Table 1. Effects of RNA interference against C. elegans homologues of bile acid biosynthetic enzymes.
| Enzyme Category# | C. elegans Genes | E-value from Blast Comparison to Mouse Protein | Summary of Effect on Defecation Rate | Effect on Defecation Rate (seconds)(p-values vs. control*) |
| Cholesterol 25-hydroxylase (AAC97482) | F35C8.5 | 3e-29 | ↓ | −18.4±4.1 (P<0.0001) |
| F49E12.10 | 3e-08 | - | +8.4±5.5 (P = 0. 1) | |
| F49E12.9 | 2e-5 | - | +7.8±5.3 (P = 0.15) | |
| 3β-Hydroxy-Δ5-C27 steroid oxidoreductase (AF277718_1) | hsd-1 | 1e-09 | - | −1.8±4.0 (P = 0.67) |
| hsd-2 | 4e-07 | - | −4.9±5.3 (P = 0.41) | |
| hsd-3 | 2e-05 | - | −4.7±4.8 (P = 0.33) | |
| Bile acid CoA ligase (NP_036108) | acs-20 | e-103 | ↓ | −13.7±3.3 (P = 0.0001) |
| acs-22 | e-101 | - | +2.4±4.2 (P = 0.57) | |
| 2-Methylacyl-CoA racemase (AAB72146) | C24A3.4 | 5e-59 | - | −0.4±4.8 (P = 0.93) |
| ZK892.4 | 3e-56 | - | −2.5±4.2 (P = 0.56) | |
| Branched-chain acyl-CoA oxidase (CAB65251) | acox-1 | e-117 | - | +1.1±4.4 (P = 0.79) |
| F08A8.2 | e-109 | - | −0.2±4.1 (P = 0.97) | |
| F59F4.1 | e-107 | ↓ | −11.1±3.7 (P = 0.005) | |
| C48B4.1 | e-105 | - | +2.6±4.2 (P = 0.53) | |
| F08A8.4 | e-104 | - | −7.0±4.4 (P = 0.12) | |
| F08A8.3 | e-101 | - | −0.2±6.5 (P = 0.97) | |
| D-bifunctional protein (CAA62015) | dhs-28 | 4e-84 | ↓ | −18.8±4.7 (P = 0.0002) |
| dhs-25 | 8e-15 | - | +10.3±6.0 (P = 0.09) | |
| F54F3.4 | 1e-13 | - | −2.1±6.4 (P = 0.75) | |
| Peroxisomal thiolase 2 (AAA40098) | daf-22 | e-134 | ↓ | −18.7±3.6 (P<0.0001) |
| nlt-1 | 2e-12 | ↓ | −26.7±4.2 (P<0.0001) | |
| B.A. CoA:a.a. N-acyltransferase (AAB58325) | W03D8.8 | 1e-27 | - | −1.9±3.6 (P = 0.59) |
| C31H5.6 | 2e-26 | - | +1.6±4.2 (P = 0.70) | |
| K05B2.4 | 2e-25 | - | −4.7±6.6 (P = 0.35) | |
| T05E7.1 | 1e-16 | - | −2.6±4.7 (P = 0.58) | |
| Δ4-3-Oxosteroid 5β-reductase (NP_663339) and 3α-Hydroxysteroid dehydrogenase (NP_085114) | Y39G8B.1 | 7e-72 | - | +0.9±3.6 (P = 0.80) |
| T08H10.1 | 3e-56 | ↑ | +10.6±3.9 (P = 0.008) | |
| C07D8.6 | 2e-55 | ↓ | −12.8±4.7 (P = 0.01) | |
| ZC443.1 | 2e-52 | - | −8.7±4.3 (P = 0.06) | |
| Y39G8B.2 | 2e-47 | - | −4.2±4.9 (P = 0.40) | |
| F53F1.3 | 5e-39 | - | −5.2±5.6 (P = 0.36) | |
| F53F1.2 | 6e-38 | ↓ | −15.4±6.3 (P = 0.02) | |
