Supplementary Table S1 - PLOS

Supplementary Table S1. Sub-set of genes found to be differently transcribed (above or below 1.5-fold) in IST439 and IST4113. CDS/Gene

mRNA IST4113 mRNA IST439

Function

Carbohydrate metabolism Electron transport and oxidative phosphorylation BCAL0030/atpB F0F1 ATP synthase subunit A BCAL0037/atpC F0F1 ATP synthase subunit epsilon BCAM2674 Putative cytochrome oxidase subunit I BCAM2675 Putative cytochrome oxidase subunit II Ubiquinol-cytochrome c reductase iron-sulfur subunit; BCAL0328/petA involved in aerobic respiration Cytochrome b of the cytochrome bc complex; BCAL0329/petB involved in aerobic respiration BCAL0330/petC Cytochrome c1 precursor BCAL0388 Ubiquinone biosynthesis hydroxylase family protein Cytochrome d ubiquinol oxidase subunit II BCAL0784/cydA (cytochrome bd) Cytochrome d ubiquinol oxidase subunit II BCAL0785/cydB (cytochrome bd) BCAL2141/cyoD Cytochrome o ubiquinol oxidase BCAL2142/cyoC Cytochrome o ubiquinol oxidase subunit III BCAL2143/cyoB Ubiquinol oxidase polypeptide I BCAL2144/cyoA Ubiquinol oxidase polypeptide II precursor Glyoxylate cycle BCAL2122/aceB BCAM1588

Malate synthase Isocitrate lyase

1.7 1.7 2.7 1.5 -1.9 -2.4 -1.6 -2.4 -1.6 -2.3 -2.2 -2.1 -2.6 -2.3 1.6 2.3

Acetoin catabolism BCAL1909/acoC BCAL1910/acoB BCAL1911/acoA BCAL1913/acoX

Branched-chain alpha-keto acid dehydrogenase subunit E2 Acetoin:2,6-dichlorophenolindophenol oxidoreductase beta subunit Acetoin:2,6-dichlorophenolindophenol oxidoreductase alpha subunit Acetoin catabolism protein

Amino acid and nitrogen metabolism Ammonium metabolism Glutamine synthetase; involved in BCAL2224/glnA reduction BCAM2301 Putative methylamine dehydrogenase; BCAM2302A Putative methylamine utilization protein BCAS0114 Putative histidine-ammonia lyase BCAM2304 Putative methylamine dehydrogenase

4.8 1.8 2.5 3.6

ammonium 1.6 2.3 2.2 1.5 1.9

CDS/Gene

Function


Glycine catabolism BCAL0075/gcvT BCAL0073/gcvP BCAL0074/gcvH

Glycine cleavage system aminomethyltransferase T; involved in ammonium reduction Glycine dehydrogenase Glycine cleavage system protein H

2.4 2.0 2.7

Histidine catabolism BCAL2240/hutG N-formylglutamate deformylase BCAL2241 N-formimino-L-glutamate deiminase BCAL2244/hutU Urocanate hydratase

1.9 1.5 1.5

Aspartate, glutamate and glutamine catabolism Argininosuccinate synthase involved in arginine BCAL2146/argT biosynthesis BCAM0746/ask Aspartate kinase BCAL0600 Putative glutamine synthetase

1.5 2.9 2.4

Phenylalanine catabolism BCAM0810 Putative aromatic oxygenase BCAM0811 Putative aromatic oxygenase Acylamide amidohydrolase; involved in putrescine BCAM1315/amiE biosynthesis BCA1979/feaB Phenylacetaldehyde dehydrogenase Sulphur metabolism BCAM1121 Putative taurine dioxygenase BCAM1122 Putative taurine dioxygenase Putative nitrite/sulfite reductase that reduces sulfite BCAM1676 into H2S; involved in cysteine biosynthesis Putative alkanesulfonate monooxygenase which BCAM1391 convert alkanesulfonates into sulfite BCAM1565 Putative alkanesulfonate monooxygenases BCAL1619/ssuD Putative alkanesulfonate monooxygenases BCAM0557 Putative alkanesulfonate monooxygenases BCAS0054 Putative alkanesulfonate monooxygenases Putative oxidoreductase presumed to be involved in BCAL2049 conversion of adenylnylsulfate into sulfite BCAL2681/cysN Putative sulfate adenylyltransferase subunit 1 BCAL2682/cysD1 Sulfate adenylyltransferase subunit 2 BCAL2683/cysH Phosphoadenosine phosphosulfate reductase

