Streamlining the immune system: How plants adapt to reduced pathogen pressure

/in /by

Although plants are sessile organisms unable to escape pathogen invasions, they are well equipped with defense mechanisms. Cell surface-localized pattern-recognition receptors (PRRs) detect extracellular signals and initiate pattern-triggered immunity (PTI), while nucleotide-binding leucine-rich repeat receptors (NLRs) sense intracellular signals and trigger effector-triggered immunity (ETI). These two layers of immune signaling were long considered distinct pathways but are now recognized as interdependent—essentially functioning as one. While numerous studies have explored the expansion of PRRs and NLRs during plant evolution, particularly during the transition from aquatic to terrestrial environments, the opposite scenario remains less examined: how plants with specialized lifestyles—such as mangrove, desert, or aquatic species—adapt to reduced pathogen pressure. Li and colleagues reassessed 808 angiosperm genomes and found that plants with specialized lifestyles and habitats (SLHs) exhibit significant reductions in PRR and NLR genes due to increased gene loss and reduced gene duplication. Evolutionary association studies further identified key immune regulatory modules, including the well-known EDS1, alongside novel components. These newly identified modules and annotated immune-related genes from 808 angiosperm species offer valuable insights into plant immunity and can be explored through the publicly available database, AirDB (https://efg.nju.edu.cn/AirDB/). (Summary by Ching Chan @ntnuchanlab) Nature Plants 10.1038/s41477-024-01901-x

Double attack! Herbivore insects feed on plants and silence their genes

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In the natural environment, plants are constantly attacked by animals. Plant immunity is regulated by a network of genes and hormones including salicylic acid (SA) and jasmonic acid (JA). A recent study suggests that herbivore insects threaten plants with concerns more than the bite. Han et al., found that the phloem-feeding whitefly (Bemisa tabaci) transfers miRNA BtmiR29-b to tobacco phloem sap during feeding. The miRNA suppresses plant defense by silencing the defense gene BAG4 and inhibits SA and JA accumulations in the host. Searching through the miRNA database miRBase, the authors found that miR29-b exists in many other insect species of various orders including Hemiptera, Coleoptera, Hymenoptera, Orthoptera, and Blattaria. Besides whitefly, miR29-b was experimentally detected in the salivary gland and saliva of aphid (Myzus persicae), which could transfer the miRNA to tobacco phloem sap during feeding. In plants, BAG4 homologs exist in various species of different families including Solanaceae, Brassicaceae, Cucurbitaceae, Euphorbiaceae, Leguminosae, and Malvaceae. Despite the different target sites, the targeting of the homologous BAG4 transcripts by miR29-b could be predicted. The transfer of BtmiR29-b from whiteflies to Arabidopsis, cotton, and tomato was also experimentally validated. The study demonstrates cross-kingdom miRNA-mediated gene silencing and suggests the conserved mechanism in different species. The findings motivate future studies in other cross-kingdom gene regulations and provide insights into pest control strategies. (Summary by Yee-Shan Ku @YeeShanKu1) Molecular Plant 10.1016/j.molp.2025.01.001

Plant Science Research Weekly: February 7, 2025

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Review: Genetic engineering for carbon assimilation in plants

Rubisco (Ribulose‐1,5‐bisphosphate carboxylase/oxygenase) is the central enzyme for photosynthesis, This enzyme poorly discriminates between CO2 and O2, which limits its efficiency.  To work around this and make carbon assimilation more efficient, scientists have been employing different engineering strategies, several of which are summarized in a new review by Qin et al. One strategy is to alter Rubisco activity, for example  by inducing mutations, combining parts of Rubisco from different organisms, engineering other enzymes involved with Rubisco activation and accumulation, and introducing Rubisco genes from lower organisms to crop plants. Another engineering approach is to create carbon-concentrating compartments, for example by using carboxysomes found in cyanobacteria and pyrenoids from eukaryotic algae. Alternatively, CO2 levels at Rubisco can be boosted by  introducing the C4 cycle in C3 plants. Scientists are also engineering the Calvin-Benson-Bassham Cycle by overexpressing specific enzymes involved in the cycle, as well as adding photorespiratory bypasses to reduce carbon loss due to photorespiration. Lastly, work has been done to design a new artificial carbon assimilation cycle by using deep learning and synthetic biology. Synthetic biology approaches can also aid in developing artificial enzyme complexes that could improve photosynthesis in plants.  (Summary by Mae Mercado @maemercado.bsky.social)  J. Integr. Plant Biol. https://onlinelibrary.wiley.com/doi/10.1111/jipb.13825

