Sex change by gene conversion in a Caenorhabditis elegans fog-2 mutant

Abstract

Caenorhabditis elegans primarily reproduces as a hermaphrodite. Independent gene conversion events in mutant obligately outcrossing populations of C. elegans [fog-2(lf)] spontaneously repaired the loss-of-function mutation in the fog-2 locus, thereby reestablishing hermaphroditism as the primary means of reproduction for the populations.

Figure 1.—

Nucleotide sequence alignments representing two independent gene conversion events at the fog-2 locus by ftr-1 resulting in a switch from obligate outcrossing to hermaphroditism in two fog-2(lf) mutant lines. In-frame nucleotide positions 200–499 of exon 3 (total length 640 bp) are displayed. The small, clear box displays the nonsense mutation G → A in the fog-2(lf)q71 allele resulting in a nonfunctional gene relative to the wild type. The larger shaded boxed area represents the minimum gene conversion tracts by the upstream ftr-1 locus in sex-revertants 1 and 2. Indels are indicated by dashed lines and dots represent identical nucleotides to the fog-2 wild-type sequence.

Figure 2.—

Schematic depicting the regions of homology between paralogs fog-2 and ftr-1. Shaded narrow rectangles denote exons; horizontal lines represent introns and duplicated flanking regions where applicable. The duplicated region is shaded. Duplicated segments as determined by shared sequence homology between the two paralogs are also depicted by the correspondence of regions with identical color and pattern. The figure is drawn to scale. ftr-1 comprises four exons encoding 314 amino acids. The exon–intron structure of fog-2, comprising five exons (encoding for 327 aa) exhibits both similarities and dissimilarities relative to ftr-1. Homology between fog-2 and ftr-1 commences ∼170 bp upstream of the start codon, encompassing the first three exons and introns and terminating at nucleotide position 91 of the terminal exon (total length 186 bp). The last 95 bp of the terminal exon of ftr-1 as well as its 3′ downstream region bear no homology to the corresponding C-terminal region of fog-2. The K_S value between ftr-1 and fog-2 over the region of homology comprising the duplication span (1248 bp) is 0.22 with the Nei–Gojobori method (Nei and Gojobori 1986) and 0.26 if corrected for multiple hits under the Jukes–Cantor model (Jukes and Cantor 1969). Regarding fog-2, the latter 66 bp of exon 4 (total 157 bp), and intron 4 (45 bp) and exon 5 (23 bp) in their entirety comprise unique sequence bearing no obvious homology to ftr-1. To determine an alternative genomic source for this nonhomologous sequence tract in the C-terminal end of fog-2, this 134 bp of unique ORF (comprising both exonic and intronic regions) in isolation as well as in conjunction with 500 bp of the fog-2 3′ downstream region was queried against the C. elegans genome sequence in WormBase using a BlastN search. In addition, we queried a 37-aa-long sequence coded by the unique exonic regions of fog-2 against WormBase using a tBlastN search. All three queries failed to yield any alternate hits, suggesting that this stretch of sequence unique to fog-2 may have been assimilated into its reading frame via recruitment of novel neighborhood sequence from its new genomic location. The loci of both paralogs, ftr-1 and fog-2, reside on chromosome V as tandem genes with positive strand orientation and are separated by a 763-bp stretch of unique sequence. The genomic proximity of fog-2 and ftr-1 suggests unequal exchange or slippage as the mechanism of duplication and conforms to the general pattern of genomic location observed for evolutionarily young gene duplicates in C. elegans (Katju and Lynch 2003, 2006).