Aldehydes with high and low toxicities inactivate cells by damaging distinct cellular targets

Review of Allelopathy in Green Tides: The Case of Ulva prolifera in the South Yellow Sea

The proliferation of large green macroalgae in marine environments has led to the occurrence of green tides, particularly in the South Yellow Sea region of China, where Ulva prolifera has been identified as the primary species responsible for the world's largest green tide events. Allelopathy among plants is a critical factor influencing the dynamics of green tides. This review synthesizes previous research on allelopathic interactions within green tides, categorizing four extensively studied allelochemicals: fatty acids, aldehydes, phenols, and terpenes. The mechanisms by which these compounds regulate the physiological processes of green tide algae are examined in depth. Additionally, recent advancements in the rapid detection of allelochemicals are summarized, and their potential applications in monitoring green tide events are discussed. The integration of advanced monitoring technologies, such as satellite observation and environmental DNA (eDNA) analysis, with allelopathic substance detection is also explored. This combined approach addresses gaps in understanding the dynamic processes of green tide formation and provides a more comprehensive insight into the mechanisms driving these phenomena. The findings and new perspectives presented in this review aim to offer valuable insights and inspiration for researchers and policymakers.

Solution and gaseous phase sensing of formaldehyde with economical triphenylmethane based sensors: a tool to estimate formaldehyde content in stored fish samples

The use of formalin to preserve raw food items such as fish, meat, vegetables etc. is very commonly practiced in the present day. Also, formaldehyde (FA), which is the main constituent of formalin solution, is known to cause serious health issues on exposure. Considering the ill effects of formaldehyde, herein we report synthesis of highly sensitive triphenylmethane based formaldehyde (FA) sensors from a single step reaction of inexpensive reagents namely 4-hydroxy benzaldehyde and 2,6-dimethyl phenol. The synthetic method also provides highly pure product in bulk quantity. The analytical activity of the triphenylmethane sensor 1 with a limit of detection (LOD) value of 2.31 × 10-6 M for FA was significantly enhanced through induced deprotonation and thereafter a LOD value of 1.82 × 10-8 M could be achieved. To the best of our knowledge, the LOD value of the deprotonated form (sensor 2) for FA was superior to those of all the FA optical sensors reported so far. The mechanism of sensing was demonstrated by 1H-NMR titration and recording mass spectra before and after addition of FA to a solution of sensor 2. Both sensor 1 and sensor 2 exhibit quenching in emission upon addition of FA. A fluorescence study also demonstrates enhancement in analytical activity of the sensor upon induced deprotonation. Then the sensor was effectively immobilized into a hydrophilic and biocompatible starch-PVA polymer matrix which enabled detection of FA in a 100% aqueous system reversibly. Again, quick and effective sensing of FA in real food samples (stored fish) with the help of a computational application was demonstrated. The sensors have significant practical applicability as they effectively detect FA in real food samples qualitatively and quantitatively.

Exocyclic DNA adducts and oxidative stress parameters: useful tools for biomonitoring exposure to aldehydes in smokers

CONTEXT

Exocyclic DNA adducts have been shown to be potential biomarkers of cancer risk related to oxidative stress and exposure to aldehydes in smokers. In fact, aldehydes potentially arise from tobacco combustion directly and endogenously through lipid peroxidation.

OBJECTIVE

This study aims to investigate the relationship between a profile of nine aldehydes-induced DNA adducts and antioxidant activities, in order to evaluate new biomarkers of systemic exposure to aldehydes.

METHODS

Using our previously published UPLC-MS/MS method, adducts levels were quantified in the blood DNA of 34 active smokers. The levels of antioxidant vitamins (A, C and E), coenzyme Q10, β-carotene, superoxide dismutase (SOD) and autoantibodies against oxidized low-density lipoprotein were measured.

RESULTS

Adducts induced by tobacco smoking-related aldehydes were quantified at levels reflecting an oxidative production from lipid peroxidation. A significant correlation between SOD and crotonaldehyde-induced adducts (p = 0.0251) was also observed. β-Carotene was negatively correlated with the adducts of formaldehyde (p = 0.0351) and acetaldehyde (p = 0.0413). Vitamin C tended to inversely correlate with acetaldehyde-induced adducts (p = 0.0584).

CONCLUSION

These results are promising, and the study is now being conducted on a larger cohort with the aim of evaluating the impact of smoking cessation programs on the evolution of adducts profile and antioxidants activities.

Enhanced chaotrope tolerance and (S)-2-hydroxypropiophenone production by recombinant Pseudomonas putida engineered with Pprl from Deinococcus radiodurans

Pseudomonas putida is a soil bacterium with multiple uses in fermentation and biotransformation processes. P. putida ATCC 12633 can biotransform benzaldehyde and other aldehydes into valuable α-hydroxyketones, such as (S)-2-hydroxypropiophenone. However, poor tolerance of this strain toward chaotropic aldehydes hampers efficient biotransformation processes. To circumvent this problem, we expressed the gene encoding the global regulator PprI from Deinococcus radiodurans, an inducer of pleiotropic proteins promoting DNA repair, in P. putida. Fine-tuned gene expression was achieved using an expression plasmid under the control of the LacIQ /Ptrc system, and the cross-protective role of PprI was assessed against multiple stress treatments. Moreover, the stress-tolerant P. putida strain was tested for 2-hydroxypropiophenone production using whole resting cells in the presence of relevant aldehyde substrates. P. putida cells harbouring the global transcriptional regulator exhibited high tolerance toward benzaldehyde, acetaldehyde, ethanol, butanol, NaCl, H2 O2 and thermal stress, thereby reflecting the multistress protection profile conferred by PprI. Additionally, the engineered cells converted aldehydes to 2-hydroxypropiophenone more efficiently than the parental P. putida strain. 2-Hydroxypropiophenone concentration reached 1.6 g L-1 upon a 3-h incubation under optimized conditions, at a cell concentration of 0.033 g wet cell weight mL-1 in the presence of 20 mM benzaldehyde and 600 mM acetaldehyde. Product yield and productivity were 0.74 g 2-HPP g-1 benzaldehyde and 0.089 g 2-HPP g cell dry weight-1  h-1 , respectively, 35% higher than the control experiments. Taken together, these results demonstrate that introducing PprI from D. radiodurans enhances chaotrope tolerance and 2-HPP production in P. putida ATCC 12633.

Mechanisms of the Formation of Nonvolatile and Volatile Oxidation Products from Methyl Linoleic Acid at High Temperatures

The impact of the oxidation of linoleic acid cannot be overlooked in daily food consumption. This study used gas chromatography-mass spectrometry (GC-MS) to identify both nonvolatile oxidation products and volatile oxidation products of methyl linoleic acid at 180 °C and density function theory to investigate oxidation mechanisms. An analysis of nonvolatile oxidation products revealed the presence of three primary oxidation products. The three primary oxidation products were identified as hydroperoxides, peroxide-linked dimers, and heterocyclic compounds in a ratio of 2.70:1:3.69 (mmol/mmol/mmol). The volatile components of secondary oxidation products were found including aldehydes (40.77%), alkanes (19.89%), alcohols (9.02%), furans (6.11%), epoxides (0.46%), and acids (2.50%). DFT calculation proved that the secondary oxidation products mainly came from peroxides (77%). Finally, we look forward to our research contributing positively to lipid autoxidation and human health.

