Mutations in the unc-52 gene of Caenorhabditis elegans affect attachment of the myofilament lattice to the muscle cell membrane. Here, we demonstrate that the unc-52 gene encodes a nematode homolog of perlecan, the mammalian basement membrane heparan sulfate proteoglycan. The longest potential open reading frame of this gene encodes a 2482-amino-acid protein with a signal peptide and four domains. The first domain is unique to the unc-52 polypeptide, whereas the three remaining domains contain sequences found in the LDL receptor (domain II) laminin (domain III) and N-CAM (domain IV). We have identified three alternatively spliced transcripts that encode different carboxy-terminal sequences. The two larger transcripts encode proteins containing all or part of domain IV, whereas the smaller transcript encodes a shortened polypeptide that completely lacks domain IV. We have determined that the disorganized muscle phenotype observed in unc-52(st196) animals is caused by the insertion of a Tcl transposon into domain IV. Two monoclonal antibodies that recognize an extracellular component of all contractile tissues in C. elegans fail to stain embryos homozygous for a lethal unc-52 allele. We have mapped the epitopes recognized by both monoclonal antibodies to a region of domain IV in the unc-52-encoded protein sequence.

Embryos homozygous for mutations in the unc-52, pat-2, pat-3, and unc-112 genes of C. elegans exhibit a similar Pat phenotype. Myosin and actin are not organized into sarcomeres in the body wall muscle cells of these mutants, and dense body and M-line components fail to assemble. The unc-52 (perlecan), pat-2 (α-integrin), and pat-3 (β-integrin) genes encode ECM or transmembrane proteins found at the cell–matrix adhesion sites of both dense bodies and M-lines. This study describes the identification of the unc-112 gene product, a novel, membrane-associated, intracellular protein that colocalizes with integrin at cell–matrix adhesion complexes. The 720–amino acid UNC-112 protein is homologous to Mig-2, a human protein of unknown function. These two proteins share a region of homology with talin and members of the FERM superfamily of proteins.We have determined that a functional UNC-112::GFP fusion protein colocalizes with PAT-3/β-integrin in both adult and embryonic body wall muscle. We also have determined that UNC-112 is required to organize PAT-3/β-integrin after it is integrated into the basal cell membrane, but is not required to organize UNC-52/perlecan in the basement membrane, nor for DEB-1/vinculin to localize with PAT-3/β-integrin. Furthermore, UNC-112 requires the presence of UNC-52/perlecan and PAT-3/β-integrin, but not DEB-1/vinculin to become localized to the muscle cell membrane.

The amino-terminal 8-kDa domain of DNA polymerase ␤ functions in binding single-stranded DNA (ssDNA), recognition of a 5-phosphate in gapped DNA structures, and as a 5-deoxyribose phosphate (dRP) lyase. NMR and x-ray crystal structures of this domain have suggested several residues that may interact with ssDNA or play a role in the dRP lyase reaction. Nine of these residues were altered by site-directed mutagenesis. Each mutant was expressed in Escherichia coli, and the recombinant protein was purified to near homogeneity. CD spectra of these mutant proteins indicated that the alteration did not adversely affect the global protein structure. Singlestranded DNA binding was probed by photochemical cross-linking to oligo(dT) 16 . Several mutants (F25W, K35A, K60A, and K68A) were impaired in ssDNA binding activity, whereas other mutants (H34G, E71Q, K72A, E75A, and K84A) retained near wild-type binding activity. The 5-phosphate recognition activity of these mutants was examined by UV cross-linking to a 5-nucleotide gap DNA where the 5 terminus in the gap was either phosphorylated or unphosphorylated. The results indicate that Lys 35 is involved in 5-phosphate recognition of DNA polymerase ␤. Finally, the dRP lyase activity of these mutants was evaluated using a preincised apurinic/apyrimidinic DNA.