1.5 1.7 2.7 1.5 3.7 4.1 1.6 1.6 1.9 1.7 3.4 4.5 1.8 -1.6 -1.8 -1.5

CDS/Gene

Function

Transport Sulphur-based compounds Periplasmic component of the ABC taurine transporter BCAL0711/tauA TauABC ATPase componenent of the ABC taurine transporter BCAL0712/tauB TauABC Permease component of taurine ABC transporter BCAL0713/tauC TauABC Permease component of the ABC transporter SsuABC BCAL1620/ssuC required for uptake of aliphatic sulfonates ATPase component of of the ABC transporter BCAL1621/ssuB SsuABC required for uptake of aliphatic sulfonates Sugars BCAL1377 BCAL1431 BCAL0781 BCAL1092 BCAM0153/kgdT BCAM2509 BCAM1986 BCAM2545 BCAM2697 BCAS0122 BCAS0343 BCAS0438

H+/citrate symporter Putative outer membrane component of an ABC transport system required for ribose uptake Phosphotransferase system IIC components; specific for glucose/maltose/N-acetylglucosamine Periplasmic component of a ABC transporter similar to a 2-aminoethylphosphonate transport system 2-keto-3-deoxygluconate permease Putative fucose transporter Putative sugar transporter of the Major Facilitator Superfamily Putative sugar transporter of the Major Facilitator Superfamily Putative sugar transporter of the Major Facilitator Superfamily Putative sugar transporter of the Major Facilitator Superfamily Putative sugar transporter of the Major Facilitator Superfamily Predicted periplamic component of an ABC sugar transporter

Amino acids and peptides BCAM0978/lysP Lysine-specific permease Predicted periplasmic component of a putative BCAL1668 arginine/ornithine/lysine ABC transporter Putative branched-chain amino acid transport system BCAL0766 permease protein BCAL1252 Putative proline/betaine transporter Putative amino acid permease predicted to be involved BCAL2729 in uptake of GABA ATPase component of a leucine/isoleucine/valine BCAM2248/livG amino acid ABC transporter


3.2 2.2 2.5 1.8 1.7

1.8 1.8 3.2 1.7 1.8 1.6 1.9 2.5 2.1 1.6 1.8 1.9

1.7 1.9 2.0 2.2 1.9 2.0

CDS/Gene BCAM2249/livM BCAM2618/argT BCAM2724/oppF BCAM2725/oppD BCAM2726/oppC BCAS0110

Function Permease component of a leucine/isoleucine/valine amino acid ABC transporter Periplasmic component of a putative arginine/ornithine/lysine ABC transporter ATPase component of Putative oligopeptide ABC transporter ATPase component of Putative oligopeptide ABC transporter Permease component of Putative oligopeptide ABC transporter Predicted periplasmic component of a putative arginine/ornithine/lysine ABC transporter

Cell envelope and outer membrane LPS and peptidoglycan biosynthesis 3-deoxy-8-phosphooctulonate synthase presumed to be involved in synthesis of 3-deoxy-D-mannoBCAL2180 octulosonic acid; required for LPS biosynthesis Putative phosphosugar-binding protein presumed to be BCAL0779 involved in peptidoglycan synthesis Tetraacyldisaccharide-1-P-kinase involved in lipid A BCAL2759 biosynthesis Putative glycosyltransferase presumed to be involved BCAM0214 in LPS biosynthesis Putative outer membrane protein presumed to be involved in the secretion of peptidoglycan-associated BCAM0220 (lipo)proteins BCAL0067 ADP-heptose:LPS heptosyltransferase D-alanyl-D-alanine endopeptidase (penicillin-binding BCAL2205 protein precursor) 3-deoxy-D-manno-octulosonic-acid transferase BCAL3110/waaA involved in biosynthesis of O-antigen Protein of unknown function that is involved in BCAL3111/wbxY biosynthesis of O-antigen Putative undecaprenyl pyrophosphate synthetase BCAM2067/uppS involved in peptidoglycan biosynthesis

mRNA IST4113 mRNA IST439 1.9 1.9 1.8 2.0 1.7 1.6

1.5 3.4 2.3 2.9 2.3 -1.6 -1.6 -1.6 -1.6 -3.7

Protein secretion BCAL1671 BCAM0180 BCAL2466/eco BCAL2867/lepA BCAM0550

Metallo peptidase Metallo peptidase Serine-protease inhibitor ecotin GTP-binding protein that functions as an exoprotease Putative exported lipase

2.5 3.3 1.8 1.5 1.9

Adhesion BCAM0184/bclB

Lectin; required for attachment to mucin

1.7

CDS/Gene BCAM0185/bclC

Function


BCAM0223 BCAL1086/bclA BCAM0224

Lectin; required for attachment to mucin Putative haemagglutinin-related autotransporter protein Putative haemagglutinin-related autotransporter protein Lectin; required for attachment to mucin Putative haemagglutinin autotransporter protein

