Molecular Mechanism Of Chromatin Remodeling Protein ZmCHB101 In Nitrate Response In Maize

Nitrogen is an essential nutrient element for plants,and it plays an important role in the growth and development of plants.Nitrate is the main nitrogen source for plants and is an essential component in fertilizer.Rapid transcriptional activation of highaffinity nitrate transport system(HATS)is an important strategy for plants to cope with nitrogen deficiency.Maize is one of the most important crops in the world,not for food,but also industrial materials.Large amounts of nitrogen fertilizer are needed in the agricultural production of maize.However,the specific transcriptional machineries participating in this process and detailed transcriptional regulatory mode for core highaffinity nitrate transport system remains unknown.ATP-dependent chromatin remodeling regulates various biological processes by changing chromatin structure,which is an important epigenetic regulation method in eukaryotes.We have found that maize SWI/SNF chromatin remodeling complex core subunit ZmCHB101 plays an important role in the growth and development of maize and the response to drought stress.Here,we demonstrate that the evolutionarily conserved core subunit of SWI/SNFtype ATP-dependent chromatin remodeling complex in maize,ZmCHB101,plays a pivotal regulatory role in nitrate-responsive gene expression in maize:(1)ZmCHB101 RNA-interference transgenic plants were treated with different concentrations of exogenous nitrate,it was found that the lateral root growth and root biomass accumulation displayed accelerated compared with wild type under low nitrate condition.(2)RNA sequencing results showed that ZmCHB101 gene silencing had a great impact on the expression of nitrate response genes in maize.A total of 862 DEGs were identified between the WT and R101 plants under the 0-h-nitrate treatment condition and 786 DEGs under the 2-h-nitrate treatment.Additionally,GO analysis revealed that different biological terms including “response to nitrogen compound”,“response to stress”,and “response to abiotic stimulus” were enriched among the DEGs under the 0-h-nitrate treatment,whereas terms such as “response to nitrate”,“response to nitrogen compound”,“nitrate metabolism process”,and “nitrate transport” were enriched among the DEGs under the 2-h-nitrate treatment.Among them,the expression levels of ZmNRT2.1 and ZmNRT2.2,which are high-affinity transport system genes,in ZmCHB101-RNAi lines were significantly higher than in the wild type.(3)We detected consensus nitrate-responsive cis-elements(NREs)in the promoters regions of both ZmNRT2.1 and ZmNRT2.2 using MEME online tool.(4)The NIN-like protein(NLP)of maize,ZmNLP3.1,recognized the consensus nitrate-responsive cis-elements(NREs)in the promoter regions of ZmNRT2.1 and ZmNRT2.2 and activated the transcription of these genes in response to nitrate.(5)Intriguingly,well-positioned nucleosomes were detected at NREs in ZmNRT2.1 and ZmNRT2.2 gene promoter regions,and nucleosome densities were reduced in ZmCHB101-RNAi compared with wild-type plants,both in the absence or presence of nitrate.(6)ZmCHB101 protein could bind to NRE regions and participate in the maintenance of nucleosome occupancies at NREs,thereby inhibiting ZmNLP3.1 binding to NREs without nitrate supply.However in the presence of nitrate,the binding affinity of ZmCHB101 for NRE regions decreased dramatically,and thus lead to reducing the nucleosome densities at NRE regions,thereby increasing the ZmNLP3.1 binding.(7)ZmCK1.1 regulated the expression of nitrate-responsive genes in maize,but ZmCK1.1 did not bind to the NREs in the of ZmNRT2.1 and ZmNRT2.2 promoter regions.Our results shed new light on understanding how a chromatin remodeler plays a role in the regulation of nitrate-responsive gene expression in plants.