gltX1 GLUTRS − − − − + + 18 (Proto-) Heme HP0509 glcD GLYCTO1 − − − − − − 3 HP0512 glnA GLNS − − + + + − 11 l-Glutamine HP0588 to HP0591 oorD, oorA, oorB, oorC OOR − − − − − − 3, 16 HP0687 feoB FE2abc − − − − + − 48 (Proto-) Heme HP0735 gpt GUAPRT, HXPRT, XPRT + + + + + − 3 HP0740 murF UGMDDS − − − − − − 3 HP0802 ribA GTPCII − − − − − − 10 HP0804 ribB DB4PS − − − − − − 10 HP0808 acpS ACPS + + + + + − 3 HP0824-0825 trx1, trxA, trxB, trxR1 TRDR − − − − − − 3 HP0829 guaB IMPD − − + + + + 18 Guanine, xanthine HP0832 speE SPMS − − − − − + 3 HP0875 katA CAT + + + + + + 13, 18 HP1011 pyrD DHORD3 − − − − + − 6 Orotate, uracil HP1038 aroD, aroQ DHQD − − − − − − 3 HP1050 thrB HSK − − − + + + 18 l-Threonine HP1052 envA, lpxC UHGADA_HP − − − − − + 18 HP1077 nixA NIabc + + + + + + 18 HP1084 pyrB ASPCT − − − − + − 2 Orotate, uracil HP1087 ribC RBFSa, RBFSb − − − − − − 10 HP1091 kgtP AKGt2r + + + + + + 18 HP1099 eda EDA + + + + + − 3 HP1100 edd EDD + + + + + − 3 HP1100 edd EDD + + + + + + 49 HP1108 to HP1111 porG, porD, porA, porB PDH2 − − − − + − 3 Thymidine + acetate HP1108 to HP1111 porG, porD, porA, porB PDH2 − − − − + + 17 Thymidine + acetate HP1118 ggt GTMLT + + + + + + 4, 18 HP1180 nupC ADNt2, ADNt2, CYTDt2, DADNt2, DCYTt2, DURIt2, THMDt2, URIt2 + + + + + + 18 HP1257 pyrE ORPT − − − − + − 3 Uracil HP1385 fbp FBP − + + + + − 3 d-Glucose HP1399 rocF ARGN − − − + + + 26 Ornithine, l-proline HP1418 murB UAPGR − − − − − − 3 HP1491 PIt2r − − − − − + 18 HP1495 tal TALA + + + + + + 3 HP1505 ribD APRAUR, DHPPDA − − − − − − 10 ↵ a Boldface indicates results of experiments that agreed with in silico predictions. Exp, in vivo study results. +, growth under the given condition; −, lethal deletion. See Table 1, footnote a, for medium abbreviations. Reaction abbreviations used here can be found in Table S2 in the supplemental data.
- TABLE 4.
Conditionally lethal mutantsa
Gene locus I (reaction) Gene locus II (reaction) HP0067 to HP0070, HP0072 to HP0073 (UREA) HP0071 (UREAt) HP0121 (PPS) HP1102 (PGL); HP0154 (ENO); HP0974 (PGM); HP1345 (PGK); HP1346, HP0921 (GAPD) HP0572 (ADPT) HP0255 (ADSS), HP1112 (ADSL1r, ADSL2r) HP0577 (FTHFLi, MTHFC, MTHFD) HP0183 (GHMT2r) HP0646 (GALU) HP0360 (UDPG4E), HP1174 (GALt2, GLCt2) HP0724 (ASNt2, ASPt2r, MALt2r, SUCCt2, SUCFUMti) HP0191-93 (FRD5) HP0735 (GUAPRT, HXPRT, XPPT) HP0409 (GMPS2) HP1169 to HP1172 (GLNabc) HP0512 (GLNS) HP1174 (GALt2, GLCt2) HP0360 (UDPG4E), HP0646 (GALU) HP1179 (PPM, PPM2) HP0574 (RPI) HP1180 (ADNt2, CYTDt2, DADNt2, DCYTt2, DURIt2, THMDt2, URIt2) HP1108 to HP1111 (PDH2), HP1533 (TMDSf) HP1189 (ASAD) HP0106 (METB1r), HSERTA HP1227, HP1538 