A note on the early transcriptional response in leaves and root of potato plants to cadmium exposure

Potato plants can accumulate a high amount of cadmium (Cd) in the tuber when grown in soils rich in Cd. The molecular mechanisms governing Cd accumulation in the potato plant are poorly understood. Here we performed an RNA-sequencing experiment to identify genes differentially expressed in the leaf and root of potato during early stages of Cd exposure. Results did not identify any significant transcriptional response in leaves under 1 or 5 mg kg−1 Cd after 72 h. However, in the roots we did identify 2,846 genes that were significantly differentially expressed after 72 h between plants grown in 5 mg kg−1 Cd and controls. These included genes involved in photosynthesis and autophagy being up-regulated, and genes involved in intracellular transport being down-regulated. This study is the first report on the transcriptome-wide response of potato to Cd stress, providing insight into the molecular mechanisms involved in the response.

Mating induces early transcriptional response in the rat endosalpinx: the role of TNF and RA

During mating, males provide not only the spermatozoa to fertilize the oocyte but also other stimuli that are essential for initiating and maintaining the reproductive programme in females. In the mammalian oviduct, mating regulates sperm storage, egg transport, fertilization, early embryonic development, and oestradiol metabolism. However, the main molecules underlying these processes are poorly understood. Using microarray analyses, we identified 58 genes that were either induced or repressed by mating in the endosalpinx at 3 h post-stimulus. RT-qPCR confirmed that mating downregulated the expression of the Oas1h and Prim1 genes and upregulated the expression of the Ceacam1, Chad, Chst10, Slc5a3 and Slc26a4 genes. The functional category ‘cell-to-cell signalling and interaction’ was over-represented in this gene list. Network modelling identified TNF and all-trans retinoic acid (RA) as upstream regulators of the mating-induced transcriptional response, which was confirmed by intraoviductal injection of TNF or RA in unmated rats. It partially mimicked the transcriptional effect of mating in the rat endosalpinx. Furthermore, mating decreased RA levels in oviductal fluid, and RA-receptor-gamma (RARG) exhibited a nuclear location in oviductal epithelium in both unmated and mated rats, indicating RA-RARG transcriptional activity. In conclusion, the early transcriptional response regulated by mating in the rat endosalpinx is mediated by TNF and RA. These signalling molecules regulate a cohort of genes involved in ‘cell-to-cell signalling and interactions’ and merit further studies to understand the specific processes activated in the endosalpinx to sustain the events that occur in the mammalian oviduct early after mating.

Quantitative description of early transcriptional response of plant cells to radiation-induced DNA damage using a Poisson initiation event model

Aim. One of the problems that have not lost their relevance is the study of the mechanisms of adaptation of higher plants to the effects of radiation associated with the modification of the DNA repair system in response to radiation. This paper presents a Poisson mathematical model of the radiation-induced early transcriptional response of genes of key enzymes, which catalyze recovery of double-stranded DNA breaks in active plant cells. Methods. We used total X-ray irradiation of a model object – 35-day-old Arabidopsis thaliana (L.) Heynh plants at sublethal doses of 3-21 Gy, total RNA extraction, reverse transcription with random hexanucleotide primers, PCR amplification of the obtained cDNA with primers to target genes, fluorescence gel densitometry of amplified products. Results. A mathematical model of transcriptional response to the genotoxic action of ionizing radiation in a subpopulation of active plant cells based on Poisson distribution, which satisfactorily describes the experimental data obtained, is proposed. Conclusions. To initiate a maximal transcriptional response to DNA damage, one two-strand lesion per chromosome, detected by DNA repair systems, is sufficient, while the absence of double-stranded lesions, or the appearance of more than one double-stranded lesion per chromosome inhibits early transcriptional response of the cell on the action of ionizing radiation. The Poisson model of the initiating event makes it possible to predict the response of subpopulations of active cells of angiosperms to the action of genotoxic factors. Keywords: ionizing radiation, DNA damage response (DDR), Arabidopsis thaliana, DNA repair, gene transcriptional activity.

EDF1 coordinates cellular responses to ribosome collisions

Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.