Table 1.
Selected genes transcriptionally regulated by Ca in MC‐RNA‐Seq and Flask‐RNA‐Seq.
| Functional group | Gene name | Locus tag | Product | MC | Flask |
|---|---|---|---|---|---|
| Twitching motility | pilG* | PD0845 | Pili chemotaxis CheY homolog PilG | Up | – |
| pilI | PD0846 | Pili chemotaxis CheW homolog Pil | Up | – | |
| ‐ | PD1077 | Fimbrial protein | Down | – | |
| pilH* | PD1632 | Regulatory protein pilH family | Up | Down | |
| pilP | PD1692 | Fimbrial assembly protein | Up | – | |
| pilO | PD1693 | Fimbrial assembly membrane protein | Up | – | |
| pilN | PD1694 | Fimbrial assembly membrane protein | Up | – | |
| pilA1 | PD1924 | Fimbrial protein | Down | Down | |
| pilA2 | PD1926 | Fimbrial protein | ‐ | Down | |
| pilR | PD1928 | Regulatory protein | Up | – | |
| Adhesins and EPS biosynthesis | xanA | PD0213 | Phosphoglucomutase | Down | – |
| xadA | PD0731 | Outer membrane protein XadA | – | Up | |
| hsf | PD0744 | Surface protein | Up | Up | |
| pspA | PD0986 | Hemagglutinin‐like secreted protein | – | Up | |
| gumM | PD1387 | GumM protein | – | – | |
| gumJ | PD1389 | GumJ protein | – | Up | |
| gumH | PD1391 | GumH protein | – | Up | |
| gumF | PD1392 | GumF protein | – | Up | |
| hxfA | PD2118 | Hemagglutinin‐like secreted protein | – | Up | |
| Regulatory function | – | PD1087 | XRE family transcriptional regulator | Down | Down |
| gacA | PD1984 | Transcriptional regulator | Down | ‐ | |
| Phage‐related proteins | – | PD0377 | Phage‐related protein | Down | Up |
| – | PD0906 | Phage‐related protein | Up | Down | |
| – | PD0916 | Phage‐related protein | Up | Down | |
| – | PD0929 | Phage‐related protein | Up | Down | |
| – | PD0932 | Phage‐related protein | Up | Down | |
| – | PD0936 | Phage‐related protein | Up | Down | |
| – | PD0943 | Phage‐related protein | Up | Down | |
| Colicin V‐like bacteriocins | cvaC | PD0215 | colicin V precursor | Up | Up |
| Recombination and competence | recF | PD0003 | Recombination protein F | Up | – |
| recJ | PD0402 | ssDNA‐specific exonuclease RecJ | – | Up | |
| recD | PD1651 | exodeoxyribonuclease V subunit alpha | – | Up | |
| comA | PD0358 | DNA uptake protein | – | Up | |
| comM | PD0464 | Competence‐like protein | Down | – | |
| comB | PD1558 | DNA transport competence protein | Down | – | |
| ruvC | PD0886 | Holliday junction resolvase | Up | Down | |
| ung | PD2049 | Uracil‐DNA glycosylase | Up | – | |
| Uncharacterized Proteins | PD0556 | hypothetical protein | Up | Down | |
| PD1111 | hypothetical protein | Down | Up |
–, No changes; Down, downregulated gene expression; Flask, Flask‐RNA‐Seq (Parker et al., 2016); MC, MC‐RNA‐Seq (this study); and Up, upregulated gene expression.
Locus tag in bold text indicates genes overlapped between MC and Flask.
Asterisk indicates q value of gene is < 0.05, but fold change is not > 1.5.