New Perspectives on Delocalization Pathways in Aromatic Molecular Chameleons.

This study comprehensively analyzes the magnetically induced current density of polycyclic compounds labeled as "aromatic chameleons" since they can arrange their π-electrons to exhibit aromaticity in both the ground and the lowest triplet state. These compounds comprise benzenoid moieties fused to a central skeleton with 4n π-electrons and traditional magnetic descriptors are biased due to the superposition of local magnetic responses. In the S0 state, our analysis reveals that the molecular constituent fragments preserve their (anti)aromatic features in agreement with two types of resonant structures: one associated with aromatic benzenoids and the other with a central antiaromatic ring. Regarding the T1 state, a global and diatropic ring current is revealed. Our aromaticity study is complemented with advanced electronic and geometric descriptors to consider different aspects of aromaticity, particularly important in the evaluation of excited state aromaticity. Remarkably, these descriptors consistently align with the general features on the main delocalization pathways in polycyclic hydrocarbons consisting of fused 4n π-electron rings. Moreover, our study demonstrates an inverse correlation between the singlet-triplet energy difference and the antiaromatic character of the central ring in S0.

Whole-Genome Duplication and Yeast's Fruitful Way of Life.

Studies on the fate of Saccharomyces cerevisiae paralogous gene pairs that arose through a whole-genome duplication event have shown diversification of retained duplicated genes. Paralogous functional specialization often results in improved function and/or novel function that could contribute to the adaptation of the organism to a new lifestyle. Here, we analyze and discuss particular case studies of paralogous functional diversification that could have played a role in the acquisition of yeast fermentative metabolism.

Synthetic negative genome screen of the GPN-loop GTPase NPA3 in Saccharomyces cerevisiae.

The GPN-loop GTPase Npa3 is encoded by an essential gene in the yeast Saccharomyces cerevisiae. Npa3 plays a critical role in the assembly and nuclear accumulation of RNA polymerase II (RNAPII), a function that may explain its essentiality. Genetic interactions describe the extent to which a mutation in a particular gene affects a specific phenotype when co-occurring with an alteration in a second gene. Discovering synthetic negative genetic interactions has long been used as a tool to delineate the functional relatedness between pairs of genes participating in common or compensatory biological pathways. Previously, our group showed that nuclear targeting and transcriptional activity of RNAPII were unaffected in cells expressing exclusively a C-terminal truncated mutant version of Npa3 (npa3∆C) lacking the last 106 residues naturally absent from the single GPN protein in Archaea, but universally conserved in all Npa3 orthologs of eukaryotes. To gain insight into novel cellular functions for Npa3, we performed here a genome-wide Synthetic Genetic Array (SGA) study coupled to bulk fluorescence monitoring to identify negative genetic interactions of NPA3 by crossing an npa3∆C strain with a 4,389 nonessential gene-deletion collection. This genetic screen revealed previously unknown synthetic negative interactions between NPA3 and 15 genes. Our results revealed that the Npa3 C-terminal tail extension regulates the participation of this essential GTPase in previously unknown biological processes related to mitochondrial homeostasis and ribosome biogenesis.

Two alpha isopropylmalate synthase isozymes with similar kinetic properties are extant in the yeast Lachancea kluyveri.

The first committed step in the leucine biosynthetic pathway is catalyzed by α-isopropylmalate synthase (α-IPMS, EC 2.3.3.13), which in the Saccaromycotina subphylum of Ascomycete yeasts is frequently encoded by duplicated genes. Following a gene duplication event, the two copies may be preserved presumably because the encoded proteins diverge in either functional properties and/or cellular localization. The genome of the petite-negative budding yeast Lachancea kluyveri includes two SAKL0E10472 (LkLEU4) and SAKL0F05170 g (LkLEU4BIS) paralogous genes, which are homologous to other yeast α-IPMS sequences. Here, we investigate whether these paralogous genes encode functional α-IPMS isozymes and whether their functions have diverged. Molecular phylogeny suggested that the LkLeu4 isozyme is located in the mitochondria and LkLeu4BIS in the cytosol. Comparison of growth rates, leucine intracellular pools and mRNA levels, indicate that the LkLeu4 isozyme is the predominant α-IPMS enzyme during growth on glucose as carbon source. Determination of the kinetic parameters indicates that the isozymes have similar affinities for the substrates and for the feedback inhibitor leucine. Thus, the diversification of the physiological roles of the genes LkLEU4 and LkLEU4BIS involves preferential transcription of the LkLEU4 gene during growth on glucose and different subcellular localization, although ligand interactions have not diverged.

