Microbial attachment and biofilm formation on microplastics (MPs <5 mm in size) in the environment have received growing attention. However, there is limited knowledge of microbial function and their effect on the properties and behavior of MPs in the environment. In this study, microbial communities in the plastisphere were explored to understand microbial ecology as well as their impact on aquatic ecosystems. Using the amplicon sequencing of 16S and internal transcribed spacer (ITS) genes, we uncovered the composition and diversity of bacterial and fungal communities in samples of MPs (fiber, film, foam, and fragment), surface water, bottom sediment, and coastal sand in two contrasting coastal areas of Japan. Differences in microbial diversity and taxonomic composition were detected depending on sample type (MPs, water, sediment, and sand) and the research site. Although relatively higher bacterial and fungal gene counts were determined in MP fragments and foams from the research sites, there were no significant differences in microbial community composition depending on the morphotypes of MPs. Given the colonization by hydrocarbon-degrading communities and the presence of pathogens on MPs, the complex processes of microbial taxa influence the characteristics of MP-associated biofilms, and thus, the properties of MPs. This study highlights the metabolic functions of microbes in MP-associated biofilms, which could be key to uncovering the true impact of plastic debris on the global ecosystem.

Outer membrane vesicles (OMVs) are small, spherical, nanoscale proteoliposomes released from Gram-negative bacteria that play an important role in cellular defense, pathogenesis, and signaling, among other functions. The functionality of OMVs can be enhanced by engineering developed for biomedical and biochemical applications. Here, we describe methods for directed packaging of enzymes into bacterial OMVs of E. coli using engineered molecular systems, such as localizing proteins to the inner or outer surface of the vesicle. Additionally, we detail some modification strategies for OMVs such as lyophilization and surfactant conjugation that enable the protection of activity of the packaged enzyme when exposed to non-physiological conditions such as elevated temperature, organic solvents, and repeated freeze/thaw that otherwise lead to a substantial loss in the activity of the free enzyme.

The enzyme-mimicking nature of versatile nanomaterials proposes a new class of materials categorized as nano-enzymes, ornanozymes. They are artificial enzymes fabricated by functionalizing nanomaterials to generate active sites that can mimic enzyme-like functions. Materials extend from metals and oxides to inorganic nanoparticles possessing intrinsic enzyme-like properties. High cost, low stability, difficulty in separation, reusability, and storage issues of natural enzymes can be well addressed by nanozymes. Since 2007, more than 100 nanozymes have been reported that mimic enzymes like peroxidase, oxidase, catalase, protease, nuclease, hydrolase, superoxide dismutase, etc. In addition, several nanozymes can also exhibit multi-enzyme properties. Vast applications have been reported by exploiting the chemical, optical, and physiochemical properties offered by nanozymes. This review focuses on the reported nanozymes fabricated from a variety of materials along with their enzyme-mimicking activity involving tuning of materials such as metal nanoparticles (NPs), metal-oxide NPs, metal-organic framework (MOF), covalent organic framework (COF), and carbon-based NPs. Furthermore, diverse applications of nanozymes in biomedical research are discussed in detail.

The identification of enzyme functions plays a crucial role in understanding the mechanisms of biological activities and advancing the development of life sciences. However, existing enzyme EC number prediction methods did not fully utilize protein sequence information and still had shortcomings in identification accuracy. To address this issue, we proposed an EC number prediction network using hierarchical features and global features (ECPN-HFGF). This method first utilized residual networks to extract generic features from protein sequences, and then employed hierarchical feature extraction modules and global feature extraction modules to further extract hierarchical and global features of protein sequences. Subsequently, the prediction results of both feature types were combined, and a multitask learning framework was utilized to achieve accurate prediction of enzyme EC numbers. Experimental results indicated that the ECPN-HFGF method performed best in the task of predicting EC numbers for protein sequences, achieving macro F1 and micro F1 scores of 95.5% and 99.0%, respectively. The ECPN-HFGF method effectively combined hierarchical and global features of protein sequences, allowing for rapid and accurate EC number prediction. Compared to current commonly used methods, this method offers significantly higher prediction accuracy, providing an efficient approach for the advancement of enzymology research and enzyme engineering applications.
酶功能的识别对理解生命活动的机制、推进生命科学的发展有重要作用。然而现有的酶EC编号预测方法，并未充分利用蛋白质序列信息，在识别精度上仍有所不足。针对上述问题，本研究提出一种基于层级特征和全局特征的EC编号预测网络(EC number prediction network using hierarchical features and global features, ECPN-HFGF)。该方法首先通过残差网络提取蛋白质序列通用特征，并通过层级特征提取模块和全局特征提取模块进一步提取蛋白质序列的层级特征和全局特征，之后结合两种特征信息的预测结果，采用多任务学习框架，实现酶EC编号的精确预测。计算实验结果表明，ECPN-HFGF方法在蛋白质序列EC编号预测任务上性能最佳，宏观F1值和微观F1值分别达到95.5%和99.0%。ECPN-HFGF方法能有效结合蛋白质序列的层级特征和全局特征，快速准确预测蛋白质序列EC编号，比当前常用方法预测精确度更高，能够为酶学研究和酶工程应用的发展提供一种高效的思路和方法。.

