Biochemical Society transactions最新文献

Critical for the regulation of eukaryotic gene transcription is the assembly and interplay of general transcription factors (GTFs) with RNA polymerases (RNAPs), leading to the formation of pre-initiation complexes (PICs) as a rate-limiting step in transcription activation. Compared with RNAPII PIC assembly involving many GTFs, activators, and co-activators, RNAPIII PIC assembly is less complex, involving mainly the four GTFs TFIIIA, TFIIIB, TFIIIC, and snRNA activating protein complex with only a few additional factors. The RNAPIII-specific GTF TFIIIC is present in type I and II promoters. One prominent area of investigation has been the dynamic interaction between TFIIIC and its promoter elements, the varying affinities of TFIIIC toward these elements, and the flexible linker within TFIIIC. Additionally, evidence suggests that TFIIIC may play a dual role, acting as an assembly factor that positions TFIIIB during PIC formation and as a barrier during RNAPIII-mediated transcription. By summarizing recent structural, biochemical, and genomic data, this review explores the mechanisms by which RNAPIII-specific GTFs, with a focus on TFIIIC, dynamically regulate RNAPIII transcription.

The endoplasmic reticulum (ER) is a vital organelle involved in the biogenesis of membrane and secreted proteins. Proteostasis (protein homeostasis) in the ER relies on finely co-ordinated mechanisms for translocation of polypeptides from the cytosol to the organelle lumen and membrane, introduction of co- and post-translational modifications, protein folding and quality control, exportation of mature proteins and disposal of unfolded or aggregated species, besides the regulation of gene expression to adjust the proteostasis network to the cellular demands for protein biogenesis. Neurodevelopmental processes involving neurogenesis, neuronal migration and differentiation, neural circuit wiring, synaptogenesis, among others, require extensive proteome diversification and remodeling, with high fluxes through the secretory pathways constantly challenging ER proteostasis. Genetic defects affecting the different nodes of the ER proteostasis network can severely disturb neurodevelopment. Here, we compile evidence illustrating how perturbations to the different steps of protein biogenesis in the ER can lead to neurological disorders and present major questions to guide research in the field.

Protein AMPylation is a post-translational modification in which adenosine monophosphate (AMP) from ATP is covalently attached to a target protein via a phosphodiester bond. This reaction is catalyzed by AMPylases, a diverse group of enzymes containing adenylyltransferase, filamentation induced by cyclic AMP (FIC), or kinase domains. As a reversible modification, AMPylation is dynamically regulated by both writer enzymes (AMPylases) and eraser enzymes (deAMPylases). Since its initial discovery in bacterial nitrogen metabolism in 1967, AMPylation has been recognized as a critical regulatory mechanism in both prokaryotic and eukaryotic systems. Recent studies link AMPylation to neurological disorders, diabetes, and cancer metastasis, underscoring its physiological and pathological significance. In this review, we present an overview of the discovery of AMPylases and deAMPylases, highlighting their role in cellular signaling, stress response, and host-pathogen interactions.

Membrane association is fundamental to Rat sarcoma (RAS) function, driving both its physiologic signaling and oncogenic transformation. This review consolidates recent advances in the study of RAS-membrane interactions, emphasizing the molecular mechanisms underlying its membrane engagement and oligomerization. We first discuss the roles of RAS lipid modification and conformational diversity of its intrinsically disordered C-terminus in these processes, and we then examine the debate surrounding RAS dimerization and its potential role in the formation of higher-order oligomers. By integrating emerging insights into these issues, we offer our own perspectives on the driving forces of RAS oligomerization and propose potential new avenues for developing targeted therapies for RAS-driven cancers.

Fusidic acid (FA) is an antibiotic used to treat staphylococcal infections, particularly Staphylococcus aureus. It acts by inhibiting protein synthesis through locking elongation factor G (EF-G) to the ribosome. In S. aureus, there are three mechanisms of resistance. Mutations in the antibiotic target, EF-G (fusA), are common. These mutations affect the FA binding or the stability of the FA-locked state of EF-G but, due to effects on the normal function of EF-G, impose a fitness cost for the pathogen. The most common mechanism, FusB-type, involves expression of a resistance protein, FusB or FusC (FusD or FusF in other staphylococci), that provides target protection. The resistance protein binds to EF-G in its FA-locked state and mediates its release from the ribosome. An uncommon resistance mechanism (FusE) involves mutations in a ribosomal protein, uL6. In other bacteria, outside of its current clinical use, resistance to FA involves efflux pumps, limited membrane permeability, or enzymes that chemically alter FA. On a global level, the prevalence of FA resistance is relatively low, indicating that the antibiotic remains effective.

