Table 1. Selected genes of interest that were significantly differentially regulated in the fixLJ deletion mutant relative to the wild-type strain AU0158 measured by RNA-seqa.
| Category/Gene name (genome designation) | Description | Fold change in fixLJ deletion mutant |
|---|---|---|
| Motility | ||
| flhD (AK34_2903) | Flagellar transcriptional activator | -2.9 |
| cheY (AK34_2899) | Chemotaxis regulator | -2.1 |
| AK34_269 | methyl-accepting chemotaxis (MCP) signaling domain protein | -2.1 |
| Type IVa pilus | ||
| pilE (AK34_2364) | Type IV pilus biogenesis protein | -2.7 |
| AK34_2365 | FIG00453045: hypothetical protein | -4.4 |
| pilW (AK34_23660 | Type IV fimbrial biogenesis protein | -9.7 |
| fimT (AK34_2368) | Tfp pilus assembly protein FimT | -3.1 |
| Type IVb pilus | ||
| AK34_1641 | Response regulator containing CheY-like receiver | 3.1 |
| tadD (AK34_1644) | Flp pilus assembly protein | 2.3 |
| tadC (AK34_1645) | Type II/IV secretion system protein | 2.4 |
| tadA (AK34_1647) | Type II/IV secretion system ATP hydrolase | 2.7 |
| AK34_1649 | Type II/IV secretion system secretin RcpA/CpaC | 2.4 |
| AK34_1652 | Probable prepilin peptidase transmembrane protein | 2.1 |
| flp (AK34_1653) | Flp pilus assembly protein, pilin Flp | 2.1 |
| Type III Secretion System | ||
| AK34_3647 | Type III secretion bridge between inner and outer membrane lipoprotein | 10.1 |
| AK34_3648 | Type III secretion cytoplasmic protein | 10.5 |
| AK34_3641 | Type III secretion inner membrane channel protein | 9.4 |
| AK34_3649 | Type III secretion cytoplasmic protein | 8.6 |
| AK34_3650 | Type III secretion cytoplasmic ATP synthase | 7.9 |
| AK34_3657 | Type III secretion inner membrane protein | 8.0 |
| AK34_3658 | Type III secretion inner membrane protein | 6.8 |
| Regulators | ||
| AK34_1304 | RNA polymerase sigma factor RpoS | 5.0 |
| AK34_3568 | Transcriptional regulator, LysR family | 3.4 |
| AK34_1422 | Transcriptional regulator, LysR family | 3.1 |
| AK34_3852 | Transcriptional regulator, MarR family | -6.1 |
| AK34_5402 | Transcriptional regulator, LysR family | -5.4 |
| AK34_2833 | Transcriptional regulator, AsnC family | -3.6 |
| AK34_1626 | Transcriptional regulator/sugar kinase | -9.5 |
| AK34_4350 | Two component system histidine kinase | -10.5 |
| Other | ||
| rbsK (AK34_5286) | Ribokinase | -9.1 |
| AK34_4362 | Putative cytochrome P450 hydroxylase | -44.7 |
| AK34_1628 | ABC-type sugar transport system, permease protein | -9.4 |
| AK34_1627 | ABC-type sugar transport system, ATP-binding protein | -9.9 |
| AK34_5433 | Outer membrane protein (porin) | -3.6 |
| AK34_3420 | Major facilitator family transporter | -3.6 |
| AK34_1355 | Outer membrane protein W precursor | 11.4 |
| AK34_3656 | Peptidoglycan hydrolase VirB1 | 11.6 |
| AK34_2361 | Probable transmembrane protein | 3.1 |
| hfq (AK34_1317) | RNA-binding protein | 2.8 |
| AK34_4984 | FOG: GGDEF domain | 2.4 |
| AK34_1354 | Dioxygenases related to 2-nitropropane dioxygenase | 5.8 |
| AK34_3566 | Enoyl-CoA hydratase | 13.6 |
| AK34_3563 | Acetyl-CoA synthetase | 13.9 |
| AK34_3562 | Butyryl-CoA dehydrogenase | 15.8 |
| AK34_3722 | 4-carboxymuconolactone decarboxylase | 11.9 |
| AK34_3721 | Phenylacetic acid degradation protein PaaY | 13.0 |
| AK34_4113 | Outer membrane protein (porin) | -4.7 |
a Significance is defined as greater than 2-fold change with q <0.05.