Design, synthesis and biological evaluation of novel cyclic malonamide derivatives as selective RIPK1 inhibitors.

Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) plays a key role in cell death and inflammation. RIPK1 is a well-established therapeutic target, due to the presence of a unique kinase-regulating allosteric pocket, which enables selective inhibition. Herein we used GSK2982772 as our starting point in our discovery campaign. Applying isosteric replacement, we successfully identified the malonamide scaffold, instead of the well-established serine template. Further structural optimization led to the design and synthesis of a series of analog inhibitors. The enantiomers of the most promising compound were tested on 97 different kinases. The active enantiomer proved to be kinase selective.

ROS-Suppression Nanoplatform Combined Activation of STAT3/Bcl-2 Pathway for Preventing Myocardial Infarction in Mice.

Myocardial infarction (MI) is the leading cause of death worldwide. The most effective way to treat myocardial infarction is to rescue ischemic cardiomyocytes. After an ischemic event, the overproduction of reactive oxygen species (ROS) is a key driver of myocardial injury. The produced ROS affects mitochondrial function and induces apoptosis in cardiomyocytes. This was accomplished by constructing platelet-membrane-encapsulated ROS-responsive drug-releasing nanoparticles (PMN@NIC-MalNPs) to deliver malonate and niclosamide (NIC). The results revealed that PMN@NIC-MalNPs degraded and released malonate and niclosamide in a high-level ROS microenvironment, effectively reducing the oxidative stress and apoptosis rate. By enhancing basal mitochondrial oxygen consumption rate (OCR), adenosine triphosphate (ATP) production, and spare respiratory capacity (SRC) in vitro, reduced the oxidative stress levels and restored mitochondrial function. In vivo studies revealed that the PMN@NIC-MalNPs improved cardiac dysfunction, inhibited succinate dehydrogenase (SDH) activity, increased ATP production, and reduced the myocardial infarct size in myocardial infarction model mice. Further, transcriptome analysis and Western blot revealed that PMN@NIC-MalNPs prevented apoptosis by activating the expressions of the signal transducer and activator of transcription 3 (STAT3) and Bcl-2, and inhibiting the expression of Bax. Thus, this study provides a novel therapeutic solution for treating myocardial infarction and predicting the viability of an antioxidant and antiapoptotic therapeutic solution in the treatment of myocardial injury.

Malonic acid shapes bacterial community dynamics in compost to promote carbon sequestration and humic substance synthesis.

The incorporation of malonic acid (MA) into compost as a regulator of the tricarboxylic acid (TCA) cycle has the potential to increase carbon sequestration. However, the influence of MA on the transformation of the microbial community during the composting process remains unclear. In this investigation, MA was introduced at different stages of chicken manure (CM) composting to characterize the bacterial community within the compost using high-throughput sequencing. We assess the extent of increased carbon sequestration by comparing the concentration of total organic carbon (TOC). At the same time, this study examines whether increased carbon sequestration contributes to humus formation, which was elucidated by evaluating the content and composition of humus. Our results show that the addition of MA significantly improved carbon sequestration within the compost, reducing the carbon loss rate (C loss (%)) from 64.70% to 52.94%, while increasing HS content and stability. High throughput sequencing and Random Forest (RF) analysis show that the introduction of MA leads to a reduction in the diversity of the bacterial communities, but enhanced the ability of bacterial communities to synthesize humus. Furthermore, the addition of MA favors the proliferation of Firmicutes. Also, the hub of operational taxonomic units (OTUs) within the community co-occurrence network shifts from Proteobacteria to Firmicutes. Remarkably, our study finds a significant decrease in negative correlations between bacteria, potentially mitigating substrate consumption due to negative interactions such as competition. This phenomenon contributes to the improved retention of TOC in the compost. This research provides new insights into the mechanisms by which MA regulates bacterial communities in compost, and provides a valuable theoretical basis for the adoption of this innovative composting strategy.

Dimethyl malonate preserves renal and mitochondrial functions following ischemia-reperfusion via inhibition of succinate dehydrogenase.

