The [4Fe4S] Cluster of Yeast DNA Polymerase ε Is Redox Active and Can Undergo DNA-Mediated Signaling

Accurately sensing analysis of active adenine DNA glycosylase (MutY) via the high identification/excision capability to specific base-mismatches of dsDNA chains

Adenine DNA glycosylase (MutY) is a crucial member of DNA glycosylase family, and the abnormal expression of the human MutY homologs is associated with the pathogenesis of various diseases, therefore, convenient and cost-effective assessing the activity of MutY holds significant biological and medical importance. Herein, the precise identification/excision capacity of MutY to mismatched G-A base pair of dsDNA chains and the DNA-template-dependant fluorescence behaviors of copper nano cluster (CuNCs) was exploited for the accurate sensing of active MutY. Hairpin DNA with G-A base mismatch was excised by MutY to produce dsDNA chains with repetitive AAT-TTA base pairs. The newly formed dsDNA provided more active sites for the growth of CuNCs compared to the original hairpin DNA, resulting in the significantly enhanced fluorescence of final CuNCs. MutY was accurately quantified with a detection limit of 9.98 nmol L-1. The developed sensing protocol exhibited excellent selectivity toward MutY over various ions, neutral biomolecules, and protein species. Most importantly, The sensing system is capable to distinguish the active MutY from other MutY homologs with low activity, e.g., de-[4Fe4S] cluster MutY (DIS-MutY), and the practicality was well demonstrated by detecting active MutY contents in various cell lysates.

Mechanisms of formation and consumption of VSCs in thermal dehydration of Lentinula edodes: A transcriptomic analysis utilizing WGCNA

The aroma of Lentinula edodes, primarily attributed to volatile sulfur compounds (VSCs), is a crucial factor influencing its commercial and culinary quality. This study investigated cellular activity and transcriptomic changes during gradient hot-air drying (40-60 °C) at various stages. AO/EB staining and tissue culture confirmed cell viability throughout the drying process. Transcriptomic analysis identified 4255 significantly different expressed genes (|log2FC| > 1, p < 0.05), including 366 associated with sulfur metabolism. WGCNA, KEGG, and GO analyses revealed that glutathione synthesis and degradation were inhibited during drying. The gene LeGGT_3 (C8R40DRAFT_1158952) was identified as a regulator of γ-GTase synthesis. Five cysteine desulfurase (C-Dase)-encoding genes were enriched in the cysteine and methionine pathways, with LeNifs_3 (C8R40DRAFT_1079603) transcriptionally modulating C-Dase activity, which positively correlates with the production of cyclic thioethers (p < 0.05). The upregulation of DNA repair genes between 4 and 8 h enhanced cyclic thioethers (e.g., lentinionine). Early drying (0-4 h) suppressed methionine biosynthesis but activated cys synthesis. Compared to fresh samples, changes in sulfur assimilation genes during 6-8 h of drying consumed VSCs. The upregulation of LeNifs_3 increased C-Dase activity, thereby promoting the formation of cyclic thioethers. This study underscores the pivotal role of LeNifs_3 in the biosynthesis of cyclic sulfides in hot-air-dried Lentinula edodes, providing valuable insights for the development of high-quality mushroom products.

Structure of human MUTYH and functional profiling of cancer-associated variants reveal an allosteric network between its [4Fe-4S] cluster cofactor and active site required for DNA repair

MUTYH is a clinically important DNA glycosylase that thwarts mutations by initiating base-excision repair at 8-oxoguanine (OG):A lesions. The roles for its [4Fe-4S] cofactor in DNA repair remain enigmatic. Functional profiling of cancer-associated variants near the [4Fe-4S] cofactor reveals that most variations abrogate both retention of the cofactor and enzyme activity. Surprisingly, R241Q and N238S retained the metal cluster and bound substrate DNA tightly, but were completely inactive. We determine the crystal structure of human MUTYH bound to a transition state mimic and this shows that Arg241 and Asn238 build an H-bond network connecting the [4Fe-4S] cluster to the catalytic Asp236 that mediates base excision. The structure of the bacterial MutY variant R149Q, along with molecular dynamics simulations of the human enzyme, support a model in which the cofactor functions to position and activate the catalytic Asp. These results suggest that allosteric cross-talk between the DNA binding [4Fe-4S] cofactor and the base excision site of MUTYH regulate its DNA repair function.

Control of Replication Stress Response by Cytosolic Fe-S Cluster Assembly (CIA) Machinery

Accurate DNA replication is essential for the maintenance of genome stability and the generation of healthy offspring. When DNA replication is challenged, signals accumulate at blocked replication forks that elicit a multifaceted cellular response, orchestrating DNA replication, DNA repair and cell cycle progression. This replication stress response promotes the recovery of DNA replication, maintaining chromosome integrity and preventing mutations. Defects in this response are linked to heightened genetic instability, which contributes to tumorigenesis and genetic disorders. Iron-sulfur (Fe-S) clusters are emerging as important cofactors in supporting the response to replication stress. These clusters are assembled and delivered to target proteins that function in the cytosol and nucleus via the conserved cytosolic Fe-S cluster assembly (CIA) machinery and the CIA targeting complex. This review summarizes recent advances in understanding the structure and function of the CIA machinery in yeast and mammals, emphasizing the critical role of Fe-S clusters in the replication stress response.

