Distinctive features and differential regulation of the DRTS genes of Arabidopsis thaliana

GwasWA: A GWAS one-stop analysis platform from WGS data to variant effect assessment

Using the accumulated whole-genome sequencing (WGS) data and assessing the functional effects of genetic variants, particularly non-coding variants, help identify new and rare variants and decipher the molecular mechanisms underlying diseases and traits but presents significant challenges. GwasWA is a comprehensive and efficient platform to identify causal variants and assess their functional effects based on WGS data. It covers the entire workflow from downloading and processing WGS data to detecting associated variants and assessing their functional effects with optimized configurations, standardized input/output formats, personalized analysis options, data visualization, and parallel processing capability that is crucial for large-scale studies. Applying GwasWA to real datasets identified three novel genes related to seed size and revealed the regulatory mechanism underlying the linkage between a human non-coding variant, rs80067372, and tumor necrosis factor levels. These results highlight the capability of GwasWA to detect novel variants based on WGS data and provide comprehensive insights into the molecular mechanisms underlying the association of variants with diseases and traits, thus contributing to medicine and biology. GwasWA and its documentation are freely available at https://github.com/unicorn-23/GwasWA.

Molecular Analysis of the E2F/DP Gene Family of Daucus carota and Involvement of the DcE2F1 Factor in Cell Proliferation

E2F transcription factors are key components of the RB/E2F pathway that, through the action of cyclin-dependent kinases, regulates cell cycle progression in both plants and animals. Moreover, plant and animal E2Fs have also been shown to regulate other cellular functions in addition to cell proliferation. Based on structural and functional features, they can be divided into different classes that have been shown to act as activators or repressors of E2F-dependent genes. Among the first plant E2F factors to be reported, we previously described DcE2F1, an activating E2F which is expressed in cycling carrot (Daucus carota) cells. In this study, we describe the identification of the additional members of the E2F/DP family of D. carota, which includes four typical E2Fs, three atypical E2F/DEL genes, and three related DP genes. Expression analyses of the carrot E2F and DP genes reveal distinctive patterns and suggest that the functions of some of them are not necessarily linked to cell proliferation. DcE2F1 was previously shown to transactivate an E2F-responsive promoter in transient assays but the functional role of this protein in planta was not defined. Sequence comparisons indicate that DcE2F1 could be an ortholog of the AtE2FA factor of Arabidopsis thaliana. Moreover, ectopic expression of the DcE2F1 cDNA in transgenic Arabidopsis plants is able to upregulate AtE2FB and promotes cell proliferation, giving rise to polycotyly with low frequency, effects that are highly similar to those observed when over-expressing AtE2FA. These results indicate that DcE2F1 is involved in the control of cell proliferation and plays important roles in the regulation of embryo and plant development.

Targeting plant DIHYDROFOLATE REDUCTASE with antifolates and mechanisms for genetic resistance

The folate biosynthetic pathway and its key enzyme dihydrofolate reductase (DHFR) is a popular target for drug development due to its essential role in the synthesis of DNA precursors and some amino acids. Despite its importance, little is known about plant DHFRs, which, like the enzymes from the malarial parasite Plasmodium, are bifunctional, possessing DHFR and thymidylate synthase (TS) domains. Here using genetic knockout lines we confirmed that either DHFR-TS1 or DHFR-TS2 (but not DHFR-TS3) was essential for seed development. Screening mutated Arabidopsis thaliana seeds for resistance to antimalarial DHFR-inhibitor drugs pyrimethamine and cycloguanil identified causal lesions in DHFR-TS1 and DHFR-TS2, respectively, near the predicted substrate-binding site. The different drug resistance profiles for the plants, enabled by the G137D mutation in DHFR-TS1 and the A71V mutation in DHFR-TS2, were consistent with biochemical studies using recombinant proteins and could be explained by structural models. These findings provide a great improvement in our understanding of plant DHFR-TS and suggest how plant-specific inhibitors might be developed, as DHFR is not currently targeted by commercial herbicides.