| Cytochrome P450s | cyp-13A1 | n/a | - | −8.9±5.5 (P = 0.12) |
| cyp-13A2 | n/a | - | −2.5±5.5 (P = 0.66) | |
| cyp-13A3 | n/a | - | +10.5±6.3 (P = 0.11) | |
| cyp-13A4 | n/a | Not avail. | ||
| cyp-13A5 | n/a | - | −1.5±5.5 (P = 0.79) | |
| cyp-13A6 | n/a | - | −2.8±5.9 (P = 0.64) | |
| cyp-13A7 | n/a | - | −3.5±4.5 (P = 0.44) | |
| cyp-13A8 | n/a | - | +2.0±6.8 (P = 0.77) | |
| cyp-13A10 | n/a | - | +2.8±4.2 (P = 0.51) | |
| cyp-13A11 | n/a | - | −7.6±5.5 (P = 0.18) | |
| cyp-13A12 | n/a | - | −5.2±5.9 (P = 0.39) | |
| cyp-13B1 | n/a | - | −7.4±5.8 (P = 0.21 | |
| cyp-13B2 | n/a | - | −4.3±6.6 (P = 0.52) | |
| cyp-14A1 | n/a | - | +10.5±5.6 (P = 0.07) | |
| cyp-14A2 | n/a | - | +6.3±6.6 (P = 0.34) | |
| cyp-14A3 | n/a | - | −9.5±4.9 (P = 0.06) | |
| cyp-14A4 | n/a | - | −4.9±5.7 (P = 0.40) | |
| cyp-14A5 | n/a | ↓ | −14.0±4.2 (P = 0.002) | |
| daf-9/cyp-22A1 | n/a | - | −0.5±3.3 (P = 0.87) | |
| cyp-23A1 | n/a | - | +7.0±5.3 (P = 0.20) | |
| cyp-25A1 | n/a | - | +2.4±4.4 (P = 0.58) | |
| cyp-25A2 | n/a | - | +6.3±6.6 (P = 0.34) | |
| cyp-25A3 | n/a | - | +0.3±5.2 (P = 0.96) | |
| cyp-25A4 | n/a | - | +6.0±4.9 (P = 0.22) | |
| cyp-25A5 | n/a | - | −2.0±4.3 (P = 0.64) | |
| cyp-25A6 | n/a | - | −1.0±3.9 (P = 0.80) | |
| cyp-29A1 | n/a | - | +10.0±6.8 (P = 0.16) | |
| cyp-29A2 | n/a | - | −2.6±3.9 (P = 0.52) | |
| cyp-29A3 | n/a | ↓ | −13.2±4.0 (P = 0.003) | |
| cyp-29A4 | n/a | - | −0.2±3.9 (P = 0.96) | |
| cyp-31A2 | n/a | - | +0.6±4.4 (P = 0.89) | |
| cyp-31A3 | n/a | ↓ | −11.0±4.0 (P = 0.01) | |
| cyp-32A1 | n/a | - | +1.4±4.6 (P = 0.75) | |
| cyp-32B1 | n/a | - | +6.5±4.5 (P = 0.17) | |
| cyp-33A1 | n/a | - | −3.6±4.7 (P = 0.45) | |
| cyp-33B1 | n/a | - | +11.8±5.9 (P = 0.06) | |
| cyp-33C1 | n/a | - | −6.2±4.3 (P = 0.16) | |
| cyp-33C2 | n/a | - | −4.6±4.1 (P = 0.27) | |
| cyp-33C3 | n/a | - | −5.9±4.9 (P = 0.24) | |
| cyp-33C4 | n/a | - | −5.0±3.9 (P = 0.20) | |
| cyp-33C5 | n/a | ↓ | −8.0±3.4 (P = 0.024) | |
| cyp-33C6 | n/a | ↓ | −13.1±3.4 (P = 0.0005) | |
| cyp-33C7 | n/a | - | +3.4±4.6 (P = 0.46) | |
| cyp-33C8 | n/a | ↑ | +12.1±4.5 (P = 0.01) | |
| cyp-33C9 | n/a | - | +7.3±5.1 (P = 0.17) | |
| cyp-33C11 | n/a | - | +1.6±4.6 (P = 0.74) | |
| cyp-33C12 | n/a | - | +9.8±5.2 (P = 0.07) | |