Redox-Guided DNA Scanning by the Dynamic Repair Enzyme Endonuclease III

Endonuclease III (EndoIII), a key enzyme in the base excision repair (BER) pathway, contains a [4Fe4S] cluster that facilitates DNA repair through DNA-mediated charge transfer. Recent findings indicate that the redox state of this cluster influences EndoIII's binding affinity for DNA, modulating the enzyme's activity. In this study, we investigated the structural and electronic changes of the [4Fe4S] cluster upon binding to double-stranded DNA (dsDNA) using Fourier transform infrared spectroscopy, density functional theory calculations, and machine learning models. Our results reveal shifts in Fe-S bond vibrational modes, suggesting stabilization of the oxidized [4Fe4S] cluster in proximity to negatively charged DNA. A machine learning model, trained on the spectral features of the EndoIII/DNA complex, predicted the enzyme-DNA binding distance, providing further insights into the structural changes upon binding. We correlated the electrochemical stabilization potential of 150 mV in the [4Fe4S] cluster with the enzyme's DNA-binding properties, demonstrating how the cluster's redox state plays a crucial role in both structural stability and DNA repair.

Fe/S proteins in microbial sulfur oxidation

Iron-sulfur clusters serve as indispensable cofactors within proteins across all three domains of life. Fe/S clusters emerged early during the evolution of life on our planet and the biogeochemical cycle of sulfur is one of the most ancient and important element cycles. It is therefore no surprise that Fe/S proteins have crucial roles in the multiple steps of microbial sulfur metabolism. During dissimilatory sulfur oxidation in prokaryotes, Fe/S proteins not only serve as electron carriers in several steps, but also perform catalytic roles, including unprecedented reactions. Two cytoplasmic enzyme systems that oxidize sulfane sulfur to sulfite are of particular interest in this context: The rDsr pathway employs the reverse acting dissimilatory sulfite reductase rDsrAB as its key enzyme, while the sHdr pathway utilizes polypeptides resembling the HdrA, HdrB and HdrC subunits of heterodisulfide reductase from methanogenic archaea. Both pathways involve components predicted to bind unusual noncubane Fe/S clusters acting as catalysts for the formation of disulfide or sulfite. Mapping of Fe/S cluster machineries on the sulfur-oxidizing prokaryote tree reveals that ISC, SUF, MIS and SMS are all sufficient to meet the Fe/S cluster maturation requirements for operation of the sHdr or rDsr pathways. The sHdr pathway is dependent on lipoate-binding proteins that are assembled by a novel pathway, involving two Radical SAM proteins, namely LipS1 and LipS2. These proteins coordinate sulfur-donating auxiliary Fe/S clusters in atypical patterns by three cysteines and one histidine and act as lipoyl synthases by jointly inserting two sulfur atoms to an octanoyl residue. This article is part of a Special Issue entitled: Biogenesis and Function of Fe/S proteins.

Iron-sulfur protein odyssey: exploring their cluster functional versatility and challenging identification

Iron-sulfur (Fe-S) clusters are an essential and ubiquitous class of protein-bound prosthetic centers that are involved in a broad range of biological processes (e.g. respiration, photosynthesis, DNA replication and repair and gene regulation) performing a wide range of functions including electron transfer, enzyme catalysis, and sensing. In a general manner, Fe-S clusters can gain or lose electrons through redox reactions, and are highly sensitive to oxidation, notably by small molecules such as oxygen and nitric oxide. The [2Fe-2S] and [4Fe-4S] clusters, the most common Fe-S cofactors, are typically coordinated by four amino acid side chains from the protein, usually cysteine thiolates, but other residues (e.g. histidine, aspartic acid) can also be found. While diversity in cluster coordination ensures the functional variety of the Fe-S clusters, the lack of conserved motifs makes new Fe-S protein identification challenging especially when the Fe-S cluster is also shared between two proteins as observed in several dimeric transcriptional regulators and in the mitoribosome. Thanks to the recent development of in cellulo, in vitro, and in silico approaches, new Fe-S proteins are still regularly identified, highlighting the functional diversity of this class of proteins. In this review, we will present three main functions of the Fe-S clusters and explain the difficulties encountered to identify Fe-S proteins and methods that have been employed to overcome these issues.