Dynamic Distribution of HIG2A between the Mitochondria and the Nucleus in Response to Hypoxia and Oxidative Stress.

Mitochondrial respiratory supercomplex formation requires HIG2A protein, which also has been associated with cell proliferation and cell survival under hypoxia. HIG2A protein localizes in mitochondria and nucleus. DNA methylation and mRNA expression of the HIGD2A gene show significant alterations in several cancers, suggesting a role for HIG2A in cancer biology. The present work aims to understand the dynamics of the HIG2A subcellular localization under cellular stress. We found that HIG2A protein levels increase under oxidative stress. H2O2 shifts HIG2A localization to the mitochondria, while rotenone shifts it to the nucleus. HIG2A protein colocalized at a higher level in the nucleus concerning the mitochondrial network under normoxia and hypoxia (2% O2). Hypoxia (2% O2) significantly increases HIG2A nuclear colocalization in C2C12 cells. In HEK293 cells, chemical hypoxia with CoCl2 (>1% O2) and FCCP mitochondrial uncoupling, the HIG2A protein decreased its nuclear localization and shifted to the mitochondria. This suggests that the HIG2A distribution pattern between the mitochondria and the nucleus depends on stress and cell type. HIG2A protein expression levels increase under cellular stresses such as hypoxia and oxidative stress. Its dynamic distribution between mitochondria and the nucleus in response to stress factors suggests a new communication system between the mitochondria and the nucleus.

The OXPHOS supercomplex assembly factor HIG2A responds to changes in energetic metabolism and cell cycle.

HIG2A promotes cell survival under hypoxia and mediates the assembly of complex III and complex IV into respiratory chain supercomplexes. In the present study, we show that human HIGD2A and mouse Higd2a gene expressions are regulated by hypoxia, glucose, and the cell cycle-related transcription factor E2F1. The latter was found to bind the promoter region of HIGD2A. Differential expression of the HIGD2A gene was found in C57BL/6 mice in relation to tissue and age. Besides, the silencing of HIGD2A evidenced the modulation of mitochondrial dynamics proteins namely, OPA1 as a fusion protein increases, while FIS1, a fission protein, decreases. Besides, the mitochondrial membrane potential (ΔΨm) increased. The protein HIG2A is localized in the mitochondria and nucleus. Moreover, we observed that the HIG2A protein interacts with OPA1. Changes in oxygen concentration, glucose availability, and cell cycle regulate HIGD2A expression. Alterations in HIGD2A expression are associated with changes in mitochondrial physiology.

Npa3/ScGpn1 carboxy-terminal tail is dispensable for cell viability and RNA polymerase II nuclear targeting but critical for microtubule stability and function.

Genetic deletion of the essential GTPase Gpn1 or replacement of the endogenous gene by partial loss of function mutants in yeast is associated with multiple cellular phenotypes, including in all cases a marked cytoplasmic retention of RNA polymerase II (RNAPII). Global inhibition of RNAPII-mediated transcription due to malfunction of Gpn1 precludes the identification and study of other cellular function(s) for this GTPase. In contrast to the single Gpn protein present in Archaea, eukaryotic Gpn1 possesses an extension of approximately 100 amino acids at the C-terminal end of the GTPase domain. To determine the importance of this C-terminal extension in Saccharomyces cerevisiae Gpn1, we generated yeast strains expressing either C-terminal truncated (gpn1ΔC) or full-length ScGpn1. We found that ScGpn1ΔC was retained in the cell nucleus, an event physiologically relevant as gpn1ΔC cells contained a higher nuclear fraction of the RNAPII CTD phosphatase Rtr1. gpn1ΔC cells displayed an increased size, a delay in mitosis exit, and an increased sensitivity to the microtubule polymerization inhibitor benomyl at the cell proliferation level and two cellular events that depend on microtubule function: RNAPII nuclear targeting and vacuole integrity. These phenotypes were not caused by inhibition of RNAPII, as in gpn1ΔC cells RNAPII nuclear targeting and transcriptional activity were unaffected. These data, combined with our description here of a genetic interaction between GPN1 and BIK1, a microtubule plus-end tracking protein with a mitotic function, strongly suggest that the ScGpn1 C-terminal tail plays a critical role in microtubule dynamics and mitotic progression in an RNAPII-independent manner.

A Fukui function-guided genetic algorithm. Assessment on structural prediction of Sin (n = 12-20) clusters.

