TABLE 2.

Proteins differentially expressed during exponential and stationary growth phases in the hfq mutant in comparison to the WT levels

ORFGenePhase (ratio)a corresponding to:Putative functionReference(s) identifying protein(s)
OverexpressionRepressionDetected in nodulesbAffected by hfq mutation in other organismsc
SMa0312Stat (0.5)Hypothetical protein
SMb20025Expo (0.5); Stat (0.35)Hypothetical protein
SMb20091Expo (0.48); Stat (0.32)Hypothetical protein
SMb20428ehuBStat (2.0)Expo (0.5)Ectoine binding protein20, 21
SMb21176phoDExpo (0.22)Phosphate binding protein20, 21, 45
SMb21181Expo (5.7); Stat (4.4)Putative glutaryl-coenzyme A dehydrogenase
SMb21441Expo (2.6)Stat (0.34)Putative inosine-5′-monophosphate dehydrogenase
SMb21549thtRStat (3.4)Putative sulfotransferase
SMb21647agpAExpo (0.19)α-Galactoside binding protein
SMc00072Expo (0.5); Stat (0.1)Hypothetical peroxiredoxin
SMc00140Expo (2.0); Stat (2.4)Amino acid binding protein20, 21
SMc00153Stat (2.0)Hypothetical protein20
SMc00242Expo (2.6); Stat (2.0)Sugar binding protein
SMc00357efpExpo (0.5)Elongation factor EF-P32 (EC, −)
SMc00419gshB1Expo (0.45); Stat (0.35)Glutathione synthetase20
SMc00421cysK1Expo (0.38); Stat (0.45)Cysteine synthase A8, 4532 (EC, +); 64 (ST, +)
SMc00595Stat (2.1)Hypothetical protein
SMc00770potFExpo (0.28)Putrescine-binding protein64 (ST, +)
SMc00784Stat (0.35)Putative iron binding ABC transport system10, 20, 21
SMc00786dppA1Expo (2.5); Stat (3.7)Dipeptide-binding protein64, 78 (ST, +); 32 (EC, +)
SMc00883Expo (0.42)Hypothetical protein
SMc00912groES1Stat (0.23)10-KDa chaperonin A protein; chaperonin GroES3 (repression); 2032 (EC, −)
SMc00948glnAStat (2.9)Glutamine synthetase I10 (absence and repression); 20, 23, 45 (absence)32 (EC, −)
SMc01028enoExpo (0.50); Stat (0.37)Enolase10 (repression)
SMc01033Stat (0.43)Probable arylesterase
SMc01169aldExpo (2.6); Stat (2.1)Probable alanine dehydrogenase2032 (EC, −)
SMc01208ppiBStat (0.5)Peptidyl-prolyl cis-trans isomerase B protein32, 74 (EC, −); 78 (ST, −); 19 (VC, +)
SMc01273Expo (0.5)S-Formylglutathione hydrolase
SMc01318rplLExpo (2.1)Stat (0.21)50S ribosomal protein L7/L122165 (ST, −)
SMc01326tufBStat (0.37)Elongation factor EF-Tu10 (repression); 11, 4565 (ST, −)
SMc01418Expo (0.33)Hypothetical signal peptide protein20
SMc01525dppA2Expo (4.1); Stat (3.2)Putative dipeptide binding periplasmic protein32 (EC, −); 64, 78 (ST, +),
SMc01700ppiAExpo (0.50); Stat (0.40)Peptidyl-prolyl cis-trans isomerase64 (ST, +); 19 (VC, +)
SMc01834Stat (2.0)Hypothetical protein20
SMc01852pfkStat (3.5)Pyrophosphate-fructose-6-phosphate 1-phosphotransferase64 (ST, −)
SMc01861murEExpo (3.7)Probable UDP-N-acetylmuramoylalanyl-d-Glutamate-2,6-diaminopimelate ligase
SMc01874ftsZ1Stat (0.48)Cell division protein FtsZ3 (repression); 20 (absence)68 (EC, +)
SMc01946livKExpo (2.6); Stat (4.7)Leucine-specific binding protein20, 2164 (ST, +)
SMc02098frrExpo (2.6)Ribosome recycling factor
SMc02100tsfExpo (4.5)Elongation factor EF-Ts32 (EC, −); 64, 78 (ST, +)
SMc02118Stat (6.4)Expo (0.29)Periplasmic binding ABC transporter20, 21
SMc02156Expo (0.07)Hypothetical protein3, 17, 21
SMc02344Stat (2.2)Periplasmic binding protein
SMc02495Stat (0.5)Putative translaldolase20
SMc02501atpDExpo (0.43); Stat (0.5)F0F1 ATP synthase subunit beta20, 3832 (EC, −)
SMc02509sitAStat (2.2)Iron-manganese binding protein3, 21
SMc02514Expo (0.5)Putative periplasmic binding protein
SMc02692rplYExpo (0.5)50S ribosomal protein L252032 (EC, −); 78 (ST, −)
SMc02720clpP2Expo (0.5)ATP-dependent Clp protease proteolytic subunit20
SMc02737Expo (3.4)Putative GB binding protein
SMc02788secBStat (0.25)Protein-export protein SecB;20, 21
SMc02884Expo (0.5)Putative lipoprotein precursor20
SMc03124Expo (3.2); Stat (4.1)Peptide/nickel transport system substrate binding
SMc03157Stat (9.9)Expo (0.31)d-Methionine transport system substrate binding
SMc03786bfrExpo (0.35); Stat (0.29)Probable bacterioferritin (BFR) (cytochrome b1) (cytochrome b557) protein3, 10 (repression)64, 78 (ST, −)
  • a The number in parentheses represents the ratio of protein abundance in the mutant strain to that in the wild-type strain. Stat, stationary phase; Expo, exponential phase.

  • b Listed are references identifying the corresponding protein in nodules in proteomic or transcriptomic studies of nodulation. The absence of the protein in nodules or the repression of transcription is indicated in parentheses.

  • c + and − denote up- and downregulation, respectively, of the corresponding protein. EC, ST, and VC correspond to Escherichia coli, Salmonella enterica serovar Typhimurium, and Vibrio cholerae, respectively.