 

Review: Geography, altitude, agriculture, and hypoxia

Hypoxia, or reduced oxygen availability, is a double-edged sword: while it disrupts metabolism and can cause cell death, it also plays a vital role in regulating development in animals and plants. With extreme flooding increasing due to climate change, understanding how genetic variation enhances hypoxia tolerance provides valuable strategies for improving crop resilience. This review by Holdsworth et al. examines how geography, altitude, and agriculture have shaped molecular responses to hypoxia, particularly through the PLANT CYSTEINE OXIDASE (PCO) N-degron pathway, and how these responses have evolved across different land plant species over time. Local adaptation plays a key role in acclimatization to humid environments, where flooding, often triggered by intense rainfall, drives acute hypoxic stress. Environmental genome-wide association studies (eGWAS) help identify genes linked to hypoxia tolerance by integrating large-scale genomic and environmental data. Altitude also influences oxygen-sensing adaptations, though no direct molecular mechanism for absolute altitude sensing has been identified. However, adaptation to altitude is at least partially linked to the PCO N-degron pathway. Agriculture has further shaped hypoxia responses, as seen in rice: the FR13A variety uses the Sub1A-1 gene to withstand full submersion by limiting growth and enhancing anaerobic metabolism, while deepwater rice employs SNORKEL1/2 genes to elongate stems and escape partial submersion. These insights drive breeding strategies for flood-resistant crops. Ultimately, understanding the conserved PCO N-degron pathway provides a foundation for future research into plant adaptation to low-oxygen environments, integrating georeferenced genomic data and biochemical findings. This article is part of the Plant Physiology focus issue on Hypoxia and Plants; a recorded webinar on this topic can be found here. (Summary by Elisa De Meo, www.linkedin.com/in/elisa-de-meo-25415a20b) Plant Physiol. https://doi.org/10.1093/plphys/kiae535

 

Structural insights into PHO1: A key regulator of phosphate translocation in plants

Phosphorus (P) is an essential macronutrient required for plant growth, development, and reproduction. It is primarily absorbed by plant roots in the form of orthophosphate (Pi). The root-to-shoot translocation of Pi depends on a crucial xylem-loading process mediated by PHOSPHATE 1 (PHO1), a Pi efflux transporter expressed in the pericycle and xylem parenchyma cells. Mutations in PHO1 result in severely impaired shoot growth and reduced seed production. Although the physiological role of PHO1 has been recognized for over two decades, its structure and gating mechanism were only recently elucidated. Using a combination of crystallography and modeling tools, Fang and colleagues resolved the Arabidopsis PHO1;H1 (AtPHO1;H1) structure, revealing an N-terminal cytoplasmic SPX domain, a transmembrane EXS domain, and a partially disordered C-terminal tail. The EXS domain facilitates Pi translocation and is gated by the residues Trp719 and Tyr610. The SPX domain binds PP-InsP molecules to regulate transport activity, while the C-terminal tail contributes to dimer formation and PP-InsP binding. These findings provide critical insights for optimizing phosphorus-use efficiency (PUE) in plants, which is essential for reducing dependence on P fertilizers and promoting sustainable, environmentally friendly agriculture. (Summary by Ching Chan @ntnuchanlab) Nature Plants 10.1038/s41477-024-01895-6

 

High-energy requiring pollen grains have specialized mitochondria

Imagine you’re on a quest to deliver a package, racing against the competition. How do you prepare? Pollen grains and the pollen tubes that they form are essentially package-delivery systems. Their purpose is to deliver genetic information (sperm cell nuclei) to the ovule. Once the task is completed, the pollen cell itself becomes obsolete. A new study by Boussardon et al. investigated the proteome of mature pollen grains which they isolated using the IMTACT protocol: Isolation of Mitochondria Tagged in specific Cell-Type. The authors showed that pollen grain mitochondria switch into a focused energy-generating program, with proteins involved in energy production (TCA cycle and electron transport chain) highly enriched, not unlike a runner carbo-loading before a race. At the same time, proteins involved in transcription and translation are strongly depleted, and the mitochondrial genome itself is actively degraded during maturation; in essence the mitochondria terminally differentiate and channel their resources into their delivery task. This observation is fascinating in light of the fact that the progeny of sexual reproduction inherit their mitochondria solely from the egg-donating parent, and not the sperm-donating parent, no pollen grain mitochondria need to be viable for transfer into the zygote. (Summary by Mary Williams @PlantTeaching.bsky.social ) Curr. Biol. 10.1016/j.cub.2024.12.037