Theoretical studies are essential for the structural characterization of clusters, when it comes to rationalize their unique size-dependent properties and composition. However, the rapid growth of local minima on the potential energy surface (PES), with respect to cluster size, makes the candidate identification a challenging undertaking. In this article, we introduce a hybrid strategy to explore the PES of clusters. This proposal involves the use of a biased initial population of a genetic algorithm procedure. Each individual in this population is built by assembling small fragments, according to the best matching of the Fukui function. The performance of a genetic algorithm procedure. The performance of the method is assessed on the PES exploration of medium-sized Sin clusters (n = 12-20). The most relevant results are: (a) the method converges at almost half of the time used by the canonical version of the GA and, (b) in all the studied cases, with the exception of Si13 and Si16 , the method allowed to identify the global minimum (GM) and other important low-lying structures. Additionally, the apparent deficiency of the proposal to identify the GM was corrected when a Si atom, or other low-lying isomers, were considered to build the clusters. © 2017 Wiley Periodicals, Inc.

Proposal of a simple and effective local reactivity descriptor through a topological analysis of an orbital-weighted fukui function.

The prediction of reactivity is one of the long-standing objectives of chemistry, contributing to enforce the link between theory and experiment. In particular, the regioselectivity of aromatic molecules has motivated the proposal of different reactivity descriptors based on foundational theories, like Frontier Molecular Orbital (FMO) theory and density functional theory, to predict and rationalize such regioselectivity. This article examines cases where reactivity descriptors, based on FMO theories, are known to have failed, specifically on electrophilic aromatic substitution reactions, through a simple but effective new reactivity model: the Orbital-weighted Fukui function ( fw-(r)) and its topological analysis. Interestingly, this descriptor proves to be effective in adequately predicting regioselectivities where other approximations failed. © 2017 Wiley Periodicals, Inc.

Three, two, one yeast fatty acid desaturases: regulation and function.

Fatty acid composition of biological membranes functionally adapts to environmental conditions by changing its composition through the activity of lipid biosynthetic enzymes, including the fatty acid desaturases. Three major desaturases are present in yeasts, responsible for the generation of double bonds in position C9-C10, C12-C13 and C15-C16 of the carbon backbone. In this review, we will report data addressed to define the functional role of basidiomycete and ascomycete yeast desaturase enzymes in response to various external signals and the regulation of the expression of their corresponding genes. Many yeast species have the complete set of three desaturases; however, only the Δ9 desaturase seems to be necessary and sufficient to ensure yeast viability. The evolutionary issue of this observation will be discussed.

Gln3 is a main regulator of nitrogen assimilation in Candida glabrata.

After Candida albicans, the yeast Candida glabrata ranks second as an aetiological agent of candidaemia and is the most frequently encountered non-Candida albicans species in patients with invasive candidiasis. Transcriptome analysis in C. albicans, C. glabrata and Cryptoccocus neoformans has revealed that, when engulfed by macrophages, these yeasts upregulate genes involved in nutrient acquisition, including nitrogen transporters such as the general amino acid permease Gap1, the dicarboxylic amino acid permease Dip5, the basic amino acid permease Can1 and the ammonium permeases Mep1 and Mep2. Nitrogen assimilation has been well studied in model species of fungi, such as Aspergillus nidulans, Neurospora crassa and Saccharomyces cerevisiae. However, little is known about nitrogen assimilation in C. glabrata. In the present study, we report a major role for Gln3 in the assimilation of glutamine, ammonium and proline. Ure2 also has a role in nitrogen assimilation, but it is only observable in ammonium and glutamine. In addition, Gat1 has a minor role, which is only observable in the absence of Ure2 and Gln3. Gln3 is absolutely necessary for full ammonium uptake from media. We have also shown that MEP2 gene expression in C. glabrata is completely dependent on Gln3, whereas GAP1 regulation is mainly exerted by Gln3, with the exception of proline where Gat1 has a minor role. In addition, in C. glabrata Ure2 appears to be a negative regulator of these NCR-sensitive genes, similarly to what has been described in S. cerevisiae. Our data place Gln3 as a key regulator of nitrogen assimilation.

Functional roles of a predicted branched chain aminotransferase encoded by the LkBAT1 gene of the yeast Lachancea kluyveri.