Multicellular life depends on the ability to activate and repress genes in a highly context-specific manner. With each cell state transition, a new transcriptional profile is established. As non-coding DNA elements, enhancers mediate their regulatory potential through the effectors they recruit. While ultimately instructed by the underlying DNA sequence, enhancer activity depends on several factors, such as transcription factor availability, chromatin state, and promoter proximity, all of which are dynamically regulated within the cell. Even when we understand the regulation of one enhancer, its genomic impact is dependent on its integration within the regulatory landscape. Thus, a full picture of enhancer dynamics can only be painted through broad, but controlled, approaches that integrate investigations into multiple levels of gene regulatory mechanisms. In this review, we will present the exit of naive pluripotency as a prime setting to do just that and contextualize how its contemporary use has been, and could be, used to reveal the intricacies of enhancer mechanistics.

Protein kinases are master regulators of myriad processes in eukaryotic cells playing critical roles in growth, metabolism, cellular differentiation, and motility. A subclass of protein kinases is regulated by their ability to be localized and activated by the phosphoinositide phosphatidylinositol (3,4,5)-trisphosphate (PIP3). This includes multiple members of the AGC and TEC family kinases, which contain PIP3 binding pleckstrin homology (PH) domains. It has been postulated that they can be activated by PIP3-mediated disruption of autoinhibitory interactions between their kinase domains and PH domains. There has been considerable controversy based on differing molecular models for how these kinases are regulated by lipid binding and post-translational modifications. This review focuses on understanding the molecular underpinnings for how the PH domains of these enzymes regulate kinase activity and what role PIP3 plays in pathway activation. A specific focus is on the integration of experimental data derived from X-ray crystallography, cryo-electron microscopy, and hydrogen deuterium exchange mass spectrometry along with recent advances in artifical intelligence enabled protein modeling. The main lipid-binding enzymes described are the AGC protein kinases 3-phosphoinositide-dependent kinase (PDK1) and Akt, and the TEC family kinase, Bruton's agammaglobulinemia tyrosine kinase (BTK).

Neurons require local protein synthesis at synapses to control their proteome in response to local inputs. Work over the past two decades has revealed that neurons can use a specialized mechanism to transfer mRNAs and ribosomes to local sites in addition to canonical mechanisms used in many cell types. Neurons initiate translation on the ribosomes in the cellular soma, pause the process, and then package these stalled ribosomes into structures known as 'neuronal RNA granules' that are transported to synapses. This review provides an overview of recent studies that characterize these ribosomes/granules biochemically and structurally. These studies provide novel insights into the unique and specialized characteristics of neuronal ribosomes that facilitate this distinct transport mechanism. Many questions remain, including the influence of mRNA sequences on the stalling process and how ribosomes in the granules avoid the physiological responses that, in other cells, recycle ribosomal subunits upon stalling. Many neurodevelopmental disorders, such as autism and intellectual disability, occur when local translation is disrupted in neurons. Understanding mechanisms underlying the stalling of neuronal ribosomes, their transport to processes, and their reactivation may enable novel therapies for neurodevelopmental diseases.

Zebrafish have been and continue to be an important model organism for studies of fundamental biology and biomedicine, including reproductive development and the cell intrinsic and extrinsic mechanisms regulating early gonocyte differentiation. Wild zebrafish strains determine sex using a ZW genetic system wherein the maternally inherited sex chromosome determines the embryo's sex. Like other species, including humans, regulation of conserved autosomal genes is crucial for gonocyte and sexual differentiation. How these conserved factors are regulated by the diverse mechanisms found throughout the animal kingdom is an active area of investigation. Domesticated zebrafish strains lack the ZW sex determination system found in wild strains and undergo gonocyte and sexual differentiation through a process exclusively governed by autosomal genes and nongenetic influences like environmental factors. Through mutational analysis, molecular genetics, and RNA sequencing, our understanding of the complexity of oocyte and spermatocyte differentiation has become clearer. In this review, we explore the most recent studies of the conserved and divergent mechanisms of gonocyte differentiation between wild and domesticated zebrafish as well as possible adaptations related to their domestication. Further, the contributions of individual genes and their molecular genetic hierarchy in regulating gonocyte differentiation are discussed and related to other species where relevant. We also address the recent characterization of a novel oocyte-progenitor and its potential implications in gonad differentiation. Finally, the role of gonocyte-extrinsic mechanisms, specifically communication between differentiating gonocytes and surrounding somatic gonad cells and the influence of resident and infiltrating immune cells, is discussed.

Intrinsic protein quality control (QC) mechanisms are essential in maintaining mitochondrial health and function. These sophisticated molecular machineries govern protein trafficking and import, processing, folding, maturation and degradation, ensuring the organelle's health. Disruption in mitochondrial protein QC can lead to severe, multisystem disorders with variable age of onset and progression. In this review, we provide a snapshot of the intrinsic molecular protein QC machineries in mitochondria detailing their function, localisation and substrate specificity. We also highlight how dysfunction of these molecular machines contributes to mitochondrial disease. Ultimately, elucidating the consequences of proteostatic failure offers critical insights into the pathogenesis of complex mitochondrial disorders.