TABLE 2

Functional classification of genes or operons differentially regulated by (p)ppGpp or DksA in H. ducreyi

Functional categoryNo. of genes differentially expressed
35000HPΔrelAΔspoT/35000HPa35000HPΔdksA/35000HPb
UpregulatedDownregulatedUpregulatedDownregulated
Amino acid biosynthesis2451
Amino acid transport and metabolism6652
Amino sugar and nucleotide metabolism41227
Cellular carbohydrate biosynthetic process7531
Carbohydrate metabolism1230
Cell division2512
Cell membrane111597
Cellular homeostasis4221
Cellular response to stress0230
DNA binding3142
DNA metabolic process8481
Fatty acid biosynthesis and metabolism7342
Intracellular trafficking and secretion11115
Ion transport3724
Iron sulfur cluster binding2603
Lipid biosynthesis and metabolism3452
Metal ion binding10875
Nucleotide binding819411
Protein fate7955
RNA binding4010
RNA processing9853
Transcription10923
Translation1527126
Transport of proteins and carbohydrates71126
Uncharacterized conserved protein61071
Hypothetical proteins75893092
  • a Genes differentially expressed in 35000HPΔrelAΔspoT mutant versus 35000HP strain at stationary phase. Fifty-two percent of the genes were downregulated genes, and 48% were upregulated genes.

  • b Genes differentially expressed in 35000HPΔdksA mutant versus 35000HP strain at stationary phase. Sixty-two percent of the genes were downregulated genes, and 38% were upregulated genes.