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Despite significant progress made in recent years, many questions still remain on how SnRK1 senses cellular energy and nutrient levels in plants, and how it translates this information to ensure optimal growth and survival. In this paper, the authors mapped a proteome-wide SnRK1 signaling network in Arabidopsis in relation to carbon availability. At the intersection of this targeted interactomics approach, the authors discovered a strong association of SnRK1 with class II T6P synthase-like proteins. They could show that these proteins function as negative regulators of SnRK1, and might have a role as carbon sensors that integrate T6P levels with SnRK1 activity.

Due to the presence of a transmembrane domain, the subcellular mobility plan of membrane-bound or membrane-tethered transcription factors (MB-TFs) differs from that of their cytosolic counterparts. The MB-TFs are mostly locked in (sub)cellular membranes, until they are released by a proteolytic cleavage event or when the transmembrane domain (TMD) is omitted from the transcript due to alternative splicing. Here, the authors review the current knowledge on the proteolytic activation mechanisms of MB-TFs in plants, with a particular focus on regulated intramembrane proteolysis (RIP), and discuss the analogy with the proteolytic cleavage of MB-TFs in animal systems. The authors present a comprehensive inventory of all known and predicted MB-TFs in the model plant Arabidopsis thaliana and examine their experimentally determined or anticipated subcellular localizations and membrane topologies.

In this study, the authors show that leaf epidermal cells acquire pavement cell identity by expressing the cell cycle inhibitory gene SIAMESE-RELATED1 (SMR1). In the absence of SMR1, apparently mature pavement cells lose their cell identity, dedifferentiate, and give rise to stomatal lineage cells. Since fine-tuning the number of stomata and pavement cells in leaves is crucial for leaf physiology under environmental stresses such as drought, the authors propose SMR1 as an exciting target for engineering climate-resilient plants.

See also press release regarding this paper.

The authors report a simple, effective strategy to create fully homozygous edited maize plants when multiplexing using CRISPR/Cas9. The authors anticipate that their strategy will facilitate the study of gene families and the identification of allele combinations to improve quantitative crop traits.

Brassinosteroids are steroidal phytohormones required for the growth and development of plants and are widely used in agriculture to improve crop yields. They are synthesized in the cell interior, but they bind their receptors at the cell surface. While brassinosteroids were discovered over 50 years ago, research on the mechanisms exporting them out of the cell lagged for decades. Researchers have now uncovered a role for the Arabidopsis ABC transporter ABCB19, formerly known as an auxin transporter, in brassinosteroid export. Future research will unravel the mechanisms regulating the ABCB19 activation and substrate preference and hopefully identify additional brassinosteroid exporters. Such mechanisms will help design more effective strategies to improve plant productivity and resilience via modulating endogenous brassinosteroid amounts and distribution.

Changes in gene expression driven by stress are fully characterized, however, the components that regulate H2O2-dependent gene expression remain largely enigmatic. The Mediator complex bridge specific transcription factors with the RNA Pol II machinery and converges different signals before channeling instructions to initiate gene transcription. Although well studied, a specific function of any of the Mediator subunits in regulating oxidative stress responses or H2O2-triggered gene expression was not yet known. Our work show that the Arabidopsis MED8 confers tolerance to stress. We demonstrate that MED8 mainly function as a repressor of H2O2-induced gene expression, negatively regulating pathways that are dependent on stress hormones such as salicylic acid and jasmonic acid. We believe that MED8 achieve its role by interacting with other components that are not necessarily required for transcription such as NOT2, a key regulator of microRNA biogenesis. Our next challenge is to comprehensively profile the Mediator interactome and to shed light on its redox regulation.

Through the application of an advanced machine learning approach for large-scale functional data integration, the authors performed, for the first time, a systematic regulatory annotation for nearly all Arabidopsis genes. Extensive validation using different types of experimental datasets revealed a strong enrichment for functional interactions. Predicting transcription factor functions based on an integrative network (iGRN) indicated that for various biological processes many known regulators could be recovered. Experimental validation confirmed 13 novel regulators involved in reactive oxygen species stress regulation, demonstrating that the iGRN offers a high-quality starting point to enhance our understanding of gene regulation in plants.

To identify regulators of thermomorphogenesis that are conserved in flowering plants, researchers at PSB mapped changes in protein phosphorylation in both dicots and monocots exposed to warm temperature. They identified MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE KINASE4 (MAP4K4)/TARGET OF TEMPERATURE3 (TOT3) as a regulator of thermomorphogenesis in Arabidopsis and wheat. This approach can contribute to ensuring food security under a changing climate.

