Host-Microbe Interactions. Plant Biology.
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Transcriptional Regulation of the Immune Receptor FLS2 Controls the Ontogeny of Plant Innate Immunity

Transcriptional Regulation of the Immune Receptor FLS2 Controls the Ontogeny of Plant Innate Immunity | Host-Microbe Interactions. Plant Biology. | Scoop.it
Innate immunity plays a vital role in protecting plants and animals from pathogen infections. Immunity varies with age in both animals and plants. However, little is known about the ontogeny of plant innate immunity during seedling development. We report here that the Arabidopsis thaliana microRNA miR172b regulates the transcription of the immune receptor gene FLAGELLIN-SENSING 2 (FLS2) through TARGET OF EAT1 (TOE1) and TOE2, which directly bind to the FLS2 promoter and inhibit its activity. The level of miR172b is very low in the early stage of seedling development, but increases over time, which results in decreased TOE½ protein accumulation and, consequently, increased FLS2 transcription and the ontogeny of FLS2-mediated immunity during seedling development. Our study reveals a role for the miR172b-TOE½ module in regulating plant innate immunity, and elucidates a regulatory mechanism underlying the ontogeny of plant innate immunity.
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Daily humidity oscillation regulates the circadian clock to influence plant physiology

Daily humidity oscillation regulates the circadian clock to influence plant physiology | Host-Microbe Interactions. Plant Biology. | Scoop.it
Humidity has been shown to influence many aspects of plant physiology. Here Mwimba et al. show that oscillating humidity entrains the circadian clock under constant light conditions and enhances clock amplitude in simulated natural environments, while also improving immunity and overall growth.
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Plant‐mediated effects of soil phosphorus on the root‐associated fungal microbiota in Arabidopsis thaliana

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Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion

Host-associated niche metabolism controls enteric infection through fine-tuning the regulation of type 3 secretion | Host-Microbe Interactions. Plant Biology. | Scoop.it
Infection of mice with Citrobacter rodentium is a common model of infection with attaching-and-effacing pathogens. Here, Connolly et al. analyse the transcriptome of C. rodentium during mouse infection, showing host-induced coordinated upregulation of virulence factors and 1,2-propanediol metabolism.
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FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana

FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana | Host-Microbe Interactions. Plant Biology. | Scoop.it
FERONIA receptor kinase plays important roles in growth, development, and stress responses,
but the transcription factor(s) mediating FERONIA signaling are not known. Guo et al.
establish that the RALF23-FER-MYC2 signaling module is employed by the host plants
to regulate coronatine-mediated host susceptibility.
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Plant functional trait change across a warming tundra biome

Plant functional trait change across a warming tundra biome | Host-Microbe Interactions. Plant Biology. | Scoop.it
Analyses of the relationships between temperature, moisture and seven key plant functional traits across the tundra and over time show that community height increased with warming across all sites, whereas other traits lagged behind predicted rates of change.
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Salicylic acid-induced transcriptional reprogramming by the HAC–NPR1–TGA histone acetyltransferase complex in Arabidopsis | Nucleic Acids Research | Oxford Academic

Salicylic acid-induced transcriptional reprogramming by the HAC–NPR1–TGA histone acetyltransferase complex in Arabidopsis | Nucleic Acids Research | Oxford Academic | Host-Microbe Interactions. Plant Biology. | Scoop.it
Abstract. Plant immunity depends on massive expression of pathogenesis-related genes (PRs) whose transcription is de-repressed by pathogen-induced signals. Sal
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Programmable protein circuits in living cells

Programmable protein circuits in living cells | Host-Microbe Interactions. Plant Biology. | Scoop.it
Synthetic genetic and biological regulatory circuits can enable logic functions to form the basis of biological computing; synthetic biology can also be used to control cell behaviors (see the Perspective by Glass and Alon). Andrews et al. used mathematical models and computer algorithms to combine standardized components and build programmable genetic sequential logic circuits. Such circuits can perform regulatory functions much like the biological checkpoint circuits of living cells. Circuits composed of interacting proteins could be used to bypass gene regulation, interfacing directly with cellular pathways without genome modification. Gao et al. engineered proteases that regulate one another, respond to diverse inputs that include oncogene activation, process signals, and conditionally activate responses such as those leading to cell death. This platform should facilitate development of “smart” therapeutic circuits for future biomedical applications.

