TABLE 3.
Genes aberrantly expressed in the Δfur mutant
| HP no. | JHP no. | Gene function and name | Avg fold change Avg
|
Identified in previous studiesa | Predicted transcriptional unitb | Transcriptional unit genes identified in previous studiesc | Remarksd | |
|---|---|---|---|---|---|---|---|---|
| Exponential | Stationary | |||||||
| HP0261 | JHP0245 | Hypothetical | 4.2 | HP0261-HP0260 | EF (HP0260) | Theoretical Fur box (HP0261) | ||
| HP0294 | JHP0279 | Aliphatic amidase, amiE | 2.8 | 5.9 | EF, MIL | Theoretical Fur box (HP0294, JHP0279) | ||
| HP0309 | JHP0294 | Conserved hypothetical protein | 2.3 | MIL | HP0309-HP0312 | MIL (HP0309, HP0310, HP0311) | Theoretical Fur box (HP0309, JHP0294) | |
| HP0588 | JHP0536 | Ferredoxin-like protein, oorD | 0.4 | HP0588-HP0591 | MIL (HP0589) | Ni (HP0588) theoretical Fur box on (JHP0536) | ||
| HP0589 | JHP0537 | Ferredoxin oxidoreductase, alpha subunit, oorA | 0.4 | MIL | ||||
| HP0591 | JHP0539 | Ferredoxin oxidoreductase, gamma subunit, oorC | 0.5 | |||||
| HP0653 | JHP0598 | Nonheme iron-containing ferritin transporters, pfr | 2.0 | EF, LF, MIL | HP0653-HP0651 | EF (HP0652, HP0653), LF (HP0653), MIL (HP0652, HP0653) | Ni (HP0653), Cu (HP0653) | |
| HP0672 | JHP0568 | Solute-binding signature and mitochondrial signature protein, aspB | 2.2 | MIL | ||||
| HP0686 | JHP0626 | Iron(III) dicitrate transport protein, fecA1 | 5.3 | 3.4 | EF, MIL | Theoretical Fur box (HP0686, JHP0626) | ||
| HP0806 | JHP0742 | Hypothetical | 4 | EF* | ||||
| HP0807 | JHP0743 | Iron(III) dicitrate transport protein, fecA2 | 16.5 | 3.8 | EF, MIL | Theoretical Fur box (HP0807, JHP0743) | ||
| HP0876 | JHP0810 | Iron-regulated outer membrane protein, frpB1 | 13 | 7.8 | EF, MIL | Theoretical Fur box (HP0876, JHP0810) | ||
| HP0877 | JHP0811 | Holliday Junction endodeoxyribonuclease, ruvC | 3 | 2 | ||||
| HP0887 | JHP0819 | Vacuolating cytotoxin, vacA | 2.2 | EF*, MIL | ||||
| HP0991 | JHP0939 | Hypothetical | 2.3 | Theoretical Fur box (JHP0939) | ||||
| HP1339 | JHP1258 | Biopolymer transport protein, exbB | 3.3 | 2.3 | EF, MIL | HP1339-HP1341 | EF (HP1339), MIL (HP1339) | Theoretical Fur box (HP1339), Ni (HP1340, HP1341), Cu (HP1340) |
| HP1340 | JHP1259 | Biopolymer transport protein, exbD | 4 | 2.8 | ||||
| HP1341 | JHP1260 | Siderophore-mediated iron transport protein, tonB2 | 2.0 | |||||
| HP1432 | JHP1321 | Histidine and glutamine-rich metal-binding protein | 3 | 3.2 | EF, MIL | |||
| HP1516 | NAe | Hypothetical | 2.6 | HP1520-HP1516 | Iron-sulfur-dependent L-serine dehydratase family | |||
| HP1520 | NA | Hypothetical | 3.9 | HP1520-HP1516 | Iron-sulfur dependent L-serine dehydratase family | |||
| HP1582 | JHP1489 | Pyridoxal phosphate biosynthetic protein J, pdxJ | 4.3 | 2.5 | MIL | HP1582-HP1584 | EF (HP1583), MIL (HP1582, HP1583) | Predicted bacterioferritin comigratory protein |
| HP1583 | JHP1490 | Pyridoxal phosphate biosynthetic protein A, pdxA | 4.4 | 3.1 | EF, MIL | HP1582-HP1584 | Predicted Iron-sulfur protein | |
| HP1584 | JHP1491 | Putative O-staloglycoprotein endopeptidase, gcp | 3 | 3.2 | HP1582-HP1584 | |||
| NA | JHP0820 | Putative lipopolysaccharide biosynthesis protein | 2.1 | JHP0823-JHP0820 | ||||
| NA | JHP0930 | Hypothetical | 2.0 | Theoretical Fur box (JHP0930) | ||||
| NA | JHP0940 | Hypothetical | 2.2 | Theoretical Fur box (JHP0940) | ||||
| NA | JHP0947 | Hypothetical | 0.5 | JHP0944-JHP0947 | ||||
| NA | JHP0951 | Integrase/recombinase (Xercd family) | 2.9 | |||||
The genes identified were compared to the H. pylori literature concentrated on iron- and/or Fur-regulated genes: EF, Ernst et al. (18); EF*, Ernst et al. (18), designated as iron dependent; LF, Lee et al. (24); MIL, Merrell et al. (33).
The genes identified were examined visually on the H. pylori strain 26695 genome and judged as being part of a transcriptional unit by assessing the number of stop codons between two adjacent genes over the span of less than 100 bp of noncoding regions between those genes at the same predicted transcriptional unit.
The genes suspected to be part of a transcriptional unit were compared to the H. pylori literature concentrated on iron- and/or Fur-regulated genes: EF, Ernst et al. (18); LF, Lee et al. (24); MIL, Merrell et al. (33). The HP gene number of the gene identified in the study according to TIGR's nomenclature of strain 26695 is given in parentheses.
Theoretical Fur box: for each gene a computerized search was conducted for a Fur box on both H. pylori strains 26695 and JHP99 published genomes. A Fur box was defined as the consensus sequence suggested by Merrell et al. (33), 250 bp upstream of the start of the predicted transcriptional unit. The HP gene number of the gene identified in the study according to TIGR's nomenclature of strain 26695 is given in parentheses. Genes identified in previous studies on nickel (Ni; Contreras et al. [11]) and copper (Cu; Waidner et al. [56]) are noted. The HP gene number of the gene identified in the study according to TIGR's nomenclature of strain 26695 is given in parentheses.
NA, not available.