Multiple DNA repair pathways prevent acetaldehyde-induced mutagenesis in yeast

Acetaldehyde is the primary metabolite of alcohol and is present in many environmental sources including tobacco smoke. Acetaldehyde is genotoxic, whereby it can form DNA adducts and lead to mutagenesis. Individuals with defects in acetaldehyde clearance pathways have increased susceptibility to alcohol-associated cancers. Moreover, a mutation signature specific to acetaldehyde exposure is widespread in alcohol and smoking-associated cancers. However, the pathways that repair acetaldehyde-induced DNA damage and thus prevent mutagenesis are vaguely understood. Here, we used Saccharomyces cerevisiae to systematically delete genes in each of the major DNA repair pathways to identify those that alter acetaldehyde-induced mutagenesis. We found that deletion of the nucleotide excision repair (NER) genes, RAD1 or RAD14, led to an increase in mutagenesis upon acetaldehyde exposure. Acetaldehyde-induced mutations were dependent on translesion synthesis as well as DNA inter-strand crosslink (ICL) repair in Δrad1 strains. Moreover, whole genome sequencing of the mutated isolates demonstrated an increase in C→A changes coupled with an enrichment of gCn→A changes in the acetaldehyde-treated Δrad1 isolates. The gCn→A mutation signature has been shown to be diagnostic of acetaldehyde exposure in yeast and in human cancers. We also demonstrated that the deletion of the two DNA-protein crosslink (DPC) repair proteases, WSS1 and DDI1, also led to increased acetaldehyde-induced mutagenesis. Defects in base excision repair (BER) led to a mild increase in mutagenesis, while defects in mismatch repair (MMR), homologous recombination repair (HR) and post replicative repair pathways did not impact mutagenesis upon acetaldehyde exposure. Our results in yeast were further corroborated upon analysis of whole exome sequenced liver cancers, wherein, tumors with defects in ERCC1 and ERCC4 (NER), FANCD2 (ICL repair) or SPRTN (DPC repair) carried a higher gCn→A mutation load than tumors with no deleterious mutations in these genes. Our findings demonstrate that multiple DNA repair pathways protect against acetaldehyde-induced mutagenesis.

Gut microbiota functional profiling in autism spectrum disorders: bacterial VOCs and related metabolic pathways acting as disease biomarkers and predictors

Background

Autism spectrum disorder (ASD) is a multifactorial neurodevelopmental disorder. Major interplays between the gastrointestinal (GI) tract and the central nervous system (CNS) seem to be driven by gut microbiota (GM). Herein, we provide a GM functional characterization, based on GM metabolomics, mapping of bacterial biochemical pathways, and anamnestic, clinical, and nutritional patient metadata.

Methods

Fecal samples collected from children with ASD and neurotypical children were analyzed by gas-chromatography mass spectrometry coupled with solid phase microextraction (GC-MS/SPME) to determine volatile organic compounds (VOCs) associated with the metataxonomic approach by 16S rRNA gene sequencing. Multivariate and univariate statistical analyses assessed differential VOC profiles and relationships with ASD anamnestic and clinical features for biomarker discovery. Multiple web-based and machine learning (ML) models identified metabolic predictors of disease and network analyses correlated GM ecological and metabolic patterns.

Results

The GM core volatilome for all ASD patients was characterized by a high concentration of 1-pentanol, 1-butanol, phenyl ethyl alcohol; benzeneacetaldehyde, octadecanal, tetradecanal; methyl isobutyl ketone, 2-hexanone, acetone; acetic, propanoic, 3-methyl-butanoic and 2-methyl-propanoic acids; indole and skatole; and o-cymene. Patients were stratified based on age, GI symptoms, and ASD severity symptoms. Disease risk prediction allowed us to associate butanoic acid with subjects older than 5 years, indole with the absence of GI symptoms and low disease severity, propanoic acid with the ASD risk group, and p-cymene with ASD symptoms, all based on the predictive CBCL-EXT scale. The HistGradientBoostingClassifier model classified ASD patients vs. CTRLs by an accuracy of 89%, based on methyl isobutyl ketone, benzeneacetaldehyde, phenyl ethyl alcohol, ethanol, butanoic acid, octadecane, acetic acid, skatole, and tetradecanal features. LogisticRegression models corroborated methyl isobutyl ketone, benzeneacetaldehyde, phenyl ethyl alcohol, skatole, and acetic acid as ASD predictors.

Conclusion

Our results will aid the development of advanced clinical decision support systems (CDSSs), assisted by ML models, for advanced ASD-personalized medicine, based on omics data integrated into electronic health/medical records. Furthermore, new ASD screening strategies based on GM-related predictors could be used to improve ASD risk assessment by uncovering novel ASD onset and risk predictors.

Fanconi anemia and Aldehyde Degradation Deficiency Syndrome: Metabolism and DNA repair protect the genome and hematopoiesis from endogenous DNA damage

We have identified a set of Japanese children with hypoplastic anemia caused by combined defects in aldehyde degrading enzymes ADH5 and ALDH2. Their clinical characteristics overlap with a hereditary DNA repair disorder, Fanconi anemia. Our discovery of this disorder, termed Aldehyde Degradation Deficiency Syndrome (ADDS), reinforces the notion that endogenously generated aldehydes exert genotoxic effects; thus, the coupled actions of metabolism and DNA repair are required to maintain proper hematopoiesis and health.

Biocompatible α-Methylenation of Metabolic Butyraldehyde in Living Bacteria

Small molecule organocatalysts are abundant in all living organisms. However, their use as organocatalysts in cells has been underexplored. Herein, we report that organocatalytic aldol chemistry can be interfaced with living Escherichia coli to enable the α-methylenation of cellular aldehydes using biogenic amines such as L-Pro or phosphate. The biocompatible reaction is mild and can be interfaced with butyraldehyde generated from D-glucose via engineered metabolism to enable the production of 2-methylenebutanal (2-MB) and 2-methylbutanal (2-MBA) by anaerobic fermentation, and 2-methylbutanol (2-MBO) by whole-cell catalysis. Overall, this study demonstrates the combination of non-enzymatic organocatalytic and metabolic reactions in vivo for the sustainable synthesis of valuable non-natural chemicals that cannot be accessed using enzymatic chemistry alone.

Computational Investigations of Reaction Mechanisms and Transformation Products of Olefins with Hypochlorous Acid

Hypochlorous acid (HOCl) as the main component in chlorination and also as the innate immune factor relevant to immune defense has attracted considerable attention. Electrophilic addition reaction of olefins with HOCl, one of the most important prototype of chemical reactions, has been intensively studied for a long time; however, it has not been fully understood yet. In this study, addition reaction mechanisms and transformation products of model olefins with HOCl were systematically investigated by the density functional theory method. The results indicate that the traditionally believed stepwise mechanism with a chloronium-ion intermediate is only suitable for olefins substituted with electron-donating groups (EDGs) and weak electron-withdrawing groups (EWGs) but it is a carbon-cation intermediate that is favorable for EDGs featuring p-π or π-π conjugation with the C═C moiety. Moreover, olefins substituted with moderate or/and strong EWGs prefer the concerted and nucleophilic addition mechanisms, respectively. Epoxide and truncated aldehyde as the main transformation products can be generated from chlorohydrin through a series of reactions involving hypochlorite; however, their generation is kinetically not as feasible as the formation of chlorohydrin. The reactivity of three chlorinating agents (HOCl, Cl₂O, and Cl₂) and the case study of chlorination and degradation of cinnamic acid were also explored. Additionally, APT charge on the double-bond moiety in olefin and energy gap (ΔE) between the highest occupied molecular orbital (HOMO) energy of olefin and the lowest unoccupied molecular orbital (LUMO) energy of HOCl were found to be good parameters to distinguish the regioselectivity of chlorohydrin and reactivity of olefin, respectively. The findings of this work are helpful in further understanding the chlorination reactions of unsaturated compounds and identifying complicated transformation products.