BACKGROUND: Acute kidney injury (AKI), often experienced at the intensive care units, is associated with high morbidity/mortality where ischemia-reperfusion injury is a main causative factor. Succinate accumulation during ischemia contributes to the excessive generation of reactive oxygen species at reperfusion. Inhibition of succinate dehydrogenase has been associated with protective outcome in cardiac ischemia-reperfusion after 24h, but the effects on kidney and mitochondrial functions are less well studied. AIM: To investigate the therapeutic potential of succinate dehydrogenase inhibition, by using dimethyl malonate (DMM), on kidney and mitochondria functions in a mouse model of AKI. METHODS: Male C57BL/6J mice were pre-treated with DMM or placebo, i.p. 30min prior to bilateral renal ischemia (20min). After 3-days of reperfusion, glomerular filtration rate (GFR) was calculated from plasma clearance of FITC-inulin. Kidney mitochondria was isolated and mass specific and intrinsic mitochondrial function were evaluated by high resolution respirometry. Kidney sections were stained (i.e., hematoxylin-eosin and TUNEL) and analyzed for histopathological evaluation of injuries and apotosis, respectively. NADPH oxidase activity in kidney and human proximal tubular cell-line (HK2) were measured luminometrically. RESULTS: DMM treatment improved GFR (p < 0.05) and reduced levels of blood urea nitrogen (p < 0.01) compared to untreated animals, which was associated with lower degree of ischemia-reperfusion-induced tubular injuries (P < 0.001) and apoptosis (P < 0.01). These therapeutic renal effects were linked with improved mitochondrial function, both mass-specific and intrinsic. Finally, DMM treatment prevented ischemia-reperfusion-induced NADPH oxidase activity in the kidney (p < 0.001), which was showed also in HK2 cells exposed to hypoxia and reoxygenation (P < 0.01). CONCLUSION: Inhibition of succinate dehydrogenase with DMM, in conjunction with the ischemia-reperfusion phase, significantly improved both renal and mitochondrial functions. These findings may have clinical implications for future therapeutic strategies to prevent development of AKI and associated adverse complications, especially in high risk hospitalized patients.

Malonate differentially affects cell survival and confers chemoresistance in cancer cells via the induction of p53-dependent autophagy.

Metabolic network intertwines with cancerous signaling and drug responses. Malonate is a prevailing metabolite in cancer and a competitive inhibitor of succinate dehydrogenase (SDH). Recent studies showed that malonate induced reactive oxygen species (ROS)-dependent apoptosis in neuroblastoma cells, but protected cells from ischemia-reperfusion injury. We here revealed that malonate differentially regulated cell death and survival in cancer cells. While high-dose malonate triggered ROS-dependent apoptosis, the low-dose malonate induced autophagy and conferred resistance to multiple chemotherapeutic agents. Mechanistically, our results showed that malonate increased p53 stability and transcriptionally up-regulated autophagy modulator DRAM (damage-regulated autophagy modulator), thus promoting autophagy. We further proved that autophagy is required for malonate-associated chemoresistance. Collectively, our findings suggest that malonate plays a double-edge function in cancer response to stressors, and highlights a pro-cancer impact of p53-induced autophagy in response to malonate.

Efficient multi-ion adsorption using chitosan-malonic acid film: Enhancement using response surface methodology.

The objective of this research is to conduct a comprehensive characterization of chitosan while also improving its attributes by crosslinking with malonic acid, with a focus on its efficacy in removing hexavalent chromium, arsenite and fluoride ions. Crosslinking chitosan in 1:0.5 mass ratio forming a film led to substantial enhancement in confiscation of these target pollutants. The characterization of the adsorbent involved several techniques, including FT-IR, TGA-DSC, SEM-EDX, XRD, and BET surface area analysis. In batch adsorption experiments, Chitosan-malonic acid (CMA) was employed to remove CrVI, AsIII and F- from aqueous solutions. These experiments were conducted while varying conditions such as pH, dosage, concentration, temperature, and time. Through the implementation of response surface methodology (RSM), parameters were optimized, resulting in over 95% removal of CrVI, AsIII and F- ions. The isotherm and kinetics data demonstrated a good fit with the Langmuir isotherm model and pseudo second-order kinetics, respectively. According to the Langmuir isotherm, the maximum adsorption capacities on CMA for CrVI, AsIII and F- were determined to be 687.05 mg g-1, 26.72 mg g-1 and 51.38 mg g-1 respectively under optimum pH of 4.0, 7.0 and 5.0 respectively under ambient temperature of 303 K. Thermodynamic analysis indicated that the adsorption process was spontaneous and driven by enthalpy. The regenerability of the adsorbent was validated through five adsorption-desorption cycles, signifying its reusability. An assessment of the adsorbent's sustainability indicated an eco-friendly synthesis, as reflected by the low E-factor value of 0.0028.

