A. Li, X. Lin, X. Tan, B. Yin, W. Han, J. Zhao, J. Yuan, B. Qiang, and X. Peng, "Circadian Gene Clock Contributes to Cell Proliferation and Migration of Glioma and Is Directly Regulated by Tumor-Suppressive miR-124," FEB...A. Li, X. Lin, X. Tan, B. Yin, W. Han, J. Zhao, J. Yuan, B. Qiang, and X. Peng, "Circadian Gene Clock Contributes to Cell Proliferation and Migration of Glioma and Is Directly Regulated by Tumor-Suppressive miR-124," FEBS Letters 587, no. 15 (2013): 2455-2460, https://doi.org/10.1016/j.febslet.2013.06.018. This Expression of Concern is for the above article, published online on 19 June 2013, in Wiley Online Library (http://onlinelibrary.wiley.com/), and has been issued by agreement between the journal Editor-in-Chief, Michael Brunner; FEBS Press; and John Wiley and Sons Ltd. A third party reported that the siNC and siCLOCK images for U87MG cells in Figure 2D shared an overlapping section. An investigation by the journal confirmed these concerns. The authors responded to an inquiry by the journal and supplied what were labeled as original data and a request for correction. The authors stated that the error in Figure 2D was caused by a mistake in the image compilation process. The journal reviewed the data provided, but they were unable to validate the experimental procedures used to generate the data. The journal reviewed the data provided, but were unable to confirm that it was acquired during the original study period. As such, the journal does not view a correction as appropriate. The Expression of Concern has been agreed to in order to inform and alert readers of the image overlap in Figure 2D. The authors disagree with the Expression of Concern.
Cutaneous leishmaniasis (CL) presents diverse clinical challenges due to species-specific drug efficacy and resistance. We propose a novel therapeutic strategy using synthetic biology to reprogram macrophage responses. B...Cutaneous leishmaniasis (CL) presents diverse clinical challenges due to species-specific drug efficacy and resistance. We propose a novel therapeutic strategy using synthetic biology to reprogram macrophage responses. By engineering an inducible TET-ON gene circuit to express immunomodulatory PeptideA (PepA), we enhance IL-12 production and parasite clearance. Peptides were identified via AI and validated through molecular dynamics simulations. This approach shifts macrophages toward a pro-inflammatory M1 phenotype, improving infection outcomes. Delivery via Tac-6 nanogel and adoptive transfer enables in vivo expression. Our method offers targeted, controllable treatment for CL, potentially overcoming current limitations. This platform also provides a versatile pipeline for studying macrophage-associated infections and inflammatory diseases, paving the way for precision immunotherapy. Impact statement We present a synthetic biology-based approach to treat cutaneous leishmaniasis by reprogramming macrophages with an inducible gene circuit expressing AI-designed peptides that boost IL-12 production and parasite clearance. Delivered via Tac-6 nanogel, this strategy offers targeted, resistance-mitigating therapy and a versatile platform for macrophage-driven diseases.
The brain vasculature is a critical barrier to maintain central nervous system (CNS) homeostasis. Parasitic infections can profoundly disrupt the brain vasculature, with consequences ranging from subtle neurological alte...The brain vasculature is a critical barrier to maintain central nervous system (CNS) homeostasis. Parasitic infections can profoundly disrupt the brain vasculature, with consequences ranging from subtle neurological alterations to severe, life-threatening pathologies. In this review, we explore the diverse mechanisms by which endoparasites interact with, modulate and breach CNS blood and lymphatic vessels. We highlight how these pathogens manipulate endothelial function, alter barrier permeability and exploit vascular surface molecules to access or influence the brain. These interactions often trigger local inflammation, endothelial activation and blood-brain barrier breakdown, with significant implications for parasite survival and host pathology. Here, we review the molecular and cellular mechanisms underlying these processes, providing an integrative view of parasite-vascular crosstalk in the brain and identifying emerging research areas. Understanding these interactions offers new insights into brain vascular disease pathogenesis and may inform future strategies for intervention.
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. Sev...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)P, PtdIns(3,5)P, and/or PtdIns(3,4,5)P. 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.