 

You’ve gotta starch somewhere: Evidence for an alternative starch granule initiation pathway

Starch is the major storage carbohydrate in plants, and in Arabidopsis leaves it forms granules in the chloroplasts to supply energy during the night when photosynthesis is inactive. These semicrystalline granules are made of glucose chains, which can be mostly unbranched (amylose) or highly branched (amylopectin). The formation of new starch granules (initiation) is achieved by building on short glucose chains called malto-oligosaccharide (MOS) primers. A key step in this process is the delivery of a glucosyltransferase STARCH SYNTHASE 4 (SS4) to the new granule by PROTEIN TARGETING TO STARCH 2 (PTST2). However, new evidence from Heutinck et al. supports an alternative route for starch granule initiation. In an Arabidopsis mutant deficient in two debranching enzymes, branched MOS in the chloroplast accumulate to levels ten times higher than in the wild type. Additional granules were also formed in these chloroplasts, which were smaller, differently shaped, and not reliant on SS4 or PTST2 to be initiated. While additional research is needed to elucidate the mechanism, the possibility of a new pathway for starch granule initiation provides huge potential for better understanding plant carbon metabolism and hence crop improvement. (Summary by Ciara O’Brien) Plant Physiol. 10.1093/plphys/kiaf002

 

Prion-like domains of sensory HSFs remember heat

The heat shock response, a rapid transcriptional response to heat, was first observed nearly 60 years ago, and has long been a paradigm for understanding gene responses to exogenous cues. The family of genes encoding heat shock factors (HSFs) is greatly expanded in plants. These HSFs serve as key regulators of the heat shock response, both initiating short-term transcriptional changes, but also serving as a molecular memory that activates heat memory genes after an earlier “priming” stress. A new study by Peng et al. examined how conformational changes in HSF protein structure contributes to both short term and memory responses to heat shock. The authors identified a transcriptional cascade, led by rapid activation HSFA1 by protein conformational changes. Within moments of heat shock, HSFA1 factors form speckles in the nucleus, suggesting that they act as heat sensors, and eliciting a very rapid transcriptional response. HSFA1 factors contain two Prion-related Domains (PrDs), which the authors showed are critical for their thermal responsiveness. PrDs are intrinsically disordered domains that are often found in proteins that undergo liquid phase separation. One of these, PrD1, is responsible for sequestering the HSFA1 proteins during ambient temperatures and maintaining them in an inactive state. The other, PrD2, is required for heat activation and thermal memory, through the formation of DNA loops that connect heat-responsive promoters with enhancer domains. This work builds on the growing recognition of the importance of intrinsically disordered domains and liquid phase separation in modulating rapid cellular responses. (Summary by Mary Williams @PlantTeaching.bsky.social) Mol Plant 10.1016/j.molp.2025.01.007

 

How a model C4 plant, Setaria viridis, copes with prolonged heat

Due to anthropomorphic global warming, 2024 was the first year during which the global mean temperature was more than 1.5° above pre-industrial levels. Clearly, understanding how high temperatures affect plant physiology is an urgent priority. In this new study, Zhang et al. did a multi-parameter study of the model C4 plant Setaria viridis. They grew two populations for two weeks at 28°, and then for the next two weeks one group was grown at 42° whilst the other remained at 28°. After this, the authors measured photosynthesis parameters, and carried out metabolomic, transcriptomic, and proteomic studies, leading to several key findings. As expected, the heat-grown plants were significantly smaller than their counterparts. Surprisingly, their photosynthetic efficiency was hardly altered. The heat-grown plants had much higher levels of hexoses, which might be a protective mechanism to retain water. The authors also found increased levels of ABA and amino-acid conjugates of IAA, which may contribute to the smaller size of the plants. There’s a LOT of interesting data, so have a look. Your favorite gene or metabolite is likely to appear in this useful and comprehensive study. (Summary by Mary Williams @plantteaching.bsky.social) Plant Cell https://doi.org/10.1093/plcell/koaf005

 

