Nucleotide Turnover Research Articles

Integration of bioinformatics and machine learning approaches for the validation of pyrimidine metabolism-related genes and their implications in immunotherapy for osteoporosis

BackgroundOsteoporosis (OP), the “silent epidemic” of our century, poses a significant challenge to public health, predominantly affecting postmenopausal women and the elderly. It evolves from mild symptoms to pronounced severity, stabilizing eventually. Unique among OP’s characteristics is the altered metabolic profile of affected cells, particularly in pyrimidine metabolism (PyM), a crucial pathway for nucleotide turnover and pyrimidine decomposition. While metabolic adaptation is acknowledged as a therapeutic target in various diseases, the specific role of PyM genes (PyMGs) in OP’s molecular response remains to be clarified.MethodsIn pursuit of elucidating and authenticating PyMGs relevant to OP, we embarked on a comprehensive bioinformatics exploration. This entailed the integration of Weighted Gene Co-expression Network Analysis (WGCNA) with a curated list of 37 candidate PyMGs, followed by the examination of their biological functions and pathways via Gene Set Variation Analysis (GSVA). The Least Absolute Shrinkage and Selection Operator (LASSO) technique was harnessed to identify crucial hub genes. We evaluated the diagnostic prowess of five PyMGs in OP detection and explored their correlation with OP’s clinical traits, further validating their expression profiles through independent datasets (GSE2208, GSE7158, GSE56815, and GSE35956).ResultsOur analytical rigor unveiled five PyMGs—IGKC, TMEM187, RPS11, IGLL3P, and GOLGA8N—with significant ties to OP. A deeper dive into their biological functions highlighted their roles in estrogen response modulation, cytosolic calcium ion concentration regulation, and GABAergic synaptic transmission. Remarkably, these PyMGs emerged as potent diagnostic biomarkers for OP, distinguishing affected individuals with substantial accuracy.ConclusionsThis investigation brings to light five PyMGs intricately associated with OP, heralding new avenues for biomarker discovery and providing insights into its pathophysiological underpinnings. These findings not only deepen our comprehension of OP’s complexity but also herald the advent of more refined diagnostic and therapeutic modalities.

Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly.

Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in guanosine triphosphate (GTP) synthesis and assembles into filaments in cells, which desensitizes the enzyme to feedback inhibition and boosts nucleotide production. The vertebrate retina expresses two splice variants IMPDH1(546) and IMPDH1(595). In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of S477 phosphorylation. The S477D mutation resensitized both variants to GTP inhibition but only blocked assembly of IMPDH1(595) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of a high-activity assembly interface, still allowing assembly of low-activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, S477 phosphorylation acts as a mechanism for downregulating retinal GTP synthesis in the dark when nucleotide turnover is decreased.

Apicomplexan phosphodiesterases in cyclic nucleotide turnover: conservation, function, and therapeutic potential.

Apicomplexa encompasses a large number of intracellular parasites infecting a wide range of animals. Cyclic nucleotide signaling is crucial for a variety of apicomplexan life stages and cellular processes. The cyclases and kinases that synthesize and respond to cyclic nucleotides (i.e., 3',5'-cyclic guanosine monophosphate and 3',5'-cyclic adenosine monophosphate) are highly conserved and essential throughout the parasite phylum. Growing evidence indicates that phosphodiesterases (PDEs) are also critical for regulating cyclic nucleotide signaling via cyclic nucleotide hydrolysis. Here, we discuss recent advances in apicomplexan PDE biology and opportunities for therapeutic interventions, with special emphasis on the major human apicomplexan parasite genera Plasmodium, Toxoplasma, Cryptosporidium, and Babesia. In particular, we show a highly flexible repertoire of apicomplexan PDEs associated with a wide range of cellular requirements across parasites and lifecycle stages. Despite this phylogenetic diversity, cellular requirements of apicomplexan PDEs for motility, host cell egress, or invasion are conserved. However, the molecular wiring of associated PDEs is extremely malleable suggesting that PDE diversity and redundancy are key for the optimization of cyclic nucleotide turnover to respond to the various environments encountered by each parasite and life stage. Understanding how apicomplexan PDEs are regulated and integrating multiple signaling systems into a unified response represent an untapped avenue for future exploration.

