Search for: All records

The widespread consumption of PET worldwide has necessitated the search for environment‐friendly methods for PET degradation and recycling. Among these methods, biodegradation stands out as a promising approach for recycling PET. The discovery of duo enzyme system PETase and MHETase in 2016, along with their engineered variants, has demonstrated significant potential in breaking down PET. Previous studies have also demonstrated that the activity of the enzyme PETase increases when it is immobilized on nanoparticles. To achieve highly efficient and complete PET depolymerization, we immobilized both FAST‐PETase and MHETase at a specific ratio on magnetic nanoparticles. This immobilization resulted in a 2.5‐fold increase in product release compared with free enzymes. Additionally, we achieved reusability and enhanced stability of the enzyme bioconjugates. 

Management of polyethylene terephthalate (PET) plastic waste remains a challenge. PET-hydrolyzing enzymes (PHEs) such as IsPETase and variants like FAST-PETase demonstrate promising PET depolymerization capabilities at ambient temperatures and can be utilized to recycle and upcycle plastic waste. Whole-cell biocatalysts displaying PHEs on their surface offer high efficiency, reusability, and stability for PET depolymerization. However, their efficacy in fully breaking down PET is hindered by the necessity of two enzymes: PETase and MHETase. Current whole-cell systems either display only one enzyme or struggle with performance when displaying larger enzymes such as the MHETase–PETase chimera. We developed a Saccharomyces cerevisiae-based whole-cell biocatalyst for complete depolymerization of PET into its constituent monomers with no accumulation of intermediate products. Leveraging a cellulosome-inspired trifunctional protein scaffoldin displayed on the yeast surface, we co-immobilized FAST-PETase and MHETase, forming a multi-enzyme cluster. This whole-cell biocatalyst achieved complete PET depolymerization at 30 °C, yielding 4.95 mM terephthalic acid (TPA) when tested on a PET film. Furthermore, we showed improved PET depolymerization ability by binding FAST-PETase at multiple sites on the scaffoldin. The whole cells had the added advantage of retained activity over multiple reusability cycles. This breakthrough in complete PET depolymerization marks a step toward a circular plastic economy. 

Computational design of functional proteins is of both fundamental and applied interest. This study introduces a generative framework for co‐designing protein sequence and structure in a unified process by modeling their joint distribution, with the goal of enabling cross‐modality interactions toward coherent and functional designs. Each residue is represented by three distinct modalities (type, position, and orientation) and modeled using dedicated diffusion processes: multinomial for types, Cartesian for positions, and special orthogonal group SO(3) for orientations. To couple these modalities, we propose a unified architecture, ReverseNet, which employs a shared graph attention encoder to integrate multimodal information and separate projectors to predict each modality. We benchmark our models, JointDiff and JointDiff‐x, on unconditional monomer design and conditional motif scaffolding tasks. Compared to two‐stage design models that generate sequence and structure separately, our models produce monomer structures with comparable or better designability, while currently lagging in sequence quality and motif scaffolding performance based on computational metrics. However, they are 1–2 orders of magnitude faster and support rapid iterative improvements through classifier‐guided sampling. To complement computational evaluations, we experimentally validate our approach through a case study on green fluorescent protein (GFP) design. Several novel, evolutionarily distant variants generated by our models exhibit measurable fluorescence, confirming functional activity. These results demonstrate the feasibility of joint sequence–structure generation and establish a foundation to accelerate functional protein design in future applications. Codes, data, and trained models are accessible athttps://github.com/Shen-Lab/JointDiff. 