Science , this issue p. [eaap8987][1], p. [1252][2]; see also p. [1199][3]

Synthetic protein-level circuits could enable engineering of powerful new cellular behaviors. Rational protein circuit design would be facilitated by a composable protein-protein regulation system in which individual protein components can regulate one another to create a variety of different circuit architectures. In this study, we show that engineered viral proteases can function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells. In this system, termed CHOMP (circuits of hacked orthogonal modular proteases), input proteases dock with and cleave target proteases to inhibit their function. These components can be connected to generate regulatory cascades, binary logic gates, and dynamic analog signal-processing functions. To demonstrate the utility of this system, we rationally designed a circuit that induces cell death in response to upstream activators of the Ras oncogene. Because CHOMP circuits can perform complex functions yet be encoded as single transcripts and delivered without genomic integration, they offer a scalable platform to facilitate protein circuit engineering for biotechnological applications.

[1]: /lookup/doi/10.1126/science.aap8987
[2]: /lookup/doi/10.1126/science.aat5062
[3]: /lookup/volpage/361/1199?iss=6408
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Robust single-cell DNA methylome profiling with snmC-seq2

Robust single-cell DNA methylome profiling with snmC-seq2 | Host-Microbe Interactions. Plant Biology. | Scoop.it
Single-cell DNA methylome profiling allows the study of epigenomic heterogeneity in tissues but has been impeded by library quality. Here the authors demonstrate snmC-seq2 which improves mapping, throughput and library complexity.
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A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses

The identification of homologous genes with functional overlap in forward genetic screens is severely limited. Here we report the generation of over 14,000 amiRNA-expressing plants that enable screens of the functionally redundant gene space in Arabidopsis . A protocol is developed here for isolating robust and reproducible amiRNA-mutants. Examples of validation approaches and essential controls are presented for two new amiRNA mutants that exhibit genetically redundant phenotypes and circumvent double mutant lethality. In a forward genetic screen for abscisic acid (ABA)-mediated inhibition of seed germination, amiRNAs that target combinations of known redundant ABA receptor and SnRK2 kinase genes were rapidly isolated, providing a strong proof of principle for this approach. A new ABA insensitive amiRNA line is isolated, which targets three genes encoding avirulence-induced gene2-like ( AIG2 ) genes. A thermal imaging screen for plants with impaired stomatal opening in response to low CO2 exposure led here to isolation of a new amiRNA targeting two essential proteasomal subunits, PAB1 and PAB2. The seed library of 14,000 T2 amiRNA lines generated here provides a new platform for forward genetic screens and is being made available to the Arabidopsis Biological Resource Center (ABRC) and optimized procedures for amiRNA screening and controls are described.
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Distinct modes of derepression of an Arabidopsis immune receptor complex by two different bacterial effectors

Distinct modes of derepression of an Arabidopsis immune receptor complex by two different bacterial effectors | Host-Microbe Interactions. Plant Biology. | Scoop.it
Plants and animals carry intracellular nucleotide-binding leucine-rich repeat (NLR) immune receptors. How NLR receptors activate defense on perceiving pathogen molecules is poorly understood, especially in plants. Some NLRs function in pairs, with one NLR carrying a domain that mimics a pathogen effector target. Effector action on this domain activates the second “helper” NLR. In the Arabidopsis RPS4 and RRS1 pair, RRS1 carries a WRKY transcription factor domain targeted by bacterial effectors AvrRps4 and PopP2. We monitored conformational changes in RPS4–RRS1 during activation and developed a “molecular padlock” to reversibly restrict such changes. This revealed domains within RRS1 required to keep the RRS1–RPS4 complex inactive prior to effector detection, and specific domain–domain interactions whose disruption or modification contributes to defense activation.
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Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control

Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control | Host-Microbe Interactions. Plant Biology. | Scoop.it
An optogenetics-based method is developed to explore the temporal requirements for
a gene product to produce a dynamic phenotype.
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ELF18‐INDUCED LONG NONCODING RNA 1 evicts fibrillarin from mediator subunit to enhance PATHOGENESIS‐RELATED GENE 1 (PR1) expression

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TIR‐NB‐LRR immune receptor SOC3 pairs with truncated TIR‐NB protein CHS1 or TN2 to monitor the homeostasis of E3 ligase SAUL1