Abstract EC.03: Distinct Molecular Signatures Of HCM- And DCM-causing Mutations At The Same Residue In The Transducer Of Cardiac Myosin

Mutations in cardiac myosin cause both hypertrophic (HCM) and dilated cardiomyopathy (DCM), and the clinical phenotype ultimately depends on the precise effect of the mutation on the function of myosin. Using recombinant human cardiac myosin, we studied the molecular effects of a novel Q222H mutation in MYH7 found in a patient with severe, early-onset DCM, and compared the effects to the Q222K mutation that was previously reported to cause HCM. The Q222 residue is located within the transducer of the head domain near the ATP binding pocket. The Q222H (DCM) mutant myosin exhibited significantly reduced steady-state actin-activated ATPase activity and a decreased rate of ATP binding in transient kinetic studies, while Q222K (HCM) mutant protein showed an increase in ATPase activity and ATP binding kinetics. In vitro motility assays showed 43% reduction and 32% increase in actin gliding velocity in Q222H and Q222K mutations, respectively. Finally, single nucleotide turnover assays revealed that the fraction of myosin with a slow ATP hydrolysis rate (super relaxed state, or SRX) thought to represent myosin in an autoinhibited state was significantly reduced in Q222K and increased in Q222H. Taken together, the Q222H/K mutations exerted contrasting effects on the motor properties of the cardiac myosin catalytic domain. Cellular characterization and molecular dynamic simulations of cardiac myosin to assess the structural impact of mutant residues are underway. These results highlight how subtle structural differences between cardiomyopathy-causing mutations can lead to significant differences in cardiac myosin motor activity and thus phenotypic expression of cardiomyopathy.

Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism

Phospholipase D3 (PLD3) polymorphisms are linked to late-onset Alzheimer’s disease (LOAD). Being a lysosomal 5’-3’ exonuclease, its neuronal substrates remained unknown as well as how a defective lysosomal nucleotide catabolism connects to AD-proteinopathy. We identified mitochondrial DNA (mtDNA) as a major physiological substrate and show its manifest build-up in lysosomes of PLD3-defective cells. mtDNA accretion creates a degradative (proteolytic) bottleneck that presents at the ultrastructural level as a marked abundance of multilamellar bodies, often containing mitochondrial remnants, which correlates with increased PINK1-dependent mitophagy. Lysosomal leakage of mtDNA to the cytosol activates cGAS–STING signaling that upregulates autophagy and induces amyloid precursor C-terminal fragment (APP-CTF) and cholesterol accumulation. STING inhibition largely normalizes APP-CTF levels, whereas an APP knockout in PLD3-deficient backgrounds lowers STING activation and normalizes cholesterol biosynthesis. Collectively, we demonstrate molecular cross-talks through feedforward loops between lysosomal nucleotide turnover, cGAS-STING and APP metabolism that, when dysregulated, result in neuronal endolysosomal demise as observed in LOAD.

Inferring mammalian tissue-specific regulatory conservation by predicting tissue-specific differences in open chromatin

