FEBS Letters最新文献

Phosphoinositides are transient signaling lipids, derived from the reversible phosphorylation of phosphatidylinositol on intracellular membranes, which serve as master regulators of many essential cellular functions. Seven distinct phosphoinositide species require precise spatiotemporal control, which is regulated by specific phosphatidylinositol kinases and phosphatases. Here, we review one such family, the inositol polyphosphate 5-phosphatases, which comprise 10 mammalian enzymes that dephosphorylate the 5-position phosphate group from the inositol head group of PtdIns(4,5)P₂, PtdIns(3,5)P₂, and/or PtdIns(3,4,5)P₃. Despite overlapping substrate specificities, the 5-phosphatases play nonredundant roles, including in development, as demonstrated by murine and zebrafish knockout studies. Mutations in several 5-phosphatase family members are associated with multisystem developmental and congenital syndromes. Associations between 5-phosphatase gene variants and diabetes and metabolic syndrome, neurodegenerative disease, and in rare cases cancer, are also emerging. Here, we provide a comprehensive discussion of the latest advances in this field, including updates on disease modeling and mechanisms.

Brain organoids, as self-organizing three-dimensional in vitro systems, offer a significant advantage over traditional models by enabling longitudinal analysis of developing human tissues. Their dynamic nature allows for the investigation of biological processes across time, a crucial 'fourth dimension' often lacking in highly reductionist in vitro models and essential to comprehensively study evolutionary and pathogenetic processes. Furthermore, the inherent genetic amenability of organoids facilitates the integration of advanced technologies, creating novel opportunities to exploit synthetic biology tools. In this regard, novel lineage tracing systems that integrate omics technologies are now dissecting complex human biological processes with unprecedented resolution. This review presents the current state of the art regarding the application of brain organoids for understanding human developmental processes related to cell lineage and temporal progression, highlighting studies that have developed dedicated lineage tracing tools. We further discuss the limitations inherent in current technologies and the potential improvements required to advance their fidelity, scalability, and translational relevance in modeling human brain development and disease.

Interleukin (IL) receptors play a pivotal role in immune regulation through coordinated interactions among multiple receptor subunits. Their cognate ligands, interleukins, orchestrate diverse immune responses by engaging distinct subunit combinations. Here, we developed a programmable IL-2 receptor surrogate ligand using a combinatorial bispecific agonist antibody strategy. By employing two complementary cell-based reporter systems that simultaneously monitor IL-2 receptor-mediated STAT5 activation and cell proliferation, we engineered a surrogate IL-2 receptor ligand that exhibits biased activation and differentiation of effector T and NK cells. This modular approach enables the development of tailored cytokine receptor surrogates with customized immunomodulatory functions.

Despite numerous studies, the biological and medical significance of inositol phosphates (InsPs) remains to be fully elucidated. One of the primary rate-limiting factors for InsP research is the difficulty in developing a method to specifically detect these molecules in complex biological matrices. Recent remarkable advancements in analytical chemistry such as nuclear magnetic resonance spectroscopy, mass spectrometry, and pertinent separation technologies have allowed the selective and sensitive differentiation of InsPs depending on the number and/or position of phosphate groups bound to the inositol ring. Thus, knowledge and experience of analytical chemistry have increasingly become a prerequisite for InsP studies. Establishing synthetic processes for functional InsPs and their analogs by organic chemists has also provided effective tools for quantitating their absolute abundances, as well as for investigating their molecular functions. This review briefly recapitulates the historical trajectory of the methodology applied to InsP research and highlights recently developed protocols using mass spectrometry coupled with liquid chromatography and capillary electrophoresis, in addition to a simple description of the chemical and chemoenzymatic synthesis of InsPs and their analogs.

The Gram-negative pathogen Burkholderia pseudomallei possesses multiple resistance-nodulation-division superfamily transporters that contribute to multidrug resistance, including BpeB and BpeF. Structural studies of BpeB and BpeF have identified a hydrophilic patch in their substrate-binding pocket. To investigate the relationship between this hydrophilic patch and substrate specificity, mutant analyses were performed using an Escherichia coli recombinant expression system. Drug susceptibility tests of BpeB and BpeF mutants showed up to a 64-fold increase in susceptibility compared with the wild type. Growth curve analyses revealed that BpeB mutants exhibited increased resistance to aminoglycosides, which are not transported by the wild type. These findings suggest that the hydrophilic patches in the substrate-binding pockets of BpeB and BpeF are involved in the substrate specificity.

