Review: Lost in translation – lessons from concepts that don’t translate from Arabidopsis

/in /by

The May 2025 issue of The Plant Cell has a focus on Arabidopsis and how this simple model plant has had an outsized impact on our understanding of pretty much everything botanical (and beyond). Alongside several articles highlighting this impact, this review by Roeder et al. features eight short vignettes on topics that do not translate from Arabidopsis. If you are at all familiar with Arabidopsis, you can probably guess what a few of these are; the first vignette highlights the incredibly easy and efficient floral dip method for transforming Arabidopsis, and discusses why it doesn’t work for most plants. Other vignettes cover Arabidopsis’ lack of mycorrhizal associations and C4 photosynthesis; challenges of orthology and transcriptional regulatory region mapping to bigger genomes; the limitations of very simple root anatomy of Arabidopsis;  challenges of studying drought responses in Arabidopsis; and finally, differences in circadian biology between Arabidopsis and other plants. It’s a fascinating and illuminating article, and should be useful to those who seek to understand the strengths and weaknesses of working with model systems. (Summary by Mary Williams @PlantTeaching.bsky.social) Plant Cell 10.1093/plcell/koaf036

Update: How to eat an idea (and translate genes to products)

/in /by

Plant biologists are critical players in the pursuit of crop enhancement and other real-world solutions to today’s pressing problems, yet few of us know how to translate our research into tangible economic or social benefits. This useful and engaging article by Jonathan Napier walks us through the many steps and obstacles along the journey from an idea to product, drawing on the author’s and others’ experiences in developing plants enriched in omega-3 long chain polyunsaturated fatty acids, which are beneficial to human health but a diminishing natural resource. One of their first challenges lay in the fact that, unlike some engineered traits, several genes had to be introduced into plants to complete the biosynthetic pathway, which intersects with many other metabolic pathways. But such obstacles are familiar to most of us. The rest of the article covers the steps that must be followed to move out of the lab and into the market, such as building a compelling economic proposal to secure funders and investors. The long timeframe of such projects, and the complex and expensive regulatory landscapes for field trials and biosafety assessment provide additional challenges and require expertise beyond those of most researchers. The author also provides a fascinating look at how to navigate the opaque world of intellectual property (IP). This article is part of the forthcoming Plant Physiology Focus Issue on Numeracy, Realism, and Relevance, which will be highlighted with a panel discussion in mid-July. More details coming soon! (Summary by Plant Teaching @PlantTeaching.bsky.social) Plant Physiol. 10.1093/plphys/kiaf178

PPR767 controls mitochondrial RNA editing to regulate growth and drought tolerance in rice

/in /by

Mitochondria are vital energy-producing organelles that depend on precise RNA processing for function. In this study, Peng et al. identify PPR767, a mitochondria-localized E-type pentatricopeptide repeat (PPR) protein in rice, as a key regulator of plant architecture and drought tolerance. Loss-of-function mutants of PPR767 displayed stunted growth, thinner stems, narrower leaves, and reduced grain yield. Molecular analyses revealed that PPR767 directly binds mitochondrial RNAs and is essential for RNA editing at four sites in three NADH dehydrogenase genes (nad1, nad3, and nad7), all of which encode core subunits of respiratory complex I. In ppr767 mutants, these editing defects impair complex I activity and disrupt mitochondrial structure. PPR767 also interacts with the editing cofactors MORF1 and MORF8, highlighting its role in assembling a functional mitochondrial editosome. As a consequence of complex I dysfunction, ppr767 mutants accumulate excess reactive oxygen species (ROS) and show increased oxidative stress and compromised drought resistance. Transcriptomic analyses indicated significant shifts in the expression of ROS-related and development genes especially in root tissues, suggesting that PPR767 shapes root architecture and stress responses. This study demonstrates how PPR767 integrates mitochondrial RNA editing with energy metabolism and stress resilience, and provides a potential molecular target for breeding rice varieties with improved drought tolerance and robust growth under adverse conditions. (Summary by Muhammad Aamir Khan @MAKNature1998) Plant Physiol. 10.1093/plphys/kiaf187/8126252

Beyond degradation: COP1 fine-tunes plant growth through non-destructive protein tagging