to HP1540 (BC10) HP0875 (CAT) HP1290 (NMNTP) HP0329 (NADS1), HP1355 (NNDPR), HP1356 (QULNS), ASPO2 HP1337 (NMNAT, NNAT) HP0329 (NADS1), HP1355 (NNDPR), HP1356 (QULNS), ASPO2 HP1461 (CCP) HP0875 (CAT) HP1495 (TALA) HP0574 (RPI), HP1386 (RPE) ADD HP0572 (ADPT) CYSabc HP0107 (CYSS), HP1210 (SERAT) FUMt3 HP1325 (FUM) GALK HP0360 (UDPG4E), HP0646 (GALU) GALTi HP0360 (UDPG4E), HP0646 (GALU) HEMEti HP0163 (PPBNGS), HP0237 (HMBS); HP0239 (GLUTRR); HP0306 (G1SATi); HP0376 (FCLT); HP0381 (PPPGO); HP0476, HP0643 (GLUTRS); HP0604 (UPPDC1, UPPDC2); HP0687 (FE2abc); HP1224 (UPP3S); HP0665, HP1226 (CPPPGO) LYSt2r HP0290 (DAPDC) PGMT HP0360 (UDPG4E), HP1174 (GALt2, GLCt2), GALK, GALTi PHEt2r HP0291 (CHORM), HP0672 (EHGLAT, PHETA1, TYRTA), PPNDH THRt2r HP0098 (THRS), HP1189 (ASAD), HP1050 (HSK) TRPt2r HP1279 (IGPS, PRAIi), HP1280 (ANPRT) TYRt2r HP0291 (CHORM), HP1380 (PPND) UPPRT HP0005 (OMPDC), HP1257 (ORPT) URAt2 HP0005 (OMPDC), HP1257 (ORPT) ↵ a A double deletion of a gene in the first column and a gene in the second column is predicted to result in a lethal phenotype. All of the genes listed here are nonessential in single-deletion studies. Reaction abbreviations used here can be found in supplemental material Table S2.
- TABLE 5.
Required reactions for the synthesis of biomass constituents in rich mediuma
Pathwayb Reaction abbreviation(s) Synthesis of biomass constituentc accoa(c) M1 btn(c) ctp(c), dctp(c) dgtp(c), gtp(c) fad(c) mqn6(c) nadp(c), nadph(c) spmd(c) succoa(c) udpg(c), utp(c) M2 ala-L(c) coa(c) dttp(c) met-L(c) nadh(c) peptido-EC(c) 5mthf(c) clpn-HP(c) pe-HP(c) pg-HP(c) ps-HP(c) lps-HP(c) Amino acid degradation VALTA X X X Amino sugar metabolism UAGDP2, GF6PTA, PGAMT, G1PACT, UAGDP, UAGCVT, UAPGR X X X X X X X X X X X X X X X X X X X ATP de novo synthesis ADK1 X X X X X X X X X X X X X X X X Biotin biosynthesis CHCOAL, AOXSr, AMAOTr, DBTSr, BTS2 X X X X X X X X X X X X X X X X X X Chorismate biosynthesis DDPA, DHQS, DHQD, SHK3Dr, SHKK, PSCVT, CHORS X X dNTP biosynthesis RNDR1, NDPK8, RNDR3, NDPK7, RNDR2, NDPK5, NDPK4 X X X X X X X X X X X X X X X X X X Fatty acid synthesis ACCOACr, MCOATA, C140SN X X X X X C160SN, C180SN X X X X X X X X X X X X X X X X X X X C181SN, C190cSN X X X X KAS-HP, KAS-HP2 X X X X X X X X X X X X X X X X X X X Folate biosynthesis DHFRi, GTPCI, DNTPPA, DNMPPA, DHNPA, ADCL, PABB, DHFS X Fucose biosynthesis MAN6PI, PMANM, MAN1PT2r, GMAND, GFUCS X X X X X X X X X X X X X X X X X X X Glycerolipid synthesis CLPNS-HP, GLYK X DASYN-HP, PSSA-HP X X X X PGSA-HP, PGPP-HP X X PSD-HP X PSSA-HP X X Glycolysis TPI X X X X GTP de novo synthesis GK1 X X X NDPK1 X