| cyp-33D1 | n/a | ↓ | −8.9±3.5 (P = 0.02) | |
| cyp-33D3 | n/a | - | −4.8±4.6 (P = 0.31) | |
| cyp-33E1 | n/a | ↑ | +12.6±5.4 (P = 0.03) | |
| cyp-33E2 | n/a | - | −2.2±5.3 (P = 0.69) | |
| cyp-33E3 | n/a | - | +4.0±6.7 (P = 0.55) | |
| cyp-34A1 | n/a | - | +1.2±6.2 (P = 0.84) | |
| cyp-34A2 | n/a | - | +0.5±5.7 (P = 0.93) | |
| cyp-34A3 | n/a | - | +1.0±4.0 (P = 0.80) | |
| cyp-34A4 | n/a | ↓ | −14.5±4.7 (P = 0.003) | |
| cyp-34A5 | n/a | - | +2.4±4.6 (P = 0.61) | |
| cyp-34A6 | n/a | ↓ | −11.5±5.0 (P = 0.03) | |
| cyp-34A7 | n/a | - | +1.1±4.2 (P = 0.80) | |
| cyp-34A8 | n/a | - | +5.6±4.4 (P = 0.22) | |
| cyp-34A9 | n/a | ↓ | −12.5±5.2 (P = 0.02) | |
| cyp-34A10 | n/a | - | +3.7±4.5 (P = 0.41) | |
| cyp-35A1 | n/a | - | +4.6±6.3 (P = 0.48) | |
| cyp-35A2 | n/a | - | −2.9±5.8 (P = 0.62) | |
| cyp-35A3 | n/a | - | −3.9±5.2 (P = 0.46) | |
| cyp-35A4 | n/a | ↓ | −12.9±4.1 (P = 0.004) | |
| cyp-35A5 | n/a | - | +5.0±6.8 (P = 0.47) | |
| cyp-35B1 | n/a | - | +9.3±6.9 (P = 0.19) | |
| cyp-35B2 | n/a | - | +1.7±6.6 (P = 0.80) | |
| cyp-35B3 | n/a | - | +12.1±7.0 (P = 0.1) | |
| cyp-35C1 | n/a | - | +10.7±6.6 (P = 0.12) | |
| cyp-35D1 | n/a | - | −1.3±6.6 (P = 0.84) | |
| cyp-36A1 | n/a | - | +3.5±5.3 (P = 0.51) | |
| cyp-37A1 | n/a | ↑ | +14.4±5.4 (P = 0.01) | |
| cyp-37B1 | n/a | - | +8.7±4.4 (P = 0.06) | |
| cyp-42A1 | n/a | - | −2.8±4.4 (P = 0.52) | |
| cyp-43A1 | n/a | - | +4.7±7.0 (P = 0.51) | |
| cyp-44A1 | n/a | - | +0.6±3.5 (P = 0.86) |
To identify C. elegans genes involved in BA synthesis, we carried out Blast homology searches for the translated products of mouse genes known to be involved in the process. In one case, the Blast results of two mouse proteins (NP_663339 and NP_085114) identified the same in worm homologues. The most homologous genes (shown in the “C. elegans genes” column) were tested by treatment of clk-1(qm30) mutants with RNAi against these genes. All cytochrome P450s were screened as they are highly similar to each other. The defecation rates are given as means ± S.E.M.
#
The accession numbers of the proteins used for the search are given.
*The p-values were obtained by comparing to control clk-1 mutants grown in parallel on HT115 bacteria harbouring only the empty pPD129.36 vector.