C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression

Abstract

To verify the genome annotation and to create a resource to functionally characterize the proteome, we attempted to Gateway-clone all predicted protein-encoding open reading frames (ORFs), or the 'ORFeome,' of Caenorhabditis elegans. We successfully cloned approximately 12,000 ORFs (ORFeome 1.1), of which roughly 4,000 correspond to genes that are untouched by any cDNA or expressed-sequence tag (EST). More than 50% of predicted genes needed corrections in their intron-exon structures. Notably, approximately 11,000 C. elegans proteins can now be expressed under many conditions and characterized using various high-throughput strategies, including large-scale interactome mapping. We suggest that similar ORFeome projects will be valuable for other organisms, including humans.

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Figure 1: Gateway cloning of the C.elegans ORFeome 1.1.
Figure 2: Genome-wide verification of gene existence.
Figure 3: Genome-wide verification of intron-exon structure.
Figure 4: Functional analysis and expression of the C.elegans ORFeome 1.1.

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Acknowledgements

We thank the C. elegans Sequencing Consortium for the genome sequence; the participants of the annual ORFeome meeting for their input and numerous suggestions; the members of M.V.'s laboratory for their input and help; C. McCowan for administrative assistance; B. Sobhian, A.-S. Nicot, N. Tzellas and the GenomeVision Service sequencing staff at Genome Therapeutics for technical assistance; and P. Braun for the protein expression plasmids. This work was supported by grants from the National Cancer Institute, the National Human Genome Research Institute, the National Institute of General Medical Sciences and the Merck Genome Research Institute awarded to M.V.

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Correspondence to Marc Vidal.

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T.M. has financial interests in Open Biosystems, one of the companies responsible for the distribution of the C. elegans ORFeome version 1.1.

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Reboul, J., Vaglio, P., Rual, J. et al. C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression. Nat Genet 34, 35–41 (2003). https://doi.org/10.1038/ng1140

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