Biochemical Society transactions最新文献

RNA and proteins are key components of all organisms. Internal ribosome entry site (IRES) elements are a diverse type of RNA regulatory structural elements that mediate end-independent, internal translation initiation in viral mRNAs and certain cellular mRNAs translated under stress conditions. Notably, viral IRES elements regulate translation initiation via a dynamic, modular RNA structure organization, which serves as the anchoring site for the ribosome guided by RNA-RNA and/or RNA-protein interactions. The implementation of advanced transcriptomics, proteomics, and computational methodologies has facilitated the identification of novel RNAs potentially translated using cap-independent mechanisms, harboring RNA structural elements with distinctive features. Here, we present a summary of the current understanding of IRES elements, focusing on the molecular functions and the RNA-binding proteins regulating IRES activity.

Deep mutational scanning (DMS), a high-throughput method leveraging next-generation sequencing, has been crucial in mapping the functional landscapes of key severe acquired respiratory syndrome-coronavirus 2 (SARS-CoV-2) proteins. By systematically assessing thousands of amino acid changes, DMS provides a framework to understand Angiotensin-converting enzyme 2 (ACE2) binding and immune evasion by the spike protein, mechanisms and drug escape potential of the main and papain-like viral proteases and has highlighted areas of concern in the nucleocapsid protein that may affect most currently available rapid antigen testing kits. Each application has required the design of bespoke assays in eukaryotic (yeast and mammalian) cell models, providing an exemplar for the application of this technique to future pandemics. This minireview examines how DMS has predicted key evolutionary changes in SARS-CoV-2 and affected our understanding of SARS-CoV-2 biology, specifically highlighting their relevance for therapeutics development.

The importance of the peroxisome as a site of oxidative metabolism in plants is well recognised, but the consequences of peroxisomal biochemistry for the broader metabolic network of plant cells are somewhat overlooked. In this review, we place a spotlight on the peroxisome as a redox-active organelle which mediates substantial flows of electrons. These electron flows not only have consequences within the peroxisome, but they also flow to and from the cytosol and at least two other major redox-active organelles, chloroplasts and mitochondria, with broad implications for metabolism and redox balance of electron carriers such as NADPH and NADH. We will outline the nature of these peroxisome-mediated electron flows and discuss the new appreciation of their quantitative significance derived from metabolic network flux analysis. We emphasise that the flows of reducing equivalents into and out of the peroxisome can be substantial - in some tissues equivalent to that to and from mitochondria. We also highlight key areas of uncertainty around specific redox reactions in the peroxisome and open questions about how redox state is balanced. Finally, we also consider the implications of peroxisomal electron flows in the context of re-engineering key metabolic processes such as photorespiration and lipid accumulation.

Neutrophils play a critical role in maintaining healthy tissue by acting as the first cellular responders to inflammatory challenges. Unfortunately, when this response is dysregulated, defects in neutrophil function can contribute to the pathogenesis of several diseases and conditions, including cancer, fibrosis, and aberrant wound healing. Understanding the factors that regulate the neutrophil response is critical for improving disease outcomes. It is becoming increasingly appreciated that the extracellular matrix (ECM) serves as a significant regulator of the neutrophil response. The ECM is a complex network of fibrous proteins and proteoglycans that provides both physical and biochemical cues that can modulate cell behavior. Importantly, the composition, structure, and mechanics of the ECM often undergo significant changes in disease. Studies have shown that matrix stiffness and composition can alter neutrophil behavior, but our understanding of how the various structural and mechanical properties of the ECM govern the neutrophil response remains incomplete. In part, this is due to the challenges involved in isolating distinct properties of the matrix to determine their individual roles in regulating the neutrophil response. In this review, we summarize the recent efforts that have been made to better understand how ECM properties affect the neutrophil inflammatory response and offer suggestions for future directions for the field.

Cells respond to thermal, chemical, and oxidative stress by activating an evolutionarily conserved adaptive mechanism known as the heat shock response (HSR) that maintains protein homeostasis and ensures cell survival. Central to the HSR is Heat Shock Factor 1 (HSF1), a highly conserved master transcription factor that up-regulates genes encoding molecular chaperones and other homeostasis factors in response to proteotoxic stress. In both yeast and mammals, the HSR is accompanied by the inducible formation of phase-separated condensates that concentrate components of the transcriptional machinery into discrete intranuclear foci. The assembly of these condensates may be driven by a combination of liquid-liquid phase separation and low-valency Interactions with spatially Clustered Binding Sites (ICBS). In budding yeast, these condensates - which contain HSF1, Mediator, and RNA polymerase II - drive concerted intraand interchromosomal interactions between HSF1 target genes, creating extensive DNA loops between regulatory and transcribed sequences. In this and other ways, yeast HSR genes resemble mammalian super-enhancers. Emerging evidence suggests that the nuclear pore complex (NPC) - a macromolecular assembly at the nuclear periphery that regulates protein and RNA transport across the nuclear membrane - serves as a scaffold for the formation of transcriptional condensates and maintains chromatin architecture. In yeast, nuclear basket proteins - which dynamically exchange between the NPC and nucleoplasm - contribute to the heat shock-induced intergenic clustering of HSF1 target loci, whereas essential NPC scaffold-associated proteins do not. Such gene clustering is accompanied by the formation of multiplexed HSR mRNAs that could potentially co-ordinate both mRNA export and translation. Here we review evidence that links genome architecture, transcriptional condensates, the NPC, and nuclear basket proteins and discuss potential implications for the treatment of disease.