Oxidative lipidomics to elucidate the non-volatile derivatives of four typical triglycerides in vegetable oils under simulated frying conditions

Vegetable oils with different saturations have varied composition of triglycerides (TGs) and produce different non-volatile derivatives during oxidation. Precise characterization of the non-volatile derivatives of TGs is essential for understanding the degradation of TGs and the production pattern of non-volatile derivatives. Oxidative lipidomics was combined with collision-induced dissociation and electron-activated dissociation to elucidate the precise structures of non-volatile derivatives produced under simulated frying conditions by 1,3-dipalmitoyl-2-oleoylglycerol (POP), triolein (OOO), trilinolein (LLL), and trilinolenin (LnLnLn). The results indicate that the unsaturated fatty acyl chains at the sn-2 position were more susceptible to oxidation compared with those at the sn-1/3 position. Species of non-volatile derivatives included epoxy-, hydroperoxy-, hydroxy-, and oxo-TGs, as well as degradation products. The potential reaction pathways of TGs and their non-volatile derivatives were also proposed. This study elucidated oxidative degradation mechanisms of the four typical TGs and provided a theoretical basis for changes of vegetable oils during frying.

Disulfide-Cross-Linked Nanogel-Based Nanoassemblies for Chemotherapeutic Drug Delivery

Although nanoparticle-based chemotherapeutic strategies have gained in popularity, the efficacy of such therapies is still limited in part due to the different nanoparticle sizes needed to best accommodate different parts of the drug delivery pathway. Herein, we describe a nanogel-based nanoassembly based on the entrapment of ultrasmall starch nanoparticles (size 10-40 nm) within disulfide-crosslinked chondroitin sulfate-based nanogels (size 150-250 nm) to address this challenge. Upon exposure of the nanoassembly to the reductive tumor microenvironment, the chondroitin sulfate-based nanogel can degrade to release the doxorubicin-loaded starch nanoparticles in the tumor to facilitate improved intratumoral penetration. CT26 colon carcinoma spheroids could be efficiently penetrated by the nanoassembly (resulting in 1 order of magnitude higher DOX-derived fluorescence inside the spheroid relative to free DOX), while in vivo experiments showed that doxorubicin-loaded nanoassemblies reduced tumor sizes by 6× relative to saline controls and 2× relative to free DOX after 21 days. Together, these data suggest that nanogel-based nanoassemblies are a viable option for improving the efficacy and safety of nanoparticle-based drug delivery vehicles treating cancer.

Optimized enantioselective (S)-2-hydroxypropiophenone synthesis by free- and encapsulated-resting cells of Pseudomonas putida

BACKGROUND

Aromatic α-hydroxy ketones, such as S-2-hydroxypropiophenone (2-HPP), are highly valuable chiral building blocks useful for the synthesis of various pharmaceuticals and natural products. In the present study, enantioselective synthesis of 2-HPP was investigated by free and immobilized whole cells of Pseudomonas putida ATCC 12633 starting from readily-available aldehyde substrates. Whole resting cells of P. putida, previously grown in a culture medium containing ammonium mandelate, are a source of native benzoylformate decarboxylase (BFD) activity. BFD produced by induced P. putida resting cells is a highly active biocatalyst without any further treatment in comparison with partially purified enzyme preparations. These cells can convert benzaldehyde and acetaldehyde into the acyloin compound 2-HPP by BFD-catalyzed enantioselective cross-coupling reaction.

RESULTS

The reaction was carried out in the presence of exogenous benzaldehyde (20 mM) and acetaldehyde (600 mM) as substrates in 6 mL of 200 mM phosphate buffer (pH 7) for 3 h. The optimal biomass concentration was assessed to be 0.006 g dry cell weight (DCW) mL^- 1. 2-HPP titer, yield and productivity using the free cells were 1.2 g L^- 1, 0.56 g 2-HPP/g benzaldehyde (0.4 mol 2-HPP/mol benzaldehyde), 0.067 g 2-HPP g^- 1 DCW h^- 1, respectively, under optimized biotransformation conditions (30 °C, 200 rpm). Calcium alginate (CA)-polyvinyl alcohol (PVA)-boric acid (BA)-beads were used for cell entrapment. Encapsulated whole-cells were successfully employed in four consecutive cycles for 2-HPP production under aerobic conditions without any noticeable beads degradation. Moreover, there was no production of benzyl alcohol as an unwanted by-product.

CONCLUSIONS

Bioconversion by whole P. putida resting cells is an efficient strategy for the production of 2-HPP and other α-hydroxyketones.

Valorization of soybean pulp for sustainable α-ketoisocaproate production using engineered Bacillus subtilis whole-cell biocatalyst

The disposal of soybean pulp (okara) (∼14 M tons annually) represents a global concern. α-ketoisocaproate (KIC) is an intrinsic l-leucine metabolite boosting mammalian muscle growth and has great potential in animal husbandry. However, the use of pure l-leucine (5000 USD/kg) for KIC (22 USD/kg) bioproduction is cost-prohibitive in practice, while okara rich in l-leucine (10%) could serve as an economical alternative. Following the concept of a circular bioeconomy, we managed to develop a cost-efficient platform to valorize okara into KIC. In this study, proteolytic Bacillus subtilis strain 168 capable of utilizing okara as a comprehensive substrate was employed as the whole-cell biocatalyst for KIC bioproduction. First, we elucidated the function of genes involved in KIC downstream metabolism in strain 168, including those encoding 2-oxoisovalerate dehydrogenase (bkdAA), 2-oxoisovalerate decarboxylase (bkdAB), enoyl-CoA hydratase (fadB), and bifunctional enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase (fadN). Among those KIC downstream metabolizing mutants of strain 168, the 2-oxoisovalerate decarboxylase gene knockout strain (ΔbkdAB) was found to have a better accumulation of KIC. To further improve the KIC yield, a soluble l-amino acid deaminase (LAAD) from Proteus vulgaris was heterologously expressed in the ΔbkdAB strain and a ∼50% conversion of total l-leucine contained in okara was catalyzed into KIC, along with a ∼50% reduction of CO₂ emission compared to the wild-type cultures. Altogether, this renovated biocatalytic system provides an alternative platform to valorize okara for producing value-added chemicals in an eco-friendly manner.

Multi-enzyme catalysed processes using purified and whole-cell biocatalysts towards a 1,3,4-substituted tetrahydroisoquinoline†‡

In this work, two multi-enzyme catalysed processes to access a 1,3,4-substituted tetrahydroisoquinoline (THIQ), using either purified enzymes or lyophilised whole-cell catalysts, are presented. A key focus was the first step in which the reduction of 3-hydroxybenzoic acid (3-OH-BZ) into 3-hydroxybenzaldehyde (3-OH-BA) was catalysed by a carboxylate reductase (CAR) enzyme. Incorporation of the CAR-catalysed step enables substituted benzoic acids as the aromatic components, which can potentially be obtained from renewable resources by microbial cell factories. In this reduction, the implementation of an efficient cofactor regeneration system of both ATP and NADPH was crucial. Two different recycling approaches, either using purified enzymes or lyophilised whole-cells, were established and compared. Both of them showed high conversions of the acid into 3-OH-BA (>80%). However, the whole-cell system showed superior performance because it allowed the combination of the first and second steps into a one-pot cascade with excellent HPLC yields (>99%, enantiomeric excess (ee) ≥ 95%) producing the intermediate 3-hydroxyphenylacetylcarbinol. Moreover, enhanced substrate loads could be achieved compared to the system employing only purified enzymes. The third and fourth steps were performed in a sequential mode to avoid cross-reactivities and the formation of several side products. Thus, (1R,2S)-metaraminol could be formed with high HPLC yields (>90%, isomeric content (ic) ≥ 95%) applying either purified or whole-cell transaminases from Bacillus megaterium (BmTA) or Chromobacterium violaceum (Cv2025). Finally, the cyclisation step was performed using either a purified or lyophilised whole-cell norcoclaurine synthase variant from Thalictrum flavum (ΔTfNCS-A79I), leading to the formation of the target THIQ product with high HPLC yields (>90%, ic > 90%). As many of the educts applied are from renewable resources and a complex product with three chiral centers can be gained by only four highly selective steps, a very step- and atom efficient approach to stereoisomerically pure THIQ is shown.

