TABLE 2

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

LocusPutative identificationFold changeb
Cell envelope
    flgL (HPYLSS1_00284)Flagellar hook-associated protein 37.64
    flgK (HPYLSS1_01062)Flagellar hook-associated protein 16.16
    flgM (HPYLSS1_01066)Anti-sigma 28 factor3.94
    flaG (HPYLSS1_00586)Polar flagellin G3.93
    flaB (HPYLSS1_00110)Flagellin B3.52
    flgE1 (HPYLSS1_00464)Flagellar hook protein 13.07
    flgB (HPYLSS1_01503)Flagellar basal body rod protein2.37
    fliL (HPYLSS1_00526)Flagellar protein of unknown function2.25
    fliK (HPYLSS1_00653)Flagellar hook-length control protein2.14
    fliD (HPYLSS1_00585)Flagellar hook-associated protein 22
    lpxB (HPYLSS1_00467)Lipid A-disaccharide synthase3.06
    lptB (HPYLSS1_00622)Lipopolysaccharide export system ATP-binding2.54
    mltD (HPYLSS1_01517)Membrane-bound lytic murein transglycosylase D precursor2
    pgdA (HPYLSS1_00299)Peptidoglycan deacetylase2.1
    HPYLSS1_00450Membrane protein3.78
    HPYLSS1_01378Outer membrane protein homD3.26
    HPYLSS1_01113Putative outer membrane protein2.91
    HPYLSS1_01021Outer membrane protein homC2.69
    HPYLSS1_01469Putative outer membrane protein2.52
Cellular processes
    cagE (HPYLSS1_00705)Type IV secretion system protein VirB4/DNA transfer2.46
    cagW (HPYLSS1_00718)cag pathogenicity island protein CagW (cag10)2.31
    cagL (HPYLSS1_00710)cag pathogenicity island protein CagL (cag18)2.02
    recR (HPYLSS1_00636)Recombination protein RecR3.7
    HPYLSS1_00410DNA polymerase I2.08
    HPYLSS1_01332CMP-N-acetylneuraminate-β-galactosamide2.2
Regulatory functions
    hrcA (HPYLSS1_00106)Heat-inducible transcription repressor HrcA4.84
    hspR (HPYLSS1_00407)Putative heat shock protein HspR2.09
    crdR (HPYLSS1_01312)Two-component response regulator CrdR2.03
    rsfS (HPYLSS1_01340)Ribosomal silencing factor S2.16
Translation
    ansA (HPYLSS1_00615)Putative l-asparaginase2.11
    cbpA (HPYLSS1_00408)Curved DNA-binding protein2.19
    HPYLSS1_00252Chaperone protein ClpB2.7
    HPYLSS1_01332CMP-N-acetylneuraminate-β-galactosamide2.2
Amino acid biosynthesis
    porC (HPYLSS1_01050)Pyruvate synthase subunit PorC2.02
Fatty acid and phospholipid metabolism
    acpS (HPYLSS1_00527)Holo-[acyl-carrier-protein] synthase2.89
    fenF (HPYLSS1_00085)Malonyl CoA-acyl carrier protein transacylase2.26
Biosynthesis of cofactors, prosthetic groups, and carriers
    thiE (HPYLSS1_00492)Thiamine-phosphate synthase4.13
    salL (HPYLSS1_00914)Adenosyl-chloride synthase2.87
DNA restriction, modification, recombination, and repair
    HPYLSS1_00696Restriction endonuclease2.19
Transport and binding proteins
    metI (HPYLSS1_01522)d-Methionine transport system permease protein2.18
    HPYLSS1_00805Putative ABC transporter ATP-binding protein2.02
Energy metabolism
    ansA (HPYLSS1_00615)Putative l-asparaginase2.11
    HPYLSS1_00772Pyrroloquinoline quinone biosynthesis protein7.5
Hypothetical proteins
    HPYLSS1_00605Hypothetical protein/putative GTPase dynamin17.63
    HPYLSS1_00355Hypothetical protein7.82
    HPYLSS1_01063Hypothetical protein7.58
    HPYLSS1_00488Hypothetical protein5.65
    HPYLSS1_01091Hypothetical protein5.34
    HPYLSS1_00197Hypothetical protein4.4
    HPYLSS1_00109Hypothetical protein4.25
    HPYLSS1_00933Hypothetical protein3.91
    HPYLSS1_01183Hypothetical protein3.37
    HPYLSS1_00583Hypothetical protein3.07
    HPYLSS1_00404Hypothetical protein2.85
    HPYLSS1_01474Hypothetical protein2.77
    HPYLSS1_00984Hypothetical protein2.56
    HPYLSS1_01009Hypothetical protein2.26
    HPYLSS1_01271Hypothetical protein2.05
    HPYLSS1_00558Hypothetical protein2.04
    HPYLSS1_01019Hypothetical protein2.03
    HPYLSS1_00777Hypothetical protein2.01
    HPYLSS1_00529Hypothetical protein2
  • a Upregulation 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.