Maintenance of genome integrity by the late-acting cytoplasmic iron-sulfur assembly (CIA) complex

Iron-sulfur (Fe-S) clusters are unique, redox-active co-factors ubiquitous throughout cellular metabolism. Fe-S cluster synthesis, trafficking, and coordination result from highly coordinated, evolutionarily conserved biosynthetic processes. The initial Fe-S cluster synthesis occurs within the mitochondria; however, the maturation of Fe-S clusters culminating in their ultimate insertion into appropriate cytosolic/nuclear proteins is coordinated by a late-acting cytosolic iron-sulfur assembly (CIA) complex in the cytosol. Several nuclear proteins involved in DNA replication and repair interact with the CIA complex and contain Fe-S clusters necessary for proper enzymatic activity. Moreover, it is currently hypothesized that the late-acting CIA complex regulates the maintenance of genome integrity and is an integral feature of DNA metabolism. This review describes the late-acting CIA complex and several [4Fe-4S] DNA metabolic enzymes associated with maintaining genome stability.

The iron-sulfur cluster is essential for DNA binding by human DNA polymerase ε

DNA polymerase ε (Polε) is a key enzyme for DNA replication in eukaryotes. Recently it was shown that the catalytic domain of yeast Polε (PolεCD) contains a [4Fe-4S] cluster located at the base of the processivity domain (P-domain) and coordinated by four conserved cysteines. In this work, we show that human PolεCD (hPolεCD) expressed in bacterial cells also contains an iron-sulfur cluster. In comparison, recombinant hPolεCD produced in insect cells contains significantly lower level of iron. The iron content of purified hPolECD samples correlates with the level of DNA-binding molecules, which suggests an important role of the iron-sulfur cluster in hPolε interaction with DNA. Indeed, mutation of two conserved cysteines that coordinate the cluster abolished template:primer binding as well as DNA polymerase and proofreading exonuclease activities. We propose that the cluster regulates the conformation of the P-domain, which, like a gatekeeper, controls access to a DNA-binding cleft for a template:primer. The binding studies demonstrated low affinity of hPolεCD to DNA and a strong effect of salt concentration on stability of the hPolεCD/DNA complex. Pre-steady-state kinetic studies have shown a maximal polymerization rate constant of 51.5 s-1 and a relatively low affinity to incoming dNTP with an apparent KD of 105 µM.

DNA Polymerase ζ without the C-Terminus of Catalytic Subunit Rev3 Retains Characteristic Activity, but Alters Mutation Specificity of Ultraviolet Radiation in Yeast

DNA polymerase ζ (pol ζ) plays a central role in replicating damaged genomic DNA. When DNA synthesis stalls at a lesion, it participates in translesion DNA synthesis (TLS), which helps replication proceed. TLS prevents cell death at the expense of new mutations. The current model indicates that pol ζ-dependent TLS events are mediated by Pol31/Pol32 pol ζ subunits, which are shared with replicative polymerase pol δ. Surprisingly, we found that the mutant rev3-ΔC in yeast, which lacks the C-terminal domain (CTD) of the catalytic subunit of pol ζ and, thus, the platform for interaction with Pol31/Pol32, retains most pol ζ functions. To understand the underlying mechanisms, we studied TLS in normal templates or templates with abasic sites in vitro in primer extension reactions with purified four-subunit pol ζ versus pol ζ with Rev3-ΔC. We also examined the specificity of ultraviolet radiation (UVR)-induced mutagenesis in the rev3-ΔC strains. We found that the absence of Rev3 CTD reduces activity levels, but does not alter the basic biochemical properties of pol ζ, and alters the mutation spectrum only at high doses of UVR, alluding to the existence of mechanisms of recruitment of pol ζ to UVR-damaged sites independent of the interaction of Pol31/Pol32 with the CTD of Rev3.

Modification of the 4Fe-4S Cluster Charge Transport Pathway Alters RNA Synthesis by Yeast DNA Primase

DNA synthesis during replication begins with the generation of an ∼10-nucleotide primer by DNA primase. Primase contains a redox-active 4Fe-4S cluster in the C-terminal domain of the p58 subunit (p58C). The redox state of this 4Fe-4S cluster can be modulated via the transport of charge through the protein and the DNA substrate (redox switching); changes in the redox state of the cluster alter the ability of p58C to associate with its substrate. The efficiency of redox switching in p58C can be altered by mutating tyrosine residues that bridge the 4Fe-4S cluster and the nucleic acid binding site. Here, we report the effects of mutating bridging tyrosines to phenylalanines in yeast p58C. High-resolution crystal structures show that these mutations, even with six tyrosines simultaneously mutated, do not perturb the three-dimensional structure of the protein. In contrast, measurements of the electrochemical properties on DNA-modified electrodes of p58C containing multiple tyrosine to phenylalanine mutations reveal deficiencies in their ability to engage in DNA charge transport. Significantly, this loss of electrochemical activity correlates with decreased primase activity. While single-site mutants showed modest decreases in activity compared to that of the wild-type primase, the protein containing six mutations exhibited a 10-fold or greater decrease. Thus, many possible tyrosine-mediated pathways for charge transport in yeast p58C exist, but inhibiting these pathways together diminishes the ability of yeast primase to generate primers. These results support a model in which redox switching is essential for primase activity.