In this work, two multi-enzyme catalysed processes to access a 1,3,4-substituted tetrahydroisoquinoline (THIQ), using either purified enzymes or lyophilised whole-cell catalysts, are presented.

Comprehensive evaluation of biopolymer immune implants for peritoneal metastasis carcinoma therapy

Immunotherapy has been widely used in the treatment of advanced stage cancers with spreading metastases, while the fully activation of immune system often requires sustained and long-acting immune stimulation by immunotherapeutic agents. In previous studies, we designed a biopolymer immune implant by dynamic covalent bonds and achieved sustained release of loaded immunotherapeutic agents, thus stimulated systemic immune activation and elicited immune memory effects. Herein, we further optimized the implants and carried out a comprehensive evaluation of the implants on peritoneal metastasis carcinoma (PMC) therapy. Our results showed that the implants fabricated with 8-arm polyethylene glycol amine (8-arm PEG-NH₂) and 40% oxidation degree dextran (ODEX) exhibited a satisfactory degradation time for activating the antitumor immunity. The drug combination of oxaliplatin (OxP) and resiquimod (R848) could be sustainably released from the implants for 18 days. The implants cured 75% of mice with PMC and elicited immune memory effects to resist tumor re-challenge without obvious side effects observed. Mechanism analysis revealed that the implants could serve as an in-situ vaccine to enhance the infiltration of activated dendritic cells (DCs), T cells and natural killer (NK) cells inside the tumor, as well as increase the serum tumor necrosis factor α (TNF-α), interferon-γ (IFN-γ) and interleukin 12 (IL-12) levels. These results strongly support the clinical translation potential of this sustained released biopolymer immune implants for PMC therapy.

Effects of amino acids on the formation and distribution of glycerol core aldehydes during deep frying

Glyceryl core aldehyde (GCAs) are hazard factors produced during the frying process using oils and fats, and GCAs control and mitigation research is very important. This study investigated the effects of adding amino acids (methionine, glycine, and histidine) at 2.5, 5, and 10 mM on the formation and distribution of four GCAs during frying. High oleic sunflower oil (HOSO) was selected as frying oil for French fries. After 12 h of frying, the content of GCAs in the tert-butylhydroquinone-treated group (0.02 wt%, 1.1 mM) decreased by 29 % compared with the control group. The addition of methionine, glycine, and histidine decreased the total GCAs by 51 %, 28 %, and 27 %, respectively. The total GCAs content was best inhibited by methionine, while glycine and histidine were not significantly different from TBHQ. Methionine addition significantly reduced GCAs (9-oxo), GCAs (10-oxo-8), and GCAs (11-oxo-9) by 39 %, 78 %, and 80 %, respectively, while histidine was the most potent inhibitor of GCAs (8-oxo), which decreased by 40 %. Methionine also proved effective in slowing degradation of frying oil quality. These results provide a new direction for decreasing GCAs in frying systems.

Determination of Carbonyl Compounds in Different Work Environments: Comparison between LC-UV/DAD and LC-MS/MS Detection Methods

There were two analytical methods for the determination of 12 carbonyl compounds (CCs) by using liquid chromatography (LC) coupled with mass spectrometry (MS/MS) and diode array detector (UV/DAD) that were developed and applied to 52 samples that were collected in 10 workplaces. Linearity (0.996 < R² < 0.999), intra-day repeatability (0.7 < RSD% < 10), and inter-day repeatability (5 < RSD% < 16) were acceptable for both techniques, but the highest sensibility of the MS/MS method allowed us to correctly quantify 98% of the samples (versus 32% by UV/DAD). The comparison of the concentrations that were obtained by quantifying the same sample with both techniques showed good agreement for acetaldehyde and formaldehyde (0.1 < % deviation < 30) but much higher for the less abundant congeners. In real samples, formaldehyde was the most abundant congener (concentrations between 2.7 and 77 µg m^-3), followed by acetaldehyde (concentrations between 1.5 and 79 µg m^-3) and butyraldehyde (concentrations between 0.4 and 13 µg m^-3). In all the beauty salon samples, instead, the most abundant congener was acetaldehyde (concentrations between 19 and 79 µg m^-3), probably associated with the use of beauty products. Principal components analysis (PCA) confirms the ubiquitous character of formaldehyde and highlights the influence of minority CCs on different workplaces.

Proteomics-based evaluation of the mechanism underlying vascular injury via DNA interstrand crosslinks, glutathione perturbation, mitogen-activated protein kinase, and Wnt and ErbB signaling pathways induced by crotonaldehyde

Crotonaldehyde (CRA)—one of the major environmental pollutants from tobacco smoke and industrial pollution—is associated with vascular injury (VI). We used proteomics to systematically characterize the presently unclear molecular mechanism of VI and to identify new related targets or signaling pathways after exposure to CRA. Cell survival assays were used to assess DNA damage, whereas oxidative stress was determined using colorimetric assays and by quantitative fluorescence study; additionally, cyclooxygenase-2, mitogen-activated protein kinase pathways, Wnt3a, β-catenin, phospho-ErbB2, and phospho-ErbB4 were assessed using ELISA. Proteins were quantitated via tandem mass tag-based liquid chromatography-mass spectrometry and bioinformatics analyses, and 34 differentially expressed proteins were confirmed using parallel reaction monitoring, which were defined as new indicators related to the mechanism underlying DNA damage; glutathione perturbation; mitogen-activated protein kinase; and the Wnt and ErbB signaling pathways in VI based on Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and protein–protein interaction network analyses. Parallel reaction monitoring confirmed significant (p < 0.05) upregulation (> 1.5-fold change) of 23 proteins and downregulation (< 0.667-fold change) of 11. The mechanisms of DNA interstrand crosslinks; glutathione perturbation; mitogen-activated protein kinase; cyclooxygenase-2; and the Wnt and ErbB signaling pathways may contribute to VI through their roles in DNA damage, oxidative stress, inflammation, vascular dysfunction, endothelial dysfunction, vascular remodeling, coagulation cascade, and the newly determined signaling pathways. Moreover, the Wnt and ErbB signaling pathways were identified as new disease pathways involved in VI. Taken together, the elucidated underlying mechanisms may help broaden existing understanding of the molecular mechanisms of VI induced by CRA.

Impact of Heating Temperature and Fatty Acid Type on the Formation of Lipid Oxidation Products During Thermal Processing

Thermal treatment of lipids rich in fatty acids contributes to the formation of lipid oxidation products (LOPs), which have potentially harmful effects on human health. This study included soybean oil (SO), palm oil (PO), olive oil (OO), and lard oil (LO) as the research objects, with an aim to investigate the impact of heating temperature and fatty acid type on the generation of LOPs (α-dicarbonyl compounds, malondialdehyde (MDA), α,β-unsaturated aldehydes, and 16 volatile aldehydes). Results showed that LOPs increased significantly (p &lt; 0.05) with the increase in temperature (100 ~ 200°C). Furthermore, the amount of 2,3-butanedione (159.53 μg/g), MDA (3.15 μg/g), 4-hydroxy-hexenal (3.03 μg/g), 2-butenal (292.18%), 2-pentenal (102.26%), hexanal (898.72%), and 2,4-heptadienal (E, E) (2182.05%) were more at 200°C in SO rich in polyunsaturated fatty acids (PUFAs) than other oils. Results from heat map analysis indicated that the 2, 4-heptadienal, and glyoxal related to the myristic acid of oil. Moreover, the MDA was in close association with PUFAs. Based on the effect of temperature and fatty acid type on the generation of LOPs, this study could serve as a control method to reduce harmful LOPs.

