Sub-cellular biochemistry最新文献

Intermediate filaments (IFs) are central to the mechanical integrity of metazoan cells and play critical roles in various fundamental cellular and multicellular processes, including cell motility, signal transduction, and wound healing. To perform their functions, IF proteins self-assemble into nanoscale biopolymers, each exhibiting unique properties that are finely tuned to their specific roles across different tissue types. However, the 3D structure of IFs has remained largely unresolved due to their intrinsic flexibility and polymorphism. This chapter reviews recent advances in the structural analysis of IFs, with a focus on vimentin IFs (VIFs), which are featuring a helical tube with a central luminal fiber. We discuss how AlphaFold-based modeling, chemical cross-linking data, and cryo-electron microscopy (cryo-EM) reconstructions have been integrated to generate a detailed structural model of VIFs, highlighting key features such as the helical symmetry of the filaments and the nature of the luminal fiber. Additionally, we explore potential sources of IF polymorphism and their implications for the analysis of IF structures.

The Golgi Associated Retrograde Protein (GARP) complex, a member of the Complexes Associated with Tethering Containing Helical Rods (CATCHR) family, is proposed to tether vesicles arriving from endosomes to the trans-Golgi network (TGN). Discovered nearly 25 years ago, this protein complex is important for sorting vacuolar hydrolases and recycling membrane proteins from the endosomal/prevacuolar compartment to the TGN; however, its exact function, molecular partners, and the nature of GARP-dependent trafficking intermediates remain understudied. GARP-dependent transport route is utilized by various plasma membrane recycling proteins, lysosomal hydrolase receptors, and pathogens, including toxins. Mutations in GARP subunits have been associated with multiple neurological disorders, although the precise mechanisms by which these mutations lead to these conditions remain unclear. This chapter reviews the current understanding of GARP's structure, function, interacting partners, mutations, and associated pathologies in both humans and model organisms.

The Golgi apparatus has important, well characterised functions in the trafficking, processing, and post-translational modification of proteins and lipids. However, roles in other cellular processes are increasingly reported, including autophagy, apoptosis, DNA repair, and cytoskeletal (microtubules and actin) function. The Golgi therefore serves as a regulatory hub for multiple signalling pathways that maintain essential cellular activities. The Golgi normally consists of flattened stacks of membrane (cisternae), but during normal physiology and pathological conditions it 'fragments', resulting in altered morphology and distribution. This is well described as an early pathological feature of many neurodegenerative diseases, including Alzheimer's (AD), Parkinson's (PD), Huntington's (HD) and prion diseases, and amyotrophic lateral sclerosis (ALS). These age-related conditions are characterised by the death of neurons: highly specialised, unique cells that form the foundation of the nervous system. Interestingly, many Golgi-related functions are also dysregulated in these diseases. However, this has received relatively little attention compared to other pathogenic mechanisms. The Golgi apparatus in neurons shares features common to other eukaryotic cells but it also has unique properties, such as the presence of distinctive assemblies: Golgi outposts and satellites, which remain poorly characterised. Here we discuss the increasing evidence describing dysfunction and fragmentation of the Golgi apparatus and its possible role in the pathogenesis of neurodegenerative diseases.

The RAB family in humans comprises approximately 70 members with about one third localizing to the Golgi apparatus and associated compartments. This significant localization reflects the number and diversity of transport pathways operating within this central cellular hub. We focus in this review on the molecular mechanisms by which RAB GTPases regulate membrane trafficking at the Golgi level.

In lower organisms (bacteria, fungi, yeast), some species that express the enzyme urease take up urea from the surrounding medium as a source of nitrogen, by energy-dependent urea transporters. In contrast, in mammals, urea is an endproduct of nitrogen metabolism, and the energy-dependent urea transports are associated with either the need to excrete nitrogen efficiently, in the case of excess nitrogen intake, or the need to conserve nitrogen and re-use it, in the case of low nitrogen supply.Three different energy-dependent urea transports have been characterized functionally in the mammalian kidney. One responsible for urea secretion in the straight segment of the proximal tubule (proximal straight tubule, PST), another for urea reabsorption in the upper third of the inner medullary collecting duct (IMCD), and one in the very late portion of the IMCD. But intriguingly, up to now, none of the membrane transporters responsible for these transports has been characterized molecularly.This review describes these urea transports functionally and proposes a candidate transporter responsible for urea secretion in the PST. Based on the study of knockout mice, SLC6A18 has been characterized as a glycine transporter, but several previous observations suggest that it may also serve another function. SLC6A18 is very likely a urea/glycine, sodium-dependent antiport. These observations are described in detail.Energy-dependent urea transport is suspected to also take place in two other organs that express facilitated urea transporters; in the testis, urea secretion could initiate a flux of fluid in seminiferous tubules to ensure sperm transport into the lumen; in the bladder, urea secretion could reclaim urea that is at permanent risk of dissipation, due to the large urea concentration difference between urine and blood and the high expression of the facilitated transporter UT-B on the basal membrane of the urothelium.The energy-dependent secretion of urea in the PST has a number of consequences. (1) It allows a better efficiency of urea excretion and thus may prevent some toxicity of urea. (2) It provides a much better understanding of the urine concentrating mechanism. (3) It explains how urea may influence glomerular filtration rate, indirectly.

