TABLE 1

Summary of COG functional classifications of genes differentially expressed in the WT relative to the misR mutant, the misS mutant relative to the misR mutant, and the WT relative to the misS mutant

COG functional class and categoryNo. of genes differentially expressed
WT/misR mutantmisS mutant/misR mutantmisS mutant/WT
UpDownUpDownUpDown
Cellular processes and signaling
    Cell cycle control, cell division, and chromosome partitioning000000
    Cell wall/membrane/envelope biogenesis61441524
    Defense mechanisms261700
    Intracellular trafficking, secretion, and vesicular transport010200
    Posttranslational modification, protein turnover, and chaperones2901002
    Signal transduction mechanisms201102
Information storage and processing
    Phage-derived proteins, transposases, and other mobilome components18011000
    Replication, recombination, and repair210200
    RNA processing and modification010100
    Transcription221200
    Translation, ribosomal structure, and biogenesis140410
Metabolism
    Amino acid transport and metabolism41231000
    Carbohydrate transport and metabolism231100
    Coenzyme transport and metabolism011101
    Energy production and conversion21411200
    Inorganic ion transport and metabolism162330
    Lipid transport and metabolism232300
    Nucleotide transport and metabolism111200
    Secondary metabolite biosynthesis, transport, and catabolism001000
Poorly characterized
    Function unknown11031000
    General function prediction only321401
Unclassified12410501
Total63944495611