Plant metabolism is a pillar of our ecosystem, food security, and economy. To understand and engineer plant metabolism, we first need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we previously created the Plant Metabolic Network (PMN), an online resource of curated and computationally predicted information about the enzymes, compounds, reactions, and pathways that make up plant metabolism. Here we report PMN 15, which contains genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants, and new tools for analyzing and viewing metabolism information across species and integrating omics data in a metabolic context. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell-type specific metabolic pathways. This work shows the continued growth and refinement of the PMN resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.

Iron deficiency hampers photosynthesis and is associated with chlorosis. We recently showed that iron deficiency-induced chlorosis depends on phosphorus availability. How plants integrate these cues to control chlorophyll accumulation is unknown. Here, we show that iron limitation downregulates photosynthesis genes in a phosphorus-dependent manner. Using transcriptomics and genome-wide association analysis, we identify two genes, a chloroplastic ascorbate transporter (PHT4;4) and a nuclear transcription factor (bZIP58), which prevent the downregulation of photosynthesis genes leading to the stay-green phenotype under iron-phosphorus deficiency. Joint limitation of these nutrients induces ascorbate accumulation by activating expression of an ascorbate biosynthesis gene, VTC4, which requires bZIP58. Exogenous ascorbate prevents iron deficiency-induced chlorosis in vtc4 mutants, but not in bzip58 or pht4;4. Our study demonstrates chloroplastic ascorbate transport is essential for preventing the downregulation of photosynthesis genes under iron-phosphorus combined deficiency. These findings uncover a molecular pathway coordinating chloroplast-nucleus communication to adapt photosynthesis to nutrient availability.

Since the entry into genome-enabled biology 20 years ago, much progress has been made in determining, describing, and disseminating functions of genes and their products. Yet, this information is still difficult to access by many, especially across genomes. To provide easy access to the status of genome function annotation for model organisms and bioenergy and food crop species, we created a web application (https://genomeannotation.rheelab.org) to visualize and download genome annotation data for 27 species. The summary graphics and data tables will be updated semi-annually and snapshots archived to provide a historical record of the progress of genome function annotation efforts.

Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. While it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs of known causal genes as training set. The model trained with orthologs could recall about 64% of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes were considered, which is similar to the performance of models trained with known causal genes. We further extended the algorithm to include polymorphisms in conserved non-coding sequences and gene presence/absence variation as additional features. Using this algorithm, QTG-Finder2, we trained and cross-validated Sorghum bicolor and Setaria viridis models. The S. bicolor model was validated by causal genes curated from the literature and could recall 70% of causal genes when the top 20% ranked genes were considered. In addition, we applied the S. viridis model and public transcriptome data to prioritize a plant height QTL and identified 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal genes in any plant species and facilitate agricultural trait improvement.

Nutrient sensing and signaling are essential for adjusting growth and development to available resources. Deprivation of the essential mineral phosphorus (P)inhibits root growth.1 The molecular processes that sense P limitation to trigger early root growth inhibition are not known yet. Target of rapamycin (TOR) kinase is a central regulatory hub in eukaryotes to adapt growth to internal and external nutritional cues.2,3 How nutritional signals are transduced to TOR to control plant growth remains unclear. Here, we identify Arabidopsis-root-specific kinase 1 (ARSK1), which attenuates initial root growth inhibition in response to P limitation. We demonstrate that ARSK1 phosphorylates and stabilizes the regulatory-associated protein of TOR 1B (RAPTOR1B), a component of the TOR complex 1, to adjust root growth to P availability. These findings uncover signaling components acting upstream of TOR to balance growth to P availability.

Summary paragraphPlacozoa is an enigmatic phylum of simple, microscopic, marine metazoans. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax H2 lives in symbiosis with two intracellular bacteria. One symbiont forms a new genus in the Midichloriaceae (Rickettsiales) and has a genomic repertoire similar to that of rickettsial parasites, but does not appear to express key genes for energy parasitism. Correlative microscopy and 3-D electron tomography revealed that this symbiont resides in an unusual location, the rough endoplasmic reticulum of its hosts internal fiber cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations. This symbiont lives in the ventral epithelial cells of Trichoplax, likely metabolizes algal lipids digested by its host, and has the capacity to supplement the placozoans nutrition. Our study shows that even the simplest animals known have evolved highly specific and intimate associations with symbiotic, intracellular bacteria, and highlights that symbioses with microorganisms are a basal trait of animal life.

