Recent reports by Orth, Pohl, et al. and Li, Garcia-Rivera et al. show that ubiquitin can mark drug-like molecules in cells. This non-canonical ubiquitination, initially discovered with proposed small-molecule HUWE1 inhibitors and a synthesis library component, respectively, offers a versatile chemical tool for probing protein regulation and developing new therapeutics.

The mitochondrial pyruvate carrier (MPC), of the SLC54 family of solute carriers, has a critical role in eukaryotic energy metabolism by transporting pyruvate, the end-product of glycolysis, into the mitochondrial matrix. Recently, structures of the human MPC1/MPC2 and MPC1L/MPC2 heterodimers in the outward-open, occluded, and inward-open states have been determined by cryo-electron microscopy (cryo-EM) and by AlphaFold modeling. In this review we discuss the membrane orientation, substrate binding site properties, and structural features of the alternating access mechanism of the carrier, as well as the binding poses of three chemically distinct inhibitor classes, which exploit the same binding site in the outward-open state. These structural studies will support drug development efforts for the treatment of diabetes mellitus, neurodegeneration, metabolic dysfunction-associated steatotic liver disease (MASLD), and some types of cancers.

Labile zinc (Zn) represents an important fraction of the total intracellular zinc pool that is readily available for binding. The signaling function of labile Zn lies in its dynamic nature. Fluctuations in labile Zn concentrations caused by either endogenous or exogenous stimuli can transiently influence cellular microenvironments, leading to modulation of signaling pathways. In this review, we focus on recent findings of zinc transients that influence cellular processes in mammalian systems. We highlight different types of zinc transients and how cellular zinc status plays regulatory roles in early development, gene expression, and kinase or neuronal signaling. Although the molecular mechanism behind how zinc transients activate signaling cascades is not clear in all cases, charting these interactions is the first step in the process.

Mitochondrial protein homeostasis (proteostasis) keeps the mitochondrial proteome functional. Thus, proteostasis is essential for mitochondrial activity and overall cellular functions, and a reduction in its function corresponds with diseases and aging in humans. Recent studies in various model organisms highlight components and mechanisms of mitochondrial proteostasis from biogenesis, through assembly, to turnover. Key findings include the identification of new components and mechanistic insights into protein import and mitochondrial translation processes, the interconnectivity of protein biogenesis and quality control, and proteolytic degradation machineries. In this review we discuss these advances that improve our current understanding of the inner workings and significance of the mitochondrial proteostasis network in maintaining functional mitochondria.

A recent study by Ding et al. harnesses cutting-edge proteomics to explore protein changes linked to human aging over 50 years across 12 tissues and plasma. It uncovered asynchronous aging clocks in different organs, redefining aging as a coordinated, targetable network.

Well-regulated transcription is essential for maintaining cellular homeostasis and genome integrity. The Integrator-PP2A complex has emerged as a major regulator of transcription by stimulating promoter-proximal termination of RNA polymerase II (Pol II). By employing dual catalytic activities, Integrator-PP2A shapes transcriptional output, limits aberrant RNA production, and suppresses R-loop-associated genome instability. Integrator-PP2A is highly modular, enabling dynamic interactions with transcription factors and epigenetic modifiers in distinct chromatin contexts and serving as a molecular hub that links transcriptional regulation to RNA quality control, chromatin state, and genome surveillance. Here, we review recent insights into the composition, mechanisms, and regulatory functions of this complex, which together establish its broad roles across both coding and noncoding transcriptional programs.

CRM1 (Exportin 1, XPO1), the best-characterized nuclear export receptor, exports hundreds of proteins and various RNA species. Its broad cargo repertoire necessitates versatile binding modes for diverse interaction partners, including nuclear export signal/sequence (NES)-containing cargoes, the GTPase Ran, nucleoporins that line nuclear pore complexes, and accessory proteins that facilitate export complex assembly or disassembly. We review the current knowledge of CRM1's protein and RNA cargoes and examine its modes of interactions in the context of the basic mechanism of nuclear export - NES recognition, recent structural studies that reveal how CRM1 engages cargoes beyond NESs, and allosteric regulation. Finally, we touch on the state of NES/cargo prediction, CRM1's interactions with nucleoporins, and its emerging roles beyond nuclear export.

Research laboratories often struggle to maintain a trusting environment which negatively affects team cohesion. Daily standup meetings provide a means to enhance communication, transparency, and psychological safety. In this article, we highlight the potential benefits of integrating daily standup meetings into your laboratory routine to promote accountability and teamwork.

