Escherichia coli uses two-component systems (TCSs) to respond to environmental signals. TCSs affect gene expression and are parts of E. coli’s global transcriptional regulatory network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and CpxAR, which were stimulated by ethanol stress; KdpDE and PhoRB, induced by limiting potassium and phosphate, respectively; and ZraSR, stimulated by zinc. We analyzed RNA-seq data using independent component analysis (ICA). ChIP-exo data were used to validate condition-specific target gene binding sites. Based on these data, we do the following: (i) identify the target genes for each TCS; (ii) show how the target genes are transcribed in response to stimulus; and (iii) reveal novel relationships between TCSs, which indicate noncognate inducers for various response regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded. IMPORTANCE E. coli is a common commensal microbe found in the human gut microenvironment; however, some strains cause diseases like diarrhea, urinary tract infections, and meningitis. E. coli’s two-component systems (TCSs) modulate target gene expression, especially related to virulence, pathogenesis, and antimicrobial peptides, in response to environmental stimuli. Thus, it is of utmost importance to understand the transcriptional regulation of TCSs to infer bacterial environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach integrating RNA sequencing (RNA-seq), independent component analysis, chromatin immunoprecipitation coupled with exonuclease treatment (ChIP-exo), and data mining, we suggest five different modes of TCS transcriptional regulation. Our data further highlight noncognate inducers of TCSs, which emphasizes the cross-regulatory nature of TCSs in E. coli and suggests that TCSs may have a role beyond their cognate functionalities. In summary, these results can lead to an understanding of the metabolic capabilities of bacteria and correctly predict complex phenotype under diverse conditions, especially when further incorporated with genome-scale metabolic models.

A plant's experience of abiotic or biotic stress can lead to stress memory in order to react faster and more efficiently to subsequent stresses. Molecularly, the memory of a stress can rely on stable inheritance through mitotic and meiotic cell divisions, thus epigenetic inheritance. The key epigenetic regulators are DNA cytosine methyltransferases and the Polycomb group (PcG) and Trithorax group (TrxG) proteins, which control numerous developmental processes. PcG and TrxG proteins act antagonistically on stable gene repression through mediating trimethylation of histone H3 lysine 27 (H3K27me3) and H3K4me3, respectively, and target thousands of genes in plants, including many genes responsive to stress. The role of PcG/TrxG proteins in regulating stress responses and memory, however, is just emerging. While it is well investigated that stress can induce changes of histone modifications at genes regulated by stress, it is largely unclear whether these changes are mitotically and/or meiotically heritable, hence confer somatic and/or transgenerational stress memory. As the literature on the role of DNA methylation in regulating stress responses has recently been extensively summarized, we focus this review on the current knowledge on the role of PcG and TrxG in stress responses and memory.

HIGHLIGHTS The PRC2 interacting protein BLISTER likely acts downstream of PRC2 to silence Polycomb target genes and is a key regulator of specific stress responses in Arabidopsis.Polycomb group (PcG) proteins are key epigenetic regulators of development. The highly conserved Polycomb repressive complex 2 (PRC2) represses thousands of target genes by trimethylating H3K27 (H3K27me3). Plant specific PcG components and functions are largely unknown, however, we previously identified the plant-specific protein BLISTER (BLI) as a PRC2 interactor. BLI regulates PcG target genes and promotes cold stress resistance. To further understand the function of BLI, we analyzed the transcriptional profile of bli-1 mutants. Approximately 40% of the up-regulated genes in bli are PcG target genes, however, bli-1 mutants did not show changes in H3K27me3 levels at all tested genes, indicating that BLI regulates PcG target genes downstream of or in parallel to PRC2. Interestingly, a significant number of BLI regulated H3K27me3 target genes is regulated by the stress hormone absciscic acid (ABA). We further reveal an overrepresentation of genes responding to abiotic stresses such as drought, high salinity, or heat stress among the up-regulated genes in bli mutants. Consistently, bli mutants showed reduced desiccation stress tolerance. We conclude that the PRC2 associated protein BLI is a key regulator of stress-responsive genes in Arabidopsis: it represses ABA-responsive PcG target genes, likely downstream of PRC2, and promotes resistance to several stresses such as cold and drought.

