Constraint-based metabolic modeling reveals metabolic properties underpinning the unprecedented growth of Chlorella ohadii.

Comparative molecular and physiological analyses of organisms from one taxonomic group grown under similar conditions offer a strategy to identify gene targets for trait improvement. While this strategy can also be performed in silico using genome-scale metabolic models for the compared organisms, we continue to lack solutions for the de novo generation of such models, particularly for eukaryotes. To facilitate model-driven identification of gene targets for growth improvement in green algae, here we present a semiautomated platform for de novo generation of genome-scale algal metabolic models.

Molecular Dynamics of the Intrinsically Disordered Protein COR15A─A Force Field Validation on Structure and Dynamics.

Intrinsically disordered proteins (IDPs) pose a challenge for structural characterization, as experimental methods lack the subnanometer/subnanosecond resolution to capture their dynamic conformational ensembles. Molecular dynamics (MD) simulations can, in principle, provide this information, but for the simulation of IDPs, dedicated protein and water force fields are needed, as traditional MD models for folded proteins prove inadequate for IDPs. Substantial effort was invested to develop IDP-specific force fields, but their performance in describing IDPs that undergo conformational changes─such as those induced by molecular partner binding or changes in solution environment─remains underexplored.

Gene co-occurrence and its association with phage infectivity in bacterial pangenomes.

Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or cannot infect a bacterial strain based on their genome sequences. Understanding the complex interactions between phages and their bacterial hosts is thus of considerable interest.

The characterization of the LEAFY COTYLEDON 2 activation domains reveals its conserved dual mode of action in flowering plants.

Seed development in Arabidopsis thaliana is largely controlled by a set of transcription factors (TFs) called LAFL, including LEAFY COTYLEDON 2 (LEC2). In this study, we investigated the structure/function relationships of the protein LEC2 outside the well-described B3 DNA-binding domain. The results presented here unveil the presence of transcription activation domains (ADs) within the unstructured ends of the protein that are conserved in eudicots.

Comprehensive analysis of DNA methylome and transcriptome reveals the epigenetic regulation of nitric oxide treatment in delaying apricot fruit senescence.

Apricot produces climacteric fruit, which are perishable after harvest. To elucidate the regulatory role of NO treatment through DNA methylation in post-harvest senescence, apricot fruits were treated with 0.2 mmol/L sodium nitroprusside (SNP) solution for 10 min, with distilled water treatment serving as the control.

Assembly-dependent translational feedback regulation of photosynthetic proteins in land plants.

In the green alga Chlamydomonas reinhardtii, the synthesis of chloroplast-encoded photosynthetic subunits is feedback regulated by their protein complex assembly state. This regulation is known as control by epistasy of synthesis (CES) and matches subunit synthesis with requirements of complex assembly in photosystem II (PSII), the cytochrome bf complex (Cyt bf), photosystem I (PSI), ATP synthase and Rubisco. In embryophytes, CES was only described for Rubisco, raising the question of whether CES exists for components of the photosynthetic electron transport chain in land plants.

Synthetic C metabolism in enables strict formatotrophy and methylotrophy via the reductive glycine pathway.

Formate and methanol are promising alternatives to sugar-based feedstocks for biotechnological applications. These one-carbon (C) substrates can be sustainably produced from CO and renewable electricity and assimilated by both native and engineered microbial systems. However, their broader adoption is limited by the narrow range of bacterial hosts capable of efficient methanol and formate utilization.

Structure, evolution, and roles of MYB transcription factors proteins in secondary metabolite biosynthetic pathways and abiotic stresses responses in plants: a comprehensive review.

Unlike mobile organisms, plants are sessile and thus more vulnerable to environmental stressors. Among these, abiotic stress represents a major constraint that profoundly affects plant growth and development. To cope with these challenges, plants have evolved sophisticated adaptive mechanisms to enhance their stress resilience.

Transient colonization by Priestia megaterium B1L5 alters the structure of the rhizosphere microbiome towards potential plant beneficial bacterial groups in apple plantlets.

Background: Plant growth-promoting bacteria (PGPB) can beneficially modulate rhizosphere microbial communities, potentially improving plant health and reducing disease incidence. Limited research exists on the influence of PGPB inoculation on the rhizosphere microbial communities of apple plants, particularly in soils affected by apple replant disease (ARD). Here, we evaluated the capacity of GFP-labelled B1 (designated as B1L5) to colonize the roots of apple plantlets grown in two soils: ARD-affected soil and ARD-unaffected grass soil.

UV-B Responsive Flavonoid Synthesis Contributes to Tartary Buckwheat High-Altitude Adaption.

High-altitude environments expose plants to increased levels of UV-B radiation, necessitating the evolution of protective mechanisms to mitigate stress. Buckwheat is a flavonoid-rich pseudocereal naturally adapted to high-altitude environments with elevated UV-B exposure. Although flavonoid biosynthesis is thought to contribute to this adaptation, the molecular and metabolic basis underlying flavonoid-mediated UV-B tolerance remains largely uncharacterized.

The fern Nephrolepis exaltata is largely unresponsive to climate change conditions at both physiological and metabolic levels.