Mitochondria act as central hubs for cell death signaling. During apoptosis and regulated necrosis (pyroptosis, necroptosis, and ferroptosis), mitochondria undergo drastic changes including membrane permeabilization, fragmentation, and loss of membrane potential. However, dissection of the mechanisms underlying these processes is challenging because they involve remodeling of mitochondrial membranes coupled to the assembly of protein complexes whose dynamics are difficult to capture. We discuss progress in our understanding of mitochondrial alterations in cell death and highlight state-of-the-art experimental approaches to study them. We focus on advanced single-molecule and correlative microscopy methods which have recently provided unprecedented details about the dynamics and structure of protein complexes in mitochondria and their impact on membrane organization.

The discovery of resistosomes has revolutionized our understanding of plant immunity by elucidating the structural and mechanistic basis of nucleotide-binding leucine-rich repeat receptor (NLR)-mediated defense. Recent structural insights and mechanistic studies highlight the pivotal role of post-translational modifications (PTMs), including phosphorylation, ubiquitination, lipidation, acetylation, and SUMOylation in regulating NLR function. Kinases, E3 ubiquitin ligases, and other PTM-modifying enzymes have emerged as key regulators that control NLR conformational dynamics, stability, and immune signaling. These findings underscore the importance of spatiotemporal regulation in balancing growth-defense trade-off during NLR-mediated immunity and provide new insights for engineering NLRs to enhance crop disease resistance.

Chemical modifications of rRNA, tRNA, and mRNA play key roles in protein synthesis by affecting the structure of these RNAs, by modulating decoding, and by influencing ribosomal efficiency. Recent advances in sequencing-based detection methods have expanded our ability to map these moieties across RNA molecules in diverse cellular states. In parallel, X-ray crystallography and the advent of high-resolution cryogenic electron microscopy have facilitated the direct visualization of RNA modifications within ribosomes. This review integrates recent structural studies with functional insights to shed light on the roles of RNA modifications in translation. Thereby, we seek to summarize current knowledge about the molecular roles of RNA modifications in gene expression and protein synthesis.

Mammalian fatty acid synthase (mFAS) supplies cells with saturated fatty acids for energy storage, membrane formation, and protein modifications. Structural studies over the past two decades have identified conformational variability as a hallmark feature of the multidomain mFAS, but how does this structural flexibility influence fatty acid synthesis? Cryo-electron microscopy (cryo-EM) snapshots of human FAS (hFAS) and a homologous polyketide synthase (PKS) reveal that efficiency is governed less by large-scale flexibility and more by the precise docking choreography of the acyl carrier protein (ACP). Three principles appear to influence the propagation of the fatty acid cycle: inherent conformational variability, scaffolding that steers ACP towards productive interactions, and ACP:domain interface complementarity.

Lysine acetylation is a post-translational modification (PTM) that is traditionally studied as a modifier of histones. In recent years, nonhistone protein acetylation has also emerged as a ubiquitous modification in eukaryotes. Recent advances in mass spectrometry (MS) workflows suggest that a majority of proteins are acetylated at some point during their life cycle. However, only a few of these acetylations have been studied for their functional significance. Here, we review the function of acetylations on key nonhistone proteins involved in chromatin remodeling and DNA damage repair, protein homeostasis, and metabolic coordination of the cell cycle in Saccharomyces cerevisiae. We discuss the diverse roles of acetylation in regulating these pathways, while highlighting emerging themes and open questions in the field.

Novel phage defense systems featuring diverse enzymatic activities are continually being discovered. Among these, defense systems employing proteolytic enzymes have been identified, revealing a previously unrecognized enzymatic activity in phage defense. These protease-associated defense systems represent an untapped reservoir for new biotechnological tools and may serve as a springboard for the development of proteome editors. This review outlines recent advancements in the discovery and characterization of protease-containing defense systems, proposes methods for further exploration and investigation of protease activity, and considers the prospect of protease defense systems for modulating protein processing and cell fate.

Autophagy enables cells to selectively degrade a wide range of macromolecules, and how this process achieves spatial precision within the densely packed cytosol is an active area of investigation. Recent advances suggest that phase separation provides a crucial organizational framework that converts autophagy into a spatiotemporally coordinated and self-organizing process. Biomolecular condensates formed by phase separation can create high-avidity binding platforms between autophagy receptors, scaffold proteins, and the cargo that stabilize transient molecular contacts. The formation of such condensates specifies the cargo and initiates autophagosome formation at defined cellular locations. Simultaneously, physical properties such as wetting govern how condensates interact with membranes, and thus influence engulfment efficiency. Viewing autophagy through the lens of condensate physics not only explains its molecular specificity but also highlights new therapeutic opportunities.