The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway plays a pivotal role in mounting an innate immune response against invading pathogens. Activation of this pathway by exogenous or endogenous...The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway plays a pivotal role in mounting an innate immune response against invading pathogens. Activation of this pathway by exogenous or endogenous stimuli triggers the downstream production of interferons and both pro-/anti-inflammatory cytokines. Over the past decade, hundreds of patents have been filed for the development and use of natural and synthetic STING agonists. For antivirals, synthetic STING agonists have been shown to be effective in both prophylactic and anaphylactic manners against viral infection and serve as vaccine adjuvants. This review summarizes the current application of STING agonists as antivirals to date against a variety of RNA and DNA viruses.
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...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.
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...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.
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...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...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 comp...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...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.
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 p...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.
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...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.
HipA-like kinases are widespread bacterial serine-threonine kinases, yet their regulatory mechanisms remain poorly understood. Here, we characterise two novel HipA-like systems, the monocistronic hipL and bicistronic hip...HipA-like kinases are widespread bacterial serine-threonine kinases, yet their regulatory mechanisms remain poorly understood. Here, we characterise two novel HipA-like systems, the monocistronic hipL and bicistronic hipIN, also encoding HipS-like and HIRAN domains. We show that the hipL gene contains an internal translation initiation site producing a smaller variant, HipL, which counteracts HipL-mediated toxicity via its HipS-like domain. Contrary to this, HipN requires both the HipS-like and the HIRAN domains to neutralise HipI-mediated toxicity. Neither system forms stable toxin-antitoxin (TA) complexes in vitro, distinguishing them from classical type II systems. Finally, we show that autophosphorylation affects HipL but not HipI-mediated toxicity. These findings reveal diverse regulatory architectures in HipA-like TA systems, shaped by domain composition and operon structure. Impact statement Kinases are increasingly recognised as key regulators in bacteria. Here, we show how complex operon and domain structures can contribute to kinase function and regulation, revealing increasingly complex regulatory networks in microbes.
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 corres...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.
Ribonucleotide reductases (RNRs) convert all four ribonucleotides to deoxyribonucleotides, providing essential building blocks for DNA biosynthesis and repair through radical-based catalysis. These functions are key to c...Ribonucleotide reductases (RNRs) convert all four ribonucleotides to deoxyribonucleotides, providing essential building blocks for DNA biosynthesis and repair through radical-based catalysis. These functions are key to cellular proliferation and have made RNRs well established targets for antimicrobial and antiviral drugs and combination chemotherapies. Here, we describe a novel highly sensitive one-pot enzymatic assay, which amplifies RNR activity by coupling it to the synthesis of a fluorogenic RNA aptamer. We validated this approach by testing RNR activity under dNTP-limiting conditions to emulate RNR's complex allosteric regulatory patterns and by detecting the dose- and time-dependent inhibition of RNR by hydroxyurea. This unique assay builds on previous high-throughput screening assays for investigation of RNR's catalytic mechanisms by improving sensitivity and reducing readout timeframes. Impact statement Ribonucleotide reductases (RNRs) are essential for controlling cellular dNTP supply and are major targets in cancer, antiviral, and antimicrobial therapy. FLARE is a novel single-tube, real-time RNR assay, coupling dNTP synthesis to the transcription of a fluorogenic aptamer for continuous monitoring of activity, regulation, and inhibition using standard microplate readers.
Cells are constantly exposed to various sources of DNA damage, including radiation, chemicals, replicative stress and oxidative stress, that threaten genome stability. To ensure faithful DNA repair, transcription regulat...Cells are constantly exposed to various sources of DNA damage, including radiation, chemicals, replicative stress and oxidative stress, that threaten genome stability. To ensure faithful DNA repair, transcription regulation needs to be tightly controlled. This regulation involves transcriptional suppression, selective activation of DNA repair-related genes and transcriptional recovery post-repair. Failure to properly modulate transcription during DNA damage can result in collisions between transcriptional and repair machineries, misregulation of repair genes and delayed recovery, ultimately compromising genomic integrity. Chromatin modifications play a central role in this process. These modifications include phosphorylation, methylation, acetylation and ubiquitination, which orchestrate DNA accessibility for repair machinery and fine-tune transcriptional responses. Absence of these modifications leads to inefficient DNA repair and transcriptional errors that are implicated in diseases such as cancer, premature ageing and neurodegenerative disorders. In this review, we delve into the role of various types of histone modifications, such as phosphorylation, methylation, acetylation and ubiquitination and how they regulate transcription in response to DNA damage. Impact Statement This review elucidates how histone modifications orchestrate transcription regulation during DNA damage response, safeguarding genome stability. We also discuss transcription dysregulation in diseases such as cancer and premature aging. Our review provide insights on chromatin-based repair pathways and guide researchers in developing therapeutic targets.