Urea transporters (UTs) facilitate the rapid transport of urea from the extracellular space to the intracellular space through a selective transport mechanism driven by urea concentration gradients. Advances in Cryo-electron microscopy and X-ray crystallography have enabled us to solve the homotrimer structures of UT-A and UT-B, which share a common feature comprising two homologous domains surrounding a continuous transmembrane pore, indicating that UTs transport urea via a channel-like mechanism. By analyzing the structures of ligand-protein complexes, results from molecular dynamics simulations, and functional data on urea analogues and small molecule permeation inhibitors, we can gain a deeper understanding of the conservation and specificity of the urea channel architecture, and clearly recognize how urea is transported by UTs and the mechanisms of small molecule inhibition. This will provide an important structural basis for drug design and development.

Urea is generated by the urea cycle enzymes, which are mainly in the liver but are also ubiquitously expressed at low levels in other tissues of mammals. Urea is then eliminated through fluids, especially urine. Urea also serves as a readily available nitrogen source for the growth of many organisms, including plants and bacteria. Urea transporters are recognized as the primary membrane proteins responsible for urea transport in organisms. However, an increasing body of studies has identified additional membrane proteins in animals, plants, and microbes that exhibit urea transport capabilities or potential. The contribution of these membrane proteins to the maintenance of physiological homeostasis and their interactions with urea transporters remains to be fully elucidated. In this chapter, transport, characteristics, regulation, as well as cellular localization of non-urea-transporter membrane proteins facilitating urea transport, are reviewed to highlight their roles in physiology and pathophysiology. Specifically, the mammalian aquaporins AQP3, AQP6, AQP7, AQP8, AQP9, AQP10, and a sodium-glucose transporter (SGLT1) in the kidney are permeable to urea. In plants, tonoplast intrinsic proteins (TIPs), a member of aquaporin family, and the DUR3 orthologue, potentially play roles in low- and high-affinity urea transport, respectively. Two urea transporters pH-independent (Yut) and pH-dependent transporters (ureI) in bacteria are known to play roles in disease conditions.

Urea transporters (UTs) UT-As (encoded by Slc14A2) and UT-B (encoded by Slc14A1), are important members of the solute carrier family. They are a group of membrane channel proteins that are selectively permeable to urea. Slc14A1 is considered the key gene determining the Kidd blood group system, and its variants can lead to the loss of Jk antigens, resulting in transfusion-related complications. Additionally, studies have shown that Slc14A1 is closely associated with cancer development and progression, with its expression level and promoter methylation status potentially serving as biomarkers for cancer progression and prognosis. Recent research suggests that UT-B functional deficiency may cause neurodegenerative diseases by accumulating urea in the brain, thereby affecting neuronal function and viability. Mutations of Slc14A2 are linked to hypertension and metabolic syndrome, due to its essential role in maintaining urea homeostasis. This chapter aims to introduce the clinical significance of UT-B and UT-A and highlight their potential roles as diagnostic and therapeutic targets.

Prion diseases are rare yet devastating neurodegenerative disorders that result from the misfolding of the cellular prion protein, PrP^C, into its infectious and pathogenic isoform, PrP^Sc. These diseases are marked by progressive neuronal damage, leading to irreversible cognitive and motor impairments and, ultimately, death. Despite extensive research into their underlying mechanisms, effective treatments for prion diseases remain elusive. Such a lack of effective therapies mainly arises from several challenges, including delayed diagnosis and the complex and poorly understood biology of prion neurotoxicity.This chapter provides an in-depth exploration of current and emerging therapeutic strategies to treat prion diseases. One promising approach involves using small molecules to inhibit prion replication by destabilizing PrP^Sc or modulating PrP^C homeostasis, possibly avoiding previously observed strain-dependent drug resistance. In parallel, immunotherapeutic approaches, including passive and active immunization, have shown potential in targeting prions. However, challenges related to brain penetration and potential neurotoxicity remain significant hurdles to their successful clinical application. Developing advanced genetic tools, such as RNA interference (RNAi) and CRISPR-based technologies, has opened up new avenues for therapeutic intervention. These approaches selectively target and reduce PrP^C expression, thereby preventing the formation and accumulation of PrP^Sc. The chapter also highlights the progress in clinical trials, such as the PrProfile trial for ION717, which tests a novel treatment based on an antisense oligonucleotide (ASO). As we look toward the future, the chapter underscores the need for a multifaceted approach to treating prion diseases. Furthermore, early detection methods, innovative drug delivery systems, and collaborative interdisciplinary research efforts will be essential for translating scientific discoveries into practical clinical breakthroughs.

Prion diseases are rapidly progressive and fatal neurodegenerative disorders caused by misfolded prion proteins. Accurate and early diagnosis is essential to distinguish these conditions from treatable dementias and to prevent iatrogenic transmission. While definitive confirmation still depends on postmortem neuropathological techniques such as immunohistochemistry and western blot, recent advances have significantly improved antemortem diagnostic capabilities. The antemortem diagnosis combines clinical evaluation, neuroimaging, electroencephalography, and cerebrospinal fluid biomarkers. The development of real-time quaking-induced conversion (RT-QuIC) has enhanced the detection of misfolded prion proteins with high specificity, complementing existing diagnostic methods. Although advancements in biomarkers and diagnostic methodologies have improved the early detection of prion diseases, challenges remain. Continued research is crucial for enhancing early identification, tracking disease progression, optimizing patient management, and further elucidating disease pathogenesis.