Influence of alkyltransferase activity and chromosomal locus on mutational hotspots in Chinese hamster ovary cells

Development of a Cucumis sativus TILLinG platform for forward and reverse genetics

Background

Cucumber (Cucumis sativus) belongs to the Cucurbitaceae family that includes more than 800 species. The cucumber genome has been recently sequenced and annotated. Transcriptomics and genome sequencing of many plant genomes are providing information on candidate genes potentially related to agronomically important traits. To accelerate functional characterization of these genes in cucumber we have generated an EMS mutant population that can be used as a TILLinG platform for reverse genetics.

Principal Findings

A population of 3,331 M2 mutant seed families was generated using two EMS concentrations (0.5% and 0.75%). Genomic DNA was extracted from M2 families and eight-fold pooled for mutation detection by ENDO1 nuclease. To assess the quality of the mutant collection, we screened for induced mutations in five genes and identified 26 mutations. The average mutation rate was calculated as 1/1147 Kb giving rise to approximately 320 mutations per genome. We focused our characterization on three missense mutations, G33C, S238F and S249F identified in the CsACS2 sex determination gene. Protein modeling and crystallography studies predicted that mutation at G³³ may affect the protein function, whereas mutations at S²³⁸ and S²⁴⁹ may not impair the protein function. As predicted, detailed phenotypic evaluation showed that the S238F and the S249F mutant lines had no sexual phenotype. In contrast, plants homozygous for the G33C mutation showed a complete sexual transition from monoecy to andromonoecy. This result demonstrates that TILLinG is a valuable tool for functional validation of gene function in crops recalcitrant to transgenic transformation.

Conclusions

We have developed a cucumber mutant population that can be used as an efficient reverse genetics tool. The cucumber TILLinG collection as well as the previously described melon TILLinG collection will prove to be a valuable resource for both fundamental research and the identification of agronomically-important genes for crop improvement in cucurbits in general.

Soybean bacterial artificial chromosome contigs anchored with RFLPs: insights into genome duplication and gene clustering

Surveying the soybean genome with 683 bacterial artificial chromosome (BAC) contiguous groups (contigs) anchored by restriction fragment length polymorphisms (RFLPs) enabled us to explore microsyntenic relationships among duplicated regions and also to examine the physical organization of hypomethylated (and presumably gene-rich) genomic regions. Numerous cases where nonhomologous RFLPs hybridized to common BAC clones indicated that RFLPs were physically clustered in soybean, apparently in less than 25% of the genome. By extension, we speculate that most of the genes are clustered in less than 275 M of the soybean genome. Approximately 40%-45% of this gene-rich portion is associated with the RFLP-anchored contigs described in this study. Similarities in genome organization among BAC contigs from duplicate genomic regions were also examined. Homoeologous BAC contigs often exhibited extensive microsynteny. Furthermore, paralogs recovered from duplicate contigs shared 86%-100% sequence identity.

Targeted recovery of mutations in Drosophila

Reverse genetic techniques will be necessary to take full advantage of the genomic sequence data for Drosophila and other experimental organisms. To develop a method for the targeted recovery of mutations, we combined an EMS chemical mutagenesis regimen with mutation detection by denaturing high performance liquid chromatography (DHPLC). We recovered mutant strains at the high rate of approximately 4.8 mutations/kb for every 1000 mutagenized chromosomes from a screen for new mutations in the Drosophila awd gene. Furthermore, we observed that the EMS mutational spectrum in Drosophila germ cells shows a strong preference for 5'-PuG-3' sites, and for G/C within a stretch of three or more G/C base pairs. Our method should prove useful for targeted mutagenesis screens in Drosophila and other genetically tractable organisms and for more precise studies of mutagenesis and DNA repair mechanisms.

A role for certain mouse Aprt sequences in resistance to toxic adenine analogs

A mouse embryonal carcinoma cell line hemizygous for the adenine phosphoribosyltransferase gene (aprt) was exposed to ultraviolet light (UV) or to the alkylating agent, ethyl methanesulfonate (EMS). Thirty eight cell lines retaining the aprt gene were isolated by selecting for resistance to 2,6-diaminopurine (DAP), an adenine analogue which selects against aprt activity. Of these, six cell lines distinguished by significant levels of aprt enzymatic activity after selection in DAP, were found to carry mutations in the aprt gene affecting the apparent Km of the enzyme for adenine in every cell line, and the apparent Km for phosphoribosylpyrophosphate in two of the six cell lines. The results indicate that the ability of these cells to survive in the presence of toxic adenine analogues while maintaining significant levels of aprt enzyme activity may be due to a reduced affinity for the adenine analogue, DAP. This biochemical analysis along with results obtained from sequencing the aprt gene from 31 DAP resistant cell lines with no detectable aprt activity were used to implicate certain amino acids within aprt in substrate binding. It was also determined that, in contrast to UV, EMS did not appear to exhibit any strand bias in the distribution of mutations.