Current Opinion in Chemical Biology最新文献

Food colorants are frequently added to processed foods since color is an important tool in the marketing of food products, influencing consumer perceptions, preferences, and purchasing behavior. While synthetic dyes currently dominate the food colorant market, consumer concern regarding their safety and sustainability is driving a demand for their replacement with naturally derived alternatives. However, natural colorants are costly compared to their synthetic counterparts as the pigment content in the native sources is usually very low and extraction can be challenging. Recent advances in the engineering of microbial metabolism have sparked interest in the development of cell factories capable of producing natural colorants from renewable resources. This review summarizes major developments within metabolic engineering for the production of nature-identical food colorants by fermentation. Additionally, it highlights common applications, formulations, and physicochemical characteristics of prevalent pigment classes. Lastly, it outlines a workflow for accelerating the optimization of cell factories for the production or derivatization of nature-identical food colorants.

O-GlcNAcylation is an essential protein glycosylation governed by two O-GlcNAc cycling enzymes: O-GlcNAc transferase (OGT) installs a single sugar moiety N-acetylglucosamine (GlcNAc) on protein serine and threonine residues, and O-GlcNAcase (OGA) removes them. Aberrant O-GlcNAcylation has been implicated in various diseases. However, the large repertoire of more than 1000 O-GlcNAcylated proteins and the elusive mechanisms of OGT/OGA in substrate recognition present significant challenges in targeting the dysregulated O-GlcNAcylation for therapeutic development. Recently, emerging evidence suggested that the non-catalytic domains play critical roles in regulating the functional specificity of OGT/OGA via modulating their protein interactions and substrate recognition. Here, we discuss recent studies on the structures, mechanisms, and related tools of the OGT/OGA non-catalytic domains, highlighting new opportunities for function-specific control.

Metalloenzymes are essential to cellular function, and their overexpression or enhanced activation are potential therapeutic targets. However, the study of metalloenzymes in vitro presents various challenges, leading many to develop tools to study them in their native cellular environment. Small-molecule fluorescence probes are commonly used to monitor metalloenzyme function, activity, and distribution in situ. These include probes that are activity-based (fluorescence is mediated by enzyme activity) or binding-based (fluorescence is mediated by interactions with the enzyme upon binding its metal cofactor). We discuss recent innovations that overcome key design challenges, such as the rapid diffusion of activity-based probes, the difficulty of probing redox-active enzymes, the selectivity of binding-based probes, and the poor penetration depth of fluorescence, and describe novel applications of these tools.

Analyzing the quantity and distribution of molecules throughout intact biological tissue is crucial for understanding various biological phenomena. Traditional methods involving destructive extraction result in the loss of spatial information. Conversely, tissue-clearing techniques combined with fluorescence imaging have recently emerged as a powerful tool for deep tissue imaging without sacrificing spatial coverage. Key to this approach is the anchoring and labeling of targets in intact tissue. In this review, methods for anchoring and labeling proteins, lipids, carbohydrates, and small molecules are presented. Future directions include the development of activity-based probes that work in vivo and mark transient events with spatial information to enable a deeper understanding of biological phenomena.

Monoclonal antibodies and antibody fragments have proven to be highly effective vectors for the delivery of radionuclides to target tissues for positron emission tomography (PET) and single-photon emission computed tomography (SPECT). However, the stochastic methods that have traditionally been used to attach radioisotopes to these biomolecules inevitably produce poorly defined and heterogeneous probes and can impair the ability of the immunoglobulins to bind their molecular targets. In response to this challenge, an array of innovative site-specific and site-selective bioconjugation strategies have been developed, and these approaches have repeatedly been shown to yield better-defined and more homogeneous radioimmunoconjugates with superior in vivo performance than their randomly modified progenitors. In this Current Opinion in Chemical Biology review, we will examine recent advances in this field, including the development — and, in some cases, clinical translation — of nuclear imaging agents radiolabeled using strategies that target the heavy chain glycans, peptide tags, and unnatural amino acids.

Pyridoxal phosphate (PLP) is a cofactor that is widely employed in enzymology. This pyridine-containing cofactor can be used for reactions ranging from transaminations to oxidations. The catalytic versatility can be understood by considering the chemical features of this cofactor. In recent years, exciting new reactions involving PLP have been discovered in natural products biosynthesis, upending our understanding of what this cofactor is capable of. Here we review some of the most exciting PLP-dependent reactions from the last five years.

Nicotinamide adenine dinucleotide (NADPH) oxidases, known for their role in generating reactive oxygen species (ROS) have emerged as key regulators of specific cellular signaling pathways. While their primary function is ROS production, recent research has highlighted the significance of their site-specific activity in governing distinct cellular signaling events.

NADPH oxidases (Nox) are found in various cell types, and both their expression and activities are tightly regulated. The generated ROS, such as superoxide anions and hydrogen peroxide, function as secondary messengers that modulate various signaling molecules, including protein kinases, transcription factors, and phosphatases.

The site-specific action of NADPH oxidases in different cellular compartments, such as the plasma membrane, endosomes, and endoplasmic reticulum, allows for precise control over specific signaling pathways. Understanding the complex interplay of NADPH oxidases in cellular signaling is essential for deciphering their roles in health and disease. Dysregulation of these enzymes can lead to oxidative stress and inflammation, making them potential therapeutic targets in various pathological conditions. Ongoing research into NADPH oxidase activation and site-specific signaling promises to unveil new insights into cellular physiology and potential treatment strategies.

Isonitrile lipopeptides discovered from Actinobacteria have attracted wide attention due to their fascinating biosynthetic pathways and relevance to the virulence of many human pathogens including Mycobacterium tuberculosis. Specifically, the identification of the new class of isonitrile-forming enzymes that belong to non-heme iron (II) and α-ketoglutarate dependent dioxygenases has intrigued several research groups to investigate their catalytic mechanism. Here we summarize the recent studies on the biosynthesis of isonitrile lipopeptides from Streptomyces and Mycobacterium. The latest research on the core and tailoring enzymes involved in the pathway as well as the isonitrile metabolic enzymes are discussed in this review.

In vivo luminescence imaging in the second near-infrared window (NIR-II, 1000–2000 nm) is a potent technique for observing deep-tissue life activities, leveraging reduced light scattering, minimized autofluorescence, and moderate absorption attenuation to substantially enhance image contrast. Pushing the frontiers of NIR-II luminescence imaging forward, moving from static to dynamic event visualization, monochromatic to multicolor images, and fundamental research to clinical applications, necessitates the development of novel luminophores featuring bright emission, extendable wavelength, and optimal biocompatibility. Recently, lanthanide-dye hybrid luminophores (LDHLs) are gaining increasing attention for their wavelength extensibility, molecular size, narrowband emission, mega stokes shift, long lifetime, and high photostability. In this review, we will summarize the recent advances of NIR-II LDHLs and their applications in imaging and analysis of living mammals, and discuss future challenges in designing new LDHLs for deep-tissue imaging.

Cofactor F₄₂₀ has been historically known as the “methanogenic redox cofactor”. It is now recognised that F₄₂₀ has essential roles in the primary and secondary metabolism of archaea and bacteria. Recent discoveries highlight the role of F₄₂₀ as a redox cofactor in the biosynthesis of various natural products, including ribosomally synthesised and post-translationally modified peptides, and a new class of nicotinamide adenine dinucleotide-based secondary metabolites. With the vast availability of (meta)genomic data, the identification of uncharacterised F₄₂₀-dependent enzymes offers the potential for discovering novel secondary metabolites, presenting valuable prospects for clinical and biotechnological applications.