Streamlining the immune system: How plants adapt to reduced pathogen pressure

Although plants are sessile organisms unable to escape pathogen invasions, they are well equipped with defense mechanisms. Cell surface-localized pattern-recognition receptors (PRRs) detect extracellular signals and initiate pattern-triggered immunity (PTI), while nucleotide-binding leucine-rich repeat receptors (NLRs) sense intracellular signals and trigger effector-triggered immunity (ETI). These two layers of immune signaling were long considered distinct pathways but are now recognized as interdependent—essentially functioning as one. While numerous studies have explored the expansion of PRRs and NLRs during plant evolution, particularly during the transition from aquatic to terrestrial environments, the opposite scenario remains less examined: how plants with specialized lifestyles—such as mangrove, desert, or aquatic species—adapt to reduced pathogen pressure. Li and colleagues reassessed 808 angiosperm genomes and found that plants with specialized lifestyles and habitats (SLHs) exhibit significant reductions in PRR and NLR genes due to increased gene loss and reduced gene duplication. Evolutionary association studies further identified key immune regulatory modules, including the well-known EDS1, alongside novel components. These newly identified modules and annotated immune-related genes from 808 angiosperm species offer valuable insights into plant immunity and can be explored through the publicly available database, AirDB (https://efg.nju.edu.cn/AirDB/). (Summary by Ching Chan @ntnuchanlab) Nature Plants 10.1038/s41477-024-01901-x

Double attack! Herbivore insects feed on plants and silence their genes

In the natural environment, plants are constantly attacked by animals. Plant immunity is regulated by a network of genes and hormones including salicylic acid (SA) and jasmonic acid (JA). A recent study suggests that herbivore insects threaten plants with concerns more than the bite. Han et al., found that the phloem-feeding whitefly (Bemisa tabaci) transfers miRNA BtmiR29-b to tobacco phloem sap during feeding. The miRNA suppresses plant defense by silencing the defense gene BAG4 and inhibits SA and JA accumulations in the host. Searching through the miRNA database miRBase, the authors found that miR29-b exists in many other insect species of various orders including Hemiptera, Coleoptera, Hymenoptera, Orthoptera, and Blattaria. Besides whitefly, miR29-b was experimentally detected in the salivary gland and saliva of aphid (Myzus persicae), which could transfer the miRNA to tobacco phloem sap during feeding. In plants, BAG4 homologs exist in various species of different families including Solanaceae, Brassicaceae, Cucurbitaceae, Euphorbiaceae, Leguminosae, and Malvaceae. Despite the different target sites, the targeting of the homologous BAG4 transcripts by miR29-b could be predicted. The transfer of BtmiR29-b from whiteflies to Arabidopsis, cotton, and tomato was also experimentally validated. The study demonstrates cross-kingdom miRNA-mediated gene silencing and suggests the conserved mechanism in different species. The findings motivate future studies in other cross-kingdom gene regulations and provide insights into pest control strategies. (Summary by Yee-Shan Ku @YeeShanKu1) Molecular Plant 10.1016/j.molp.2025.01.001

 

Review. Unraveling plant-microbe interaction dynamics: Insights from the Tripartite Symbiosis Model

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Plants naturally interact with a diverse array of microorganisms, which influence their fitness in various ways. However, understanding these plant-microbe interactions and applying the knowledge in real-world agricultural systems has been challenging. Most experimental research focuses on bipartite systems, where a single plant species is paired with one microbial species. This oversimplification fails to capture the complexity of natural ecosystems, where plants typically engage with multiple microorganisms simultaneously. One promising model for exploring these complex interactions is the tripartite symbiosis between legumes, arbuscular mycorrhizal fungi (AMF), and nitrogen-fixing rhizobia. This tripartite system provides valuable insights into the intricate relationships that govern plant-microbe dynamics and brings researchers closer to understanding how these multifactorial interactions shape plant health and productivity. In their review, Gorgia and Tsikou examine current knowledge and challenges associated with this system. They highlight that the effects of dual inoculation with both AMF and rhizobia cannot be predicted by simply adding the individual contributions of each microorganism, as indicated by multi-omics analyses. Moreover, factors such as partner compatibility, nutrient availability, environmental conditions, plant autoregulation, and the interactions between microbes inside (intraradical) and outside (extraradical) the root tissue all play critical roles. Together, these factors shape the rhizosphere community, influence root morphology, and ultimately affect the competitive dynamics of plants. Although the tripartite system remains relatively simple, it serves as a foundational model for studying more complex multispecies interactions that could have important applications in agriculture, particularly in enhancing crop productivity and sustainability. (Summary by Ching Chan @ntnuchanlab) Plant, Cell & Environment 10.1111/pce.15341

