To distinguish wild-type and mutant genes, one needs to define a wild-type strain. To this end, we worm breeders use the convention that N2 is the wild type. Now, when people order N2 from the Caenorhabditis Genetics Center, they usually request a hermaphrodite stock, but there is also a male stock available (strain: “N2 male”); for convenience, we will refer to these two lines as N2H and N2M. A problem here is that these lines are not genetically identical: N2M hermaphrodites are longer lived (+11% median lifespan) (Gems and Riddle, 2000). So which is wild type, N2H or N2M? This is a problem, and we have been looking into it.
Under standard culture conditions N2 hermaphrodites exhibit two forms of death, with either a swollen or an atrophied pharynx (P and p death, respectively). P death occurs earlier and results from bacterial infection, facilitated by mechanical senescence of the pharynx due to the high, wild-type pumping rate (Zhao et al., 2017). We have found that the greater lifespan of N2M hermaphrodites is due to lower P death frequency (and therefore reduced early mortality).
This turns out to be due to a single recessive mutation in the X-linked gene fln-2 (filamin) in N2M, as revealed initially by Variant Discovery Mapping. fln-2(ot611) is a nonsense allele resulting from a C to A transversion, creating a stop codon at Y800 in the FLN-2A isoform. Thus, N2H is wild type and N2M is mutant. This conclusion is confirmed by examination of the fln-2 sequence in multiple C. elegans wild isolates (Cook et al., 2017). It would therefore be advisable to discontinue the use of N2M (“N2 male”).
Although people mainly use N2H as their wild type, N2M is sometimes used for strain construction and backcrossing. To get an idea of the prevalence of fln-2(ot611) we checked a sample of strains in our collection and found fln-2(ot611) in 23/50, particularly in strains generated by the C. elegans Gene Knockout Project and the C. elegans Expression Project.
Variation at the fln-2 locus is a potential confounding variable, especially in studies of lifespan genetics. We have so far found it to confound the effects on lifespan of alteration of eat-2, sir-2.1 and daf-12. For this reason we advise the use of routine checks of fln-2 genotype in studies of the genetics of lifespan. Here is information about how to do this.
The relevant fln-2 sequence information is:
Wild-type fln-2: GGCGCTGGTCAATA[C]AAAATCCACGTTCTT
fln-2(ot611): GGCGCTGGTCAATA[A]AAAATCCACGTTCTT with a C to A change in the bracket.
To genotype fln-2, we used the following primers to PCR amplify the region containing the mutation: forward 5’-GGTGTTCGATTCTGGTCTGG; reverse 5’-ACATCGACGAGAAGACAACAC. The PCR product can be sequenced using the primer 5’-TGTACCCAGAAATTGACAAGATAC.
Allele-specific PCR can also be used to discriminate between the alleles, using the following primers: wild-type-specific forward 5′-taccattccgagcttattgattgttacctGGACGGCGCTGGTCCATAC-3′; ot611-specific forward 5′-GGACGGCGCTGGTCTATAA-3′; reverse 5′-ATCGCATGAACCATAAATGATG-3′. Each forward primer contains an additional mismatch to make it different from both the template and the other forward primer to ensure allele specificity (Neagu and Maier, 2011). The wild-type PCR product is 30bp longer than the mutant product, and can be readily distinguished on a 2% agarose gel.
Neagu A and Maier W. (2011). snPCR for reliable one-step genotyping of single nucleotide differences. The Worm Breeder’s Gazette 19, 1.
Zhao Y, Gilliat AF, Ziehm M, Turmaine M, Wang H, Ezcurra M, Yang C, Phillips G, McBay D, Zhang WB, Partridge L, Pincus Z, and Gems D. (2017). Two forms of death in ageing Caenorhabditis elegans. Nature Comm. 8, 15458.