/in /by

In the dark (e.g., under soil), hypocotyls elongate, but when exposed to light, they stop elongation. The biosynthesis of the plant hormone auxin is implicated in the elongation of hypocotyls in the dark. In the light, however, auxin action is inhibited, thereby limiting hypocotyl elongation. The E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) promotes elongated hypocotyl in the dark, but is inactivated in light. Ubiquitins are small, evolutionarily conserved (“ubiquitous”) proteins that, through the action of ubiquitin ligases like COP1, are attached to target proteins. When the link is made at lysine 48 (K48) of ubiquitin, the tagged proteins are targeted for degradation in the proteasome. In this article, Liu et al., showed that COP1 is not all about protein degradation as seen in the more common K48 linkage, but can also play a non-proteolytic role via linkage at lysine 63 (K63). The authors experimentally showed that to promote hypocotyl elongation in the dark, COP1 adds a specific molecular tag (K63-linked ubiquitin) to the enzyme GRETCHEN HAGEN 3.5 (GH3.5). This tagging inhibits the activity of GH3.5, thereby limiting the conjugation of amino acids to auxin (indole-3-acetic acid: IAA), suppressing hypocotyl elongation. However, in the light, COP1 inactivation disrupts K63 ubiquitination of GH3.5, leading to the activation of GH3.5, leading to increased amino acid conjugation to IAA, thus limiting IAA levels that promote hypocotyl elongation. Here, the authors showed a mechanism by which light regulates auxin metabolism to modulate hypocotyl elongation. (Summary by Nathaniel Oragbon @NathanIgwe) Nature Comms. 10.1038/s41467-025-58767-6 

When CLV walked in fields of gold

/in /by

A recent study by Vardanega et al. focuses on the development of the unique barley inflorescence architecture and unveils key molecular controls underlying meristematic determinacy. The CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) – CLAVATA1 (CLV1) interaction has been tied to meristem size and maintenance throughout the grasses. Using a variety of techniques such as phylogenetics, smRNA-FISH, RNA sequencing and CRISPR-Cas9, Vardenega et al. show the role of the CLE/CLV1 pathway in barley to coordinate meristem activities and direct the development of distinct inflorescence architecture. Initially, a candidate CLE peptide, HvFCP1, and ortholog for AtCLV1, HvCLV1, were identified. These were found to localise to similar positions within the inflorescence and their mutants had multi-floret spikelets, as well as indeterminate rachilla with enhanced proliferation. From transcriptomic analysis, these phenotypes were attributed to auxin signalling and trehalose-6-phosphate metabolism, indicating that this CLV pathway regulates meristems through sugar allocation and developmental timing. This research described how different meristems are likely controlled by interactions of CLV1 with different CLE peptides (with distinct expression patterns) to regulate inflorescence architecture development. Vardanega et al. highlight the opportunity to uncover and exploit these diverse mechanisms regulating different meristems to allow for precise engineering of inflorescence architecture in barley. (Summary by Kes Maio @kesmaio.bsky.social) Nature Comms 10.1038/s41467-025-59330-z

Untangling cell-specific root responses to stress

/in , /by

Single-cell technologies have brought our understanding of complex tissues to whole new levels. Previous methods showed how gene expression in tissues changes over time or after challenges, whereas now these patterns can be assigned to specific cell types, revealing intricate, elegant processes. Here, Zhu and Hsu et al. examined rice root responses to heterogenous soil or a homogeneous gel matrix. The authors found that while inner cell layers did not differ much between growth conditions, the outer cell layers of soil-grown plants showed elevated expression of defence, nutrient and cell wall-related genes as compared to the gel-grown samples. The authors also examined roots grown in more compact soils (1.6 g cm−3 compared to 1.2 g cm−3). Interestingly, the endodermis and exodermis cells showed the greatest impact of the higher density soils. Some of the more highly expressed genes are those involved in cell wall expansion (e.g., expansins). Genes involved in water stress responses were also elevated, including ABA synthesis and response genes, suggesting that the higher soil density leads to water stress. Interestingly, ABA synthesis genes were elevated in inner cell layers, while ABA response genes were elevated the outer cell layers, suggesting that ABA moves outward. Finally, the authors found that in the compacted soils, there was an increase in expression of biosynthetic genes for lignin and suberin in the endodermis and exodermis, potentially mediated by ABA, helping to prevent water movement out of the root. (Summary by Mary Williams @PlantTeaching.bsky.social) Nature 10.1038/s41586-025-08941-z