Tuberculosis (TB) is a serious and fatal disease caused by Mycobacterium tuberculosis (Mtb). The World Health Organization reported an estimated 1.30 million TB-related deaths in 2022. The escalating prevalence of Mtb strains classified as being multi-, extensively, extremely, or totally drug resistant, coupled with the decreasing efficacies of conventional therapies, necessitates the development of novel treatments. As viruses that infect Mycobacterium spp., mycobacteriophages may represent a strategy to combat and eradicate drug-resistant TB. More exploration is needed to provide a comprehensive understanding of mycobacteriophages and their genome structure, which could pave the way toward a definitive treatment for TB. This review focuses on the properties of mycobacteriophages, their potential in diagnosing and treating TB, the benefits and drawbacks of their application, and their use in human health. Specifically, we summarize recent research on mycobacteriophages targeted against Mtb infection and newly developed mycobacteriophage-based tools to diagnose and treat diseases caused by Mycobacterium spp.

Enzymatic reaction kinetics are central in analyzing enzymatic reaction mechanisms and target-enzyme optimization, and thus in biomanufacturing and other industries. The enzyme turnover number (kcat) and Michaelis constant (Km), key kinetic parameters for measuring enzyme catalytic efficiency, are crucial for analyzing enzymatic reaction mechanisms and the directed evolution of target enzymes. Experimental determination of kcat and Km is costly in terms of time, labor, and cost. To consider the intrinsic connection between kcat and Km and further improve the prediction performance, we propose a universal pretrained multitask deep learning model, MPEK, to predict these parameters simultaneously while considering pH, temperature, and organismal information. Through testing on the same kcat and Km test datasets, MPEK demonstrated superior prediction performance over the previous models. Specifically, MPEK achieved the Pearson coefficient of 0.808 for predicting kcat, improving ca. 14.6% and 7.6% compared to the DLKcat and UniKP models, and it achieved the Pearson coefficient of 0.777 for predicting Km, improving ca. 34.9% and 53.3% compared to the Kroll_model and UniKP models. More importantly, MPEK was able to reveal enzyme promiscuity and was sensitive to slight changes in the mutant enzyme sequence. In addition, in three case studies, it was shown that MPEK has the potential for assisted enzyme mining and directed evolution. To facilitate in silico evaluation of enzyme catalytic efficiency, we have established a web server implementing this model, which can be accessed at http://mathtc.nscc-tj.cn/mpek.

The present study was aimed at assessing the impact of azoxystrobin-a fungicide commonly used in plant protection against pathogens (Amistar 250 SC)-on the soil microbiota and enzymes, as well as plant growth and development. The laboratory experiment was conducted in three analytical terms (30, 60, and 90 days) on sandy clay (pH-7.0). Azoxystrobin was applied to soil in doses of 0.00 (C), 0.110 (F) and 32.92 (P) mg kg-1 d.m. of soil. Its 0.110 mg kg-1 dose stimulated the proliferation of organotrophic bacteria and actinobacteria but inhibited that of fungi. It also contributed to an increase in the colony development index (CD) and a decrease in the ecophysiological diversity index (EP) of all analyzed groups of microorganisms. Azoxystrobin applied at 32.92 mg kg-1 reduced the number and EP of microorganisms and increased their CD. PP952051.1 Bacillus mycoides strain (P), PP952052.1 Prestia megaterium strain (P) bacteria, as well as PP952052.1 Kreatinophyton terreum isolate (P) fungi were identified in the soil contaminated with azoxystrobin, all of which may exhibit resistance to its effects. The azoxystrobin dose of 0.110 mg kg-1 stimulated the activity of all enzymes, whereas its 32.92 mg kg-1 dose inhibited activities of dehydrogenases, alkaline phosphatase, acid phosphatase, and urease and stimulated the activity of catalase. The analyzed fungicide added to the soil at both 0.110 and 32.92 mg kg-1 doses inhibited seed germination and elongation of shoots of Lepidium sativum L., Sinapsis alba L., and Sorgum saccharatum L.

Competency-based physiology and biochemistry education can benefit from the creative integration of imaginative narratives into traditional teaching methods. This paper proposes an innovative model using a pen and palm analogy to visualize enzyme function theories. The pen (substrate) must fit snugly into the palm (enzyme\'s active site) for catalysis to occur, akin to induced-fit theory. Pressing the pen\'s top button with the thumb represents the strain needed to convert substrate (pen with nib inside) into product (pen with nub out, ready to write). By leveraging everyday objects creatively, students can enhance their understanding and engagement with enzymatic reactions.NEW & NOTEWORTHY Understanding how enzymes work can be tricky, but a new teaching method using everyday objects like pens and palms helps make it easier. Two main theories explain this: the induced-fit model and the substrate-strain model. To visualize this, imagine a pen as the substrate and your palm as the enzyme. When you hold the pen with your fingers (induced-fit), it\'s like the enzyme changing shape to hold the substrate. Pressing the pen\'s button with your thumb (substrate-strain) is like the enzyme applying pressure to make the pen ready to write. This simple analogy helps students better understand these complex processes, making learning more engaging and accessible.

