Annual review of biochemistry最新文献

Microproteins are polypeptides of 100-150 amino acids or fewer that have not been annotated by genome annotation consortia, given their small size and other noncanonical properties. Translated microproteins are now known to number in the thousands in the human genome, to function in critical cellular and physiological processes, and to be dysregulated or mutated in diseases including neurodegeneration and cancer. Knowledge about microproteins has rapidly accumulated since the advent of ribosome profiling enabled their global discovery 15 years ago. In this review, we summarize what is known about eukaryotic microprotein discovery, the sequences and expression mechanisms of small open reading frames, and microprotein functions from yeast to human.

Genetic recombination involves the exchange of genetic material between homologous sequences of DNA. It is employed during meiosis in sexually reproducing organisms or in somatic cells to accurately repair toxic DNA lesions like double-strand breaks and stalled replication forks. In these separate roles, recombination drives genetic diversity by enabling reshuffling of parental genetic information while also serving as a molecular safeguard against the deleterious effects of gross chromosomal rearrangements or mutagenic insults arising for either endogenous or exogenous reasons. In both cases, efficient recombination ensures faithful transmission of genetic information to subsequent generations. In this review, we provide an exploration of the biochemical mechanisms driving genetic recombination, elucidating the molecular intricacies of fundamental processes involved therein with a focus on mechanistic insights gained into these processes using biochemical and single-molecule techniques.

Gram-negative bacteria are intrinsically resistant to many antibiotics because they are surrounded by an outer membrane that creates a robust permeability barrier. The outer membrane has an unusual asymmetric structure with a periplasmic leaflet composed of phospholipids and an outer leaflet composed of lipopolysaccharides. Because lipid biosynthesis is completed in the inner membrane of these didermic bacteria, these components must be transported across the cell envelope and properly assembled to expand the outer membrane during growth and division. Lipopolysaccharide molecules are transported over a multi-protein transenvelope bridge that is powered by ATP hydrolysis in the cytoplasm. This review discusses how this bridge is assembled and functions and how lipopolysaccharide transport is regulated to ensure balanced growth of all envelope layers. A combination of approaches and new experimental tools have significantly advanced our understanding of this molecular machine and contributed to the development of new antimicrobials that interfere with transport.

Under hyperproliferative conditions, escalation of genomic activity provokes high levels of DNA mechanical stress. Cancer cells cope with this stress through topoisomerase activity. Topoisomerases support genome-wide programs, including those driven by oncogenes and tumor suppressors, by adjusting the supercoiling and by interacting with the regulatory complexes involved in transcription, replication, and chromatin transactions. Topoisomerases also manage DNA conformational alterations that control gene activity. However, when the topological stress from oncogene-driven processes exceeds topoisomerase capacity, aberrant structures associated with DNA damage arise. These abnormalities include R-loop formation during transcription and replication. Excessive supercoiling also creates transcription-replication conflicts triggering DNA damage. Topoisomerase catalytic failure elicits topological dysregulation and DNA damage. This damage contributes further to tumorigenesis and tumor progression. The roles of topoisomerases in various genetic processes have been widely described, but the cancer-specific functions of topoisomerases are incompletely understood. Here, we summarize the crucial roles played by topoisomerases in cancer.

I present a theory of Alzheimer's disease (AD) that explains its symptoms, pathology, and risk factors. To do this, I introduce a new theory of brain plasticity that elucidates the physiological roles of AD-related agents. New events generate synaptic and branching candidates competing for long-term enhancement. Competition resolution crucially depends on the formation of membrane lipid rafts, which requires astrocyte-produced cholesterol. Sporadic AD is caused by impaired formation of plasma-membrane lipid rafts, preventing the conversion of short- to long-term memory and yielding excessive tau phosphorylation, intracellular cholesterol accumulation, synaptic dysfunction, and neurodegeneration. Amyloid β (Aβ) production is promoted by cholesterol during the switch to competition resolution, and cholesterol accumulation stimulates chronic Aβ production, secretion, and aggregation. The theory addresses all of the major established facts known about the disease and is supported by strong evidence.

