Table 2

Gene clusters with purported roles in carbon transport and metabolism downregulated in M. smegmatis in response to VapC

Predicted carbon substrate(s)Gene ID or locus tagGene namen-fold changeaP valueDescriptionb
FructoseMSMEG_0084ptsH1.284.97E−02Phosphocarrier protein hpr
MSMEG_0085fruA1.372.74E−02PTS system, Fru family protein, IIABC components
MSMEG_0086fruK1.241.35E−011-Phosphofructokinase
MSMEG_0087fruR1.063.34E−01Glucitol operon repressor
MSMEG_0088ptsI1.812.11E−03Phosphoenolpyruvate-protein phosphotransferase
GlycerolMSMEG_15421.232.60E−02Transcriptional regulator
MSMEG_15432.184.70E−03EPTC-inducible aldehyde dehydrogenase
MSMEG_15441.352.08E−01PduO protein
MSMEG_15451.121.50E−01Conserved hypothetical protein
MSMEG_15461.981.30E−03Coenzyme B12-dependent glycerol dehydrogenase small subunit
MSMEG_15472.022.14E−03Glycerol dehydratase large subunit
MSMEG_15481.971.01E−02Propanediol utilization: dehydratase, medium subunit
MSMEG_15491.681.56E−02Glycerol dehydratase reactivation factor large subunit; this gene contains a frameshift which is not the result of sequencing error
XyloseMSMEG_1704xylF21.632.66E−02ABC transporter
MSMEG_1705xylG21.472.52E−02d-Xylose transport ATP-binding protein XylG
MSMEG_1706xylH21.411.76E−02Xylose transport system permease protein XylH
ArabinoseMSMEG_1707pho(1.23)7.29E−02Phosphatase YfbT
MSMEG_1708araR1.07.60E−01Ribose operon repressor, putative
MSMEG_1709araG1.077.50E−01Inner membrane ABC transporter permease protein YjfF
MSMEG_1710araF1.276.67E−02Ribose transport system permease protein RbsC
MSMEG_1711araK1.853.03E−02ATP-binding protein of ABC transporter
MSMEG_1712araE3.288.23E−04ABC transporter periplasmic binding protein YtfQ
MSMEG_1713araB1.393.19E−01l-Ribulokinase
MSMEG_1714araD1.301.84E−01l-Ribulose-5-phosphate 4-epimerase UlaF
MSMEG_1715araA1.481.80E−01l-Ribulose-5-phosphate 4-epimerase UlaF
Glucose, trehalose, N-acetylglucosamineMSMEG_21141.251.57E−02Glucose-6-phosphate isomerase, putative
MSMEG_2115(1.11)6.32E−01Conserved hypothetical protein
MSMEG_2116ptsG1.331.21E−02PTS system, glucose-specific IIBC component
MSMEG_2117crr1.322.54E−02b-Glucoside-specific EII permease
MSMEG_2118nagB21.373.29E−02Glucosamine-6-phosphate isomerase
MSMEG_2119nagA1.381.07E−02N-Acetylglucosamine-6-phosphate deacetylase
MSMEG_2120pstR(1.16)3.51E−01Tetratricopeptide repeat family protein
DihydroxyacetoneMSMEG_2121ptsT2.133.74E−04Multiphosphoryl transfer protein (MTP)
MSMEG_2122dhaL1.962.03E−03Dihydroxyacetone kinase, L subunit
MSMEG_2123dhaK2.216.61E−05Dihydroxyacetone kinase, DhaK subunit
MSMEG_2124dhaF2.736.19E−04Glycerol uptake facilitator, MIP channel
MSMEG_2125dhaR1.025.76E−01Glycerol operon regulatory protein
Ribose, ribonucleosidesMSMEG_3089deoC1.066.80E−01Deoxyribose-phosphate aldolase
MSMEG_3090rbsC21.751.54E−02Ribose transport permease protein RbsC
MSMEG_3091rbsA21.038.12E−01Ribose transport ATP-binding protein RbsA
MSMEG_3092rbsR2(2.08)5.16E−01Transcriptional regulator, sugar-binding family protein
MSMEG_3093sugK1.155.30E−01Putative sugar kinase protein
MSMEG_3094sugD1.584.08E−02Oxidoreductase, zinc-binding dehydrogenase family protein
MSMEG_3095rbsB21.802.30E−03d-Ribose-binding periplasmic protein
UnknownMSMEG_3264abcR1.073.92E−01Transcriptional regulator
MSMEG_3265sugK1.383.32E−03Arabitol-phosphate dehydrogenase
MSMEG_3266abcE1.421.78E−02Maltose/maltodextrin-binding protein
MSMEG_3267abcF1.694.34E−02Transporter
MSMEG_3268abcG1.195.50E−02ABC transporter, permease protein
MSMEG_3269abcK11.691.58E−02Putative sugar ABC transporter ATP-binding protein
MSMEG_3270abcK21.262.10E−01sn-Glycerol-3-phosphate ABC transporter, ATP-binding protein