BackgroundEvolutionary conservation is an invaluable tool for inferring functional significance in the genome, including regions that are crucial across many species and those that have undergone convergent evolution. Computational methods to test for sequence conservation are dominated by algorithms that examine the ability of one or more nucleotides to align across large evolutionary distances. While these nucleotide alignment-based approaches have proven powerful for protein-coding genes and some non-coding elements, they fail to capture conservation of many enhancers, distal regulatory elements that control spatial and temporal patterns of gene expression. The function of enhancers is governed by a complex, often tissue- and cell type-specific code that links combinations of transcription factor binding sites and other regulation-related sequence patterns to regulatory activity. Thus, function of orthologous enhancer regions can be conserved across large evolutionary distances, even when nucleotide turnover is high.ResultsWe present a new machine learning-based approach for evaluating enhancer conservation that leverages the combinatorial sequence code of enhancer activity rather than relying on the alignment of individual nucleotides. We first train a convolutional neural network model that can predict tissue-specific open chromatin, a proxy for enhancer activity, across mammals. Next, we apply that model to distinguish instances where the genome sequence would predict conserved function versus a loss of regulatory activity in that tissue. We present criteria for systematically evaluating model performance for this task and use them to demonstrate that our models accurately predict tissue-specific conservation and divergence in open chromatin between primate and rodent species, vastly out-performing leading nucleotide alignment-based approaches. We then apply our models to predict open chromatin at orthologs of brain and liver open chromatin regions across hundreds of mammals and find that brain enhancers associated with neuron activity have a stronger tendency than the general population to have predicted lineage-specific open chromatin.ConclusionThe framework presented here provides a mechanism to annotate tissue-specific regulatory function across hundreds of genomes and to study enhancer evolution using predicted regulatory differences rather than nucleotide-level conservation measurements.

Effects of hypercapnia / ischemia and dissection on the rat brain metabolome

It is known that brain energy metabolites such as ATP are quickly depleted during postmortem ischemia; however, a comprehensive assessment on the effects of preceding hypercapnia/ischemia and the dissection process on the larger brain metabolome remains lacking. This study sought to address this unknown by measuring aqueous metabolites impacted by hypercapnia/ischemia and brain dissection using Nuclear Magnetic Resonance. Metabolites were measured in rats subjected to 1) high energy head-focused microwave irradiation (control group); 2) CO2–induced hypercapnia/ischemia followed by immediate microwave irradiation; 3) CO2 followed by decapitation and then microwave irradiation ∼6.4 min later, to simulate a postmortem interval equivalent to typical dissection times; and 4) CO2–induced hypercapnia/ischemia followed by dissection within ∼6 min (no microwave fixation) to test the effects of brain dissection on the metabolome. Compared to control rats subjected to head-focused microwave irradiation, concentrations of high-energy phosphate metabolites and glucose were significantly reduced, while β-hydroxybutyrate and lactate were increased in rats subjected to all other treatments. Several amino acids and neurotransmitters (GABA) increased by hypercapnia/ischemia and dissection. Sugar donors involved in glycosylation decreased and nucleotides decreased or increased following hypercapnia/ischemia and dissection. sn-Glycero-3-phosphocholine decreased and its choline byproduct increased in all groups relative to controls, indicating postmortem changes in lipid turnover. Antioxidants increased following hypercapnia/ischemia but decreased to control levels following dissection. This study demonstrates substantial post-mortem changes in brain energy and glycosylation pathways, as well as protein, nucleotide, neurotransmitter, lipid, and antioxidant turnover due to hypercapnia/ischemia and dissection. Changes in phosphate donors, glycosylation and amino acids reflect post-translational modification and protein degradation processes that persist post-mortem. Microwave irradiation is necessary for accurately capturing in vivo brain metabolite concentrations.

Markov State Models and Molecular Dynamics Simulations Provide Understanding of the Nucleotide-Dependent Dimerization-Based Activation of LRRK2 ROC Domain.