Solid-state synthesis represents an alternative to solution-phase chemistry that can provide routes to materials typically unobtainable by conventional methods. However, multiple competing reaction pathways under high-pressure conditions makes the targeted synthesis of chemically homogeneous systems a challenge. Nanothreads, one-dimensional diamondoid polymers formed through the compression of aromatic hydrocarbons present a unique opportunity to carry out high pressure reactions in a controlled and predictable manner. We hypothesize that through careful consideration of molecular stacking and intermolecular forces (e.g., H-bonding), it is possible to form chemically homogeneous nanothreads that retain precisely located chemical functionality. Herein, we report the scalable solid-state polymerization of 2,5-furandicarboxylic acid through sequential [4 + 2] Diels Alder cycloaddition reactions. The resulting nanothread product is decorated with a high density of pendant carboxylate groups, presenting new opportunities for post-synthetic processing and functional applications. Transition metal coordination is demonstrated for the functionalized threads, representing proof-of-concept for the utilization of nanothreads as independent synthons and the possibility for novel, extended multidimensional networks.

Context. The current period is conducive to exploring our Solar System's origins with recent and future space sample return missions, which provide invaluable information from known Solar System asteroids and comets The Hayabusa2 mission of the Japan Aerospace Exploration Agency (JAXA) recently brought back samples from the surface of the Ryugu carbonaceous asteroid.Aims. We aim to identify the different forms of chemical composition of organic matter and minerals that constitute these Solar System primitive objects, to shed light on the Solar System's origins.Methods. In this work, we recorded infrared (IR) hyper-spectral maps of whole-rock Ryugu asteroid samples at the highest achievable spatial resolution with a synchrotron in the mid-IR (MIR). Additional global far-IR (FIR) spectra of each sample were also acquired.Results. The hyper-spectral maps reveal the variability of the functional groups at small scales and the intimate association of phyl-losilicates with the aliphatic components of the organic matter present in Ryugu. The relative proportion of column densities of the identified IR functional groups (aliphatics, hydroxyl + interlayer and/or physisorbed water, carbonyl, carbonates, and silicates) giving access to the composition of the Ryugu samples is estimated from these IR hyper-spectral maps. Phyllosilicate spectra reveal the presence of mixtures of serpentine and saponite. We do not detect anhydrous silicates in the samples analysed, at the scales probed. The carbonates are dominated by dolomite. Aliphatics organics are distributed over the whole samples at the micron scale probed with the synchrotron, and intimately mixed with the phyllosilicates. The aromatic C=C contribution could not be safely deconvolved from OH in most spectra, due to the ubiquitous presence of hydrated minerals. The peak intensity ratios of the organics methylene to methyl (CH2/CH3) of the Ryugu samples vary between about 1.5 and 2.5, and are compared to the ratios in chondrites from types 1 to 3. Overall, the mineralogical and organic characteristics of the Ryugu samples show similarities with those of CI chondrites, although with a noticeably higher CH2/CH3 in Ryugu than generally measured in C1 chondrites collected on Earth, and possibly a higher carbonate content.

Skeletal muscles can regenerate throughout life time from resident Pax7-expressing (Pax7+) muscle stem cells (MuSCs)1-3. Pax7+ MuSCs are normally quiescent and localized at a niche in which they are attached to the extracellular matrix basally and compressed against the myofiber apically3-5. Upon muscle injury, MuSCs lose apical contact with the myofiber and re-enter cell cycle to initiate regeneration. Prior studies on the physical niche of MuSCs focused on basal elasticity6,7, and significance of the apical force exerted on MuSCs remains unaddressed. Here we simulate MuSCs’ mechanical environment in vivo by applying physical compression to MuSCs’ apical surface. We demonstrate that compression drives activated MuSCs back to a quiescent stem cell state, even when seeded on different basal elasticities. By mathematical modeling and manipulating cell tension, we conclude that low overall tension combined with high edge tension generated by compression lead to MuSC quiescence. We further show that apical compression results in up-regulation of Notch downstream genes, accompanied by increased levels of nuclear Notch. The compression induced nuclear Notch is ligand-independent, as it does not require the canonical S2 cleavage of Notch by ADAM10/17. Our results fill the knowledge gap on the role of apical tension for MuSC fate. Implications to how stem cell fate and activity are interlocked with the mechanical integrity of its resident tissue are discussed.

The 2021 La Palma eruption provided an unpreceded opportunity to test the relationship between earthquake hypocenters and the location of magma reservoirs. We performed density measurements on CO2-rich fluid in-clusions (FIs) hosted in olivine crystals that are highly sensitive to pressure via calibrated Raman spectroscopy. This technique can revolutionize our knowledge of magma storage and transport during an ongoing eruption, given that it can produce precise magma storage depth constraints in near real time with minimal sample prep-aration. Our FIs have CO2 recorded densities from 0.73 to 0.98 g/cm3, translating into depths of 15 to 27 km, which falls within the reported deep seismic zone recording the main melt storage reservoir.