MSMEG_3271sugK1.242.90E−01Dihydroxyacetone kinase
RiboseMSMEG_3598rbsB31.284.65E−03Periplasmic sugar-binding proteins
MSMEG_3599rbsR31.421.01E−02Sugar-binding transcriptional regulator, LacI family protein
MSMEG_3600(1.02)7.80E−01Hypothetical protein
MSMEG_3601rbsC31.536.94E−03Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
MSMEG_3602rbsA31.222.29E−01Ribose transport ATP-binding protein RbsA
MSMEG_4170rbsA4(1.08)5.15E−01Ribose transport ATP-binding protein RbsA
MSMEG_4171rbsC41.212.61E−01Ribose transport system permease protein RbsC
MSMEG_4172rbsB41.463.36E−02d-Ribose-binding periplasmic protein RbsB
MSMEG_4173rbsR4(1.13)1.63E−01MaoC family protein
Unknown sugarMSMEG_4655(1.19)1.89E−01Transcriptional regulator, AraC family protein
MSMEG_46561.379.08E−03Sugar ABC transporter ATP-binding protein
MSMEG_46571.421.60E−02ABC transporter membrane protein
MSMEG_46581.494.33E−04Sugar ABC transporter substrate-binding protein
MSMEG_46591.026.77E−01GntR family protein transcriptional regulator
MSMEG_46601.143.38E−01Hypothetical protein
MSMEG_46611.471.02E−02Sugar kinase, ribokinase family protein
MSMEG_46621.271.67E−01Deoxyribose-phosphate aldolase superfamily protein
MSMEG_4663iolB1.781.88E−03IolB protein
MSMEG_4664iolD1.534.17E−02IolD protein
MSMEG_4665iolE1.304.81E−03IolE protein
MSMEG_46661.068.33E−01myo-Inositol 2-dehydrogenase
MSMEG_50571.361.46E−03Conserved hypothetical protein
MSMEG_5058sugK1.524.32E−04ABC transporter, ATP-binding protein SugC
MSMEG_5059sugG1.468.71E−05ABC transporter, permease protein SugB
MSMEG_5060sugF1.371.24E−04ABC transporter, permease protein SugA
MSMEG_5061sugE1.302.96E−04Bacterial extracellular solute-binding protein
MSMEG_50621.111.62E−02Conserved hypothetical protein
SuccinateMSMEG_5302dctA1.732.57E−02Aerobic C4-dicarboxylate transport protein
Sugar alcoholMSMEG_5571smoK1.803.06E−03ABC transporter ATP-binding protein
MSMEG_5572smoG1.761.37E−02Sugar ABC transporter permease protein
MSMEG_5573smoF1.992.01E−02Sugar ABC transporter permease protein
MSMEG_5574somE1.921.20E−03Substrate-binding protein
MSMEG_5575smoR1.682.30E−03Repressor
XyloseMSMEG_6018xylG11.602.39E−02Xylose transport permease protein XylH
MSMEG_6019xylF1(1.20)7.50E−01ABC-type sugar transport system ATPase component
MSMEG_6020xylE11.115.15E−01d-Xylose-binding periplasmic protein
MSMEG_6021xylA11.652.57E−02Xylose isomerase
MSMEG_6022xylR1(1.08)3.13E−01Xylose repressor, ROK family protein transcriptional regulator
GlycerolMSMEG_62381.703.49E−02Putative two-component system sensor kinase
MSMEG_62391.771.44E−021,3-Propanediol dehydrogenase
MSMEG_62401.441.84E−01Conserved hypothetical protein
MSMEG_62411.731.15E−01ATPase associated with various cellular activities
MSMEG_62422.023.94E−02Alcohol dehydrogenase containing iron
MSMEG_62431.274.33E−02Response regulator receiver domain protein
MSMEG_6756glpK21.191.88E−02Glycerol kinase
MSMEG_6757glpR1.475.86E−04Glycerol operon regulatory protein
MSMEG_6758glpF1.712.11E−04Transport integral membrane protein
MSMEG_6759glpK12.108.12E−04Glycerol kinase
MSMEG_6760glpD1.139.60E−01Conserved hypothetical protein
MSMEG_6761glpD22.107.42E−04Glycerol-3-phosphate dehydrogenase 2
RiboseMSMEG_6802(1.18)7.28E−01ABC transporter ATP-binding protein
MSMEG_68031.414.11E−02Ribose transport system permease protein RbsC
MSMEG_68041.455.03E−03Sugar ABC transporter substrate-binding protein
  • a Boldface values indicate a downregulation of 1.5-fold or greater in gene expression. Shading indicates significant fold changes with P value of <0.05. The values in parentheses are upregulated genes.

  • b PTS, phosphotransferase; EPTC, S-ethyl dipropylcarbamothioate; EII, enzyme II; MIP, major intrinsic protein family.