Phosphorylation plays a central role in regulating signal transduction across all kingdoms of life, allowing organisms to sense and respond to their environment. In mammals, the signalling research field is dominated by the functions of pSer, pThr and pTyr, due to both historical and technological factors. Mostly ignored are the labile phosphosites (LaPhs), made up of six other phosphorylatable amino acids: His, Lys, Arg, Asp, Glu and Cys. This group is characterised by an acid and/or heat-labile phosphate linkage, forming a distinct group from the highly stable phosphomonoesters of pSer, pThr and pTyr. LaPhs have distinct thermal and pH stability profiles, which may contribute to, or even dictate, their functions. Here, we review the contribution of LaPhs to mammalian signalling networks, highlighting their currently defined diverse functions.

Long non-coding RNAs (lncRNAs) play crucial roles in cellular processes; however, the mechanisms controlling their stability are not well understood. Since the appropriate levels of lncRNAs in cells are required to carry out their functions, it is critical that their degradation is tightly controlled. Extensive research has shown that translation and degradation of messenger RNAs (mRNAs) are intricately linked, with repression of translation usually leading to degradation of the RNA. Recently, evidence has emerged to suggest that translation may also affect lncRNA stability. Ribosome engagement may stabilise lncRNAs by protecting them from nucleases or by promoting their degradation via ribosome-associated decay pathways such as nonsense-mediated decay. In this review, we first highlight specific human diseases that result from misregulation of lncRNA stability. We then explore the mechanisms underlying ribosome association and lncRNA stability, drawing comparisons with canonical mRNA mechanisms and highlighting emerging hypotheses that may be particularly relevant to lncRNAs. We also discuss how advanced techniques such as ribosome profiling can be applied to investigate whether lncRNAs are translated. Finally, we suggest future strategies to aid further understanding of lncRNA stability and its relationship with development and disease. Understanding the dynamic relationship between translation and lncRNA decay offers broad implications for RNA biology and provides new insights into the regulation of lncRNAs in both cellular and disease contexts.

Fas-activated serine/threonine kinase (FASTK) proteins comprise one of the largest families of mitochondrial post-transcriptional regulators. Members are classified based on their conserved C-terminus, which shows homology with the PD-(D/E)XK superfamily of endoribonucleases. However, it is still uncertain which of these FASTK members are catalytic. The six human FASTK homologs rely on their RNA-binding activity to regulate distinct stages of mitochondrial gene expression, including early processing of nascent RNA, 3'-end messenger RNA (mRNA) maturation, ribosomal RNA (rRNA) modification, mRNA stability, and translation. Genetic and genomic studies have highlighted the crucial role of FASTK proteins in balancing the mitochondrial transcriptome and controlling oxidative phosphorylation. However, until recently, the molecular mechanisms governing their RNA metabolic activities have remained elusive. New biochemical and structural advances have provided molecular insights into the architecture and regulation of FASTK proteins. Here, we summarize the current understanding of the FASTK family's specialized roles in gene regulation, with an emphasis on mitochondrial mRNA metabolism by the proteins FASTK, FASTK domain-containing protein 4 (FASTKD4), and FASTKD5. Additionally, we leverage recent experimental structures and artificial intelligence-based prediction models to explore the molecular organization of FASTK proteins and highlight the family's signature C-terminus, a region essential for their RNA-binding activity.

Pseudokinases, once considered catalytically inactive remnants of evolution, have emerged as key regulators of numerous fundamental biological processes. While eukaryotic pseudokinases have attracted significant attention, bacterial pseudokinases remain largely unexplored experimentally. Recent advances in sequence analysis and structural modeling have identified and characterized multiple conserved bacterial pseudokinase families, each with distinct predicted catalytic impairments but unknown functions. This review delves into their classification, structural features, and evolutionary adaptation. We also highlight the significance of bacterial pseudokinases in host-microbe interactions and their emerging potential as therapeutic targets. By integrating bioinformatics with experimental approaches, future research is poised to uncover the biological functions of bacterial pseudokinases, providing new insights into microbial signaling mechanisms and revealing new strategies to interrogate bacterial cell signaling, including pseudokinase drivers of infection and antimicrobial drug resistance.

The GID/C-terminal to LisH (CTLH) E3 is an emerging family of evolutionarily conserved multiprotein E3 ligase complexes implicated in various biological processes including metabolic rewiring, stress-responsive regulation, cellular differentiation, and immunity. Pioneering biochemical reconstitution, cryo-EM, and cell-based studies have illuminated many aspects of the compositional and structural dynamics of GID/CTLH E3 complexes. GID/CTLH E3 undergoes sophisticated regulation through incorporation of interchangeable substrate receptors and association with supramolecular assembly factors enabling higher-order complex formation. Furthermore, paralogous subunits vary and may modulate function across cell types. Additionally, an assortment of regulatory factors fine-tune substrate selection, underscoring the adaptability of this E3 ligase system. Here, we review these distinct ubiquitin ligase features, examine the mechanistic implications of GID/CTLH E3 regulation and the exquisite targeting of oligomeric substrates, and discuss potential for therapeutic application in targeted protein degradation.