TABLE 2.
Upregulated genes in H. pylori SS1 biofilm using RNA-seq analysis, grouped by functional role categoriesa
| Locus | Putative identification | Fold changeb |
|---|---|---|
| Cell envelope | ||
| flgL (HPYLSS1_00284) | Flagellar hook-associated protein 3 | 7.64 |
| flgK (HPYLSS1_01062) | Flagellar hook-associated protein 1 | 6.16 |
| flgM (HPYLSS1_01066) | Anti-sigma 28 factor | 3.94 |
| flaG (HPYLSS1_00586) | Polar flagellin G | 3.93 |
| flaB (HPYLSS1_00110) | Flagellin B | 3.52 |
| flgE1 (HPYLSS1_00464) | Flagellar hook protein 1 | 3.07 |
| flgB (HPYLSS1_01503) | Flagellar basal body rod protein | 2.37 |
| fliL (HPYLSS1_00526) | Flagellar protein of unknown function | 2.25 |
| fliK (HPYLSS1_00653) | Flagellar hook-length control protein | 2.14 |
| fliD (HPYLSS1_00585) | Flagellar hook-associated protein 2 | 2 |
| lpxB (HPYLSS1_00467) | Lipid A-disaccharide synthase | 3.06 |
| lptB (HPYLSS1_00622) | Lipopolysaccharide export system ATP-binding | 2.54 |
| mltD (HPYLSS1_01517) | Membrane-bound lytic murein transglycosylase D precursor | 2 |
| pgdA (HPYLSS1_00299) | Peptidoglycan deacetylase | 2.1 |
| HPYLSS1_00450 | Membrane protein | 3.78 |
| HPYLSS1_01378 | Outer membrane protein homD | 3.26 |
| HPYLSS1_01113 | Putative outer membrane protein | 2.91 |
| HPYLSS1_01021 | Outer membrane protein homC | 2.69 |
| HPYLSS1_01469 | Putative outer membrane protein | 2.52 |
| Cellular processes | ||
| cagE (HPYLSS1_00705) | Type IV secretion system protein VirB4/DNA transfer | 2.46 |
| 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 RecR | 3.7 |
| HPYLSS1_00410 | DNA polymerase I | 2.08 |
| HPYLSS1_01332 | CMP-N-acetylneuraminate-β-galactosamide | 2.2 |
| Regulatory functions | ||
| hrcA (HPYLSS1_00106) | Heat-inducible transcription repressor HrcA | 4.84 |
| hspR (HPYLSS1_00407) | Putative heat shock protein HspR | 2.09 |
| crdR (HPYLSS1_01312) | Two-component response regulator CrdR | 2.03 |
| rsfS (HPYLSS1_01340) | Ribosomal silencing factor S | 2.16 |
| Translation | ||
| ansA (HPYLSS1_00615) | Putative l-asparaginase | 2.11 |
| cbpA (HPYLSS1_00408) | Curved DNA-binding protein | 2.19 |
| HPYLSS1_00252 | Chaperone protein ClpB | 2.7 |
| HPYLSS1_01332 | CMP-N-acetylneuraminate-β-galactosamide | 2.2 |
| Amino acid biosynthesis | ||
| porC (HPYLSS1_01050) | Pyruvate synthase subunit PorC | 2.02 |
| Fatty acid and phospholipid metabolism | ||
| acpS (HPYLSS1_00527) | Holo-[acyl-carrier-protein] synthase | 2.89 |
| fenF (HPYLSS1_00085) | Malonyl CoA-acyl carrier protein transacylase | 2.26 |
| Biosynthesis of cofactors, prosthetic groups, and carriers | ||
| thiE (HPYLSS1_00492) | Thiamine-phosphate synthase | 4.13 |
| salL (HPYLSS1_00914) | Adenosyl-chloride synthase | 2.87 |
| DNA restriction, modification, recombination, and repair | ||
| HPYLSS1_00696 | Restriction endonuclease | 2.19 |
| Transport and binding proteins | ||
| metI (HPYLSS1_01522) | d-Methionine transport system permease protein | 2.18 |
| HPYLSS1_00805 | Putative ABC transporter ATP-binding protein | 2.02 |
| Energy metabolism | ||
| ansA (HPYLSS1_00615) | Putative l-asparaginase | 2.11 |
| HPYLSS1_00772 | Pyrroloquinoline quinone biosynthesis protein | 7.5 |
| Hypothetical proteins | ||
| HPYLSS1_00605 | Hypothetical protein/putative GTPase dynamin | 17.63 |
| HPYLSS1_00355 | Hypothetical protein | 7.82 |
| HPYLSS1_01063 | Hypothetical protein | 7.58 |
| HPYLSS1_00488 | Hypothetical protein | 5.65 |
| HPYLSS1_01091 | Hypothetical protein | 5.34 |
| HPYLSS1_00197 | Hypothetical protein | 4.4 |
| HPYLSS1_00109 | Hypothetical protein | 4.25 |
| HPYLSS1_00933 | Hypothetical protein | 3.91 |
| HPYLSS1_01183 | Hypothetical protein | 3.37 |
| HPYLSS1_00583 | Hypothetical protein | 3.07 |
| HPYLSS1_00404 | Hypothetical protein | 2.85 |
| HPYLSS1_01474 | Hypothetical protein | 2.77 |
| HPYLSS1_00984 | Hypothetical protein | 2.56 |
| HPYLSS1_01009 | Hypothetical protein | 2.26 |
| HPYLSS1_01271 | Hypothetical protein | 2.05 |
| HPYLSS1_00558 | Hypothetical protein | 2.04 |
| HPYLSS1_01019 | Hypothetical protein | 2.03 |
| HPYLSS1_00777 | Hypothetical protein | 2.01 |
| HPYLSS1_00529 | Hypothetical protein | 2 |
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.