Abstract Effective nitrogen fertilizer management is crucial for reducing nitrous oxide (N₂O) emissions while ensuring food security within planetary boundaries. However, climate change might also interact with management practices to alter N₂O emission and emission factors (EFs), adding further uncertainties to estimating mitigation potentials. Here, we developed a new hybrid modeling framework that integrates a machine learning model with an ensemble of eight process‐based models to project EFs under different climate and nitrogen policy scenarios. Our findings reveal that EFs are dynamically modulated by environmental changes, including climate, soil properties, and nitrogen management practices. Under low‐ambition nitrogen regulation policies, EF would increase from 1.18%–1.22% in 2010 to 1.27%–1.34% by 2050, representing a relative increase of 4.4%–11.4% and exceeding the IPCC tier‐1 EF of 1%. This trend is particularly pronounced in tropical and subtropical regions with high nitrogen inputs, where EFs could increase by 0.14%–0.35% (relative increase of 11.9%–17%). In contrast, high‐ambition policies have the potential to mitigate the increases in EF caused by climate change, possibly leading to slight decreases in EFs. Furthermore, our results demonstrate that global EFs are expected to continue rising due to warming and regional drying–wetting cycles, even in the absence of changes in nitrogen management practices. This asymmetrical influence of nitrogen fertilizers on EFs, driven by climate change, underscores the urgent need for immediate N₂O emission reductions and further assessments of mitigation potentials. This hybrid modeling framework offers a computationally efficient approach to projecting future N₂O emissions across various climate, soil, and nitrogen management scenarios, facilitating socio‐economic assessments and policy‐making efforts. 

This dataset contains yearly projections of emission factors (EFs) for fertilizer-induced direct nitrous oxide (N2O) emissions across the global agricultural lands with a spatial resolution of 0.5° × 0.5° from 1990 to 2050. Emission factor (EF) is defined as the amount of N2O emitted per unit of nitrogen (N) fertilizer applied, expressed in percentage (%). They are developed from a hybrid modeling framework, Dym-EF (more details can be found in Li et al., 2024). The framework integrates machine learning approaches with an ensemble of eight process-based models from The Global N2O Model Intercomparison Project phase 2 (NMIP2) to learn the relationship between EF dynamics and multiple environmental factors, such as climate, soil properties, nitrogen fertilizer input, and other agricultural management practices. After the hybrid modeling framework was extensively validated, we applied it to develop EF projections under different nitrogen management policies and climate change scenarios, including future climate data from 37 Global Climate Models (GCMs). The annual median and standard deviation (SD) of EF under each scenario represent the projection median and variability derived from climate input data using the 37 GCMs.The dataset filenames follow the structure: 'Scenario'_'N regulation'_'Median/SD', where 'Scenario' corresponds to the different nitrogen management and climate scenarios (e.g., INMS1, INMS2, and INMS3), 'N regulation' corresponds to the different nitrogen management levels (e.g., BAU, LowNRegul, and MedNRegul), and 'Median/SD' indicates whether the file contains the median (Median) or standard deviation (SD) of the projections. All relevant data and further details can be found in the supplementary materials and the cited references.INMS1: Business-as-usual, Land use regulation: Medium, Diet: Meat & dairy-rich, Ambition level: LowINMS2: Low-nitrogen regulation, Land use regulation: Medium, Diet: Medium meat & dairy, Ambition level: LowINMS3: Medium-nitrogen regulation, Land use regulation: Medium, Diet: Medium meat & dairy, Ambition level: ModerateINMS4: High-nitrogen regulation, Land use regulation: Medium, Diet: Medium meat & dairy, Ambition level: HighINMS5: Best-case, Land use regulation: Strong, Diet: Low meat & dairy, Ambition level: HighINMS6: Best-case “Plus”, Land use regulation: Strong, Diet: Ambitious diet shift and food-loss/waste reductions, Ambition level: HighINMS7: Bioenergy, Land use regulation: Strong, Diet: Low meat & dairy, Ambition level: HighWe developed this data using the “ranger” package in R 4.1.1, which is accessible at https://cran.r-project.org/web/packages/ranger/. The optimization of the two hyperparameters (ntree and mtry) was performed using the ‘caret’ package, available at https://topepo.github.io/caret/.This database is developed by Li, L., C. Lu, W. Winiwarter, H. Tian, J. Canadell, A. Ito, A.K. Jain, S. Kou-Giesbrecht, S. Pan, N. Pan, H. Shi, Q. Sun, N. Vuichard, S. Ye., S. Zaehle, Q. Zhu. Enhanced nitrous oxide emission factors due to climate change increase the mitigation challenge in the agricultural sector Global Change Biology (In Press)