The nematode Caenorhabditis elegans is a powerful model system to study contemporary biological problems. This system would be even more useful if we had mutations in all the genes of this multicellular metazoan. The combined efforts of the C. elegans Deletion Mutant Consortium and individuals within the worm community are moving us ever closer to this goal. At present, of the 20,377 protein-coding genes in this organism, 6764 genes with associated molecular lesions are either deletions or null mutations (WormBase WS220). Our three laboratories have contributed the majority of mutated genes, 6841 mutations in 6013 genes. The principal method we used to detect deletion mutations in the nematode utilizes polymerase chain reaction (PCR). More recently, we have used array comparative genome hybridization (aCGH) to detect deletions across the entire coding part of the genome and massively parallel short-read sequencing to identify nonsense, splicing, and missense defects in open reading frames. As deletion strains can be frozen and then thawed when needed, these strains will be an enduring community resource. Our combined molecular screening strategies have improved the overall throughput of our gene-knockout facilities and have broadened the types of mutations that we and others can identify. These multiple strategies should enable us to eventually identify a mutation in every gene in this multicellular organism. This knowledge will usher in a new age of metazoan genetics in which the contribution to any biological process can be assessed for all genes.

SUMMARYNeuroligins are postsynaptic cell adhesion proteins that bind specifically to presynaptic membrane proteins called neurexins. Mutations in human neuroligin genes are associated with autism spectrum disorders in some families. The nematode Caenorhabditis elegans has a single neuroligin gene (nlg-1), and approximately a sixth of C. elegans neurons, including some sensory neurons, interneurons and a subset of cholinergic motor neurons, express a neuroligin transcriptional reporter. Neuroligin-deficient mutants of C. elegans are viable, and they do not appear deficient in any major motor functions. However, neuroligin mutants are defective in a subset of sensory behaviors and sensory processing, and are hypersensitive to oxidative stress and mercury compounds; the behavioral deficits are strikingly similar to traits frequently associated with autism spectrum disorders. Our results suggest a possible link between genetic defects in synapse formation or function, and sensitivity to environmental factors in the development of autism spectrum disorders. RESEARCH ARTICLENLG-1 is 26-28% identical (45-47% similar) to the four human neuroligins and is most similar overall (28% identical, 47% similar) to human neuroligin 4 (supplementary material Fig. S1).Through a combination of cDNA sequencing and reverse transcription PCR (RT-PCR) analysis of transcripts, we documented several types of nlg-1 alternative splicing (Figs 1, 2). Exons 13 and 14 are variably present in nlg-1 transcripts; the skipping of these two exons occurs independently, and we have detected transcripts containing only exon 13, only exon 14, both exons, and neither exon. In addition, we have identified tandem alternative splice acceptor sites at the 5Ј-ends of exons 4 and 16, and tandem alternative splice donor sites at the 3Ј-end of exon 14 (Figs 1, 2). If these splicing events are independent, there could be as many as 24 distinct NLG-1 isoforms. nlg-1 is expressed in a subset of neurons and muscle cellsWe used a transgenic transcriptional reporter, with the nlg-1 promoter driving YFP expression (FRM77, Fig. 1), to examine the cellular expression of nlg-1. We found that nlg-1 is expressed in a subset of neurons in C. elegans adults, including ~20 cells in the ventral nerve cord and ~20 cells in the head (Fig. 3). We identified the nlg-1-expressing cells in the ventral nerve cord as the cholinergic VA and DA motor neurons (Fig. 3). We also identified the two AIY and two URB interneurons and the four URA motor neurons in the head, and the two PVD mechanosensory and two HSN motor neurons in the body, as nlg-1-expressing cells. Of these cells, the AIY interneurons are cholinergic (Altun-Gultekin et al., 2001), the PVD neurons are glutamatergic (Lee et al., 1999), and the HSN neurons release both serotonin and acetylcholine (ACh) (Desai et al., 1988;Duerr et al., 2001). Neurotransmitter assignments have not been reported for the remaining nlg-1-expressing neurons; however, they do not express GABAergic, dopaminergic, serotonergic or glutamatergic repo...