Mutations in leucine-rich repeat kinase 2 (LRRK2) are recognized as the most frequent cause of Parkinson’s disease (PD). As a multidomain ROCO protein, LRRK2 is characterized by the presence of both a Ras-of-complex (ROC) GTPase domain and a kinase domain connected through the C-terminal of an ROC domain (COR). The bienzymatic ROC–COR–kinase catalytic triad indicated the potential role of GTPase domain in regulating kinase activity. However, as a functional GTPase, the detailed intrinsic regulation of the ROC activation cycle remains poorly understood. Here, combining extensive molecular dynamics simulations and Markov state models, we disclosed the dynamic structural rearrangement of ROC’s homodimer during nucleotide turnover. Our study revealed the coupling between dimerization extent and nucleotide-binding state, indicating a nucleotide-dependent dimerization-based activation scheme adopted by ROC GTPase. Furthermore, inspired by the well-known R1441C/G/H PD-relevant mutations within the ROC domain, we illuminated the potential allosteric molecular mechanism for its pathogenetic effects through enabling faster interconversion between inactive and active states, thus trapping ROC in a prolonged activated state, while the implicated allostery could provide further guidance for identification of regulatory allosteric pockets on the ROC complex. Our investigations illuminated the thermodynamics and kinetics of ROC homodimer during nucleotide-dependent activation for the first time and provided guidance for further exploiting ROC as therapeutic targets for controlling LRRK2 functionality in PD treatment.

How can the commercial potential of microalgae from the Dunaliella genus be improved? The importance of nucleotide metabolism with a focus on nucleoside diphosphate kinase (NDPK)

Over recent decades, wide-ranging research has been focused on algae due to their potential applications, e.g., for biomass, extract and “third”-generation biofuel production. In particular, microalgae, which are very fast-growing organisms with low nutrient requirements, are ideal research objects. This review focuses on one of the most significant microalgae genus, i.e., Dunaliella, which includes D. salina and D. tertiolecta. The valuable components of these unicellular eukaryotes include glycerol, carotenoids (such as zeaxanthin and β-carotene) and many others, which mainly accumulate when these microalgae are affected by stress conditions (i.e., hypersaline and oxidative stress). The rapid growth of these microalgae in artificial/natural systems certainly has to be based not only on nutrient uptake and photosynthesis rates but also on efficient nucleotide metabolism. Nucleoside diphosphate kinases (NDPKs), which are considered conserved housekeeping proteins responsible for nucleotide turnover, could play an important role in this context, together with proper mitochondrial and chloroplast function. A more detailed understanding of the biochemical nature of Dunaliella spp. will help optimize the massive cultivation of these microorganisms. Ultimately, it will facilitate the greater use of coastal waters to multiply Dunaliella biomass production significantly. This strategy will save freshwater resources, e.g., in obtaining land plant oils to make biofuels. Greater access to different algal bioactive compounds may support the treatment of various diseases, such as asthma, eye diseases, cancer, and viral infections.

Urate Transporters in the Kidney: What Clinicians Need to Know.

Urate is produced in the liver by the degradation of purines from the diet and nucleotide turnover and excreted by the kidney and gut. The kidney is the major route of urate removal and has a pivotal role in the regulation of urate homeostasis. Approximately 10% of the glomerular filtered urate is excreted in the urine, and the remainder is reabsorbed by the proximal tubule. However, the transport of urate in the proximal tubule is bidirectional: reabsorption and secretion. Thus, an increase in reabsorption or a decrease in secretion may induce hyperuricemia. In contrast, a decrease in reabsorption or an increase in secretion may result in hyperuricosuria. In the proximal tubule, urate reabsorption is mainly mediated by apical URAT1 (SLC22A12) and basolateral GLUT9 (SLC2A9) transporter. OAT4 (SLC22A11) also acts in urate reabsorption in the apical membrane, and its polymorphism is associated with the risk of hyperuricemia. Renal hypouricemia is caused by SLC22A12 or SLC2A9 loss-of-function mutations, and it may be complicated by exercise-induced acute kidney injury. URAT1 and GLUT9 are also drug targets for uricosuric agents. Sodium-glucose cotransporter inhibitors may induce hyperuricosuria by inhibiting GLUT9b located in the apical plasma membrane. Urate secretion is mediated by basolateral OAT1 (SLC22A6) and OAT3 (SLC22A8) and apical ATP-binding cassette super-family G member 2 (ABCG2), NPT1 (SLC17A1), and NPT4 (SLC17A3) transporter in the proximal tubule. NPT1 and NPT4 may be key players in renal urate secretion in humans, and deletion of SLC22A6 and SLC22A8 in mice leads to decreased urate excretion. Dysfunctional variants of ABCG2 inhibit urate secretion from the gut and kidney and may cause gout. In summary, the net result of urate transport in the proximal tubule is determined by the dominance of transporters between reabsorption (URAT1, OAT4, and GLUT9) and secretion (ABCG2, NPT1, NPT4, OAT1, and OAT3).