Review: High-yield farming is essential to slow biodiversity loss

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It’s 2025, and although we live in a world saturated with information, is increasingly difficult to sort fact from propaganda or fiction. This is true in all arenas, including plant science. Calls for strategies to improve crop yields are sometimes met with criticisms that higher yielding crops would only serve “big ag” or further harm biodiversity. That’s why I enjoyed reading this well-researched but accessible review article by Bamford et al. that lays out the need for high-yield farming to “bend the curve” of biodiversity loss, part of a special issue honoring the legacy of biodiversity researcher Georgina Mace. (You can find the rest of this special issue here https://royalsocietypublishing.org/toc/rstb/2025/380/1917). The authors address several issues, including the fact that feeding the human population “remains the pre-eminent threat to wild nature” and that so-called “land sharing” strategies (in which wildlife cohabitates with agriculture) don’t work very well. Therefore, they call for “land sparing”, which means keeping farming’s footprint as small as possible, through increasing yields. These yield increases can come aboutthrough crop improvement but also through making sure farmers have access to and are using best practices, such as integrated pest management and drip irrigation. The final paragraph of their article sums up the social challenges eloquently, have a look. (Summary by Mary Williams @PlantTeaching.bksy.social @PlantTeaching) Phil. Trans. R. Soc. B. https://doi.org/10.1098/rstb.2023.0216

Single cell multiomic analysis of plant immunity reveals PRIMER cells

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Single cell mutiomics are radically changing our understanding of pretty much every cellular process. Here, Nobori et al. integrated single-cell transcriptomic, epigenomic and spatial transcriptomic data to investigate plant responses to pathogens. The authors used three different strains of Pseudomonas syringae pv. tomato DC3000; the wild-type (referred to as DC3000) which causes disease, and two avirulent variants, DC3000 AvrRpt2 and AvrRpm1 that produce effectors that trigger the plant immune response. Nuclei were isolated at various times after inoculation for single-nucleus RNA-seq and Single-nucleus assay for transposase-accessible chromatin followed by sequencing (snATAC–seq), a method for identifying chromosome regions accessible to transcription factors and likely to indicate active genes. These large datasets revealed a wealth of information, including the fact that a subset of cellsact as primary immune responder (PRIMER) cells. These PRIMER cells express a novel transcription factor and are surrounded by “bystander” cells that activate systemic responses. The datasets are publicly available at (https://plantpathogenatlas.salk.edu). (Summary by Mary Williams) Nature https://doi.org/10.1038/s41586-024-08383-z

Dioecious dynamics: How male and female poplars shape microbial networks under stress

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Plants actively shape the microbial community in their rhizosphere to optimize nutrient acquisition and enhance resilience against environmental stresses. Interestingly, in dioecious plants, male and female individuals play distinct ecological roles and evolve different environmental adaptability. For instance, female poplar trees tend to allocate more resources to vegetative growth and reproduction, whereas male poplars prioritize defense and stress adaptation. However, the molecular mechanisms driving these differences remain largely unexplored. In a recent study, Yan and colleagues uncovered a fascinating aspect of this dimorphism under salinity stress. They observed that male poplars secrete higher levels of citric acid, which facilitates the recruitment of specific bacterial species in the rhizosphere. These bacteria form a keystone node in the microbial network, positively correlating with the male plants’ health index under stress. In contrast, female poplars showed a different interaction: fungal keystone nodes negatively correlated with their health index, suggesting harmful microbial associations. This study sheds light on the sexually dimorphic responses in plants and the intricate dynamics of plant-microbe interactions. It also highlights how poplars deploy a “cry for help” strategy to recruit beneficial microbes under stress conditions. (Summary by Ching Chan @ntnuchanlab) Plant, Cell & Environment 10.1111/pce.15350

Plant Science Research Weekly: January 24, 2025

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Review. Unraveling plant-microbe interaction dynamics: Insights from the Tripartite Symbiosis Model

Plants naturally interact with a diverse array of microorganisms, which influence their fitness in various ways. However, understanding these plant-microbe interactions and applying the knowledge in real-world agricultural systems has been challenging. Most experimental research focuses on bipartite systems, where a single plant species is paired with one microbial species. This oversimplification fails to capture the complexity of natural ecosystems, where plants typically engage with multiple microorganisms simultaneously. One promising model for exploring these complex interactions is the tripartite symbiosis between legumes, arbuscular mycorrhizal fungi (AMF), and nitrogen-fixing rhizobia. This tripartite system provides valuable insights into the intricate relationships that govern plant-microbe dynamics and brings researchers closer to understanding how these multifactorial interactions shape plant health and productivity. In their review, Gorgia and Tsikou examine current knowledge and challenges associated with this system. They highlight that the effects of dual inoculation with both AMF and rhizobia cannot be predicted by simply adding the individual contributions of each microorganism, as indicated by multi-omics analyses. Moreover, factors such as partner compatibility, nutrient availability, environmental conditions, plant autoregulation, and the interactions between microbes inside (intraradical) and outside (extraradical) the root tissue all play critical roles. Together, these factors shape the rhizosphere community, influence root morphology, and ultimately affect the competitive dynamics of plants. Although the tripartite system remains relatively simple, it serves as a foundational model for studying more complex multispecies interactions that could have important applications in agriculture, particularly in enhancing crop productivity and sustainability. (Summary by Ching Chan @ntnuchanlab) Plant, Cell & Environment 10.1111/pce.15341