Direct photodegradation of internally mixed sodium chloride and malonic acid single aerosols: Impact of the photoproducts on the hygroscopic properties of the particles.

Sea-salt aerosols (SSA) are one of the key natural aerosols in our atmosphere, consisting predominantly of sodium chloride (NaCl). Throughout their atmospheric transport, these aerosols undergo complex internal mixing, giving rise to a rich variety of inorganic and organic species, including dicarboxylic acids. This study investigates firstly the composition and deliquescence properties of coarse particles containing pure malonic acid (MA2, CH2(COOH)2) and internally mixed NaCl and MA2, by means of an acoustic levitation system coupled with a Raman microspectrometer. Secondly, we report here the first experimental observation and characterization of the products arising from photochemical reactions under UV-Visible irradiation (338 ≤ λ ≤ 414 nm) in the absence of an oxidant under acoustic levitation conditions in MA2 and NaCl/MA2 aerosols. Furthermore, the impact of photodegradation on the hygroscopic properties of these particles is examined. We confirmed the irreversible formation of monosodium malonate (NaMA, HOOCCH2COONa), which coexists with NaCl or MA2 on non-irradiated particles. We also demonstrated the formation of oxalic acid (OA2, HOOC-COOH) within irradiated MA2 droplets and the appearance of glyoxylic acid (GlyA, HCOCOOH) in NaCl containing droplets. The photolysis process exerts a marked effect on the hygroscopic properties of the particles, resulting in a shift in deliquescence transitions toward higher relative humidity (RH) values. This study contributes to the understanding of the intricate physicochemical processes involved in SSA during their atmospheric transport. Likewise, this work sheds light on the impacts of these types of aerosols on cloud formation and climate change.

Dimethyl malonate protects the lung in a murine model of acute respiratory distress syndrome.

BACKGROUND: Succinate is a proinflammatory citric acid cycle metabolite that accumulates in tissues during pathophysiological states. Oxidation of succinate after ischemia-reperfusion leads to reversal of the electron transport chain and generation of reactive oxygen species. Dimethyl malonate (DMM) is a competitive inhibitor of succinate dehydrogenase, which has been shown to reduce succinate accumulation. We hypothesized that DMM would protect against inflammation in a murine model of ARDS. METHODS: C57BL/6 mice were given ARDS via 67.7 µg of intratracheally administered lipopolysaccharide. Dimethyl malonate (50 mg/kg) was administered via tail vein injection 30 minutes after injury, then daily for 3 days. The animals were sacrificed on day 4 after bronchoalveolar lavage (BAL). Bronchoalveolar lavage cell counts were performed to examine cellular influx. Supernatant protein was quantified via Bradford protein assay. Animals receiving DMM (n = 8) were compared with those receiving sham injection (n = 8). Cells were fixed and stained with FITC-labeled wheat germ agglutinin to quantify the endothelial glycocalyx (EGX). RESULTS: Total cell counts in BAL was less for animals receiving DMM (6.93 × 10 6 vs. 2.46 × 10 6 , p = 0.04). The DMM group had less BAL macrophages (168.6 vs. 85.1, p = 0.04) and lymphocytes (527.7 vs. 248.3; p = 0.04). Dimethyl malonate-treated animals had less protein leak in BAL than sham treated (1.48 vs. 1.15 µg/µl, p = 0.03). Treatment with DMM resulted in greater staining intensity of the EGX in the lung when compared with sham (12,016 vs. 15,186 arbitrary units, p = 0.03). Untreated animals had a greater degree of weight loss than treated animals (3.7% vs. 1.1%, p = 0.04). Dimethyl malonate prevented the upregulation of monocyte chemoattractant protein-1 (1.66 vs. 0.92 RE, p = 0.02) and ICAM-1 (1.40 vs. 1.01 RE, p = 0.05). CONCLUSION: Dimethyl malonate reduces lung inflammation and capillary leak in ARDS. This may be mediated by protection of the EGX and inhibition of monocyte chemoattractant protein-1 and ICAM-1. Dimethyl malonate may be a novel therapeutic for ARDS.