The LH2 complex is essential for light harvesting in many photosynthetic bacteria. To elucidate the specific structural role of carotenoids, we analyzed LH2 complexes from Ectothiorhodospira haloalkaliphila with inhibite...The LH2 complex is essential for light harvesting in many photosynthetic bacteria. To elucidate the specific structural role of carotenoids, we analyzed LH2 complexes from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis. This approach allowed us to study complexes incorporating the colorless carotenoid phytoene instead of the native, colored pigments. A 1.92 Å cryo-EM reconstruction revealed that phytoene fully substitutes for the native carotenoids while maintaining the octameric symmetry of the complex and the precise arrangement of bacteriochlorophylls. These results demonstrate that the architectural function of carotenoids in LH2 complexes is maintained even when their light-absorption capability is altered, providing new mechanistic insight into the structural basis of pigment-protein interactions in photosynthetic antenna complexes.
Circadian transcription factors (TFs) orchestrate daily rhythms in gene expression to drive rhythmic biological functions. In mammals, this system relies on the TF CLOCK:BMAL1, which binds E-boxes to initiate rhythmic tr...Circadian transcription factors (TFs) orchestrate daily rhythms in gene expression to drive rhythmic biological functions. In mammals, this system relies on the TF CLOCK:BMAL1, which binds E-boxes to initiate rhythmic transcription. While traditionally viewed as a master activator, CLOCK:BMAL1 is now recognized to engage in additional regulatory functions that are essential for its activity. This perspective focuses on the mammalian circadian clock and integrates genomic, structural, and single-molecule footprinting data to highlight emerging insights into how CLOCK:BMAL1 regulates chromatin architecture, cooperates with other TFs, and coordinates complex enhancer dynamics. We propose an updated framework for how circadian TFs operate within dynamic and multifactorial chromatin landscapes, and prime cis-regulatory elements for rhythmic transcriptional bursts. We also discuss how this framework underlies circadian reprogramming and transcriptional plasticity.
F. Zhang , H. Ni , X. Li , H. Liu , T. Xi and L. Zheng , "LncRNA FENDRR Attenuates Adriamycin Resistance via Suppressing MDR1 Expression Through Sponging HuR and miR-184 in Chronic Myelogenous Leukaemia Cells," FEBS Lett...F. Zhang , H. Ni , X. Li , H. Liu , T. Xi and L. Zheng , "LncRNA FENDRR Attenuates Adriamycin Resistance via Suppressing MDR1 Expression Through Sponging HuR and miR-184 in Chronic Myelogenous Leukaemia Cells," FEBS Letters 593, no. 15 (2019): 1993-2007, https://doi.org/10.1002/1873-3468.13480. The above article, published online on 10 June 2019 in Wiley Online Library (wileyonlinelibrary.com), has been retracted by agreement between the authors, T. Xi and L. Zheng; the journal Editor-in-Chief, Michael Brunner; the Federation of European Biochemical Societies; and John Wiley & Sons Ltd. The retraction has been agreed upon following an investigation into concerns raised by a third party. Several duplications were identified between Figures 1B, 2C, 2D, 2G, 3A, 3B, and 7D of this article and figures published in another article by two of the same authors. The authors contacted the journal and explained this was an inadvertent error that occurred during figure preparation as the studies were conducted simultaneously. However, due to the nature and extent of the duplications, the editors no longer have confidence in the results and conclusions reported in the paper. The co-authors, F. Zhang, H. Ni, X. Li and H. Liu did not respond to our notice of retraction.