Review: High-yield farming is essential to slow biodiversity loss

It’s 2025, and although we live in a world saturated with information, is increasingly difficult to sort fact from propaganda or fiction. This is true in all arenas, including plant science. Calls for strategies to improve crop yields are sometimes met with criticisms that higher yielding crops would only serve “big ag” or further harm biodiversity. That’s why I enjoyed reading this well-researched but accessible review article by Bamford et al. that lays out the need for high-yield farming to “bend the curve” of biodiversity loss, part of a special issue honoring the legacy of biodiversity researcher Georgina Mace. (You can find the rest of this special issue here https://royalsocietypublishing.org/toc/rstb/2025/380/1917). The authors address several issues, including the fact that feeding the human population “remains the pre-eminent threat to wild nature” and that so-called “land sharing” strategies (in which wildlife cohabitates with agriculture) don’t work very well. Therefore, they call for “land sparing”, which means keeping farming’s footprint as small as possible, through increasing yields. These yield increases can come about through crop improvement but also through making sure farmers have access to and are using best practices, such as integrated pest management and drip irrigation. The final paragraph of their article sums up the social challenges eloquently, have a look. (Summary by Mary Williams @PlantTeaching.bksy.social @PlantTeaching) Phil. Trans. R. Soc. B. 10.1098/rstb.2023.0216

How nitrogenase stays active

One of the great dilemmas of science is the fact that nitrogen gas, though very abundant in the atmosphere, is limiting for most forms of life. Of course, this lack of availability is because N2 gas has an extremely strong triple bond holding the two nitrogen atoms together; it’s so strong that N2 gas is considered “inert” and foods are often packaged in N2 to prolong shelf life. Fortunately, some prokaryotes produce an enzyme, nitrogenase, that can break this triple bond to produce ammonium (NH4+), which can be taken up and used by other organisms. However, this essential enzyme has an Achilles heel, which is that it is rapidly inactivated by oxygen. Fortunately, many nitrogen-fixing organisms produce a protein called FeSII (also known as Shethna protein II) that protects nitrogenase from oxygen, in a mechanism that has just been revealed in two back-to-back articles by Franke et al. and Narehood et al. Nitrogenase is made up of two protein complexes [iron protein (FeP) and molybdenum–iron protein (MoFeP)] containing several metal cofactors. The authors used cryo-EM to image this complex in the presence and absence of oxygen, and they found that in the presence of oxygen, FeSII reversibly binds to these metal-containing regions, protecting them from oxidative damage. Interestingly, the authors also found that the single protected structures can multimerize further into higher-order filaments. Not only is this beautiful work, but it also provides key insights that can one day be used to engineer plants that can fix nitrogen on their own. (Summary by Mary Williams @PlantTeaching.bksy.social @PlantTeaching) Nature10.1038/s41586-024-08355-3 and 10.1038/s41586-024-08311-1.

Capsella rubella: My Fruity Valentine

Most shapes in plant organs are pre-determined at the primordial stage and from this point, growth will establish and maintain this shape. Rarely will re-shaping of an organ occur post-organogenesis. However, Hu et al. describe a notable exception in Capsella rubella, a close relative of Arabidopsis thaliana. Capsella’s female reproductive organ, the gynoecium, undergoes a geometric rearrangement where its initially flat, spheroidal structure is re-shaped into a heart-shape upon fertilization. Hu et al. used a complex of technologies from single cell RNA sequencing to whole-organ live cell imaging to piece together the mechanisms underlying re-shaping. At the cellular level, this paper provides evidence that a gradient of differentiation, as well as regional anisotropic growth (different growth in different directions), support the re-shaping of the gynoecium. Molecularly, they identified an important gene supporting this process: SHOOTMERISTEMLESS (CrSTM). CrSTM expression is induced by local auxin signaling. CrSTM then binds a specific region in its own promoter to maintain its expression through an autoregulatory positive feedback loop. Intriguingly, this STM self-binding site is conserved throughout Brassicaceae species which re-shape their gynoecia post-fertilization. Altogether these findings demonstrate the evolutionary significance of STM autoregulation, coordinated cell division, and localized growth in re-shaping. (Summary by Kes Maio @KestrelMaio @kesmaio.bsky.social) Nature Plants 10.1038/s41477-024-01854-1