Abstract 226: Pathways of nucleotide synthesis in NSCLC

Abstract Tracer-based mapping of metabolic networks is a powerful approach for revealing metabolic reprogramming in human cancer. Nucleotide synthesis and turnover is critical for cell proliferation and is tightly regulated [1,2]. We have developed NMR and tandem MS methods for determining the active pathways of the synthesis of free nucleotides and nucleotide sugars including UDP-Glucose and UDPGlcNAc using multiplexed stable isotope resolved metabolomics (mSIRM)[3] in a variety of models including freshly resected lung tumor tissue, mouse PDX and organoids. Using multiple isotopic labels (13C, 2H and 15N) we determined the relative contributions to purine and pyrimidine nucleotide synthesis of both exogenous glucose, glutamine, serine and glycine and metabolically-derived intracellular precursors. We have used these approaches to compare the relative importance of different metabolic pathways in NSCLC under various conditions to assess the role of the tumor microenvironment, and how these pathways are impacted by arsenite and selenite. Our findings indicate that the substrates for de novo nucleotide synthesis may differ profoundly between cancer cell lines and fresh human lung cancer tissues; for purines, the latter preferred glucose to exogenous serine or glycine but not the former. Pyrimidine nucleotides also utilize glucose for ribose synthesis via the pentose phosphate pathway, but both glucose and glutamine for the pyrimidine rings depending on the conditions and cell type. This distinction in substrate utilization in nucleotide synthesis in human cancer tissues should be considered when targeting one-carbon metabolism for cancer therapy. Acknowledgements: This work was supported in part by grants: 1R01ES022191-01 (to TWMF and RMH), 1P01CA163223-01A1 (to ANL and TWMF), and 1U24DK097215-01A1 (to RMH, TWMF, and ANL).

Deletion of the N-Terminus of Myosin Essential Light Chain (N-ELC) in the Background of HCM-A57G Mutation in Double Mutant Mice Rescues Hypercontractile Myosin Phenotype

Cardiac pathologic remodeling including fibrosis, diastolic dysfunction and increased Ca2+ sensitivity of force has been observed in mice expressing the A57G mutation in myosin ventricular ELC (MYL3 gene) with clinical phenotype of hypertrophic cardiomyopathy (HCM). Our previous investigation showed that the lack of the unique 43 amino acid-long N-terminus ELC (N-ELC) in >7-month-old Δ43 mice results in non-pathological cardiac hypertrophy. Papillary muscles (PM) from ∼8 mo-old Δ43 hearts were subjected to mantATP-chase assay and compared to those from age-matched WT-ELC and A57G mice. The data showed that Δ43 fibers favor the super-relaxed (SRX) state of myosin with increased population of slowly cycling heads compared to PM from age-matched WT-ELC mice. The opposite was true for A57G mice whose PM demonstrated a pathologic hypercontractile behavior with significantly inhibited SRX. We then tested the effect of N-ELC deletion in A57G mice on the SRX in offspring resulting from breeding Δ43 with A57G mice (Δ43xA57G) and expressing 0-22% of Δ43 and 0-84% of A57G. Single nucleotide turnover assays on PM from all Δ43xA57G animals showed stabilization of the SRX state that was reminiscent of Δ43 alone, and different from all other groups of mice. Interestingly, echocardiographic evaluation of ∼8-month-old Δ43xA57G mice revealed a decrease in cardiac hypertrophy (decrease in LV mass) compared to A57G and Δ43 animals. Myocardial performance index was also improved in Δ43xA57G crosses compared to HCM-A57G mice, and not different compared to WT or Δ43 mice. Our studies suggest that the deletion of N-ELC in the background of HCM-ELC mutation may be beneficial in reversing some of the pathological myosin motor phenotypes associated with HCM. Supported by NIH R01HL123255 and R56HL146133 (DSC).

