Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins

Authors: GRANA, ELISA - University Of Vigo; DIAZ-TIELAS, CARLA - University Of Vigo; SANCHEZ-MOREIRAS, ADELA - University Of Vigo; REIGOSA, MANUEL - University Of Vigo; CELEIRAO, MARIA - University Of Vigo; ABAGYAN, RUBEN - University Of California, San Diego; TEIJEIRA, MARTA - University Of Vigo; Duke, Mary; CLERK, TRACY - Former ARS Employee; Pan, Zhiqiang - Peter; Duke, Stephen

Submitted to: Physiologia Plantarum
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/28/2019
Publication Date: 12/11/2019
Citation: Grana, E., Diaz-Tielas, C., Sanchez-Moreiras, A.M., Reigosa, M.J., Celeirao, M., Abagyan, R., Teijeira, M., Duke, M.V., Clerk, T., Pan, Z., Duke, S.O. 2019. Transcriptome and binding data indicate that citral inhibits single strand DNA-binding proteins. Physiologia Plantarum. 169(1):99-109. https://doi.org/10.1111/ppl.13055.
DOI: https://doi.org/10.1111/ppl.13055

Interpretive Summary: There are few effective herbicides for organic agriculture and little is known of the mode of action of these products. Citral is the most active ingredient of several bioherbicides, but its mode of action is unknown. This mixture of two organic compounds (neral and geranial) was found to shut down many plant genes. Analysis of binding of these two compounds to DNA binding proteins indicated citral’s effects on gene expression is the result of this binding. This is a novel mode of action.

Technical Abstract: The mode of action of the terpenoid phytotoxin citral (composed of the isomers neral and geranial) was probed in Arabidopsis thaliana with RNA-Seq transcriptome and in silico binding analyses. The concentration of citral that inhibited growth by 50% (202 µM) down regulated transcription of 9156 and 5541 genes in roots and shoots, respectively, at the p = 0.001 level after 1 h. Only 56 and 62 genes in roots and shoots, respectively, were upregulated. In the roots, these effects dissipated after 3 and 6 h, but similar effects began again at 12 and continued until 24 h. In the shoots, the down regulation increased at 3 h (6239 genes downregulated, vs. 66 upregulated) with the effect decreasing at from 6 to 24 h, with only 1 gene downregulated at 24 h. Of all genes affected in roots at 1 h and shoots at 3 h (times of greatest effect), 6.5 and 9.2 %, respectively, of affected genes were for DNA and RNA binding functions. Genes for single strand DNA binding proteins (SSBP) WHY1, WHY 2 and WHY3 were strongly downregulated in the shoot up until 12 h after citral exposure. Effects were strong in the root at just 1 h after the treatment and then at 12, and 24 h. Similar effect occurred with the binding proteins MYC-2, ANAC and SCR-SHR, which were also significantly downregulated for the first hour of treatment, and downregulation was significantly important again after 12 and 24 h treatment. Specially relevant is the down-regulation of ANAC in the first hour of treatment that was more than eight times significantly decreased (p < 0.0001) compared to the control. In silico molecular docking analysis suggests binding of citral isomers to the SSBPs WHY1, WHY2, and WHY3, as well as with other transcription factors such as MYC-2, ANAC, and SCR-SHR. Such effects could account for the profound and unusual effects on down-regulation of gene transcription.