Modular and diverse synthesis of amino acids via asymmetric decarboxylative protonation of aminomalonic acids.

Stereoselective protonation is a challenge in asymmetric catalysis. The small size and high rate of transfer of protons mean that face-selective delivery to planar intermediates is hard to control, but it can unlock previously obscure asymmetric transformations. Particularly, when coupled with a preceding decarboxylation, enantioselective protonation can convert the abundant acid feedstocks into structurally diverse chiral molecules. Here an anchoring group strategy is demonstrated as a potential alternative and supplement to the conventional structural modification of catalysts by creating additional catalyst-substrate interactions. We show that a tailored benzamide group in aminomalonic acids can help build a coordinated network of non-covalent interactions, including hydrogen bonds, π-π interactions and dispersion forces, with a chiral acid catalyst. This allows enantioselective decarboxylative protonation to give α-amino acids. The malonate-based synthesis introduces side chains via a facile substitution of aminomalonic esters and thus can access structurally and functionally diverse amino acids.

Metabolomics analysis of human cumulus cells obtained from cumulus-oocyte complexes with different developmental potential.

STUDY QUESTION: Is the abundance of certain biochemical compounds in human cumulus cells (CCs) related to oocyte quality? SUMMARY ANSWER: Malonate, 5-oxyproline, and erythronate were positively associated with pregnancy potential. WHAT IS KNOWN ALREADY: CCs are removed and discarded prior to ICSI, thereby constituting an interesting biological material on which to perform molecular analysis aimed to predict oocyte developmental competence. Mitochondrial DNA content and transcriptional analyses in CC have been shown to provide a poor predictive value of oocyte competence, but the untargeted analysis of biochemical compounds (metabolomics) has been unexplored. STUDY DESIGN, SIZE, DURATION: CCs were obtained from three groups of cumulus-oocyte complexes (COCs) of known developmental potential: oocytes not developing to blastocyst following ICSI (Bl-); oocytes developing to blastocyst but failing to establish pregnancy following embryo transfer (P-); and oocytes developing to blastocyst able to establish a pregnancy (P+). Metabolomics analyses were performed on 12 samples per group, each sample comprising the CC recovered from a single COC. PARTICIPANTS/MATERIALS, SETTING, METHODS: Human CC samples were obtained from IVF treatments. Only unfrozen oocytes and embryos not submitted to preimplantation genetic testing were included in the analysis. Metabolomics analysis was performed by ultra-high performance liquid chromatography-tandem mass spectroscopy. MAIN RESULTS AND THE ROLE OF CHANCE: The analysis identified 98 compounds, five of which were differentially abundant (P < 0.05) between groups: asparagine, proline, and malonate were less abundant in P- compared to Bl-, malonate and 5-oxoproline were less abundant in P- group compared to P+, and erythronate was less abundant in Bl- group compared to P+. No significant association between the abundance of the compounds identified and donor age or BMI was noted. LIMITATIONS, REASONS FOR CAUTION: Data dispersion and the lack of coherence between developmental groups preclude the direct use of metabolic markers in clinical practice, where the uterine environment plays a major role in pregnancy outcome. The abundance of other compounds not detected by the analysis may be associated with oocyte competence. As donors were lean (only two with BMI > 30 kg/m2) and young (<34 years old), a possible effect of obesity or advanced age on the CC metabolome could not be determined. WIDER IMPLICATIONS OF THE FINDINGS: The abundance of malonate, 5-oxyproline, and erythronate in CC was significantly higher in COCs ultimately establishing pregnancy, providing clues on the pathways required for oocyte competence. The untargeted analysis uncovered the presence of compounds that were not expected in CC, such as ß-citrylglutamate and the neurotransmitter N-acetyl-aspartyl-glutamate, which may play roles in chromatin remodeling and signaling, respectively. STUDY FUNDING/COMPETING INTEREST(S): Research was supported by the Industrial Doctorate Project IND2017/BIO-7748 funded by Madrid Region Government. The authors declare no competing interest. TRIAL REGISTRATION NUMBER: N/A.

