Functional and phylogenetic analysis of the ubiquitylation system in Caenorhabditis elegans: ubiquitin-conjugating enzymes, ubiquitin-activating enzymes, and ubiquitin-like proteins

Table 1 RNAi with C. elegans ubiquitin-conjugating enzyme genes

Cosmid	Gene name	dsRNA source	Fragment size (bp)	Chromosome	Number of RNAi trials	Embryonic lethality %	Secondary phenotype	Embryonic lethality (%) brood A	Embryonic lethality (%)brood B	Secondary phenotype
					Feeding method			Injection method
UBC proteins
B0403.2	ubc-17	gen PCR	591	X	2	3.4	Normal	-	-	-
C06E2.3	ubc-21	gen PCR	1131	X	2	0	Normal	-	-	-
C06E2.7	ubc-22	gen PCR	1075	X	2	0	Normal	-	-	-
C28G1.1	ubc-23	gen PCR	491	X	2	0	Normal	-	-	-
C35B1.1	ubc-1	pR1.7	593	IV	2	0	Normal	0	0	Normal
D1022.1	ubc-6	yk640 h7	750	II	2	6.9	Normal	-	-	-
F29B9.6	ubc-9	yk312e11	1160	IV	4	60.2	Evl, abnormal morphology	2.7	18.2	Evl, Egl, abnormal morphology
F40G9.3	ubc-20	yk246g3	835	III	4	0	Rare arrest at L3 stage	4.8	0	Some arrest at L3 to L4 stage^*
F49E12.4	ubc-24	gen PCR	842	II	2	0	Normal	-	-	-
F58A4.10	ubc-7	yk486g12	500	III	2	0	Normal	-	-	-
M7.1	let-70	cDNA	444	IV	-	-	-	-	51	L3 stage arrest
	(ubc-2)
R01H2.6	ubc-18	yk461f2	584	III	2	0	Normal	-	-	-
R09B3.4	ubc-12	yk486f10	630	I	6	85.3	Evl, abnormal morphology	5.8	52.3	Evl, abnormal morphology
Y110A2AR.2	ubc-15	yk602e10	644	II	2	0	Normal	-	-	-
Y54E5B.4	ubc-16	yk137b4	679	I	2	0	Normal	1.0	1.4	Normal
Y54G2A.23	ubc-13	yk659d2	499	IV	2	0	Normal	-	-	-
Y69H2.6	ubc-19	yk290g1	635	V	2	0	Normal	0.8	1.1	Normal
Y71G12B.15	ubc-3	yk255b2	1053	I	2	0	Normal	1.6	2.0	Normal
Y87G2A.9	ubc-14	yk573c8	532	I	6	54.1	Abnormal morphology	-	-	-
Y94H6A.6	ubc-8	gen PCR	890	IV	2	0	Normal	-	-	-
UEV proteins
F39B2.2	uev-1	yk593d12	499	I	2	0	Normal	-	-	-
F56D2.4	uev-2	gen PCR	1074	III	2	0	Normal	-	-	-
F26H9.7	uev-3	RT-PCR	660	I	2	0	Normal		-	--

Gene names have been assigned as indicated in the text. DNA fragments of the indicated sizes were obtained from the cDNA sources shown or from fragments obtained by genomic PCR (gen PCR), or by reverse transcription from RNA (RT-PCR). Phenotypes include Evl (everted vulva) and Egl (egg-laying defect). Embryonic lethality for broods A and B are shown separately. A dash indicates experiment not done. ^*Variable penetrance. Two potential C. elegansubc genes that have recently come to light are not included in this table. F25H2.8 encodes a protein that is 25% identical to UBC-1 over 100 amino acids spanning the active site. This UBC domain is not recognized by Pfam, but is recognized by SMART (UBCc domain). The protein is 56% identical in amino-acid sequence to Drosophila BG:25E8.2 and therefore belongs in group I of Figures 1 and 2. RNAi experiments with F25H2.8 produce paralysis in the adult stage and premature death of the hermaphrodites 4 to 5 days after the beginning of oviposition [85]. YAC clone Y110A2AM may contain another ubc gene (currently uncurated) encoding a protein 52% identical over 143 amino acids to Y110A2AR.2 (group XVIII).

ISSN: 1474-760X