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CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization | Host-Microbe Interactions. Plant Biology. | Scoop.it
An engineered CRISPR-based platform for inducible recruitment of specific genomic
loci to distinct nuclear compartments reveals positional effects on gene expression
and cellular function.
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Quantitative phosphoproteomic analysis reveals common regulatory mechanisms between effector‐ and PAMP‐triggered immunity in plants

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The interaction landscape between transcription factors and the nucleosome

The interaction landscape between transcription factors and the nucleosome | Host-Microbe Interactions. Plant Biology. | Scoop.it
A method for systematically exploring interactions between the nucleosome and transcription factors identifies five major interaction patterns.
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Strain-level diversity drives alternative community types in millimetre-scale granular biofilms

Strain-level diversity drives alternative community types in millimetre-scale granular biofilms | Host-Microbe Interactions. Plant Biology. | Scoop.it
Using millimetre-scale replicate granules from an enhanced biological phosphorus removal reactor, the authors observe strain-level variability providing insights into the intrinsic drivers of microbial assembly at relevant spatial scales.
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Bacterial antagonism in host-associated microbial communities

Bacterial antagonism in host-associated microbial communities | Host-Microbe Interactions. Plant Biology. | Scoop.it
The gut microbiota of mammals is diverse and dynamic, and gut bacteria respond sensitively to diet and drug intake. Nevertheless, in a healthy adult, microbial community composition remains remarkably stable over time, despite being highly individual. García-Bayona and Comstock review the mechanisms that gut bacterial species use to jostle for space and resources and maintain their populations in the face of intense and varied competition. Bacteria have evolved a range of antibiotics, bacteriocins, toxins, and delivery devices to enable interspecies conflict. These interbacterial weapons possess a spectrum of specificities and range from those that target strains of their own species to broad-acting bacteriocides. This toxic armamentarium provides a valuable resource for potential therapeutic development.

Science , this issue p. [eaat2456][1]

### BACKGROUND

Microbial communities are ubiquitous on Earth. The microbiota of different habitats are diverse and have distinct functional traits, but there are common ecological principles that govern their composition. The ability of a microbe to compete with other members of its community for resources is paramount to its success. Competition through the production of molecules that harm other members, known as interference competition, is also important in the assembly and maintenance of microbial communities. As new technologies allow for more in-depth analyses of microbial communities and their genetic content, we are better able to identify new antimicrobial toxins and analyze the effects of their production. Here, we explore the range of antibacterial protein/peptide toxins and toxin-secretion systems, together with the fitness benefits they confer to the producing organisms. Because human-associated microbial communities have been intensely studied over the past decade, our focus is on the growing body of data regarding bacterial antagonism in these and other host-associated microbial communities.

### ADVANCES

Studies continue to reveal the large arsenal of antibacterial peptides and proteins that bacteria produce and the secretion systems that they use to deliver these toxins to competing cells. Bacterially produced antimicrobial peptides and proteins are diverse in terms of their structures, cellular targets, mechanisms of action, and spatial range. Their antagonistic range also varies; some are limited to intraspecies killing, whereas others are able to kill across genera, families, and orders. Through a combination of mathematical modeling and experimental model systems, the ecological outcomes of bacterial antagonism are being elucidated. In vivo analyses in host models have shown that some antimicrobial toxins play a role in microbiota-mediated colonization resistance by preventing invasion of pathogens. Some pathogens, however, also use toxins to battle with the resident microbiota to invade an ecosystem and cause disease. Antagonism has also been shown to facilitate genome evolution; the DNA released from killed cells can be taken up and incorporated into the aggressor’s genome. In some cases, antagonism has been shown to increase rather than reduce microbial diversity, potentially through promotion of spatial segregation of competing strains, facilitating the exchange of signals and secreted products between related cells (kin). The factors that regulate the production and release of some antibacterial toxins are also becoming better understood. Studies are revealing that toxin producers respond to various environmental signals, including signals that indicate host occupancy, that nutrients are limiting, or that they may be attacked by other bacterial community members.