Malonate induces the browning of white adipose tissue in high-fat diet induced obesity model.

Obesity increases the risk of various diseases, and many studies have examined prevention and treatment strategies. Browning of white adipocytes promotes triglyceride (TG) metabolism and is the new focus for treating obesity. This study investigated the role of malonate-a modulator of mitochondrial function-in adipocyte browning, and its potential as a therapeutic agent in obesity. Our findings revealed that malonate increased oxygen consumption without inhibiting ATP synthesis. Malonate induced expression of PRDM16-an important transcription factor for browning-and uncoupling protein 1 (beige adipocyte marker), suggesting that malonate induces browning in white adipocytes. In an obesity mouse model induced by a high-fat diet, malonate significantly reduced body weight and white adipose tissue weight, as well as improved insulin resistance. Importantly, malonate stimulated browning in white adipose tissue and maintained the mass of brown adipose tissue in the high-fat diet-induced obesity mouse model. We propose that manipulation of mitochondrial function by malonate is a promising therapeutic approach for obesity.

Exploring the hygroscopicity and chemical composition evolution in organic-inorganic aerosols: A study on internally mixed malonic acid-metal (Na+, Ca2+, Mg2+) nitrates.

Chemical transformations in mixed aerosols alter the particulate physical properties. Nitrates and water soluble dicarboxylic acids, such as malonic acid (MA), are major components of ambient aerosol particles. Various metal ions such as, Na+, Ca2+, Mg2+ also become part of these complex aerosol systems during their atmospheric lifetime. Interactions among the co-existing ionic and molecular species govern the chemical changes in the aerosol particles. In this work, we provide a comparative account of the effect of metal ion identity (Na+, Ca2+, Mg2+) on such chemical changes arising from ion-molecular interactions in NaNO3-MA, Ca(NO3)2-MA and Mg(NO3)2-MA mixed inorganic-organic aerosols. In-situ micro-Raman spectroscopy has enabled us to gain molecular level insight on formation of organic salt and simultaneously estimate nitrate depletion in these mixed aerosols during different stages of their hygroscopic cycle. In addition to the nitrate depletion often reported during the drying phase, this study has brought to light an intriguing observation: depletion of nitrate in the humidification phase as well, a phenomenon that has hitherto remained undocumented. For the mixed systems studied here, the extent of nitrate depletion follows the order Mg-MA (58%) > Ca-MA (43%) > Na-MA (15%). The comparatively huge forward shift in the acid displacement reaction equilibrium for the systems, Ca-MA and Mg-MA is driven by complexation. Our results highlight the profound effect of ion-molecular interactions on the acid displacement reaction equilibria in aerosols.

The Enzyme Lysine Malonylation of Calvin Cycle and Gluconeogenesis Regulated Glycometabolism in Nostoc flagelliforme to Adapt to Drought Stress.

Lysine malonylation (Kmal) is an evolutionarily conserved post-translational modification (PTM) that has been demonstrated to be involved in cellular and organismal metabolism. However, the role that Kmal plays in response to drought stress of the terrestrial cyanobacteria N. flagelliforme is still unknown. In this study, we performed the first proteomic analysis of Kmal in N. flagelliforme under different drought stresses using LC-MS/MS. In total, 421 malonylated lysine residues were found in 236 different proteins. GO and KEGG enrichment analysis indicated that these malonylated proteins were highly enriched in several metabolic pathways, including carbon metabolism and photosynthesis. Decreased malonylation levels were found to hinder the reception and transmission of light energy and CO2 fixation, which led to a decrease in photosynthetic activity. Kmal was also shown to inhibit the flux of the TCA cycle and activate the gluconeogenesis pathway in response to drought stress. Furthermore, malonylated antioxidant enzymes and antioxidants were synergistically involved in reactive oxygen species (ROS) scavenging. Malonylation was involved in lipid degradation and amino acid biosynthesis as part of drought stress adaptation. This work represents the first comprehensive investigation of the role of malonylation in dehydrated N. flagelliforme, providing an important resource for understanding the drought tolerance mechanism of this organism.

