PCH1 and PCHL Directly Interact with PIF1,Promote Its Degradation,and Inhibit Its Transcriptional Function during Photomorphogenesis

PHOTOPERIODIC CONTROL OF HYPOCOTYL 1(PCH1)and PCH1-LIKE(PCHL)were shown to directly bind to phytochrome B(phyB)and suppress phyB thermal reversion,resulting in plants with dramatically enhanced light sensitivity.Here,we show that PCH1 and PCHL also positively regulate various light responses,including seed germination,hypocotyl gravitropism,and chlorophyll biosynthesis,by physically interacting with PHYTOCHROME INTERACTING FACTOR 1(PIF1)and CONSTITUTIVE PHOTOMORPHO-GENIC 1(COP1).PCH1 and PCHL interact with PIF1 both in the dark and light,and regulate PIF1 abundance.Moreover,PCH1 and PCHL facilitate the physical interaction between phyB and PIF1 in vivo to promote the light-induced degradation of PIF1.PCH1 and PCHL also inhibit the DNA-binding ability of PIF1 to negatively regulate the expressions of PIF1 target genes.In addition,PCH1 and PCHL interact with COP1 and undergo degradation through the 26S proteasome pathway in the dark.Consistently,pch1 suppresses cop1 phenotype in darkness.Collectively,our study reveals a novel mechanism by which PCH1 and PCHL regulate diverse light responses not only by stabilizing phyB Pfrform but also by directly interacting with PIF1 and COP1,providing a molecular understanding of the control of hypocotyl growth by these proteins.

Arabidopsis FHY1 and FHY1-LIKE Are Not Required for Phytochrome A Signal Transduction in the Nucleus

Photoreceptors of the phytochrome family control a multitude of responses in plants.Phytochrome A(phyA)is essential for far-red light perception,which is important for germination and seedling establishment in strong canopy shade.Translocation of phyA from the cytosol into nucleus is a key step in farred light signaling and requires FAR-RED ELONGATED HYPOCOTYL 1(FHY1)and FHY1-LIKE(FHL).FHY1/FHL bind to phyA downstream signaling components.Therefore,it has been suggested that FHY1/FHL also have a function in assembling phyA transcription factor complexes in the nucleus.Yet,in this study,we show that constitutively nuclear-localized phyA is active in the absence of FHY1 and FHL.Furthermore,an artificial FHY1,consisting of an SV40 NLS,a phyA binding site,and a YFP tag as spacer between them,complements the fhy1-3 fhl-1 double mutant.These findings show that FHY1 and FHL are not required for phyA downstream signaling in the nucleus.However,we found that lines expressing phyA-NLS-YFP are hypersensitive to red and far-red light and that slightly increased levels of constitutively nuclear-localized phyA result in photomorphogenic development in the dark.Thus,restricting phyA to the cytosol and inducing nuclear transport in light by interaction with FHY1/FHL might be important to suppress photomorphogenesis in the dark.

finDr:A web server for in silico D-peptide ligand identification

In the rapidly expanding field of peptide therapeutics,the short in vivo half-life of peptides represents a considerable limitation for drug action.D-peptides,consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids(AAs),do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation,resulting in a favourable pharmacokinetic profile.To experimentally identify D-peptide binders to interesting therapeutic targets,so-called mirror-image phage display is typically performed,whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage display.This technique is extremely powerful,but it requires the synthesis of the target in D-form,which is challenging for large proteins.Here we present finDr,a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure(https://findr.biologie.uni-freiburg.de/).finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank(PDB)for their ability to bind to the target.In a separate,heuristic approach to search the chemical space of 12-mer peptides,finDr executes a customizable evolutionary algorithm(EA)for the de novo identification or optimization of D-peptide ligands.As a proof of principle,we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3(PSMα3),a toxin of methicillin-resistant Staphylococcus aureus(MRSA).We validate the predictions using in vitro binding assays,supporting the success of this approach.Compared to conventional methods,finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size limitation.We believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.

LAZing around: The intricate dance of amyloplast sedimentation and gravity sensing in plants

Gravitropism,the remarkable ability of plants to adjust their growth in response to gravity,is fundamental to their existence on Earth.Pioneering research on gravitropism can date back to the work in the 1880s,notably by Charles and Francis Darwin.

Novel pathomechanistic insights into lysosomal storage disorders:how neuron-intrinsic cGAS-STING signaling drives disease progression

In their recent paper published in Nature Cell Biology,1 Wang and colleagues defined a pathogenetic mechanism among a variety of lysosomal storage disorders(LSDs)mediating neuronal death and disease progression.The authors observed neuron-intrinsic activated cGAS-STING signaling triggered by accumulating cytosolic dsDNA,and thus,they provide a valuable target for directed therapies.

Microglia out of place—mapping macrophages across the developing human body

Macrophages(MΦs)are versatile cells found in every organ.Throughout the body,they work tirelessly to maintain tissues.To this end,they are instructed by their respective niches to express organ-specific genes and proteins,resulting in a variety of cell morphologies and highly specialized functions across different tissues[1].A recent study by Wang et al.used single-cell RNA sequencing to comprehensively profile human MΦphenotypes across 19 organs between postconception weeks(PCW)4 and 26[2].This study revealed a surprising diversity of these cells and suggests new avenues of research.