Nuclear envelope formations on missegregated chromosomes or chromosome fragments produce micronuclei. Although they exist largely in an autonomous state, they maintain aspects of chromosome biology that are found in the major nucleus. Aberrant micronuclear envelope behaviors alter communication with the cytoplasm. Micronuclear envelope rupture exposes entrapped chromosomes to DNA-interacting factors, resulting in DNA damage and massive chromosome shattering. Exposure of micronuclear DNA to innate immune sensors has been proposed to trigger inflammatory cytokine production. Such events can direct tumor microenvironments in response to genotoxic therapies. Understanding the formation, rupture, DNA integrity, and detection of micronuclei by immune sensors will provide insights into human disease and suggest approaches for therapeutic intervention. Here we discuss basic studies on micronuclei stability and transactions that affect their chromosomal DNA content.

Proteins of unknown function (PUFs) remain a persistent blind spot in molecular biology. Emerging evidence implicates many PUFs in crucial but poorly characterised roles in biomedical contexts, particularly cancer and infectious diseases. Here, we explore integrative strategies combining high-throughput experimental platforms with computational models to address this gap. We outline how functional insights can be derived across a molecular hierarchy, spanning individual proteins, interaction networks, and transient assemblies, and evaluate the distinct opportunities and challenges faced at each level. Framing these advances within a systems biology lens, we argue that characterising PUFs could redefine therapeutic discovery pipelines. We call for data-driven discovery methods and community efforts to support reproducible, scalable annotation of the 'dark' proteome.

The cyclic GMP-AMP (cGAMP) synthase (cGAS)-stimulator of interferon (IFN) genes (STING) pathway detects cytoplasmic DNA and elicits the innate immune response. Several recent studies show that cGAS-STING signaling not only terminates at the lysosome but also regulates lysosomal function. Here, we discuss the interplay of the cGAS-STING pathway with the lysosome.

Owing to minuscule differences in ionic radius and coordination numbers, separation of the lanthanides is technologically critical but rife with chemical and geopolitical challenges. Methylotrophic bacteria have evolved pathways for lanthanide acquisition and intracellular sorting of preferred from non-preferred lanthanides. Characterization of two proteins in this pathway, lanmodulin and landiscernin, has revealed mechanisms by which cells differentiate lanthanides. This review focuses on two modes of protein dimerization mediated by lanthanide ion binding at protein interfaces, which propagate picometer-scale differences in ionic radius to quaternary structure. Characterization of these interfaces has led us to propose a lanthanide trafficking pathway that ensures metalation of lanthanide-dependent enzymes. Finally, we discuss how metal ion-mediated protein dimerization may be applied toward improving industrial-scale lanthanide separations.

The ubiquitin-proteasome system (UPS) is a central regulator of protein turnover and signaling, with E3 ubiquitin ligases conferring substrate specificity and chain-type control. Recent advances have revealed new mechanistic classes of E3 ligases and expanded our understanding of their roles in disease, including cancer, neurodegeneration, and immune dysfunction. These insights have fueled the development of targeted protein degradation strategies that harness the UPS to eliminate disease-associated proteins. Approaches such as proteolysis-targeting chimeras (PROTACs), molecular glues, and antibody-based degraders are broadening the druggable proteome. Despite this progress, key challenges remain, including limited E3 ligase diversity, difficulties in degrader delivery, and resistance mechanisms. This review outlines recent advances in E3 ligase biology and therapeutic degradation, emphasizing opportunities to expand and refine UPS-targeted interventions.

Cells organize their biochemical activities by assembling proteins into both membrane-bound organelles and membrane-less condensates. These compartments enable specialized chemical environments that support unique biochemical functions. Recent evidence indicates that proteins carry encoded instructions for not only protein folding, but also selective distribution into condensate compartments. The dynamic movement of proteins into and within compartments is essential for normal function, while disruptions that reduce protein mobility can impair biochemical rates and cause dysfunction and disease. Here, we review these principles of condensate compartmentalization, emphasizing how encoded protein properties, chemical environments, and dynamic movement shape both cellular health and disease pathology.