3.8 -2.1 -1.6

Protein synthesis BCAL0115/rpsU1 BCAL0222/rplK BCAL0224/rplJ BCAL0225/rplL BCAL0229/rpsL BCAL230/rpsG BCAL0233/rpsJ BCAL0234/rplC BCAL0235/rplD BCAL0236/rplW BCAL0237/rplB BCAL0238/rpsS BCAL0239/rplV BCAL0240/rpsC BCAL0241/rplP BCAL0242/rpmC BCAL0243/rpsQ BCAL0244/rplN BCAL0245/rplX BCAL0246/rplE BCAL0247/rpsN BCAL0248/rpsH BCAL0249/rplF BCAL0250/rplR BCAL0251/rpsE BCAL0252/rpmD BCAL0253/rplO BCAL0256/rpmJ BCAL0257/rpsM BCAL0258/rpsK BCAL0259/rpsD BCAL0261/rplQ BCAL0799 BCAL0990/rpmF BCAL1483/rpmI BCAL1484/rpiT BCAL1905/rpmE2 BCAL1942/rplI

Structural component of the ribosome 50S ribosomal protein L11 50S ribosomal protein L10 50S ribosomal protein L7/L12 30S ribosomal protein S12 30S ribosomal protein S12 30s ribosomal protein S10 50S ribosomal protein L3 50S ribosomal protein L4 50S ribosomal protein L23 50S ribosomal protein L2 30S ribosomal protein S19 50S ribosomal protein L22 30S ribosomal protein S3 50S ribosomal protein L16 50S ribosomal protein L29 30S ribosomal protein S17 50S ribosomal protein L14 50S ribosomal protein L24 50S ribosomal protein L5 30S ribosomal protein S14 30S ribosomal protein S8 50S ribosomal protein L6 50S ribosomal protein L18 30S ribosomal protein S5 50S ribosomal protein L30 50S ribosomal protein L15 50S ribosomal protein L36 30S ribosomal protein S13 30S ribosomal protein S11 30S ribosomal protein S4 50S ribosomal protein L17 50S ribosomal protein L25/general stress protein Ctc 50S ribosomal protein L32 50S ribosomal protein L35 50S ribosomal protein L20 50S ribosomal protein L31 type B 50S ribosomal protein L9

2.0 1.7 2.2 2.4 1.9 1.8 1.6 2.3 2.8 2.5 2.9 2.7 2.8 2.9 2.0 2.3 2.6 1.8 1.5 1.8 2.2 2.1 1.9 2.1 1.9 1.7 1.9 1.8 1.9 2.2 1.7 1.5 1.9 1.9 2.3 2.2 2.7 2.0

BCAM0219

1.5 1.5

BCAL1943/rpsR BCAL1945/rpsF BCAL2715/rpmG BCAL2765/rpsT BCAL2928/rpsP BCAL2950/rpsA BCAL3347/rpsI BCAL3348/rplM BCAL3442/rplU BCAL0219/tufA1 BCAL0231/fusA BCAL0232/tuf BCAl1012/efp2 BCAL0255/infA BCAL1507/infB

30S ribosomal protein S18 30S ribosomal protein S6 50S ribosomal protein L33 30S ribosomal protein S20 30S ribosomal protein S16 30S ribosomal protein S1 30S ribosomal protein S9 50S ribosomal protein L13 50S ribosomal protein L21 Elongation factor Tu Elongation factor G Elongation factor Tu Elongation factor P Translation initiation factor IF-1 Translation initiation factor IF-2

1.8 1.8 1.5 1.6 1.6 1.7 1.6 1.7 1.6 1.8 2.5 1.8 1.9 2.1 1.8

Ion homeostasis Iron assimilation BCAL1697/orbJ BCAL1698/orbK BCAL1699/pvdA BCAL1700/orbA BCAL1701/orbF BCAL1702/orbL BCAM2626/huvA BCAM2627/hmuS BCAM0564 BCAL1371 BCAM1571 BCAM2227/phcG BCAM2230/phcE

Non-ribosomal peptide synthase required for ornibactin biosynthesis Protein of unknown function involved in ornibactin biosynthesis L-ornithine-oxygenase involved in ornibactin biosynthesis Ornibactin receptor; presumably involved in the transport of iron-ornibactin complexes Ornibactin synthetase Protein of unknown function involved in ornibactin biosynthesis Putative heme receptor protein Putative hemin ABC transport system protein TonB-dependent receptor TonB-dependent receptor TonB-dependent receptor Putative pyochelin biosynthetic protein Dihydroaeruginoic acid synthetase PchE involved in pyochelin biosynthesis

1.9 3.0 4.9 5.9 4.1 3.1 2.0 1.7 1.5 1.6 1.9 -1.6 -1.5