The biosynthesis of plant specialized metabolites is strictly regulated in time and space. We have identified a robust transcriptional network, composed of multiple redundant transcriptional activators, co-activators and repressors, which steers cell-specific and jasmonate-inducible triterpene biosynthesis in the outer tissues of the root tips of the model plant Arabidopsis. This network is a beautiful example of the robustness of the regulatory networks that not only determine the establishment and proper employment of the arsenal of bioactive plant metabolites essential for plant survival but also protect the producing plants from their own chemical weapons.

In this multi-disciplinary paper, the authors show how single cell sequencing allows to identify procambium specific regulators controlling active hormone levels during vascular development. These regulators would not have been selected using bulk approaches given their tissue specific expression. This is a beautiful example of how single cell approaches can boost developmental biology research.

Polyploid organisms abound, but long-term polyploid establishment is much rarer and likely not random. Hence, polyploidy is considered either an evolutionary dead end or a force helping organisms survive environmental changes and stress. How and why polyploids, especially autopolyploids, might outcompete nonpolyploids during times of environmental upheaval is unclear. On a longer timescale, whole-genome duplications may increase genetic robustness and variation, but their benefits on the short term are harder to explain. We show that duplicating genomes and their encoded gene regulatory networks increase signal output variation, leading to niche expansion and increased potential for surviving environmental turmoil. These findings highlight how polyploidy might help organisms adapt to changing conditions and survive disruption but might be maladaptive under stable conditions.

Clathrin-mediated endocytosis is an essential transport pathway that functions to internalize material on the cell surface. The generation of clathrin-coated vesicles during endocytosis requires the co-ordinated recruitment of dozens of proteins to the plasma membrane within seconds. Importantly, the efficient assembly of endocytic vesicles requires that these endocytic components can be dynamically rearranged during the different stages of the process. The evolutionary ancient octameric TPLATE complex occupies a central position in endocytosis in plants. We discovered that the TPLATE complex undergoes biomolecular condensation through interactions with plasma membrane phospholipids and, via weak multivalent interactions, recruits clathrin and other endocytic proteins to facilitate the efficient progression of endocytosis.

See also research briefing that accompanies manuscript: https://doi.org/10.1038/s41556-024-01355-5

Multiplex amplicon sequencing is a versatile method to identify genetic variation in natural or mutagenized populations through eco-tilling or multiplex CRISPR screens. Such genotyping screens require reliable and specific primer designs, combined with simultaneous gRNA design for CRISPR screens. Unfortunately, current tools are unable to combine multiplex gRNA and primer design in a high-throughput and easy-to-use manner with high design flexibility. Here, the authors report the development of a bioinformatics tool called SMAP design to overcome these limitations. They tested SMAP design on several plant and non-plant genomes and obtained designs for more than 80–90% of the target genes, depending on the genome and gene family. The authors validated the designs with Illumina multiplex amplicon sequencing and Sanger sequencing in Arabidopsis, soybean, and maize and used SMAP design to perform eco-tilling by tilling PCR amplicons across nine candidate genes putatively associated with haploid induction in Cichorium intybus. SMAP design is an easy-to-use command-line tool that generates highly specific gRNA and/or primer designs for any number of loci for CRISPR or natural variation screens and is compatible with other SMAP modules for seamless downstream analysis.

Lignocellulosic biomass is a promising renewable resource for the production of primary sugars to be fermented to biobased products. Lignin is the main factor limiting the enzymatic deconstruction of the biomass. To reduce the recalcitrance engendered by the lignin polymer, lignin structure can be engineered such that is is easier to degrade and remove from the lignocellulosic matrix. Through the simultaneous expression of FERULOYL-CoA 6'-HYDROXYLASE 1 (F6'H1) and COUMARIN SYNTHASE (COSY) in lignifying cells in Arabidopsis, the transgenic lines overproduced the coumarin scopoletin and incorporated it into the lignin polymer, without adversely affecting plant growth. About 3.3% of the lignin units in the transgenic lines were derived from scopoletin, thereby exceeding the levels of the traditional p-hydroxyphenyl units. Saccharification efficiency of alkali-pretreated scopoletin-overproducing lines was 40% higher than for wild type.

Lorenzo et al., 2023 describes a gene discovery pipeline, denominated BREEDIT, which combines multiplex gene editing of large sets of genes with crossing schemes to improve complex traits such as yield and drought tolerance. Phenotyping the edited populations and multiplex amplicon sequencing of all target genes allowed for the identification of putative gene combinations that govern the traits of interest. The paper provides proof of concept data in maize but a similar approach can be used for many other crops.