Programmed cell death-1 (PD-1)/programmed death-ligand 1 (PD-L1) checkpoint signaling and its blockade by checkpoint inhibitors are dependent on molecular interactions at the binding interface. In this work, the two complete complex structures in the protein native state of PD-1 with PD-L1, and the anti-PD-L1 antibody atezolizumab were investigated by atomic force microscopy (AFM) single-molecule force spectroscopy and predicted by AlphaFold modeling. AFM revealed that the PD-1/PD-L1 binding interface displayed greater stability than the atezolizumab/PD-L1 complex due to hydrogen bonding, while the hydrophobic effect enhanced binding flexibility at the atezolizumab/PD-L1 interface. The two complexes exhibited different bond lifetimes reflecting binding interface stability and transition distance related to the interface flexibility. This work provides relevant methodology to evaluate single-molecule macromolecular interactions. Impact statement Our research developed a novel and close-to-native physiological platform to evaluate protein interactions from structural, mechanical, and kinetic perspectives at the single-molecule level. This could be applied in the design of more effective checkpoint inhibitory molecules and provides relevant methodologies for evaluating single-molecule macromolecular interactions.

CLOCK, BMAL1, and HIFs are basic helix-loop-helix and Per-Arnt-Sim domain (bHLH-PAS) proteins, which function as transcription factors. bHLH-PAS proteins are designated in two classes. Many class I proteins are regulated by environmental signals via their PAS domains, but such signals have not been identified for all. Class II (ARNTs and BMALs) are partners for Class I and can be regulated by synthetic PAS ligands. Previous studies suggested restricted dimerization for bHLH-PAS proteins. BMAL1 and BMAL2 were believed to dimerize only with CLOCK and NPAS2, while ARNT was thought to dimerize with most Class I proteins except for CLOCK and NPAS2. The logic underlying these assumptions was flawed, and evidence supports dimerization of both HIF1α and HIF2α with BMAL1.

The long lifespan of humans is often not matched with health span. Thus, there is a need for rejuvenation strategies. Here, we first discuss the evolutionary benefits of the long human lifespan, particularly when coupled with an extended health span. We then highlight the importance of understanding the complexity of aging before interfering with it. This raises the question of the optimal target for rejuvenation. We propose the blood system and hematopoietic stem cells (HSCs). Their decline is associated with dysfunction and disease in other organs, crystallizing them as a central player in organismal aging. We present rejuvenation strategies targeting the hematopoietic system, especially HSCs, and explore their systemic benefits. Overall, we summarize the potential of the blood system to reverse aging. Impact statement There is a current need to reduce the economic burden caused by aging-related diseases. In this perspective article, we discuss the evidence that supports that rejuvenating or delaying aging of the blood system has a beneficial and systemic impact on human health.

Intrinsically disordered protein regions (IDRs) are found across all domains of life and are characterized by a lack of stable 3D structure. Nevertheless, IDRs play critical roles in the most tightly regulated cellular processes, including in the core circadian clock. The molecular oscillator at the heart of circadian regulation leverages IDRs as dynamic interaction modules-for activation and repression, alike-to support robust timekeeping and expand clock output and regulation. Here, we cover the biophysical mechanisms conferred by IDRs and their modulators. We survey the IDRs in clock proteins that are widely prevalent from fungi to mammals and discuss the importance of IDRs to the core clock and beyond.

Protein pyrophosphorylation is an emerging, unusual posttranslational modification. This signaling mechanism can be driven by inositol pyrophosphate messengers, which can convert a prephosphorylated protein to the corresponding pyrophosphoprotein. Endogenous protein pyrophosphorylation influences various cellular processes and signaling pathways, including the regulation of rRNA synthesis and the modulation of vesicular trafficking. Herein, we will summarize the current detection and analysis methods that have established the occurrence of pyrophosphorylation. These methods have also been used to explore the effects of pyrophosphorylation on protein structure and function. Putative mechanisms for the regulation of this intriguing, understudied modification will be discussed. Finally, the future needs for this developing area of signal transduction research are highlighted.