The roles of microglia in viral encephalitis:from sensome to therapeutic targeting

Viral encephalitis is a devastating disease with high mortality,and survivors often suffer from severe neurological complications.Microglia are innate immune cells of the central nervous system(CNS)parenchyma whose turnover is reliant on local proliferation.Microglia express a diverse range of proteins,which allows them to continuously sense the environment and quickly react to changes.Under inflammatory conditions such as CNS viral infection,microglia promote innate and adaptive immune responses to protect the host.However,during viral infection,a dysregulated microglia-T-cell interplay may result in altered phagocytosis of neuronal synapses by microglia that causes neurocognitive impairment.In this review,we summarize the current knowledge on the role of microglia in viral encephalitis,propose questions to be answered in the future and suggest possible therapeutic targets.

Is the Prform of phytochrome biologically active in the nucleus?

The sessile nature of plants has promoted the evolution of a wide range of mechanisms that enable plants to adapt to the changing environment.In particular,the light environment is highly dynamic and,therefore,plants have evolved several families of photoreceptors to detect almost all facets of light,such as quality,quantity,direction,and duration.Phytochromes are red(R)and far-red(FR)light photoreceptors in plants that play fundamental roles in modulating adaptive growth of plants in response to their changing light environment(Li et al.,2011).In the model plant Arabidopsis thaliana there are five phytochrome photoreceptors,named phytochrome A(phyA)to phyE.PhyA is photolabile,whereas phyB to phyE are photostable.PhyA and phyB,the two most abundant phytochromes,account for-95% of total phytochrome proteins in etiolated Arabidopsis seedlings and play the most important role in regulating seedling photomorphogenesis(Li et al.,2011).

Dose-Dependent AGO1-Mediated Inhibition of the miRNA165/166 Pathway Modulates Stem Cell Maintenance in Arabidopsis Shoot Apical Meristem

Pluripotent stem cells localized in proliferating growth centers, the meristems, are the origin of life-long organ formation and growth in higher plants. In the shoot apical meristem of Arabidopsis thaliana, the closelyrelated ARGONAUTE proteins AGO1 and ZLL/AGO10 bind miR165/166 species to regulate mRNAs of HDZIP III transcription factors that are essential to maintaining stem cells. Several genetic studies showed thatAGO1 and ZLL/AGO10 act redundantly to maintain stem cells. By contrast, the reported biochemical datasuggested antagonistic functions: AGO1 utilizes miR165/166 to slice HD-ZIP III mRNAs, whereas ZLL/AGO10 promotes degradation of miR165/166 and thus stabilizes HD-ZIP III mRNAs. How these differentfunctions are balanced in stem cell regulation has remained enigmatic. Here, we show that autorepressionof AGO1 through miR168-mediated slicing of its own RNA is required to maintain the ability of AGO1 to suppress HD-ZIP III mRNAs. Increased AGO1 expression, either in the miR168a-2 mutant or by transgenicexpression, inhibits this ability despite the presence of high levels of miR165/166, effectively uncouplingHD-ZIP III and miR165/166 expression. AGO1 activity can be restored, however, by increasing the levelsof chaperones SQN and HSP90, which promote assembly of RNA-induced silencing complex (RISC). Thissuggests that cellular abundance of SQN and HSP chaperones limits AGO1-mediated RNA interferencein shoot meristem stem cell regulation. Localized misexpression of AGO1 indicates that the cells surrounding the shoot meristem primordium play a crucial role in stem cell development. Taken together, our studyprovides a framework that reconciles biochemical and genetic data, showing that restriction of AGO1 levelsby miR168-mediated autorepression is key to RISC homeostasis and the function of AGO1 in stem cellregulation.

Hypoxia Is a Developmental Regulator in Plant Meristems

Despite the presence of about 21%O2 in the atmosphere,organs of plants and mammals are inevitably subject to lower O2 tensions(pO2)due to high O2 demand in metabolic active cells and limited O2 transport efficiency.In humans,for example,the p O2 decreases from the ambient 21%(160 mm Hg)of the inhaled air to 2%-9%in the internal organs(Brahimi-Horn and Pouyssegur,2007).To cope with this limited oxygen supply,aerobic organisms have developed a variety of adaptive responses at cellular,tissue,and organismal levels(Bailey-Serres et al.,2012).Although low O2 tensions are the normal conditions for organs,the ambient 21%O2 is usually referred to as normoxia and the lower internal concentrations as hypoxia(van Dongen and Licausi,2015).

Beyond borders:the choroid plexus-immune communication during neuroinflammation

In their paper published in Cell,1 Xu et al.leveraged single-cell sequencing and cell lineage tracing tools combined with two-photon live imaging to characterise the spatiotemporal immune recruitment and infiltration to the choroid plexus(ChP).They provide seminal insights into the communication between specialised ChP epithelial and macrophage populations,which coordinate the stepwise response to inflammation and its resolution.