Cell communication lockdown: How plants close plasmodesmata in MAMP immune response

/in /by

How do plants protect themselves from microbial invaders? One response is the closure of plasmodesmata to stop the spread of microbial effector proteins that help pathogens evade the immune response, protecting neighboring uninfected cells. While the phenomenon of plasmodesmata closure in response of microbe-associated molecular patterns (MAMPs) is well-documented, the underlying signaling and mechanisms need further investigation. Li et al. have determined that in Arabidopsis this process is mediated by Synaptotagmin 1 (Syt1), a transmembrane protein that connects to both the endoplasmic reticulum and the plasma membrane. Upon exposure to flagellin peptide, a MAMP, the levels of plasma membrane phospholipid PI(4,5)P2 increase. This increase is detected by Syt1, causing it to a form a complex with annexin 4 and initiating calcium signaling, increasing callose deposition within the plasmodesmata. Because the aperture of the plasmodesmata pore is controlled by callose deposition, this MAMP response decreases the pore size and prevents the MAMPs from spreading to nearby cells. This study helps elucidate the underlying mechanisms of plant innate immune responses and could inform future work on local regulation specific to the plasmodesmata and on the heterogeneity of intracellular calcium signaling. (Summary by Elise Krespan) Cell Reports 10.1016/j.celrep.2025.115672

Uncovering the kinase switch to coordinate symbiosis and immunity

/in /by

Biological nitrogen fixation is a vital natural process that converts atmospheric nitrogen into bioavailable forms, enabling its assimilation into essential biomolecules such as amino acids and nucleic acids. This unique capability is primarily carried out by specialized microbes, often through their symbiotic association with legume plants. The success of this symbiosis depends on the plants’ ability to accurately recognize and selectively interact with beneficial microbial partners while actively excluding potential pathogens. In Medicago truncatula, recognition of nitrogen-fixing rhizobia occurs through the interaction between the bacterial Nod factor signals and the plant receptor kinases MtLYK3and MtNFP. Although this selective recognition is a well-established concept, the molecular mechanisms mediating the switch between symbiotic and immune signaling remain elusive. In a recent study, Wang and colleagues used yeast two-hybrid cDNA library screening to identified MtLICK1 and MtLICK2 as MtLYK3 interactors. Functional studies revealed that mutations in MtLICK1/2 impair the expression of symbiotic marker genes and reduce nodule formation. Using further genetic and biochemical assays, the authors demonstrated that MtLICKs and MtLYK3 form a reciprocal trans-phosphorylation module. This module activates symbiotic signaling while simultaneously repressing immune responses. These findings position MtLICK1/2 as critical kinases that activate MtLYK3, thus resolving a long-standing question in legume symbiosis research. (Summary by Ching Chan @ntnuchanlab) Nature 10.1038/s41586-025-09057-0

A roadmap to get fruit and veg back on the table

/in /by

We all know that a healthy body requires a diet rich in fruits and vegetables., yet the vast majority of people living in the US don’t eat the recommended daily amounts of these plant foods. This deficit, and the accompanying over-reliance on grain-based and ultraprocessed foods, means that America is experiencing a health epidemic of obesity and accompanying type 2 diabetes. This article, by Gunter et al., explores the causes of these problems. Their key finding is that fruits and vegetables are simply too expensive, leading people to rely on cheaper, low-quality foods, a trend that is even more pronounced among people in socioeconomically disadvantaged groups. Several factors contribute to the high costs including the fact that domestic production is inadequate, and horticultural research grossly underfunded. The authors call for increased funding for fruit and vegetable improvement, targeting nutrient content, palatability, shelf life, and traits that make them more available to mechanical harvesting to reduce labor costs. They also call for better community outreach to help reverse people’s bad eating habits, and more research to explore how to reverse chronic health problems through better nutrition.  (Summary by Mary Williams @PlantTeaching.bsky.social) Proc. Natl. Acad. Sci. USA 10.1073/pnas.2501723122