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A temporal hierarchy underpins the transcription factor-DNA interactome of the maize UPR.

ABSTRACT: Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large-scale systems-level analysis of the protein-DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high-throughput enhanced yeast one-hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis-regulatory elements (CREs) in ER stress-responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Finally, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription-regulatory mechanisms in the stress responses and crop improvement.

SUBMITTER: Ko DK

PROVIDER: S-EPMC7942231 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:UNLABELLED:Understanding cellular responses to environmental stimuli requires not only the knowledge of specific regulatory components but also the quantitative characterization of the magnitude and timing of regulatory events. The two-component system is one of the major prokaryotic signaling schemes and is the focus of extensive interest in quantitative modeling and investigation of signaling dynamics. Here we report how the binding affinity of the PhoB two-component response regulator (RR) to target promoters impacts the level and timing of expression of PhoB-regulated genes. Information content has often been used to assess the degree of conservation for transcription factor (TF)-binding sites. We show that increasing the information content of PhoB-binding sites in designed phoA promoters increased the binding affinity and that the binding affinity and concentration of phosphorylated PhoB (PhoB~P) together dictate the level and timing of expression of phoA promoter variants. For various PhoB-regulated promoters with distinct promoter architectures, expression levels appear not to be correlated with TF-binding affinities, in contrast to the intuitive and oversimplified assumption that promoters with higher affinity for a TF tend to have higher expression levels. However, the expression timing of the core set of PhoB-regulated genes correlates well with the binding affinity of PhoB~P to individual promoters and the temporal hierarchy of gene expression appears to be related to the function of gene products during the phosphate starvation response. Modulation of the information content and binding affinity of TF-binding sites may be a common strategy for temporal programming of the expression profile of RR-regulated genes. IMPORTANCE:A single TF often orchestrates the expression of multiple genes in response to environmental stimuli. It is not clear how different TF-binding sites within the regulon dictate the expression profile. Our studies of Escherichia coli PhoB, a response regulator that controls expression of a core set of phosphate assimilation genes in response to phosphate starvation, showed that expression levels of PhoB-regulated genes are under sophisticated control and do not follow a simple correlation with the binding affinity of PhoB~P to individual promoters. However, the expression timing correlates with the PhoB-binding affinity and gene functions. Genes involved in direct Pi uptake contain high-affinity sites and are transcribed earlier than genes involved in phosphorus scavenging. This illustrates an elaborate mechanism of temporally programmed gene expression, even for nondevelopmental pathways.

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A temporal hierarchy underpins the transcription factor-DNA interactome of the maize UPR.

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