The association between dietary fiber intake and the concentrations of aldehydes in serum

Aldehydes have been shown to be potentially carcinogenic, mutagenic, and cardiotoxic to humans. Dietary fiber reduces exposure to certain environmental pollutants and has been widely used to improve various metabolic disorders. However, the effects of dietary fiber on serum concentrations of aldehydes remain unexplored. Data was collected from the National Health and Nutrition Examination Survey (NHANES) 2013-2014. Generalized linear regression and restricted cubic spline models were performed to elucidate the association of dietary fiber intake with the serum concentration of aldehydes. After fully adjusting for age, sex, education level, race, smoking status, alcohol use, diabetes, hypertension, body mass index, energy intake, poverty-income ratio, and physical activity, dietary fiber intake had a strong negative association with serum levels of isopentanaldehyde and propanaldehyde and a positive association with serum levels of benzaldehyde. The estimated increases in the mean log2-unit (ng/mL) of aldehydes for each fold increase in dietary fiber were -0.140 (95% confidence interval [CI]: -0.195 to -0.085) for isopentanaldehyde, -0.060 (95% CI: -0.099 to -0.015) for propanaldehyde, and 0.084 (95% CI: 0.017 to 0.150) for benzaldehyde, respectively. No significant association was observed between dietary fiber intake and the concentration of any other aldehydes. These results demonstrate that dietary fiber reduces the concentration of certain aldehydes in serum.

Effects of temperature and ferric ion on the formation of glycerol core aldehydes during simulated frying

Glycerol core aldehydes (GCAs) are toxins widely formed in oils at high temperature. This study investigated the effects of frying time, temperature, and Fe³⁺ content on the GCAs formation in high-oleic sunflower oil. The results showed that the GCAs (8-oxo, 9-oxo, 10-oxo-8, 11-oxo-9) concentrations increased with time following the pseudo-first-order kinetics. Frying at 160 °C without Fe³⁺ and at 180 °C with 0.0005 mol·L^-1 Fe³⁺ yielded the lowest and highest total GCA content. The concentrations of GCAs (8-oxo) and GCAs (9-oxo) or GCAs (10-oxo-8) and GCAs (11-oxo-9) changed similarly with different frying temperature and Fe³⁺ concentration. The major GCAs was GCAs (9-oxo) (40-70%), which also had the highest formation rate (5.42 × 10^-4 mg·g^-1·h^-1). However, GCA (10-oxo-8) and GCAs (11-oxo-9) with similar proportion (ca. 10-20%) and GCAs (8-oxo) made up the least proportions (<10%).

Stalling of Eukaryotic Translesion DNA Polymerases at DNA-Protein Cross-Links

DNA-protein cross-links (DPCs) are extremely bulky adducts that interfere with replication. In human cells, they are processed by SPRTN, a protease activated by DNA polymerases stuck at DPCs. We have recently proposed the mechanism of the interaction of DNA polymerases with DPCs, involving a clash of protein surfaces followed by the distortion of the cross-linked protein. Here, we used a model DPC, located in the single-stranded template, the template strand of double-stranded DNA, or the displaced strand, to study the eukaryotic translesion DNA polymerases ζ (POLζ), ι (POLι) and η (POLη). POLι demonstrated poor synthesis on the DPC-containing substrates. POLζ and POLη paused at sites dictated by the footprints of the polymerase and the cross-linked protein. Beyond that, POLζ was able to elongate the primer to the cross-link site when a DPC was in the template. Surprisingly, POLη was not only able to reach the cross-link site but also incorporated 1–2 nucleotides past it, which makes POLη the most efficient DNA polymerase on DPC-containing substrates. However, a DPC in the displaced strand was an insurmountable obstacle for all polymerases, which stalled several nucleotides before the cross-link site. Overall, the behavior of translesion polymerases agrees with the model of protein clash and distortion described above.

Glyoxal damages human aortic endothelial cells by perturbing the glutathione, mitochondrial membrane potential, and mitogen-activated protein kinase pathways

Background

Exposure to glyoxal, the smallest dialdehyde, is associated with several diseases; humans are routinely exposed to glyoxal because of its ubiquitous presence in foods and the environment. The aim of this study was to examine the damage caused by glyoxal in human aortic endothelial cells.

Methods

Cell survival assays and quantitative fluorescence assays were performed to measure DNA damage; oxidative stress was detected by colorimetric assays and quantitative fluorescence, and the mitogen-activated protein kinase pathways were assessed using western blotting.

Results

Exposure to glyoxal was found to be linked to abnormal glutathione activity, the collapse of mitochondrial membrane potential, and the activation of mitogen-activated protein kinase pathways. However, DNA damage and thioredoxin oxidation were not induced by dialdehydes.

Conclusions

Intracellular glutathione, members of the mitogen-activated protein kinase pathways, and the mitochondrial membrane potential are all critical targets of glyoxal. These findings provide novel insights into the molecular mechanisms perturbed by glyoxal, and may facilitate the development of new therapeutics and diagnostic markers for cardiovascular diseases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12872-021-02418-3.

Luminescence turn-on response of naphthalene diimide based chemosensor with Formaldehyde: A novel stratagem for estimation of formaldehyde in storage fish samples

A new strategy has been developed for selective estimation of toxic Formaldehyde (FA) in storage fish samples by a simple chemosensor (BNDI) based on naphthalene diimide core in aqueous medium at neutral pH. The rapid "lightning-up" fluorescence feature of BNDI has been implied to detect and estimate aqueous FA selectively at very low concentration. The chemosensing properties of BNDI with aqueous FA have been established through a unique interaction pattern which is proven by different spectroscopic and theoretical analysis.

Production of the Carboxylate Reductase from Nocardia otitidiscaviarum in a Soluble, Active Form for in vitro Applications

Accessing aldehydes from carboxylate moieties is often a challenging task. In this regard, carboxylate reductases (CARs) are promising catalysts provided by nature that are able to accomplish this task in just one step, avoiding over-reduction to the alcohol product. However, the heterologous expression of CARs can be quite difficult due to the excessive formation of insoluble protein, thus hindering further characterization and application of the enzyme. Here, the heterologous production of the carboxylate reductase from Nocardia otitidiscaviarum (NoCAR) was optimized by a combination of i) optimized cultivation conditions, ii) post-translational modification with a phosphopantetheinyl transferase and iii) selection of an appropriate expression strain. Especially, the selection of Escherichia coli tuner cells as host had a strong effect on the final 110-fold increase in the specific activity of NoCAR. This highly active NoCAR was used to reduce sodium benzoate to benzaldehyde, and it was successfully assembled with an in vitro regeneration of ATP and NADPH, being capable of reducing about 30 mM sodium benzoate with high selectivity in only 2 h of reaction.

In-depth understanding of molecular mechanisms of aldehyde toxicity to engineer robust Saccharomyces cerevisiae

Aldehydes are ubiquitous electrophilic compounds that ferment microorganisms including Saccharomyces cerevisiae encounter during the fermentation processes to produce food, fuels, chemicals, and pharmaceuticals. Aldehydes pose severe toxicity to the growth and metabolism of the S. cerevisiae through a variety of toxic molecular mechanisms, predominantly via damaging macromolecules and hampering the production of targeted compounds. Compounds with aldehyde functional groups are far more toxic to S. cerevisiae than all other functional classes, and toxic potency depends on physicochemical characteristics of aldehydes. The yeast synthetic biology community established a design-build-test-learn framework to develop S. cerevisiae cell factories to valorize the sustainable and renewable biomass, including the lignin-derived substrates. However, thermochemically pretreated biomass-derived substrate streams contain diverse aldehydes (e.g., glycolaldehyde and furfural), and biological conversions routes of lignocellulosic compounds consist of toxic aldehyde intermediates (e.g., formaldehyde and methylglyoxal), and some of the high-value targeted products have aldehyde functional group (e.g., vanillin and benzaldehyde). Numerous studies comprehensively characterized both single and additive effects of aldehyde toxicity via systems biology investigations, and novel molecular approaches have been discovered to overcome the aldehyde toxicity. Based on those novel approaches, researchers successfully developed synthetic yeast cell factories to convert lignocellulosic substrates to valuable products, including aldehyde compounds. In this mini-review, we highlight the salient relationship of physicochemical characteristics and molecular toxicity of aldehydes, the molecular detoxification and macromolecules protection mechanisms of aldehydes, and the advances of engineering robust S. cerevisiae against complex mixtures of aldehyde inhibitors. KEY POINTS: • We reviewed structure-activity relationships of aldehyde toxicity on S. cerevisiae. • Two-tier protection mechanisms to alleviate aldehyde toxicity are presented. • We highlighted the strategies to overcome the synergistic toxicity of aldehydes.

