FEBS Letters最新文献

Fanzor proteins represent the first confirmed family of RNA-guided DNA endonucleases in eukaryotes. Originally identified in 2013 as TnpB homologs, Fanzors remained functionally uncharacterized until 2023, when three independent research groups demonstrated their activity as programmable nucleases. Comprehensive bioinformatic analysis revealed over 3000 unique Fanzor sequences across diverse eukaryotic phyla and viruses. Fanzors share core mechanisms with their prokaryotic counterparts, utilizing a RuvC domain for DNA cleavage and requiring a Fanzor RNA (ωRNA) for targeting. However, they exhibit distinctive features, including diverse target adjacent motif preferences, extended ωRNA structure, and RuvC domain rearrangements. The eukaryotic origins of Fanzors make them promising tools for mammalian genome editing, with initial studies demonstrating successful editing in human cells without extensive engineering.

Biological processes are often spatially regulated, ensuring molecular and cellular events occur in their most strategically advantageous locations. Cellular senescence, marked by cell cycle arrest and hypersecretion, is recognized as an important part of physiological processes like development and healing, but it also contributes to aging and disease. However, the spatial distribution of senescent cells and its physiological and pathological impact remain unclear. Here we compile evidence on senescent cell localization in development, healing, and aging. We emphasize the significance of their spatial patterns and speculate on the effects of disrupted spatial positioning of senescence in relation to pathologies. To summarize the specific spatial functions of senescent cells, we propose to refer to them as 'barrier' and 'conductor' functions. The 'barrier' function of senescent cells, due to their altered morphology and apoptosis resistance, separates tissues and builds a border between two environments. The conductor function, with the secretion of signaling factors, influences the surrounding area and stimulates migration, differentiation, or proliferation, among other processes. Overall, this Review explores the spatial patterning of cellular senescence in biological processes, highlighting its dual roles as 'barrier' and 'conductor' functions, and examines the implications of senescent cell distribution in development, healing, aging, and disease.

Ion channels are among the main targets of venom peptides. Extensive functional screening has identified a number of these peptides as modulators of the voltage-gated sodium channel subtype Na_V1.7, a potential target for the treatment of chronic pain. In this study, we used a bioinformatic approach that can automatically identify Na_V1.7 gating modifier toxins from sequence information alone. The method further enables the incorporation of evolutionarily accessible sequence space in structure-activity relationship studies. The in silico method identified a putative Na_V1.7 inhibitor, μ-theraphotoxin Cg4a, which we produced recombinantly and confirmed as a Na_V1.7 inhibitor. Using structural and mutagenesis studies, we propose an improved definition of the pharmacophore of this class of Na_V1.7 inhibitors, aiding future in silico screening and classification of Na_V1.7 inhibitors.

The hyperthermophile Thermotoga maritima possesses a unique peptidoglycan containing an unusual d-lysine. Previously, we identified enzymes involved in the production of d-lysine and d-glutamate, respectively, but the biosynthetic pathway of d-alanine remains unclear. Herein, we characterized two amino acid aminotransferases, aspartate aminotransferase (TM1255), and alanine aminotransferase (TM1698). TM1255 has specific aminotransferase activities toward l-aspartate and l-glutamate as amino donors, while TM1698 has broad substrate specificity with high activities toward l-alanine and l-aminobutyrate as amino donors. Intriguingly, these two enzymes possess racemase activities toward several amino acids and aspartate 4-decarboxylase activity. The catalytic efficiency of both enzymes was highest for aminotransferase activity, followed by aspartate 4-decarboxylase activity. Therefore, TM1255 and TM1698 are novel multifunctional enzymes that have three different activities.

Expression of concern: C. Soto, L. Anderes, S. Suardi, F. Cardone, J. Castilla, M.-J. Frossard, S. Peano, P. Saa, L. Limido, M. Carbonatto, J. Ironside, J.-M. Torres, M. Pocchiari, and F. Tagliavini, "Pre-Symptomatic Detection of Prions by Cyclic Amplification of Protein Misfolding," FEBS Letters 579, no. 3 (2005): 638-642, https://doi.org/10.1016/j.febslet.2004.12.035. This Expression of Concern is for the above article, published online on 25 December 2004, 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. The journal received a report from a third party that there was evidence of undeclared spliced sections in Figure 2 and Figure 4 as well as a duplication of bands between those two figures. An investigation by the journal confirmed these concerns and detected additional evidence of undeclared splicing in Figure 3. The investigation also uncovered evidence of manipulation on non-data-containing portions of the western blot images in Figure 1. The authors responded to an inquiry by the publisher and have stated that they are not able to supply the original data due to the length of time since publication. In their response, the authors proposed a correction to change the duplicated lanes in Figure 4 to lanes from alternate experiments performed at the time, for which the authors have the original data. However, the parties concluded that this correction would not be appropriate. The authors also stated that non-data-containing elements of the western blots in Figure 1 may have been altered to improve readability, but the journal is not able to confirm this in the absence of raw data. The parties are concerned about the issues identified but also believe that they do not necessarily invalidate the conclusions of the paper. The parties agree with an Expression of Concern because the veracity of the experimental data could not be confirmed by viewing the original raw data. Authors C. Soto, J. Castilla, and F. Tagliavini agree with the Expression of Concern. All other authors could not be reached regarding the Expression of Concern.