Enzymes serve as pivotal components in various biotechnological applications across several industries. Understanding enzyme inhibition sheds light on how certain compounds disrupt biochemical pathways, facilitating the design of targeted drugs for combating diseases. On the other hand, reversible inhibition or enhancement of activity can unlock new ways of controlling industrial reactions and boosting the catalytic activity of native enzymes that are taken out of their natural environments. Over the last two decades, immobilizing enzymes on nanomaterial-based solid supports has emerged as an especially promising approach for tuning enzyme activity. Nanomaterials not only inhibit enzymes but also enhance their performance, showcasing their versatility.  This Concept highlights significant advancements in utilizing nanomaterials for enzyme modulation and discusses future prospects for leveraging this phenomenon in developing sophisticated molecular systems and downstream applications.

The stratum corneum (SC), the outermost epidermal layer, plays a pivotal role in skin barrier function. This review delves into the intricate process of protein degradation within the stratum corneum, elucidating the roles of specific enzymes, regulatory mechanisms and the consequent impact on various skin conditions. Protein degradation is a finely tuned process, orchestrated by a suite of proteolytic enzymes like kallikreins. These enzymes are responsible for the breakdown of corneodesmosomes and the orderly desquamation of corneocytes, a process essential for skin homeostasis. Another critical enzymatic process is the breakdown of proteins like filaggrin and the generation of amino acids and their derivatives, required in the physiological water-handling properties of the SC. Regulation of these proteolytic activities is complex, involving a balance between endogenous inhibitors and other factors like pH, hydration and environmental stressors. Dysregulation of protease activity is linked to a spectrum of skin conditions, ranging from xerosis to inflammatory diseases like atopic dermatitis and psoriasis. Aberrant protein degradation can lead to compromised skin barrier function, increased tissue water loss and heightened susceptibility to infections and allergens. Understanding the factors affecting protein degradation can inform the development of targeted skincare products. Advances in biochemistry and dermatology have paved the way for the search for active ingredients designed to modulate protease activity. Such innovations may offer promising therapeutic avenues for enhancing skin barrier function and treating skin disorders. This review underscores the significance of enzymatic protein degradation in the SC and its regulatory mechanisms. It provides insights into the pathophysiology of skin diseases and outlines the potential for novel skincare interventions. By bridging the gap between fundamental research and practical applications, this article aims to inspire further investigation for better understanding of skin physiology and innovation in the realm of skincare product development.
La couche cornée (stratum corneum, SC), la couche épidermique la plus externe, joue un rôle essentiel dans la fonction de barrière cutanée. Cette revue se penche sur le processus complexe de dégradation des protéines au sein de la couche cornée, ce qui explique les rôles des enzymes spécifiques, les mécanismes de régulation et l\'impact qui en résulte sur diverses affections cutanées. La dégradation des protéines est un processus subtil, orchestré par une série d\'enzymes protéolytiques telles que les kallikréines. Ces enzymes sont responsables de la décomposition des cornéodesmosomes et de la desquamation ordonnée des cornéocytes, un processus essentiel à l\'homéostasie de la peau. Un autre processus enzymatique essentiel est la dégradation des protéines telles que la filaggrine et la génération d\'acides aminés et de leurs dérivés, nécessaires aux propriétés physiologiques de traitement de l\'eau de la SC. La régulation de ces activités protéolytiques est complexe, impliquant un équilibre entre les inhibiteurs endogènes et d\'autres facteurs tels que le pH, l\'hydratation et les facteurs de stress environnementaux. Le dérèglement de l\'activité de la protéase est lié à un spectre d\'affections cutanées, allant de la xérose à des maladies inflammatoires telles que la dermatite atopique et le psoriasis. Une dégradation aberrante des protéines peut compromettre la fonction de barrière cutanée, augmenter la perte d\'eau tissulaire et augmenter la sensibilité aux infections et aux allergènes. Comprendre les facteurs affectant la dégradation des protéines peut contribuer au développement de produits de soins de la peau ciblés. Les progrès en biochimie et en dermatologie ont ouvert la voie à la recherche de principes actifs conçus pour moduler l\'activité de la protéase. Ces innovations peuvent offrir des pistes thérapeutiques prometteuses pour améliorer la fonction de la barrière cutanée et traiter les troubles cutanés. Cette revue souligne l\'importance de la dégradation enzymatique des protéines dans la SC et ses mécanismes de régulation. Elle fournit des informations sur la physiopathologie des maladies cutanées et souligne le potentiel de nouvelles interventions pour soins de la peau. En comblant le fossé entre la recherche fondamentale et les applications pratiques, cet article vise à inspirer des recherches supplémentaires pour mieux comprendre la physiologie de la peau et l\'innovation dans le domaine du développement de produits de soins de la peau.