Table 1. Enrichment of genes involved in flagellar biosynthesis in the CsrA coIP data.
|
C. jejuni
NCTC11168 |
C. jejuni
81-176 |
|||
|---|---|---|---|---|
| Enrichment (reads) | 5′UTR | ORF | 5′UTR | ORF |
| Regulation of expression (class 1) | ||||
| rpoN (Cj0670) | 1.5 × (26) | 25 × (1,747) | − | 8 × (634) |
| fliA (Cj0061c) | − | 1.1 × (121) | − | 0.7 × (79) |
| flgS (Cj0793) | − | 1.7 × (43) | 1.3 × (1) | 1.7 × (15) |
| flgR (Cj1024) | 1.2 × (4) | 1.1 × (137) | 1.3 × (4) | 1.2 × (101) |
| Flagellar protein secretion (class 1) | ||||
| flgM (Cj1464) | − | 5 × (1429) | − | 2.3 × (380) |
| fliF (Cj0318) | − | 6.1 × (1,005) | − | 7.8 × (1,105) |
| flhA (Cj0882c) | − | 1.2 × (82) | − | 0.9 × (53) |
| flhB (Cj0335) | 0.6 × (3) | 1.2 × (99) | 0.7 × (1) | 1.0 × (67) |
| fliO (Cj0352) | − | 1.4 × (41) | − | 0.7 × (1) |
| fliP (Cj0820c) | − | 1.2 × (29) | − | 0.5 × (15) |
| fliQ (Cj1675) | − | 1.3 × (45) | − | 0.9 × (29) |
| fliR (Cj1179c) | − | 1.2 × (6) | − | 0.5 × (5) |
| fliH (Cj0320) | − | 4.8 × (202) | − | 1.3 × (100) |
| fliI (Cj0195) | − | 3.6 × (442) | − | 0.6 × (86) |
| Basal body components (classes 1 and 2) | ||||
| fliE (Cj0526c) | − | 2.4 × (268) | − | 1.4 × (120) |
| flgC (Cj0527c) | − | 1.2 × (397) | − | 0.9 × (217) |
| flgB (Cj0528c) | 1.6 × (7) | 1.6 × (181) | 0.7 × (2) | 0.9 × (61) |
| flgG2 (Cj0697) | − | 43.9 × (8,133) | − | 77.4 × (9,670) |
| flgG (Cj0698) | 1.2 × (1) | 1.4 × (253) | 5.3 × (4) | 1.3 × (165) |
| flgJ (Cj1463) | − | 4.4 × (180) | − | 1.0 × (26) |
| flgI (Cj1462) | 170.5 × (5,750) | 52.7 × (12,087) | 157.1 × (1,666) | 61.5 × (5,401) |
| flgA (Cj0769c) | 0.8 × (2) | 15.8 × (410) | 0.9 × (4) | 3.7 × (104) |
| flgH (Cj0687c) | 200.9 × (1,911) | 20.1 × (3,288) | 110.1 × (917) | 27.6 × (2,487) |
| Flagellar hook components (class 2) | ||||
| flgE (Cj1729c) | − | 68.2 × (104,324) | − | 7.1 × (3,967) |
| flgD (Cj0042) | − | 3.6 × (1015) | − | 2.0 × (284) |
| flgE2 (Cj0043) | − | 2.5 × (1045) | − | 1.1 × (250) |
| fliK (Cj0041) | − | 4.1 × (613) | − | 1.2 × (89) |
| Cj0040* | 356.2 × (3,389) | 110.6 × (9,277) | 38 × (230) | 20.4 × (727) |
| flgK (Cj1466) | − | 0.7 × (4) | − | 1.0 × (141) |
| flgL (Cj0887c) | − | 2.0 × (484) | 2.3 × (74) | 0.9 × (193) |
| Flagellar filament components (classes 2 and 3) | ||||
| flaA (Cj1339c) | 304.5 × (693,471) | 111 × (473,588) | 324.7 × (158,590) | 45.3 × (138,159) |
| flaB (Cj1338c) | 58.8 × (915) | 14.1 × (17,880) | 59.4 × (1,170) | 14.9 × (29,530) |
| fliD (Cj0548) | − | 6.8 × (4,348) | − | 5.4 × (3,929) |
| fliS (Cj0549) | 1.6 × (149) | 1.3 × (165) | ||
| flaC (Cj0720) | 1.2x (344) | 1.2 × (1,298) | 1.3 × (239) | 1.2 × (1,237) |
| Other enriched genes (>5x) involved in flagella formation | ||||
| pseB (Cj1293) | 119.7 × (2,298) | 9.5 × (2,280) | 34.5 × (470) | 4.1 × (759) |
| pseI (Cj1317) | 1.7 × (22) | 7.2 × (864) | 2.3 × (14) | 0.8 × (111) |
| flaG (Cj0547) | 346.1 × (11,077) | 72.4 × (18,150) | 168.5 × (3,701) | 84.2 × (16,012) |
| motA (Cj0337c) | 10.3 × (89) | 1.8 × (660) | 1.4 × (16) | 0.8 × (271) |
| Cj0951c | − | 15.2 × (79) | 2 × (3) | 1.3 × (194) |
| Cj0248 | 5.5 × (120) | 1.8 × (387) | 1.1 × (38) | 0.9 × (257) |
| flhX (Cj0848c) | − | 7.5 × (13) | − | 1.5 × (7) |
CoIP, co-immunoprecipitation; UTR, untranslated region; ORF, open reading frame.
Classification of flagellar genes is based on ref. 75. Transcripts with >5-fold enrichment in cDNA read counts in the CsrA-3xFLAG versus control coIP libraries are highlighted in bold. Numbers in brackets indicate the absolute cDNA read counts in the CsrA-3xFLAG coIP libraries.
*Cj0040 (unknown function) is the first gene of the hook gene operon.