A complex suite of loci and elements in eukaryotic type II topoisomerases determine selective sensitivity to distinct poisoning agents.

Type II topoisomerases catalyze essential DNA transactions and are proven drug targets. Drug discrimination by prokaryotic and eukaryotic topoisomerases is vital to therapeutic utility, but is poorly understood. We developed a next-generation sequencing (NGS) approach to identify drug-resistance mutations in eukaryotic topoisomerases. We show that alterations conferring resistance to poisons of human and yeast topoisomerase II derive from a rich mutational ‘landscape’ of amino acid substitutions broadly distributed throughout the entire enzyme. Both general and discriminatory drug-resistant behaviors are found to arise from different point mutations found at the same amino acid position and to occur far outside known drug-binding sites. Studies of selected resistant enzymes confirm the NGS data and further show that the anti-cancer quinolone vosaroxin acts solely as an intercalating poison, and that the antibacterial ciprofloxacin can poison yeast topoisomerase II. The innate drug-sensitivity of the DNA binding and cleavage region of human and yeast topoisomerases (particularly hTOP2β) is additionally revealed to be significantly regulated by the enzymes’ adenosine triphosphatase regions. Collectively, these studies highlight the utility of using NGS-based methods to rapidly map drug resistance landscapes and reveal that the nucleotide turnover elements of type II topoisomerases impact drug specificity.

The negative and detrimental effects of high fructose on the liver, with special reference to metabolic disorders.

The increased consumption of fructose in the average diet through sweeteners such as high-fructose corn syrup (HFCS) and sucrose has resulted in negative outcomes in society through producing a considerable economic and medical burden on our healthcare system. Ingestion of fructose chronically has contributed to multiple health consequences, such as insulin resistance, obesity, liver disorders, and diabetes. Fructose metabolism starts with fructose phosphorylation by fructose kinase in the liver, and this process is not feedback regulated. Therefore, ingestion of high fructose can deplete ATP, increase uric acid production, and increase nucleotide turnover. This review focuses the discussion on the hepatic manifestations of high fructose-implicated liver metabolic disorders such as insulin resistance, obesity due to enhanced lipogenesis, non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and type 2 diabetes. The detrimental effects of high fructose on the liver, contributed potentially by microbiome and leptin, were also discussed. The authors believe that, together with diet management, further studies focusing on disrupting or blocking fructose metabolism in the liver may help with designing novel strategies for prevention and treatment of fructose-induced chronic liver metabolic diseases.

Parts list for a microtubule depolymerising kinesin.

The Kinesin superfamily is a large group of molecular motors that use the turnover of ATP to regulate their interaction with the microtubule cytoskeleton. The coupled relationship between nucleotide turnover and microtubule binding is harnessed in various ways by these motors allowing them to carry out a variety of cellular functions. The Kinesin-13 family is a group of specialist microtubule depolymerising motors. Members of this family use their microtubule destabilising activity to regulate processes such as chromosome segregation, maintenance of cilia and neuronal development. Here, we describe the current understanding of the structure of this family of kinesins and the role different parts of these proteins play in their microtubule depolymerisation activity and in the wider function of this family of kinesins.

