TABLE 3.
Downregulated genes in H. pylori SS1 biofilm using RNA-seq analysis, grouped by functional role categoriesa
| Locus | Putative identification | Fold 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_00758 | Putative 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_00145 | Recombinase 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_00188 | Hypothetical protein | −3.92 |
| HPYLSS1_00885 | Hypothetical protein | −3.15 |
| HPYLSS1_00325 | Hypothetical protein/putative β-lactamase | −2.95 |
| HPYLSS1_00036 | Hypothetical protein/putative nucleoid-associated protein | −2.79 |
| HPYLSS1_01458 | Hypothetical protein | −2.79 |
| HPYLSS1_01225 | Hypothetical protein | −2.71 |
| HPYLSS1_00259 | Hypothetical protein | −2.66 |
| HPYLSS1_01321 | Hypothetical protein | −2.44 |
| HPYLSS1_01060 | Hypothetical protein | −2.32 |
| HPYLSS1_00657 | Hypothetical protein | −2.27 |
| HPYLSS1_01143 | Hypothetical protein | −2.21 |
| HPYLSS1_00296 | Hypothetical protein/putative FoF1-ATPase subunit | −2.2 |
| HPYLSS1_00945 | Hypothetical protein | −2.16 |
| HPYLSS1_00057 | Hypothetical protein | −2.03 |
| HPYLSS1_00569 | Hypothetical 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.