The endothelial glycocalyx, a glycan-rich layer on the luminal surface of endothelial cells lining blood and lymphatic vessels, plays a crucial role in vascular homeostasis by regulating vascular permeability, immune cell trafficking, and vascular tone. Dysregulated endothelial glycocalyx turnover-whether through altered synthesis, intracellular degradation, or shedding-contributes to endothelial dysfunction in conditions such as sepsis, ischemic events, and chronic inflammatory disorders including diabetes and atherosclerosis. In this review, we examine the structure, function, and turnover of the endothelial glycocalyx, emphasizing how pathological changes in its turnover drive vascular dysfunction. We also highlight diagnostic approaches to evaluate dysregulated endothelial glycocalyx turnover in connection with vascular diseases and discuss therapeutic strategies aimed at preventing endothelial glycocalyx degradation and restoring endothelial function.

Extracellular electron transfer is an ancient and ubiquitous process that is used by a range of microorganisms to exchange electrons between the cell and environment. These electron transfer reactions can impact the solubility and speciation of redox-active molecules in the environment, such as metal oxides, while allowing bacteria to survive in areas of limited nutrient availability. Controlled transfer of electrons across the cell envelope requires assembly of electron transport chains that must pass through the outer membrane of Gram-negative bacteria or the S-layer of Gram-positive bacteria, but the mechanisms used by bacteria are still far from understood. Here, we review the literature surrounding characterized extracellular electron transfer pathways and use protein modeling tools to investigate novel electron transfer proteins and protein complexes. While these protein models are hypothetical, they provide new insight into features that may explain how extracellular electron transfer complexes interact with a range of different environmental substrates.

The visualization and manipulation of proteins in live cells are critical for studying complex biological processes. Self-labeling proteins do so by enabling the specific and covalent attachment of synthetic probes, offering unprecedented flexibility in the chemical labeling of proteins in live cells and in vivo. By combining the excellent photophysical properties of synthetic dyes with genetic targetability, these tags provide a modular and innovative toolbox for live-cell and high-resolution fluorescence imaging. In this review, we explore the development and diverse applications of the key self-labeling protein technologies, HaloTag7, SNAP-tag, and CLIP-tag, as well as the covalent trimethoprim (TMP)-tag. We discuss recent innovations in both protein engineering and substrate design that have introduced new functionalities to enable multiplexed imaging, super-resolution microscopy, and the design of novel biosensors and recorders.

Gene expression is essential for life and development, allowing the cell to modulate mRNA production in response to intrinsic and extracellular cues. Initiation of gene transcription requires a highly regulated molecular process to assemble multisubunit complexes into the preinitiation complex (PIC). Attempts to visualize these processes have been driven largely by electron microscopy, with near atomic-level resolution producing static snapshots complemented by low-resolution fluorescence cell imaging. Here, we review how new advances in superresolution single-molecule imaging in live cells can track transcription across vast spatiotemporal scales. We discuss how recent imaging research has fundamentally recast our understanding of PIC assembly from a stable, ordered process to one constantly in flux, dominated by multivalent weak interactions. We also discuss future advancements that will further expand our ability to measure PIC assembly in concert with cellular behavior, predict complex interactions computationally, and target undruggable transcription factors to treat human disease.

Heme oxygenase (HO)-like metalloenzymes are an emerging protein superfamily diverse in reaction outcome and mechanism. Found primarily in bacterial biosynthetic pathways, members conserve a flexible protein scaffold shared with the heme catabolic enzyme, HO, and a set of metal-binding residues. Most HO-like metalloenzymes assemble a diiron cluster, although manganese-iron and mononuclear iron cofactors can also be accommodated. In the canonical HO-like diiron oxygenases/oxidases (HDOs), an Fe₂(II/II) complex reacts with O₂ to form a peroxo-Fe₂(III/III) intermediate (P), common to all HDOs studied to date. The HO-like scaffold confers both distinctive metal-binding properties, allowing for dynamic cofactor assembly and disassembly, and unusual reactivity to its associated metallocofactor. These features may prove to be important in HDO-mediated catalysis of the fragmentation and rearrangement reactions that remain unprecedented among other dinuclear iron enzymes. Much of the sequence space in the HO-like metalloenzyme superfamily remains unexplored, offering exciting opportunities for the discovery of new mechanisms and reactivities.