Global Transcriptional Response of Methylorubrum extorquens to Formaldehyde Stress Expands the Role of EfgA and Is Distinct from Antibiotic Translational Inhibition

The potency and indiscriminate nature of formaldehyde reactivity upon biological molecules make it a universal stressor. However, some organisms such as Methylorubrum extorquens possess means to rapidly and effectively mitigate formaldehyde-induced damage. EfgA is a recently identified formaldehyde sensor predicted to halt translation in response to elevated formaldehyde as a means to protect cells. Herein, we investigate growth and changes in gene expression to understand how M. extorquens responds to formaldehyde with and without the EfgA-formaldehyde-mediated translational response, and how this mechanism compares to antibiotic-mediated translation inhibition. These distinct mechanisms of translation inhibition have notable differences: they each involve different specific players and in addition, formaldehyde also acts as a general, multi-target stressor and a potential carbon source. We present findings demonstrating that in addition to its characterized impact on translation, functional EfgA allows for a rapid and robust transcriptional response to formaldehyde and that removal of EfgA leads to heightened proteotoxic and genotoxic stress in the presence of increased formaldehyde levels. We also found that many downstream consequences of translation inhibition were shared by EfgA-formaldehyde- and kanamycin-mediated translation inhibition. Our work uncovered additional layers of regulatory control enacted by functional EfgA upon experiencing formaldehyde stress, and further demonstrated the importance this protein plays at both transcriptional and translational levels in this model methylotroph.

Animal models of Fanconi anemia: A developmental and therapeutic perspective on a multifaceted disease

Fanconi anemia (FA) is a genetic disorder characterized by developmental abnormalities, progressive bone marrow failure, and increased susceptibility to cancer. FA animal models have been useful to understand the pathogenesis of the disease. Herein, we review FA developmental models that have been developed to simulate human FA, focusing on zebrafish and mouse models. We summarize the recapitulated phenotypes observed in these in vivo models including bone, gametogenesis and sterility defects, as well as marrow failure. We also discuss the relevance of aldehydes in pathogenesis of FA, emphasizing on hematopoietic defects. In addition, we provide a summary of potential therapeutic agents, such as aldehyde scavengers, TGFβ inhibitors, and gene therapy for FA. The diversity of FA animal models makes them useful for understanding FA etiology and allows the discovery of new therapies.

Evaluation of glycerol core aldehydes formation in edible oils under restaurant deep frying

Glycerol core aldehydes (GCAs) are potentially toxic lipid oxidation products characterized by aldehydic acids bonded to glycerol via acyl groups. This study investigated the profile and change of GCAs in rapeseed oil (RO), high-oleic sunflower oil (HOSO) and cottonseed oil (CO) after frying chicken nuggets (CNs), fish nuggets (FNs) and French fries (FFs) for 60 h in real restaurant frying systems. Three GCAs (8-oxo, 9-oxo, and 10-oxo-8) were identified, with the GCAs (9-oxo) accounting for the highest value (60%), followed by GCAs (10-oxo-8) and GCAs (8-oxo). The total GCAs increased from 1.12 to 2.02 mg/g with frying time from 0 to 60 h in RO used for frying FNs. The FN frying systems produced the largest amount of GCAs, whereas the FF frying systems produced the least. RO contained more GCAs than CO and HOSO owing to its higher unsaturated fatty acid content (91.81%). Furthermore, the GCAs showed a high correlation with polymerized and oxidized products, indicating that the formation of GCAs were related to the oxidative stability of oils. These results may provide insight into the formation of GCAs and their control during frying.

Genotoxicity of aldehyde mixtures: profile of exocyclic DNA-adducts as a biomarker of exposure to tobacco smoke

Electrophilic compounds present in humans, originating from endogenous processes or pollutant exposures, pose a risk to health though their reaction with nucleophilic sites in protein and DNA. Among this chemical class, aldehydes are mainly present in indoor air and they can also be produced by endogenous lipid peroxidation arising from oxidative stress. Known to be very reactive, aldehydes have the ability to form exocyclic adducts to DNA that, for the most if not repaired correctly, are mutagenic and by consequence potential agents involved in carcinogenesis. The aim of this work was to establish profiles of exocyclic DNA adducts induced by aldehyde mixtures, which could ultimately be considered as a genotoxic marker of endogenous and environmental aldehyde exposure. Adducts were quantified by an accurate, sensitive and validated ultra high performance liquid chromatography-electrospray ionization analytical method coupled to mass spectrometry in the tandem mode (UHPLC-ESI-MS/MS). We simultaneously measured nine exocyclic DNA adducts generated during the exposure in vitro of calf thymus DNA to different concentrations of each aldehyde along, as well as, to an equimolar mixture of these aldehydes. This approach has enabled us to establish dose-response relationships that allowed displaying the specific reactivity of aldehydes towards corresponding adducts formation. Profiles of these adducts determined in DNA of current smokers and non-smokers blood samples supported these findings. These first results are encouraging to explore genotoxicity induced by aldehyde mixtures and can furthermore be used as future reference for adductomic approaches.

Chemical Compositions of Commercial Essential Oils From Coriandrum sativum Fruits and Aerial Parts

Coriander and cilantro, the fruit and herb of Coriandrum sativum, are popular additives in various cuisines worldwide. The essential oils derived from coriander and cilantro are also popular and have shown some remarkable biological properties and health benefits. In this report, we have analyzed the essential oil compositions of 19 commercial coriander and 28 commercial cilantro essential oil samples by gas chromatography–mass spectrometry (GC–MS) techniques. In addition, 5 coriander and 4 cilantro commercial essential oil samples were analyzed by chiral GC–MS. Commercial coriander essential oil is dominated by linalool (62.2%-76.7%) with lesser quantities of α-pinene (0.3%-11.4%), γ-terpinene (0.6%-11.6%), and camphor (0.0%-5.5%). Commercial cilantro essential oil is composed largely of (2 E)-decenal (16.0%-46.6%), linalool (11.8%-29.8%), (2 E)-decen-1-ol (0.0%-24.7%), decanal (5.2%-18.7%), (2 E)-dodecenal (4.1%-8.7%), and 1-decanol (0.0%-9.5%). The enantiomeric distribution of linalool was 87% (+)-linalool:13% (−)-linalool in both coriander and cilantro essential oils, while α-pinene was 93% (+):7% (−) in coriander, 90% (+):10% (−) in cilantro; and (+)-camphor:(−)-camphor was 13%:87% in both essential oils. Chiral GC–MS analysis was able to detect an adulterated coriander essential oil sample. The data provided in this study serves to establish a baseline for future evaluations of these essential oils as well as a screen for authenticity or adulteration.