### OUTLOOK

Although bacterial antagonism is an active area of research, we are still in the early stages of understanding the impacts of these interactions in natural community settings and how they influence the overall structure, dynamics, and composition of complex microbial communities. The rapid increase in the number of available metagenomic datasets derived from diverse microbial communities and the expanding capability to culture and genetically modify these organisms is allowing for the identification and characterization of new . The protective function of microbiota-produced toxins in warding off pathogens indicates a potential for applications in medical, agricultural, and other industrial settings. In addition, the inclusion of antibacterial toxins in genetically engineered bacteria (live biotherapeutics) may allow for specific targeting of harmful community members, including those involved in therapeutic failures, and may also allow a live biotherapeutic to compete with members of the microbiota to deliver various health-promoting functions.

![Figure][2]

Intra- and interspecies antagonism—the example of Bacteroides species in the human gut.
Bacteroides fragilis and Bacteroides uniformis use MACPF (membrane attack complex/perforin) toxins—BSAP-1 and BSAP-2, respectively—for intraspecies killing. Producer strains carry a modified receptor [outer membrane protein (OMP) or lipopolysaccharide (LPS) glycan] that confers resistance to its cognate toxin. B. fragilis can also kill other B. fragilis strains and most gut Bacteroidales species via type VI secretion systems (T6SSs).



Antagonistic interactions are abundant in microbial communities and contribute not only to the composition and relative proportions of their members but also to the longer-term stability of a community. This Review will largely focus on bacterial antagonism mediated by ribosomally synthesized peptides and proteins produced by members of host-associated microbial communities. We discuss recent findings on their diversity, functions, and ecological impacts. These systems play key roles in ecosystem defense, pathogen invasion, spatial segregation, and diversity but also confer indirect gains to the aggressor from products released by killed cells. Investigations into antagonistic bacterial interactions are important for our understanding of how the microbiota establish within hosts, influence health and disease, and offer insights into potential translational applications.

[1]: /lookup/doi/10.1126/science.aat2456
[2]: pending:yes
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Sugar Turns Bacteria Sweet: A Peace Offering in the Gut

Sugar Turns Bacteria Sweet: A Peace Offering in the Gut | Host-Microbe Interactions. Plant Biology. | Scoop.it
Following an infection, a subset of individuals can remain disease free despite harboring
a pathogen for a prolonged period. In this issue of Cell, Sanchez et al. demonstrate
that a metabolically favorable host response can drive an otherwise lethal bacterial
pathogen to abandon virulence and become a commensal microorganism.
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Identification of cell populations necessary for leaf-to-leaf electrical signaling in a wounded plant

Identification of cell populations necessary for leaf-to-leaf electrical signaling in a wounded plant | Host-Microbe Interactions. Plant Biology. | Scoop.it
Numerous modes of long-distance electrical signaling exist in nature. The best known of these, axonal conduction, requires one primary cell population, i.e., neurons. In contrast, the cell types that mediate leaf-to-leaf electrical signaling in wounded plants have not been defined rigorously. Using genetic approaches, we find that two distinct populations of cells in the vasculature matrix are needed to perform this function. Surprisingly, these cells do not contact each other directly. As we further defined the plant wound response, we found that wound-induced membrane depolarizations preceded large intravasculature calcium fluxes. We reveal a two-cell-type mode of electrical signaling in leaves and discuss parallels and differences in electrical signaling outside the plant kingdom.

The identity of the cell files necessary for the leaf-to-leaf transmission of wound signals plants has been debated for decades. In Arabidopsis , wounding initiates the glutamate receptor-like (GLR)–dependent propagation of membrane depolarizations that lead to defense gene activation. Using a vein extraction procedure we found pools of GLR-fusion proteins in endomembranes in phloem sieve elements and/or in xylem contact cells. Strikingly, only double mutants that eliminated GLRs from both of these spatially separated cell types strongly attenuated leaf-to-leaf electrical signaling. glr3.3 mutants were also compromised in their defense against herbivores. Since wounding is known to cause increases in cytosolic calcium, we monitored electrical signals and Ca2+ transients simultaneously. This revealed that wound-induced membrane depolarizations in the wild-type preceded cytosolic Ca2+ maxima. The axial and radial distributions of calcium fluxes were differentially affected in each glr mutant. Resolving a debate over which cell types are necessary for electrical signaling between leaves, we show that phloem sieve elements and xylem contact cells function together in this process.
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Removal of soil biota alters soil feedback effects on plant growth and defense chemistry

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