Synthesis, Characterization, and Bioactivity of the Lichen Pigments Pulvinamide, Rhizocarpic Acid, and Epanorin and Congeners.

The lichen natural products pulvinamide, rhizocarpic acid, and epanorin have been synthesized and characterized spectroscopically and by X-ray crystallography. The syntheses, by ring-opening of pulvinic acid dilactone (PAD), may well be biomimetic, given the well-known occurrence of PAD in lichen. The enantiomers, ent-rhizocarpic acid and ent-epanorin, and corresponding carboxylic acids, norrhizocarpic acid and norepanorin, were similarly prepared. All compounds were assessed for growth inhibitory activity against selected bacteria, fungi, a protist, a mammalian tumor cell line, and normal cells. Rhizocarpic acid is weakly antibacterial (Bacillus subtilis MIC = 50 µg/mL) and possesses modest but selective antitumor activity (NS-1 murine myeloma MIC = 3.1 µg/mL) with >10-fold potency relative to its enantiomer (MIC = 50 µg/mL).

Enantioselective conjugate addition of malonates to α,ß-unsaturated aldehydes catalysed by 4-oxalocrotonate tautomerase.

The enantioselective conjugate addition of malonates to α,ß-unsaturated aldehydes catalysed by 4-oxalocrotonate tautomerase is described. High conversions, high enantioselectivities, and good isolation yields were achieved for a range of substrates. We further completed a four-step synthesis of the antidepressant (+)-femoxetine by utilizing this reaction and an enzymatic reductive amination reaction.

Engineering a Novel Metabolic Pathway for Improving Cellular Malonyl-CoA Levels in Escherichia coli.

Cellular pool of malonyl-CoA in Escherichia coli is small, which impedes its utility for overproduction of natural products such as phenylpropanoids, polyketides, and flavonoids. In this study, we report the use of a new metabolic pathway to increase the malonyl-CoA concentration as a limiting metabolite in E. coli. For this purpose, the malonate/sodium symporter from Malonomonas rubra, and malonyl-CoA synthetase (MCS) from Bradyrhizobium japonicum were co-expressed in E. coli. This new pathway allows the cell to actively import malonate from the culture medium and to convert malonate and CoA to malonyl-CoA via an ATP-dependent ligation reaction. HPLC analysis confirmed elevated levels of malonyl-CoA and (2S)-naringenin as a malonyl-CoA-dependent metabolite, in E. coli. A 6.8-fold and more than 3.5-fold increase in (2S)-naringenin production were achieved in the engineered host in comparison with non-engineered E. coli and previously reported passive transport MatBMatC pathway, respectively. This observation suggests that using active transporters of malonate not only improves malonyl-CoA-dependent production but also makes it possible to harness low concentrations of malonate in culture media.

Directed evolution of tripartite ATP-independent periplasmic transporter for 3-Hydroxypropionate biosynthesis.

Our previous study's introduction of the malonic acid assimilation pathway into Escherichia coli enabled biosynthesis of 3-Hydroxypropionate (3-HP) from malonate. However, the relatively low uptake activity of tripartite ATP-independent periplasmic (TRAP) malonic acid transporter (MatPQM) is considered rate-limiting in malonate utilization. Here, to improve the transport performance of this importer, MatP variants were obtained via directed evolution and a novel developed enzyme-inhibition-based high throughput screening approach. This plate chromogenic screening method is based on the fact that malonic acid inhibits both of succinate dehydrogenase activity and further the capability of the reduction of methylene-blue to methylene-white. The best mutant E103G/S194G/Y218H/L235P/N272S showed twofold increased transport efficiency compared to the wild-type. ITC assay and structural analysis revealed that increased binding affinity of the mutant to the ligand was the reason for improved uptake activity of MatPQM. Finally, the engineered strain harboring the evolved mutant produced 20.08 g/L 3-HP with the yield of 0.87 mol/mol malonate in a bioreactor. Therefore, the well-established directed evolution strategy can be regarded as the reference work for other TRAP-type transporters engineering. And, this transporter mutant with enhanced malonic acid uptake activity has broad applications in the microbial biosynthesis of malonyl-CoA-derived valuable compounds in bacteria. KEY POINTS: • We reported directed evolution of a TRAP-type malonic acid transporter. • We found the enhanced malonate uptake activity of mutant lies in improved affinity. • We enhanced 3-HP bioproduction with high yield by employing the best mutant.