Participation of TDP1 in the repair of formaldehyde-induced DNA-protein cross-links in chicken DT40 cells

Proteins are covalently trapped on DNA to form DNA-protein cross-links (DPCs) when cells are exposed to DNA-damaging agents. Aldehyde compounds produce common types of DPCs that contain proteins in an undisrupted DNA strand. Tyrosyl-DNA phosphodiesterase 1 (TDP1) repairs topoisomerase 1 (TOPO1) that is trapped at the 3’-end of DNA. In the present study, we examined the contribution of TDP1 to the repair of formaldehyde-induced DPCs using a reverse genetic strategy with chicken DT40 cells. The results obtained showed that cells deficient in TDP1 were sensitive to formaldehyde. The removal of formaldehyde-induced DPCs was slower in tdp1-deficient cells than in wild type cells. We also found that formaldehyde did not produce trapped TOPO1, indicating that trapped TOPO1 was not a primary cytotoxic DNA lesion that was generated by formaldehyde and repaired by TDP1. The formaldehyde treatment resulted in the accumulation of chromosomal breakages that were more prominent in tdp1-deficient cells than in wild type cells. Therefore, TDP1 plays a critical role in the repair of formaldehyde-induced DPCs that are distinct from trapped TOPO1.

Potential Adverse Public Health Effects Afforded by the Ingestion of Dietary Lipid Oxidation Product Toxins: Significance of Fried Food Sources

Exposure of polyunsaturated fatty acid (PUFA)-rich culinary oils (COs) to high temperature frying practices generates high concentrations of cytotoxic and genotoxic lipid oxidation products (LOPs) via oxygen-fueled, recycling peroxidative bursts. These toxins, including aldehydes and epoxy-fatty acids, readily penetrate into fried foods and hence are available for human consumption; therefore, they may pose substantial health hazards. Although previous reports have claimed health benefits offered by the use of PUFA-laden COs for frying purposes, these may be erroneous in view of their failure to consider the negating adverse public health threats presented by food-transferable LOPs therein. When absorbed from the gastrointestinal (GI) system into the systemic circulation, such LOPs may significantly contribute to enhanced risks of chronic non-communicable diseases (NCDs), e.g. cancer, along with cardiovascular and neurological diseases. Herein, we provide a comprehensive rationale relating to the public health threats posed by the dietary ingestion of LOPs in fried foods. We begin with an introduction to sequential lipid peroxidation processes, describing the noxious effects of LOP toxins generated therefrom. We continue to discuss GI system interactions, the metabolism and biotransformation of primary lipid hydroperoxide LOPs and their secondary products, and the toxicological properties of these agents, prior to providing a narrative on chemically-reactive, secondary aldehydic LOPs available for human ingestion. In view of a range of previous studies focused on their deleterious health effects in animal and cellular model systems, some emphasis is placed on the physiological fate of the more prevalent and toxic α,β-unsaturated aldehydes. We conclude with a description of targeted nutritional and interventional strategies, whilst highlighting the urgent and unmet clinical need for nutritional and epidemiological trials probing relationships between the incidence of NCDs, and the frequency and estimated quantities of dietary LOP intake.

DNA-protein crosslink formation by endogenous aldehydes and AP sites

Covalent binding between proteins and a DNA strand produces DNA-protein crosslinks (DPC). DPC are one of the most deleterious types of DNA damage, leading to the blockage of DNA replication and transcription. Both DNA lesions and endogenous products with carbonyl functional groups can produce DPC in genomic DNA under normal physiological conditions. For example, formaldehyde, the most abundant endogenous human carcinogen, and apurinic/apyrimidinic (AP) sites, the most common type of endogenous DNA lesions, has been shown to crosslink proteins and/or DNA through their carbonyl functional groups. Unfortunately, compared to other types of DNA damage, DPC have been less studied and understood. However, a recent advancement has allowed researchers to determine accurate yields of various DNA lesions including formaldehyde-derived DPC with high sensitivity and specificity, paving the way for new developments in this field of research. Here, we review the current literature and remaining unanswered questions on DPC formation by endogenous formaldehyde and various aldehydic 2-deoxyribose lesions.

DNA-protein cross-link repair: what do we know now?

When a protein is covalently and irreversibly bound to DNA (i.e., a DNA–protein cross-link [DPC]), it may obstruct any DNA-based transaction, such as transcription and replication. DPC formation is very common in cells, as it can arise from endogenous factors, such as aldehyde produced during cell metabolism, or exogenous sources like ionizing radiation, ultraviolet light, and chemotherapeutic agents. DPCs are composed of DNA, protein, and their cross-linked bonds, each of which can be targeted by different repair pathways. Many studies have demonstrated that nucleotide excision repair and homologous recombination can act on DNA molecules and execute nuclease-dependent DPC repair. Enzymes that have evolved to deal specifically with DPC, such as tyrosyl-DNA phosphodiesterases 1 and 2, can directly reverse cross-linked bonds and release DPC from DNA. The newly identified proteolysis pathway, which employs the proteases Wss1 and SprT-like domain at the N-terminus (SPRTN), can directly hydrolyze the proteins in DPCs, thus offering a new venue for DPC repair in cells. A deep understanding of the mechanisms of each pathway and the interplay among them may provide new guidance for targeting DPC repair as a therapeutic strategy for cancer. Here, we summarize the progress in DPC repair field and describe how cells may employ these different repair pathways for efficient repair of DPCs.

Chemoselective probe for detailed analysis of ketones and aldehydes produced by gut microbiota in human samples

New strategies are required for the discovery of unknown bioactive molecules produced by gut microbiota in the human host. Herein, we utilize a chemoselective probe immobilized to magnetic beads for analysis of carbonyls in human fecal samples. We identified 112 metabolites due to femtomole analysis and an increased mass spectrometric sensitivity by up to six orders of magnitude.

DNA-protein cross-links: Formidable challenges to maintaining genome integrity

DNA is associated with proteins that are involved in its folding and transaction processes. When cells are exposed to chemical cross-linking agents or free radical-generating ionizing radiation, DNA-associated proteins are covalently trapped within the DNA to produce DNA-protein cross-links (DPCs). DPCs produced by these agents contain cross-linked proteins in an undisrupted DNA strand. Some DNA-metabolizing enzymes that form covalent reaction intermediates can also be irreversibly trapped in the presence of inhibitors or DNA damage to give rise to abortive DPCs. The abortive DPCs often contain cross-linked proteins attached to the 5' or 3' end of a DNA strand break. In vitro studies show that steric hindrance caused by cross-linked proteins impedes the progression of DNA helicases and polymerases and of RNA polymerases. The modes and consequences by which DPCs impede replication and transcription processes are considerably different from those with conventional DNA lesions. Thus, DPCs are formidable challenges to maintaining genome integrity and faithful gene expression. Current models of DPC repair involve direct and indirect removal of DPCs. The direct mechanism works for DPCs that contain topoisomerase 2 attached to the 5' end of DNA. The Mre11-Rad50-Nbs1 complex cleaves the site internal to the DPC and directly releases a DPC-containing oligonucleotide. The indirect mechanism involves degradation of cross-linked proteins by proteasomes or the recently identified DPC proteases Wss1 and Sprtn to relieve steric hindrance of DPCs. The resulting peptide-cross-links might be processed by translesion synthesis or other canonical repair mechanisms: however, the exact mechanism remains to be elucidated.

Cigarette sidestream smoke delays nucleotide excision repair: inhibited accumulation of repair proteins at DNA lesions

Cigarette sidestream smoke (CSS) contains many carcinogens that induce DNA damage. DNA damage plays an important role in the initiation of cancer and several diseases, and repair is the major defense mechanism; however, the relationship between CSS and the repair of DNA damage remains unclear. We herein investigated whether CSS influences nucleotide excision repair (NER) in vivo and in vitro. HR-1 hairless mouse skin treated with CSS was exposed to UVB, as a result of which pyrimidine dimers (cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs)) were formed and repaired via the NER pathway. The immunohistochemical staining of CPDs revealed that their repair was delayed by the CSS treatment. This delay in NER and the underlying mechanisms were examined in the human skin cell lines, HaCaT and HSC-1. Dot-blot assays, enzyme-linked immunosorbent assay and local ultraviolet irradiation assays demonstrated that CSS delayed the repair of CPDs and 6-4PPs. The recruitment of the repair molecules, TFIIH, XPA and XPG to pyrimidine dimers was markedly inhibited by CSS. Semicarbazide, which reacts with aldehydes, recovered the CSS-induced inhibition of NER, and formaldehyde exerted similar inhibitory effects to those of CSS. These results suggest that aldehydes in CSS interfere with the recruitment of NER molecules to damaged sites, leading to a delay in the repair of pyrimidine dimers.