SOS1, salt, and cryo-imaging of subcellular element distribution

For living organisms, proper control of element location is just as important as the control of enzyme location, but harder to study. A new study by Ramakrishna et al. uses an exciting new technology, cryo nanoscale secondary ion mass spectrometry ion microprobe, to investigate elemental distribution (measured by their major isotopes) in Arabidopsis and rice roots. The images are beautiful, and different elements can be clearly seen localized within different subcellular compartments, including the cytosol, vacuole, and apoplast. Here, the authors investigated the subcellular distribution of sodium (Na+) in root cells. Plant cells are very sensitive to cytosolic sodium levels and use pumps to maintain a low concentration in the cytosol. In wild-type plants in mild salt stress (2.5 mM), sodium is almost entirely found in the apoplast, whereas when the salt concentration is moderate (25mM) the sodium mainly accumulates in the vacuole. The authors also examined mutants of a sodium transporter SOS1 (SODIUM OVERLY SENSITIVE 1). SOS1 was previously shown to be a sodium/proton antiporter localized in the plasma membrane that contributes to sodium export from the cytosol. In these sos1 mutant plants the authors observed a very different pattern of sodium accumulation at moderate salt levels; the salt remained elevated in the apoplast with very little accumulating in the vacuole, indicating a role for SOS1 in moving sodium into the vacuole. This study demonstrates a new role for SOS1, and introduces a powerful new imaging technology. (Summary by Mary Williams @PlantTeaching.bksy.social @PlantTeaching) Nature 10.1038/s41586-024-08403-y

Repairing a detrimental domestication variant improves tomato harvests

Domesticated plants and animals are remarkable human achievements but were achieved with rather blunt instruments. With the benefit of hindsight, we can now see that some of the genes and alleles that passed through the population bottlenecks and artificial selection process are deleterious. Glaus et al. looked at several tomato wild species, land races, and domesticated varieties. They found large numbers of non-synonymous mutations (coding for a different amino acid) and focused on the genes involved in flowering time, the florigen-activation complex. In tomato, the SELF-PRUNING (SP) gene acts as an anti-florigen that suppresses flowering. Another gene, SUPPRESSOR OF SP (SSP), has previously been used to control plant architecture and time of flowering. The authors identified a related gene, SSP2, that shows a deleterious mutation (S to F) in the DNA-binding domain in domesticated tomatoes. Introgressing the ancestral allele from wild tomatoes led to earlier flowering and a more compact inflorescence. The authors subsequently showed that the deleterious mutation interferes with the ability of SSP2 to bind DNA and act as a transcription factor. Next, they used CRISPR/Cas9 base editing to repair this mutation and restore the ancestral allele in domesticated tomato. The resulting plants showed a more compact growth, earlier flowering, and higher proportion of ripe fruit at harvest. This study shows that today’s powerful genomic tools can identify and repair deleterious alleles that are prevalent in domesticated plants and animals, correcting some unintended outcomes of our ancestors. (Summary by Mary Williams @PlantTeaching.bksy.social @PlantTeaching) Nature Genetics 10.1038/s41588-024-02026-9

Interconnected memories: How heat stress and bacterial infection shape plant resilience

Memory—a mysterious cognitive process that retains information over time and shapes future interpretations and actions—is not exclusive to animals. In plants, a similar phenomenon occurs where past exposure to environmental stressors is “memorized,” enabling plants to respond more effectively to subsequent challenges. This adaptive capability is exemplified by acquired thermotolerance (ATT) and systemic acquired resistance (SAR), two well-documented cases of plant memory. Fascinatingly, Nishad and colleagues uncovered an unexpected crosstalk between these seemingly distinct processes, revealing how they can prime one another. On one side, bacterial infection enhances plant tolerance to heat stress by promoting the sustained upregulation of heat shock proteins, with effects that persist longer than typical ATT responses. Conversely, heat stress influences SAR in an opposite direction, decreasing reactive oxygen species (ROS) production and consequently diminishing plant resistance to bacterial pathogens. Moreover, experiments in mutants deficient in heat shock memory regulators demonstrated that SAR is abolished in the absence of these factors, underscoring the pivotal role of heat shock proteins in mediating immune responses. This study highlights the intricate connections between heat stress signaling and plant immunity, offering exciting possibilities for cross-protection strategies. By understanding these interconnected mechanisms, researchers could develop innovative approaches to enhance crop resilience against combined stressors, improving agricultural sustainability in a changing climate. (Summary by Ching Chan @ntnuchanlab) Plant, Cell & Environment 10.1111/pce.15364