Exploring a potential allosteric inhibition mechanism in the motor domain of human Eg-5

Kinesin-5 (Eg-5), microtubule motor protein, is one of the emerging drug targets in cancer research. Several inhibitors have been reported to bind the hEg-5 “motor domain” in two different locations that are potentially allosteric. Interestingly, the crystal structure of Eg-5 bound to benzimidazole unveils two chemically different allosteric pockets (PDB ID: 3ZCW). The allosteric modulators inhibit Eg-5 activity by causing conformational changes that affect nucleotide turnover rate. In the present work, three allosteric inhibitors were simulated along with the substrate nucleotides (ADP and ATP) to capture conformation changes induced by the allosteric inhibitors. To analyze the allosteric inhibition mechanism, we used dynamics cross-correlation, principal component analysis (PCA), and enthalpic calculations. The loop L5 interaction is determined by the type of substrate bind at the nucleotide binding site. The SW-II flexibility increased upon dual allosteric inhibition by SB-743921 and 6a. The ionic interaction between R221-E116 is observed only in the presence of two allosteric inhibitors. Also, we noticed that the α2/α3 helical orientation is responsible for the SW-1 loop position and substrate binding. Our simulation data suggest the critical chemical features required to block the motor domain by the allosteric inhibitors. The results summarized in this work will help the researchers to design better therapeutic agents targeting hEg-5.Communicated by Ramaswamy H. Sarma

7-Methylguanosine monophosphate analogues with 5′-(1,2,3-triazoyl) moiety: Synthesis and evaluation as the inhibitors of cNIIIB nucleotidase

The hydrolysis of nucleoside 5′-monophosphates to the corresponding nucleosides and inorganic phosphate is catalysed by 5′-nucleotidases, thereby contributing to the control of endogenous nucleotide turnover and affecting the fate of exogenously delivered nucleotide- and nucleoside-derived therapeutics in cells. A recently identified nucleotidase cNIIIB shows preference towards 7-methylguanosine monophosphate (m7GMP) as a substrate, which suggests its potential involvement in mRNA degradation. However, the extent of biological functions and the significance of cNIIIB remains to be elucidated. Here, we synthesised a series of m7GMP analogues carrying a 1,2,3-triazole moiety at the 5′ position as the potential inhibitors of human cNIIIB. The compounds were synthesised by using the copper-catalysed azide-alkyne cycloaddition (CuAAC) between 5′-azido-5′-deoxy-7-methylguanosine and different phosphate or phosphonate derivatives carrying terminal alkyne. The analogues were evaluated as cNIIIB inhibitors using HPLC and malachite green assays, demonstrating that compound 1a, carrying a 1,2,3-triazoylphosphonate moiety, inhibits cNIIIB activity at micromolar concentrations (IC50 87.8 ± 7.5 µM), while other analogues showed no activity. In addition, compound 1d was identified as an artifical substrate for HscNIIIB. Further characterization of inhibitor 1a revealed that it is poorly recognised by other m7G-binding proteins, eIF4E and DcpS, indicating its selectivity towards cNIIIB. The first inhibitor (1a) and unnatural substrate (1d) of cNIIIB, identified here, can be used as molecular probes for the elucidation of biological roles of cNIIIB, including the verification of its proposed function in mRNA metabolism.

Mechanisms of subzero growth in the cryophile Planococcus halocryophilus determined through proteomic analysis.

The eurypsychrophilic bacterium Planococcus halocryophilus is capable of growth down to -15°C, making it ideal for studying adaptations to subzero growth. To increase our understanding of the mechanisms and pathways important for subzero growth, we performed proteomics on P. halocryophilus grown at 23°C, 23°C with 12% w/v NaCl and -10°C with 12% w/v NaCl. Many proteins with increased abundances at -10°C versus 23°C also increased at 23C-salt versus 23°C, indicating a closely tied relationship between salt and cold stress adaptation. Processes which displayed the largest changes in protein abundance were peptidoglycan and fatty acid (FA) synthesis, translation processes, methylglyoxal metabolism, DNA repair and recombination, and protein and nucleotide turnover. We identified intriguing targets for further research at -10°C, including PlsX and KASII (FA metabolism), DD-transpeptidase and MurB (peptidoglycan synthesis), glyoxalase family proteins (reactive electrophile response) and ribosome modifying enzymes (translation turnover). PemK/MazF may have a crucial role in translational reprogramming under cold conditions. At -10°C P. halocryophilus induces stress responses, uses resources efficiently, and carefully controls its growth and metabolism to maximize subzero survival. The present study identifies several mechanisms involved in subzero growth and enhances our understanding of cold adaptation.