Systematic analysis of lysine malonylation in Streptococcus mutans.

Protein lysine malonylation (Kmal) is a novel post-translational modification (PTM) that regulates various biological pathways such as energy metabolism and translation. Malonylation in prokaryotes, however, is still poorly understood. In this study, we performed a global Kmal analysis of the cariogenic organism Streptococcus mutans by combining antibody-based affinity enrichment and high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis. Altogether, 392 malonyllysine sites in 159 proteins were identified. Subsequent bioinformatic analysis revealed that Kmal occurs in proteins involved in various metabolic pathways including translation machinery, energy metabolism, RNA degradation, and biosynthesis of various secondary metabolites. Quantitative analysis demonstrated that Kmal substrates were globally altered in the biofilm growth state compared to the planktonic growth state. Furthermore, a comparative analysis of the lysine malonylome of our study with previously determined lysine acetylome in S. mutans revealed that a small proportion of Kmal sites overlapped with acetylated sites, whereby suggesting that these two acylations have distinct functional implications. These results expand our knowledge of Kmal in prokaryotes, providing a resource for researching metabolic regulation of bacterial virulence and physiological functions by PTM.

Proteome-wide analyses reveal diverse functions of protein acetylation and succinylation modifications in fast growing stolons of bermudagrass (Cynodon dactylon L.).

BACKGROUND: Bermudagrass (Cynodon dactylon L.) is an important warm-season turfgrass species with well-developed stolons, which lay the foundation for the fast propagation of bermudagrass plants through asexual clonal growth. However, the growth and development of bermudagrass stolons are still poorly understood at the molecular level. RESULTS: In this study, we comprehensively analyzed the acetylation and succinylation modifications of proteins in fast-growing stolons of the bermudagrass cultivar Yangjiang. A total of 4657 lysine acetylation sites on 1914 proteins and 226 lysine succinylation sites on 128 proteins were successfully identified using liquid chromatography coupled to tandem mass spectrometry, respectively. Furthermore, 78 proteins and 81 lysine sites were found to be both acetylated and succinylated. Functional enrichment analysis revealed that acetylated proteins regulate diverse reactions of carbohydrate metabolism and protein turnover, whereas succinylated proteins mainly regulate the citrate cycle. These results partly explained the different growth disturbances of bermudagrass stolons under treatment with sodium butyrate and sodium malonate, which interfere with protein acetylation and succinylation, respectively. Moreover, 140 acetylated proteins and 42 succinylated proteins were further characterized having similarly modified orthologs in other grass species. Site-specific mutations combined with enzymatic activity assays indicated that the conserved acetylation of catalase and succinylation of malate dehydrogenase both inhibited their activities, further implying important regulatory roles of the two modifications. CONCLUSION: In summary, our study implied that lysine acetylation and succinylation of proteins possibly play important regulatory roles in the fast growth of bermudagrass stolons. The results not only provide new insights into clonal growth of bermudagrass but also offer a rich resource for functional analyses of protein lysine acetylation and succinylation in plants.

Regiodivergent Palladium-Catalyzed Alkene Difunctionalization Reactions for the Construction of Methylene Cyclobutanes and Methylene Cyclopentanes.

Regiodivergent palladium-catalyzed alkene difunctionalization reactions between diethyl malonate and 1,5-dienes bearing a triflate group at C2 are described. Use of tris(2,4-di-tert-butylphenyl)phosphite as a ligand leads to 4-exo-cyclization/functionalization to afford malonate-substituted methylene cyclobutanes. In contrast, the 1,2-bis(diphenylphosphino)benzene ligand provides methylene cyclopentanes via 5-endo-cyclization/functionalization. The five-membered ring-forming reactions occur via anti-carbopalladation of the enolate nucleophile, whereas four-membered ring-forming reactions proceed through syn-4-exo-migratory insertion of the tethered alkene, followed by C(sp3)-C(sp3) bond-forming reductive elimination from an (alkyl)Pd(II)(malonate) complex.