Climate change is impacting the performance of plants worldwide. However, the impact on ferns, the second-most diverse lineage of vascular plants, has received little attention. Here, we investigated the effects of one of the most claimed scenarios of the climatic change: drought (D), high temperature (HT) and high CO concentration (CO) on a fern (Nephrolepis exaltata) and a commonly studied angiosperm (Brassica oleracea) at photosynthetic, anatomical, and metabolic levels.

Evaluating plant growth-defense trade-offs by modeling the interaction between primary and secondary metabolism.

Understanding the molecular mechanisms behind plant response to stress can enhance breeding strategies and help us design crop varieties with improved stress tolerance, yield, and quality. To investigate resource redistribution from growth- to defense-related processes in an essential tuber crop, potato, here we generate a large-scale compartmentalized genome-scale metabolic model (GEM), potato-GEM. Apart from a large-scale reconstruction of primary metabolism, the model includes the full known potato secondary metabolism, spanning over 566 reactions that facilitate the biosynthesis of 182 distinct potato secondary metabolites.

Circulating epigenetic signatures classifying brain insulin resistance in humans.

Brain insulin action plays an important role in metabolic and cognitive health, but there is no biomarker available to assess brain insulin resistance in humans. Here, we developed a machine learning framework based on blood DNA methylation profiles of participants who did not have type 2 diabetes with and without brain insulin resistance and detailed metabolic phenotyping. We identified 540 DNA methylation sites (CpGs) as classifiers of brain insulin resistance in a discovery cohort ( = 167), results that were validated in two replication cohorts ( = 33 and 24) with high accuracy (83 to 94%).

Transcription factor CitMYB16 positively regulates cutin and wax biosynthesis in citrus by directly activating CitDCR and CitKCS2.

The cuticle forms a protective barrier on fruit surfaces, playing crucial roles in limiting water loss, reducing fruit cracking, and resisting pathogen invasion. However, the molecular mechanisms underlying cuticle accumulation in citrus fruits remain unclear due to the challenges associated with isolating and analyzing cuticle components. In this study, ZK (Citrus trifoliata) and HJ (Citrus reticulata) with extremely different cuticle contents were identified from nine citrus varieties, providing ideal materials for studying cuticle accumulation in citrus.

Rapid origin and turnover of genomic imprinting by transposable elements.

Genomic imprinting, the preferential expression of alleles based on their parent-of-origin, is an epigenetic mechanism that plays a key role in endosperm development and establishment of hybridization barriers. While imprinting is frequently associated with DNA methylation asymmetries and transposable elements (TEs), growing evidence suggests that this connection is not applying to all imprinted genes. This review synthesizes recent findings across different plant species, highlighting how TEs not only initiate imprinting through epigenetic reprogramming but also participate in its turnover, driving rapid evolutionary changes.

Wave-like SnRK1 Activation and Tre6P-Sucrose Imbalance Shape Early Salt Stress Response in Growing Alfalfa Leaves.

Alfalfa (Medicago sativa L.) is a key forage crop valued for its adaptability and nutritional quality, yet salinity significantly limits its productivity, particularly in arid regions. Understanding early stress responses is crucial for improving resilience.

The source of nitrogen conditions transcriptomic responses to water deficit in common bean roots.

Drought stress reduces plant growth and yield of crops. Common bean (Phaseolus vulgaris L.) establishes symbiosis with rhizobia, ensuring an adequate nitrogen supply without fertilizers.

Positional C enrichment analysis of aspartate determines PEPC activity in vivo.

Photoautotrophic organisms fix inorganic carbon (Ci) by RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) and PHOSPHOENOLPYRUVATE CARBOXYLASE (PEPC). Monitoring Ci assimilation rates in vivo is a major challenge in analyzing photoautotrophic metabolism and engineering improved photosynthesis, as conventional methods do not distinguish between these two fluxes. We explored widely applied gas chromatography mass spectrometry (GC-MS) metabolite profiling for C-positional fractional C enrichment (EC) analyses of aspartate to differentiate within one molecule between PEPC, RUBISCO, and CBB cycle activities by C pulse-labeling.

Towards a comprehensive view of the pocketome universe-biological implications and algorithmic challenges.

With the availability of reliably predicted 3D-structures for essentially all known proteins, characterizing the entirety of compound-binding sites (binding pockets on proteins) has become a possibility. The aim of this study was to identify and analyze all compound-binding sites, i.e.

Integrated biotechnological and AI innovations for crop improvement.

Crops provide food, clothing and other important products for the global population. To meet the demands of a growing population, substantial improvements are required in crop yield, quality and production sustainability. However, these goals are constrained by various environmental factors and limited genetic resources.

The biosynthesis and diversity of taxanes: From pathway elucidation to engineering and synthetic biology.

Taxanes are diterpenoid natural products found in yew trees (Taxus spp.) and include three anticancer agents: paclitaxel, docetaxel, and cabazitaxel. Despite nearly 500 reported taxane compounds, only the biosynthetic pathway of the type I taxane skeleton leading to paclitaxel is close to being fully elucidated.

Towards genetic architecture and genomic prediction of crop traits from time-series data: Challenges and breakthroughs.

Advances in remote and proximal sensing have facilitated temporal high-throughput phenotyping of crop populations grown in field conditions. The resulting time-series phenotypic data capture single or multiple growth- and yield-related traits at different temporal resolution. Whilst classical quantitative genetics approaches can readily be used with these temporal data by considering the measurement of a character at a given time point as a separate trait, this strategy fully neglects inter-trait integration over time.