The aldehyde group of gossypol induces mitochondrial apoptosis via ROS-SIRT1-p53-PUMA pathway in male germline stem cell

As a widely grown economic crop, cotton is the major oil and protein resource for human and livestock. But the highly toxic of gossypol in cottonseed severely restricts its effective utilization, consequently creating huge resource waste. Previous studies have shown the male germline stem cells were the most vulnerable cells in gossypol damages, but the mechanism was still unclear. We found gossypol induced cell viability decline resulted from apoptosis. And the increase of Caspase-9 activity in gossypol treatment hinted the mitochondrial apoptosis. So the mitochondrial dysfunction was confirmed by the decreased mitochondrial membrane potential and ATP concentration. We found the higher intracellular H₂O₂ level did not accompany with the O₂^·- associated increase in gossypol-treated, which indicated that gossypol obstructed the intracellular reactive oxygen species (ROS) elimination. Manipulated gossypol-induced H₂O₂ level by H₂O₂ and α-lipoic acid, we demonstrated that the mitochondrial dysfunction resulted from the excessive intracellular H₂O₂. Treated with Apogossypolone (ApoG2), an aldehyde group removed derivative of gossypol, the GSH/GSSG ratio and H₂O₂ did not decrease. ApoG2 also did not cause the mitochondrial apoptosis. So the aldehyde group is key factor in gossypol cytotoxicity. We respectively detected the NAD⁺/NADH ratio, SIRT1 activity, the relative protein level and apoptosis. Comparing with the specific inhibitors groups, the data illustrated that gossypol induced apoptosis through SIRT1-P53-PUMA pathway. This study helped to overcome barriers of gossypol cytotoxicity, which is crucial in feed and food use of cottonseed. This also provides a reference for the gossypol derivatives using in male contraception and anticancer.

Radiation-induced DNA-protein cross-links: Mechanisms and biological significance

Ionizing radiation produces various DNA lesions such as base damage, DNA single-strand breaks (SSBs), DNA double-strand breaks (DSBs), and DNA-protein cross-links (DPCs). Of these, the biological significance of DPCs remains elusive. In this article, we focus on radiation-induced DPCs and review the current understanding of their induction, properties, repair, and biological consequences. When cells are irradiated, the formation of base damage, SSBs, and DSBs are promoted in the presence of oxygen. Conversely, that of DPCs is promoted in the absence of oxygen, suggesting their importance in hypoxic cells, such as those present in tumors. DNA and protein radicals generated by hydroxyl radicals (i.e., indirect effect) are responsible for DPC formation. In addition, DPCs can also be formed from guanine radical cations generated by the direct effect. Actin, histones, and other proteins have been identified as cross-linked proteins. Also, covalent linkages between DNA and protein constituents such as thymine-lysine and guanine-lysine have been identified and their structures are proposed. In irradiated cells and tissues, DPCs are repaired in a biphasic manner, consisting of fast and slow components. The half-time for the fast component is 20min-2h and that for the slow component is 2-70h. Notably, radiation-induced DPCs are repaired more slowly than DSBs. Homologous recombination plays a pivotal role in the repair of radiation-induced DPCs as well as DSBs. Recently, a novel mechanism of DPC repair mediated by a DPC protease was reported, wherein the resulting DNA-peptide cross-links were bypassed by translesion synthesis. The replication and transcription of DPC-bearing reporter plasmids are inhibited in cells, suggesting that DPCs are potentially lethal lesions. However, whether DPCs are mutagenic and induce gross chromosomal alterations remains to be determined.

Maintenance of genome stability by Fanconi anemia proteins

Persistent dysregulation of the DNA damage response and repair in cells causes genomic instability. The resulting genetic changes permit alterations in growth and proliferation observed in virtually all cancers. However, an unstable genome can serve as a double-edged sword by providing survival advantages in the ability to evade checkpoint signaling, but also creating vulnerabilities through dependency on alternative genomic maintenance factors. The Fanconi anemia pathway comprises an intricate network of DNA damage signaling and repair that are critical for protection against genomic instability. The importance of this pathway is underlined by the severity of the cancer predisposing syndrome Fanconi anemia which can be caused by biallelic mutations in any one of the 21 genes known thus far. This review delineates the roles of the Fanconi anemia pathway and the molecular actions of Fanconi anemia proteins in confronting replicative, oxidative, and mitotic stress.

The mechanism of a formaldehyde-sensing transcriptional regulator

Most organisms are exposed to the genotoxic chemical formaldehyde, either from endogenous or environmental sources. Therefore, biology has evolved systems to perceive and detoxify formaldehyde. The frmRA(B) operon that is present in many bacteria represents one such system. The FrmR protein is a transcriptional repressor that is specifically inactivated in the presence of formaldehyde, permitting expression of the formaldehyde detoxification machinery (FrmA and FrmB, when the latter is present). The X-ray structure of the formaldehyde-treated Escherichia coli FrmR (EcFrmR) protein reveals the formation of methylene bridges that link adjacent Pro2 and Cys35 residues in the EcFrmR tetramer. Methylene bridge formation has profound effects on the pattern of surface charge of EcFrmR and combined with biochemical/biophysical data suggests a mechanistic model for formaldehyde-sensing and derepression of frmRA(B) expression in numerous bacterial species.

Photosensitized UVA-Induced Cross-Linking between Human DNA Repair and Replication Proteins and DNA Revealed by Proteomic Analysis

Long wavelength ultraviolet radiation (UVA, 320-400 nm) interacts with chromophores present in human cells to induce reactive oxygen species (ROS) that damage both DNA and proteins. ROS levels are amplified, and the damaging effects of UVA are exacerbated if the cells are irradiated in the presence of UVA photosensitizers such as 6-thioguanine (6-TG), a strong UVA chromophore that is extensively incorporated into the DNA of dividing cells, or the fluoroquinolone antibiotic ciprofloxacin. Both DNA-embedded 6-TG and ciprofloxacin combine synergistically with UVA to generate high levels of ROS. Importantly, the extensive protein damage induced by these photosensitizer+UVA combinations inhibits DNA repair. DNA is maintained in intimate contact with the proteins that effect its replication, transcription, and repair, and DNA-protein cross-links (DPCs) are a recognized reaction product of ROS. Cross-linking of DNA metabolizing proteins would compromise these processes by introducing physical blocks and by depleting active proteins. We describe a sensitive and statistically rigorous method to analyze DPCs in cultured human cells. Application of this proteomics-based analysis to cells treated with 6-TG+UVA and ciprofloxacin+UVA identified proteins involved in DNA repair, replication, and gene expression among those most vulnerable to cross-linking under oxidative conditions.

Defects in homologous recombination repair behind the human diseases: FA and HBOC

Hereditary breast and ovarian cancer (HBOC) syndrome and a rare childhood disorder Fanconi anemia (FA) are caused by homologous recombination (HR) defects, and some of the causative genes overlap. Recent studies in this field have led to the exciting development of PARP inhibitors as novel cancer therapeutics and have clarified important mechanisms underlying genome instability and tumor suppression in HR-defective disorders. In this review, we provide an overview of the basic molecular mechanisms governing HR and DNA crosslink repair, highlighting BRCA2, and the intriguing relationship between HBOC and FA.