Associations of cord blood metabolites with perinatal characteristics, newborn anthropometry, and cord blood hormones in project viva

ContextMetabolomics has emerged as a powerful tool to characterize biomarkers and elucidate physiological processes underlying adverse health outcomes. Little is known of these relationships during gestation and infancy, which are critical period for development of metabolic disease risk. ObjectivesTo identify cord blood metabolite patterns associated with birth size; and to investigate relations of the birth size-associated metabolite patterns, and a branched chain amino acid (BCAA) metabolite pattern with a range of newborn and perinatal characteristics. MethodsUsing untargeted mass-spectrometry, we quantified metabolites in cord blood of 126 mother-child pairs. After excluding 103 xenobiotics, we used principal components analysis (PCA) to consolidate the remaining 606 metabolites into principal components (“factors”). Next, we identified factors associated with gestational age-and sex-standardized birthweight z-score (BW/GA) and examined associations of the BW/GA-associated pattern(s) and the BCAA pattern with cord blood insulin, leptin, adiponectin, insulin-like growth factor (IGF)-1, IGF-2, and IGF binding protein 3 (IGFBP-3) using multivariable linear regression. Finally, we examined associations of maternal/perinatal characteristics with the cord blood metabolite patterns. ResultsMean BW/GA z-score was 0.27±0.98 units. About half of the infants were male (52.4%) and white (57.1%). Of the 6 factors identified from PCA, one was associated with higher BW/GA: Factor 5, which comprised metabolites involved in energy production (malate, succinate, fumarate) and nucleotide turnover (inosine 5-monophosphate, adenosine 5-monophosphate, cytidine 5-monophosphate) pathways. In multivariable analysis, Factor 5 was related to higher cord blood leptin (1.64 [95% CI: 0.42, 2.87] ng/mL) and IGF-1 even after adjusting for IGFBP-3 (3.35 [0.25, 6.44] ng/mL). The BCAA pattern was associated with higher BW/GA (0.20 [0.03, 0.36] z-scores) and IGFBP-3 (106.5 [44.7, 168.2] ng/mL). No maternal characteristics were associated with either metabolite pattern; however, infants born via Cesarean delivery exhibited a higher score for Factor 5, and gestation length was inversely associated with the BCAA pattern. ConclusionsMetabolites in energy production and DNA/RNA turnover pathways in cord blood are associated with larger size at birth, and higher leptin and IGF-1. Similarly, the BCAA pattern was associated with larger birth size and IGFBP-3.

Allosteric Coupling of Nucleotide Turnover to Bimolecular Recognition in Kinesin Motors and G Protein Switches

Kinesin motors and homologous G proteins switches coordinate a wide array of important subcellular processes, from division and growth to intracellular communication and self-organization. These functionally diverse families contain a similar core structure supporting a common mode of nucleotide dependent allostery. However, a complete atomistic scale picture of key structural dynamic mechanisms and their adaptation to control distinct functional interactions remains elusive. Here we describe results from a comparative approach that couples bioinformatics, molecular simulation and experimental protein engineering across kinesin and G protein families. This includes the prediction and experimental engineering of allosterically decoupled constitutively active heterotrimeric G proteins. Prediction and experimental verification of allosterically enhanced and mechanochemically distinct kinesin-5. Computational and experimental dissection of kinesin-microtubule interactions along with the rational modulation of kinesin processive motility - the ability of an individual motor to take multiple steps along its microtubule filament. Collectively, this work furthers our understanding of the evolutionary adaptation of a ubiquitous allosteric motif and informs mechanistic studies on many related nucleotide triphosphatases that constitute nearly 5% of human protein coding genes.Software and other material related to this work can be found at:http://thegrantlab.org/.