TABLE 3

Downregulated genes in H. pylori SS1 biofilm using RNA-seq analysis, grouped by functional role categoriesa

LocusPutative identificationFold changeb
Cell envelope
    murB (HPYLSS1_01344)UDP-N-acetylenolpyruvoylglucosamine reductase−2.52
    fliM (HPYLSS1_00401)Flagellar motor switch protein FliM−2.25
    fliI (HPYLSS1_01346)Flagellum-specific ATP synthase−2.16
    yohD-1 (HPYLSS1_00775)Inner membrane protein YohD−2.14
Cellular processes
    mreB (HPYLSS1_01316)Rod shape-determining protein MreB−2.95
    ureA (HPYLSS1_00068)Urease subunit α−2.28
    groEL (HPYLSS1_00013)60-kDa chaperonin−2.17
    hcpC (HPYLSS1_01039)Cysteine-rich protein HcpC−3.78
    cmmA (HPYLSS1_01486)Polymer-forming cytoskeletal family protein−2.58
    typA (HPYLSS1_00442)GTP-binding protein−2.02
Regulatory functions
    hslV (HPYLSS1_00733)ATP-dependent protease subunit−3.33
    HPYLSS1_00758Putative TrmH family tRNA/rRNA−2.24
Translation
    rplR (HPYLSS1_01253)50S ribosomal protein L18−3.09
    rpsE (HPYLSS1_01252)30S ribosomal protein S5−3.06
    rpsG (HPYLSS1_01140)30S ribosomal protein S7−2.52
    rpsC (HPYLSS1_01262)30S ribosomal protein S3−2.49
    rpsK (HPYLSS1_01246)30S ribosomal protein S11−2.44
    rplW (HPYLSS1_01266)50S ribosomal protein L23−2.29
    rplN (HPYLSS1_01258)50S ribosomal protein L14−2.29
    rplD (HPYLSS1_01267)50S ribosomal protein L4−2.23
    rplB (HPYLSS1_01265)50S ribosomal protein L2−2.22
    rplF (HPYLSS1_01254)50S ribosomal protein L6−2.21
    rpmF (HPYLSS1_00189)50S ribosomal protein L32−2.14
    rpsD (HPYLSS1_01245)30S ribosomal protein S4−2.12
    rplS (HPYLSS1_01093)50S ribosomal protein L19−2.09
    rplE (HPYLSS1_01256)50S ribosomal protein L5−2.07
    rplV (HPYLSS1_01263)50S ribosomal protein L22−2.02
    rpmG (HPYLSS1_01151)50S ribosomal protein L33−2.02
    fusA (HPYLSS1_01139)Elongation factor G−2.23
    tufA (HPYLSS1_01152)Elongation factor Tu−2.14
    yigZ (HPYLSS1_01411)Elongation factor−2.05
Amino acid biosynthesis
    trpB (HPYLSS1_01240)Tryptophan synthase β chain−2.68
Fatty acid and phospholipid metabolism
    acpP_2 (HPYLSS1_00944)Acyl carrier protein−2.96
    plsX (HPYLSS1_00190)Phosphate acyltransferase−2.71
    scoB (HPYLSS1_00895)3-Oxoacid coenzyme A-transferase, subunit B−2.11
Biosynthesis of cofactors, prosthetic groups, and carriers
    birA (HPYLSS1_01084)Bifunctional ligase/repressor BirA−3.29
    ribH (HPYLSS1_00002)6,7-Dimethyl-8-ribityllumazine synthase−2.47
    folK (HPYLSS1_00396)2-Amino-4-hydroxy-6-hydroxymethyldihydropteridine
pyrophosphokinase
−2.13
    ggt (HPYLSS1_01061)γ-Glutamyl transpeptidase−2.06
DNA restriction, modification, recombination, and repair
    HPYLSS1_00145Recombinase A−2.46
Energy metabolism
    atpC (HPYLSS1_01075)ATP synthase ε chain−2.78
    atpE (HPYLSS1_01164)ATP synthase subunit c−2.48
    nifU (HPYLSS1_00210)NifU-like protein−2.15
    adhA (HPYLSS1_00)Alcohol dehydrogenase−2.12
    mdaB (HPYLSS1_00836)Modulator of drug activity B−2.05
Purine, pyrimidine, nucleosides, and nucleotide
    pyrD_2 (HPYLSS1_01468)Dihydroorotate dehydrogenase B [NAD(+)], catalytic subunit−2.13
Hypothetical proteins
    HPYLSS1_00188Hypothetical protein−3.92
    HPYLSS1_00885Hypothetical protein−3.15
    HPYLSS1_00325Hypothetical protein/putative β-lactamase−2.95
    HPYLSS1_00036Hypothetical protein/putative nucleoid-associated protein−2.79
    HPYLSS1_01458Hypothetical protein−2.79
    HPYLSS1_01225Hypothetical protein−2.71
    HPYLSS1_00259Hypothetical protein−2.66
    HPYLSS1_01321Hypothetical protein−2.44
    HPYLSS1_01060Hypothetical protein−2.32
    HPYLSS1_00657Hypothetical protein−2.27
    HPYLSS1_01143Hypothetical protein−2.21
    HPYLSS1_00296Hypothetical protein/putative FoF1-ATPase subunit−2.2
    HPYLSS1_00945Hypothetical protein−2.16
    HPYLSS1_00057Hypothetical protein−2.03
    HPYLSS1_00569Hypothetical protein−2.07
  • a Downregulation was determined as a cutoff ratio of ≤−1 log2 fold change and P value of <0.05.

  • b Fold change represents the difference in gene expression between biofilm (n = 3) and planktonic (n = 3) populations.