The nitrate response of marchantia polymorpha
Authors:   , Zapata Romero Valentina Paz 
Published: June 2024

Nitrogen (N) is an essential nutrient for plant growth and development, and nitrate is the main source of N. Understanding how plants uptake and reduce nitrate to assimilate N is important to improve N use efficiency. Besides its role as a nutrient, nitrate acts as a signal molecule that regulates gene expression and many biological processes in the plant. Extracellular nitrate is sensed by Nitrate Transporter 1 (NRT)/ Peptide Transporter (PTR) family 6.3 (NPF6.3), which is a dual affinity transporter. Intracellular nitrate can be sensed by Nin-Like Protein 7 (NLP7). The nitrate signaling pathway involves an increase in cytoplasmatic Ca+2 levels, which activates several transcription factors. These transcription factors, such as NLP7, can activate or repress nitrate transporters, nitrate reduction and assimilation enzymes, as well as other effectors related to carbon and hormone pathways. Regulation of gene expression is key for orchestrating environmental responses in land plants. Changes in gene expression require coordinating transcriptional and epigenetic processes. Chromatin modifications have been characterized to have a role in modulating plant development and response to environmental changes. Tri-methylation of lysine 4 in histone 3 (H3K4me3) and tri-methylation of lysine 27 in histone 3 (H3K27me3) are widely studied due to the high correlation between their abundance with gene expression in A. thaliana, rice, and soybean. H3K27me3 has been characterized as an effective mechanism for gene silencing, while H3K4me3 is associated with highly expressed genes. The strong association between gene expression and specific histone modifications has led to the prediction of gene expression with great confidence. Here, we provided a first insight into the characterization of the nitrate response in Marchantia polymorpha under contrasting (0.5 and 5mM) and acute treatments (5mM for 0, 15, 30, 60, and 120 minutes). We evaluated genome-wide changes of two histone modifications and mRNA levels under contrasting nitrate concentrations. Moreover, we determined transcriptomic changes in response to acute nitrate treatments over time. Genome-wide characterization under contrasting nitrate concentrations identified 17,178 occupied regions for H3K4me3 and 12,083 occupied regions for H3K27me3 among all samples. The location of these H3K4me3 peaks was associated with 13,899 genes, which were primarily expressed. In comparison, H3K27me3 peaks were associated with 4,011 genes, which were primarily repressed. Genes that possessed both histone modifications tend to have low transcript abundance. However, histone modifications were not differentially occupied between nitrate conditions. Furthermore, only 24 genes were differentially expressed between contrasting nitrate concentrations. Hence, growth under contrasting nitrate concentrations in M. polymorpha does not significantly change transcript levels and histone post-translational modifications. After acute nitrate treatment over the time course, we identified 399 male and 367 female genes that specifically respond to nitrate. Male and female exclusive genes changed their expression after nitrate treatment, including exclusive nitrate-induced genes per sex. Moreover, 116 genes were shared between male and female accessions. Among these shared genes, 108 genes were induced after acute nitrate treatments and enriched in biological processes associated with nitrate and carbon metabolism. To determine whether nitrate acts as a signaling molecule in M. polymorpha, we used a nitrate-reductase null mutant. We identified 31 nitrate-responsive genes in the wild-type plants, which did not change their transcript abundance in the nitrate reductase-null mutant. Our results indicate nitrate is not sensed as a signal in M. polymorpha under our experimental conditions. However, we found 1,514 misregulated genes in the nitrate reductase-null mutant compared to wild-type plants. The magnitude of the changes indicates that a subproduct of nitrate reduction is necessary to maintain proper gene expression. Our study provides the first insight into the contrasting and acute nitrate response in M. polymorpha. Our results shed light on understanding the ancestral nitrate response in land plants, allowing us to determine some conserved and not conserved mechanisms across land plants.