FEBS Letters最新文献

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.

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.

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.

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 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.

RETRACTION: 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.

Photosystem II (PSII) water oxidation includes proton and electron transfer pathways, occurring during the sequential S-state transitions of Mn₄CaO₆. Here, we investigate the charge separation events during the S₂ to S₃ transition that take place via the S₂TyrZ^• intermediate, utilizing electron paramagnetic resonance (EPR) spectroscopy. The increasing number of cycles of S₂TyrZ^• formation and decay results in a gradual diminution of the S₂TyrZ^• signal intensity which is proportional to the amount of S₃ state. Our results point to the progressive accumulation of a different configuration of the donor side of PSII at the S₂ state that allows the Mn₄CaO₆ to be oxidized. These results consolidate previous investigations supporting that, during the lifetime of the S₂TyrZ^•, a proton from Mn₄CaO₆ is removed, prior to the advancement to the S₃ state.

It was previously shown that a fructose-rich diet (FRD) induces prediabetes, cardiac dysfunction, and hypertrophy (CH) in males. We assessed FRD and estrogen depletion on female metabolism and cardiovascular function. Females on FRD or control diet (CD) did not develop prediabetes or cardiac dysfunction, although FRD-fed mice showed CH vs. CD. One month of ovariectomy (OVX) did not induce prediabetes, but FRD impaired glucose tolerance in OVX mice without additional metabolic or cardiac changes. Calcium transient amplitude decreased in OVX-FRD vs. SHAM-FRD, with delayed decay, suggesting reduced activity of the sarcoplasmic/endoplasmic reticulum Ca²⁺ ATPase (SERCA2a). Sodium-hydrogen exchanger 1 (NHE1) expression also decreased in OVX-FRD. These findings indicate estrogen loss does not cause dysfunction but modifies glycemic response to FRD, while reduced NHE1 may help preserve cardiac function. Impact statement In ovariectomized (OVX) mice, estrogen deficiency leads to insulin resistance and impaired glucose tolerance only when combined with a fructose-rich diet (FRD); neither OVX nor FRD alone is sufficient to induce these alterations. However, despite hormonal changes, OVX mice fed a FRD do not develop significant cardiac dysfunction.