Clioquinol has been thought of as the causative drug of subacute myelo-optic neuropathy (SMON). The underlying mechanisms of clioquinol toxicity, however, have not been elucidated in detail. Here, we revealed that clioquinol (20 μm) suppressed the expression of SCO1 and SCO2 copper chaperones for mitochondrial respiratory chain Complex IV (cytochrome c oxidase) in SH-SY5Y neuroblastoma cells. The assembly of Complex IV components and Complex IV activity were suppressed in clioquinol-treated cells. Clioquinol (10-50 μm) decreased cellular ATP levels in glucose-free media. Clioquinol (10-50 μm) induced OMA1 mitochondrial protease-dependent degradation of the dynamin-related GTPase OPA1 and suppressed the expression of CHCHD10 and CHCHD2 involved in the maintenance of cristae structure. These results suggest that mitochondrial toxicity is one of the mechanisms of clioquinol-induced neuronal cell death.

α2 → 8 polysialic acid (polySia), the capsular polysaccharide on Neisseria meningitidis serogroup B and Escherichia coli K1, elicits poor immunogenic properties. A solution structure might clarify the cause. From X-ray and neutron small-angle scattering, we find that the solution supramolecular structure of polySia exhibits parallel-chain binding. Also, striking structural changes occur upon the addition of calcium to these solutions but still with the parallel motif. The major histocompatibility complex requires entities in the molecular weight range of 600-3000 Da, but the solution structures determined here argue that in endosomes polySia oligomers of the correct size to be immunologically effective are instead bound up as parallel chains. This is expected to reduce the possible concentrations of the effective oligomers and so reduce the immunogenic capability of α2 → 8 polysialic acid.

Immunoglobulin G1 (IgG1) antibodies undergo denaturation in acidic conditions, resulting in an alternatively folded state (AFS). The AFS structure is more compact than the native state. However, the prevalence of AFS in other subclasses remains largely unexplored. This study provides evidence that humanized IgG4 can also adopt the AFS structure, as demonstrated through size-exclusion chromatography coupled with small-angle X-ray scattering (SEC-SAXS) analysis. These findings suggest that the anomalous compaction of immunoglobulins G (IgGs) is resilient to variations in sequence and structure among subclasses.

The phycobilisome (PBS) captures light energy and transfers it to photosystem I (PSI) and photosystem II (PSII). Which and how many copies of protein subunits in PBSs, PSI, and PSII remain unbound in thylakoids are unknown. Here, quantitative mass spectrometry (QMS) was used to quantify substantial pools of free extrinsic subunits of PSII and PSI. Interestingly, the membrane intrinsic PsaL is 3-fold higher than PsaA/B. This scenario complements the static structures of these complexes as revealed by X-ray crystallography and cryo-EM. The ratios of ApcG and photoprotective OCP over PBS indicate a pool of extra ApcG. The 2.5 ratio of CpcG-PBS over CpcL-PBS improves our understanding of these light-harvesting complexes involved in energy capture and photoprotection in cyanobacteria. Impact statement Our study presents the first quantitative inquiry of the free pools of proteins associated with the three major photosynthetic complexes in Synechocystis 6803. This study increases our understanding of the unbound thylakoid proteome, guiding future research into the functions of these proteins, which will facilitate efforts to enhance photosynthetic efficiency.

The ribosome-associated endoribonuclease Rae1 cleaves the Bacillus subtilis yrzI operon mRNA in a translation-dependent manner. This operon encodes up to four small peptides, S1027, YrzI, S1025, and S1024, whose functions are unknown. Here, we identified the function of YrzI and S1025 and deciphered the degradation pathways of the yrzI polycistronic mRNA. We show that YrzI is toxic at high concentrations, but co-expression with S1025 abolishes its toxicity, and that, in the absence of Rae1, S1025 is the major antidote to the YzI toxin. We show that a highly stable mRNA species containing the YrzI and S1025 open reading frames results from endoribonucleolytic cleavage upstream of yrzI followed by the arrest of 5'-exoribonucleolytic processing by ribosomes bound to its exceptionally strong Shine-Dalgarno sequence. Degradation of this mRNA requires either translation-dependent cleavage within S1025 by Rae1 or direct attack from the structured 3'-end by 3'-exoribonucleases. Neither pathway is common for a B. subtilis mRNA.