X X X X X X X X X X X X X X X X X X IMP synthesis PRPPS X X X X X X X X X X X X X X X X X X Isoprenoid biosynthesis DXPS, DXPRIi, MEPCT, CDPMEK, MECDPS, MECOPDH, DMPPS, IPDPS X LPS biosynthesis S7PI, GMHEPK, GMHEPPA, GMHEPAT, AGMHE, RFA-HP, A5PISO, KDOPS, KDOPP, KDOCT, UAGAAT-HP, UHGADA-HP, U23GAAT-HP, USHD-HP, U2GAAT, U2GAAT2, LPADSS-HP, MOAT-HP, RFAC-HP, LPSSYN-HP X X X X X X X X X X X X X X X X X X X Lysine/threonine biosynthesis DHDPS, DHDPRy, THDPS, SDPTA, SDPDS, DAPE X X X X X X X X X X X X X X X X X X Menaquinone biosynthesis ICHORSi, OXGDC2, SHCHCS2, SUCBZS, SUCBZL, NPHS, DHNAOT2, AMMQT6 X Methionine salvage pathway DKMPPD, MDRPDr, MTAN, MTRI, MTRK, UNK2 X X X X X X X X X X X X X X X X X X Nucleotide Interconversion CYTK1, NDPK3 X X X X X X X X X DTMPK X X X X X X X X X X X X X X X X X X Nicotinate biosynthesis NADK X Others GCALDDr, GLYCTO1 X GLUR X X X X X X X X X X X X X X X X X X PPA X X X X X X X X X X X X X X X X X X X X Pantothenate/CoA biosynthesis MOHMT, DPR, ASP1DC, PANTS, PNTK, PPNCL2, PPCDC, PTPATi, DPCOAK X X X Peptidoglycan biosynthesis UAMAS, UAMAGS, UAAGDS, ALAALAr, UGMDDS, PAPPT3, UAGPT3, PPTGS, UDCPDP X X X X X X X X X X X X X X X X X X Respiratory chain FRDO X X X X X X X X X X X X X X X X X X X Riboflavin metabolism GTPCII, DHPPDA, APRAUR, PMDPHT, D84PS, RBFSa, RBFSb, RBFK, FMNAT X Spermidine biosynthesis ARGDC, AGMT, ADMDCr, SPMS X X X X X X X X X X X X X X X X X X METAT X X X X X X X X TCA cycle OOR X X X X X X X X X X X X X X X X X X TCA cycle MALS X THF metabolism MTHFR2 X Thioredoxin system TRDR X X X X X X X X X X X X X X X X X X Transport O21 X X PIMEtr X X X X X X X X X X X X X X X X X X PII2r X X X X X X X X X X X X X X X X HISabc, ILEabc, LEUabc, THMabc, VALabc X X X X X X X X X X X X X X X X X X METabc X X X X X X X Tyr, Phe, Trp biosynthesis CHORM UTP/CTP de novo synthesis UMPK X X X X X X X X X X X X X X X X X X X NDPK2 X X X X CTPS1 X Others DMATT, GRTT, OCTDPS X sink-ahcys(c) X X X X X sink-amob X X X X X X X X X X X X X X X X X X X ↵ a Reaction and metabolite abbreviations used here can be found in Table S2 in the supplemental material.
↵ b dNTP, deoxynucleoside triphosphate; TCA, tricarboxylic acid.
↵ c X, lethal deletion; blank cell, viable deletion. M1 and M2 columns represent the two largest clusters. M1: amp(c), atp(c), datp(c), and nad(c). M2: thm(c), thr-L(c), trp-L(c), tyr-L(c), arg-L(c), asn-L(c), asp-L(c), val-L(c), cys-L(c), gln-L(c), h2o(c), his-L(c), ile-L(c), leu-L(c), lys-L(c), phe-L(c), pheme(c), pro-L(c), ptrc(c), ser-L(c), glu-L(c), and gly(c). The symbol (c) signifies a cytosolic localization of the metabolite.