The unfolded protein response (UPR) is required for protein homeostasis in the endoplasmic reticulum (ER) when plants are challenged by adverse environmental conditions. Inositol-requiring enzyme 1 (IRE1), the bifunctional protein kinase / ribonuclease, is an important UPR regulator in plants mediating cytoplasmic splicing of the mRNA encoding the transcription factor bZIP60. This activates the UPR signaling pathway and regulates canonical UPR genes. However, how the protein activity of IRE1 is controlled during plant growth and development is largely unknown. In the present study, we demonstrate that the nuclear and Golgi-localized protein BLISTER (BLI) negatively controls the activity of IRE1A/IRE1B under normal growth condition in Arabidopsis. Loss-of-function mutation of BLI results in chronic up-regulation of a set of both canonical UPR genes and non-canonical UPR downstream genes, leading to cell death and growth retardation. Genetic analysis indicates that BLI-regulated vegetative growth phenotype is dependent on IRE1A/IRE1B but not their canonical splicing target bZIP60. Genetic complementation with mutation analysis suggests that the D570/K572 residues in the ATP-binding pocket and N780 residue in the RNase domain of IRE1A are required for the activation of canonical UPR gene expression, in contrast, the D570/K572 residues and D590 residue in the protein kinase domain of IRE1A are important for the induction of non-canonical UPR downstream genes in the BLI mutant background, which correlates with the shoot growth phenotype. Hence, our results reveal the important role of IRE1A in plant growth and development, and BLI negatively controls IRE1A's function under normal growth condition in plants.

23Escherichia coli uses two-component systems (TCSs) to respond to environmental 24 signals. TCSs affect gene expression and are parts of E. coli's global transcriptional regulatory 25 network (TRN). Here, we identified the regulons of five TCSs in E. coli MG1655: BaeSR and 26 CpxAR, which were stimulated by ethanol stress; KdpDE and PhoRB, induced by limiting 27 potassium and phosphate, respectively; and ZraSR, stimulated by zinc. We analyzed RNA-seq 28 data using independent component analysis (ICA). ChIP-exo data was used to validate condition-29 specific target gene binding sites. Based on this data we (1) identify the target genes for each 30 TCS; (2) show how the target genes are transcribed in response to stimulus; and (3) reveal novel 31 relationships between TCSs, which indicate non-cognate inducers for various response 32 regulators, such as BaeR to iron starvation, CpxR to phosphate limitation, and PhoB and ZraR to 33 cell envelope stress. Our understanding of the TRN in E. coli is thus notably expanded. 35Importance 36 E. coli is a common commensal microbe found in human gut microenvironment; 37 however, some strains cause diseases like diarrhea, urinary tract infections and meningitis. E. 38 coli's two-component system (TCS) modulates target gene expression, specially related to 39 virulence, pathogenesis and anti-microbial peptides, in response to environmental stimuli. Thus, 40 it is of utmost importance to understand the transcriptional regulation of the TCSs to infer its 41 environmental adaptation and disease pathogenicity. Utilizing a combinatorial approach 42 integrating RNAseq, independent component analysis, ChIP-exo and data mining, we show that 43 TCSs have five different modes of transcriptional regulation. Our data further highlights non-44 cognate inducers of TCSs emphasizing cross-regulatory nature of TCSs in E. coli and suggests 45 that TCSs may have a role beyond their cognate functionalities. In summary, these results when 46 further incorporated with genome scale metabolic models can lead to understanding of metabolic 47 capabilities of bacteria and correctly predict complex phenotype under diverse conditions. 48 49 Keywords 50 51 Two-component systems, E. coli, independent component analysis, transcriptomics, ChIP-exo, 52 transcriptional regulatory network, gene targets 53 54 Introduction 55 56Bacterial survival and resilience across diverse conditions relies upon environmental 57 sensing and a corresponding response. One pervasive biological design towards this goal consists 58 of a histidine kinase unit to sense the environment and a related response regulator unit to receive 59 the signal and translate it into gene expression changes. This signaling process is known as a 60 two-component system (TCS) (1). In the case of Escherichia coli (E. coli) strain K12 MG1655, 61 there are 30 histidine kinases and 32 response regulators involved in 29 complete two-62 component systems that mediate responses to various environmental stimuli such as metal 63 sen...