Single cell multiomic analysis of plant immunity reveals PRIMER cells

Single cell mutiomics are radically changing our understanding of pretty much every cellular process. Here, Nobori et al. integrated single-cell transcriptomic, epigenomic and spatial transcriptomic data to investigate plant responses to pathogens. The authors used three different strains of Pseudomonas syringae pv. tomato DC3000; the wild-type (referred to as DC3000) which causes disease, and two avirulent variants, DC3000 AvrRpt2 and AvrRpm1 that produce effectors that trigger the plant immune response. Nuclei were isolated at various times after inoculation for single-nucleus RNA-seq and single-nucleus assay for transposase-accessible chromatin followed by sequencing (snATAC–seq), a method for identifying chromosome regions accessible to transcription factors and likely to indicate active genes. These large datasets revealed a wealth of information, including the fact that a subset of cells act as primary immune responder (PRIMER) cells. These PRIMER cells express a novel transcription factor and are surrounded by “bystander” cells that activate systemic responses. The datasets are publicly available at https://plantpathogenatlas.salk.edu. (Summary by Mary Williams @PlantTeaching.bksy.social @PlantTeaching) Nature 10.1038/s41586-024-08383-z

Dioecious dynamics: How male and female poplars shape microbial networks under stress

Plants actively shape the microbial community in their rhizosphere to optimize nutrient acquisition and enhance resilience against environmental stresses. Interestingly, in dioecious plants, male and female individuals play distinct ecological roles and evolve different environmental adaptability. For instance, female poplar trees tend to allocate more resources to vegetative growth and reproduction, whereas male poplars prioritize defense and stress adaptation. However, the molecular mechanisms driving these differences remain largely unexplored. In a recent study, Yan and colleagues uncovered a fascinating aspect of this dimorphism under salinity stress. They observed that male poplars secrete higher levels of citric acid, which facilitates the recruitment of specific bacterial species in the rhizosphere. These bacteria form a keystone node in the microbial network, positively correlating with the male plants’ health index under stress. In contrast, female poplars showed a different interaction: fungal keystone nodes negatively correlated with their health index, suggesting harmful microbial associations. This study sheds light on the sexually dimorphic responses in plants and the intricate dynamics of plant-microbe interactions. It also highlights how poplars deploy a “cry for help” strategy to recruit beneficial microbes under stress conditions. (Summary by Ching Chan @ntnuchanlab) Plant, Cell & Environment 10.1111/pce.15350

 

How nitrogenase stays active

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One of the great dilemmas of science is the fact that nitrogen gas, though very abundant in the atmosphere, is limiting for most forms of life. Of course, this lack of availability is because N2 gas has an extremely strong triple bond holding the two nitrogen atoms together; it’s so strong that N2 gas is considered “inert” and foods are often packaged in N2 to prolong shelf life. Fortunately, some prokaryotes produce an enzyme, nitrogenase, that can break this triple bond to produce ammonium (NH4+), which can be taken up and used by other organisms. However, this essential enzyme has an Achilles heel, which is that it is rapidly inactivated by oxygen. Fortunately, many nitrogen-fixing organisms produce a protein called FeSII (also known as Shethna protein II) that protects nitrogenase from oxygen, in a mechanism that has just been revealed in two back-to-back articles by Franke et al. and Narehood et al. Nitrogenase is made up of two protein complexes [iron protein (FeP) and molybdenum–iron protein (MoFeP)] containing several metal cofactors. The authors used cryo-EM to image this complex in the presence and absence of oxygen, and they found that in the presence of oxygen, FeSII reversibly binds to these metal-containing regions, protecting them from oxidative damage. Interestingly, the authors also found that the single protected structures can multimerize further into higher-order filaments. Not only is this beautiful work, but it also provides key insights that can one day be used to engineer plants that can fix nitrogen on their own. (Summary by Mary Williams @PlantTeaching.bksy.social @PlantTeaching) Nature https://doi.org/10.1038/s41586-024-08355-3 and https://doi.org/10.1038/s41586-024-08311-1.