TABLE 2.

Genes whose expression was strongly upregulated (>10-fold) in P. aeruginosa in the absence of sulfate relative to growth with inorganic sulfatea

Gene nameFold change in expression% of S-amino acidsbCOGcProtein description
PA0183 (atsA)32.951.873119Arylsulfatase
PA0184 (atsC)41.301.431116Probable ATP-binding component of ABC transporter
PA0185 (atsB)16.181.86600Probable permease of ABC transporter
PA0186 (atsR)24.030.00715Probable binding protein component of ABC transporter
PA019225.420.511629Probable TonB-dependent receptor
PA0193 (atsK)42.400.002175Alkylsulfatase
PA019426.920.002175Hypothetical protein
PA0197 (tonB2)38.600.74810Hypothetical protein
PA0198 (exbB1)55.970.42811Transport protein ExbB
PA0199 (exbD1)35.721.50848Transport protein ExbD
PA208511.080.595517Probable ring-hydroxylating dioxygenase small subunit
PA208613.532.00596Probable epoxide hydrolase
PA208712.162.75NoneHypothetical protein
PA208813.072.134106Hypothetical protein
PA209212.031.762814Probable MFS transporter
PA229213.414.303536Hypothetical protein
PA229320.701.251413Hypothetical protein
PA229422.323.871116Probable ATP-binding component of ABC transporter
PA229535.523.40600Probable permease of ABC transporter
PA229644.800.85715Hypothetical protein
PA229718.5213.582221Probable ferredoxin
PA229814.834.701053Probable oxidoreductase
PA229919.462.412188Probable transcriptional regulator
PA230715.120.69600Probable permease of ABC transporter
PA230815.432.131116Probable ATP-binding component of ABC transporter
PA230911.830.00715Hypothetical protein
PA231010.811.022175Hypothetical protein
PA232426.100.481960Hypothetical protein
PA232514.640.001960Hypothetical protein
PA232611.141.072141Hypothetical protein
PA234624.300.731960Conserved hypothetical protein
PA234734.830.491960Hypothetical protein
PA234846.961.522141Conserved hypothetical protein
PA234936.850.001464Conserved hypothetical protein
PA235019.241.901135Probable ATP-binding component of ABC transporter
PA235110.544.612011Probable permease of ABC transporter
PA235416.041.063829Probable transcriptional regulator
PA2355 (msuC)22.581.781960Probable FMNH2-dependent monooxygenase
PA2356 (msuD)18.441.052141Methanesulfonate sulfonatase
PA2357 (msuE)17.800.00431NADH-dependent FMN reductase
PA344713.472.411116Probable ATP-binding component of ABC transporter
PA344814.590.73600Probable permease of ABC transporter
PA395420.210.272141Hypothetical protein
  • a Other sulfur sources were supplied for growth of P. aeruginosa. For a complete list of P. aeruginosa genes upregulated and downregulated (greater than twofold) under the conditions tested, see Table S3 in the supplemental material. Analysis was performed using Genespring GX 7.3, with a Benjamini-Hochberg multiple-testing correction and a false detection rate of 5%. Significance of the called genes was also assessed using SAM (49), giving q values of <0.05.

  • b Percentages of sulfur-amino acids were calculated as the proportion of cysteine/methionine residues in the encoded protein, not including the initiating formylmethionine.

  • c COG to which the gene has been assigned (46).