Branched chain amino acid aminotransferases (BCATs) catalyze the last step of the biosynthesis and the first step of the catabolism of branched chain amino acids. In Saccharomyces cerevisiae, BCATs are encoded by the ScBAT1 and ScBAT2 paralogous genes. Analysis of Lachancea kluyveri genome sequence, allowed the identification of the LkBAT1 locus, which could presumably encode a BCAT. A second unlinked locus (LkBAT1bis), exhibiting sequence similarity to LkBAT1 was also identified. To determine the function of these putative BCATs, L. kluyveri mutant strains lacking LkBAT1, LkBAT1bis or both genes were generated and tested for VIL metabolism. LkBat1 displayed branched chain aminotransferase activity and is required for VIL biosynthesis and catabolism. However, Lkbat1Δ mutant is a valine and isoleucine auxotroph and a leucine bradytroph indicating that L. kluyveri harbors an alternative enzyme(s) involved in leucine biosynthesis. Additionally, heterologous reciprocal gene complementation between S. cerevisiae and L. kluyveri orthologous LkBAT1, ScBAT1 and ScBAT2 genes, confirmed that the mitochondrial LkBat1 functions as BCAT in S. cerevisiae, restoring wild type phenotype to the ScBAT1 null mutant. Conversely, LkBAT1bis did not display a role in BCAAs metabolism. However, when ethanol was used as carbon source, deletion of LkBAT1bis in an Lkbat1Δ null strain resulted in an extended 'lag' growth phase, pointing to a potential function of LkBAT1 and LkBAT1bis in the aerobic metabolism of L. kluyveri. These results confirm the BCAT function of LkBAT1 in L. kluyveri, and further support the proposition that the BCAT function in ancestral-type yeasts has been distributed in the two paralogous genes present in S. cerevisiae.

Gastroprotective activity of ent-beyerene derivatives in mice: Effects on gastric secretion, endogenous prostaglandins and non-protein sulfhydryls.

Seventeen compounds (2-18) synthetized from the diterpenoid ent-beyer-15-en-18-ol (1) isolated from aerial part of Baccharis tola were tested for their gastroprotective activity on the model of HCl/EtOH-induced gastric lesions in mice. Furthermore cytotoxicity test toward fibroblasts and AGS cells were performed. The results showed that compound 1 (ED50=50 mg/kg), 2, 6 and 13 were the most active regarding gastroprotective activity. Compounds 8-10 and 17-18 showed the lowest cytotoxicity toward fibroblasts and AGS cells. Regarding to mode of gastroprotective action, the effect elicited by 6 (50 mg/kg) was reversed by Indomethacin but not by N-ethylmaleimide, N(G)-nitro-L-arginine methyl ester or ruthenium red, which suggests that prostaglandins are involved in the mode of gastroprotective action of 6.

Li7(BH)5(+): a new thermodynamically favored star-shaped molecule.

The potential energy surfaces (PESs) of Lin(BH)5(n-6) systems (where n = 5, 6, and 7) were explored using the gradient embedded genetic algorithm (GEGA) program, in order to find their global minima conformations. This search predicts that the lowest-energy isomers of Li6(BH)5 and Li7(BH)5(+) contain a (BH)5(6-) pentagonal fragment, which is isoelectronic and structurally analogous to the prototypical aromatic hydrocarbon anion C5H5(-). Li7(BH)5(+), along with Li7C5(+), Li7Si5(+) and Li7Ge5(+), joins a select group of clusters that adopt a seven-peak star-shape geometry, which is favored by aromaticity in the central five-membered ring, and by the preference of Li atoms for bridging positions. The theoretical analysis of chemical bonding, based on magnetic criteria, supports the notion that electronic delocalization is an important stabilization factor in all these star-shaped clusters.

Seco-taondiol, an unusual meroterpenoid from the Chilean seaweed Stypopodium flabelliforme and its gastroprotective effect in mouse model.

Ten known meroterpenoids and the new meroterpenoid 7 were isolated from the Chilean seaweed Stypopodium flabelliforme as their acetylated derivatives. Furthermore, the known metabolite taondiol has been isolated for the first time from this species. The molecular structure of the new metabolite was determined by spectroscopic methods based on 1D- and 2D-NMR. Isolation of 7 represents a key step toward a better understanding of the biogenesis of this class of meroterpenoids. Among the meroditerpenoids isolated, stypodiol, isoepitaondiol, epitaondiol and sargaol exhibited gastroprotective activity on the HCl/Ethanol-induced gastric lesions model in mice. Regarding the mode of gastroprotective action, the activity of epitaondiol was reversed significantly when animals were pretreated with indomethacin, N-ethylmaleimide and N-nitro-l-arginine methyl ester (L-NAME) suggesting that prostaglandins, sulfhydryl groups and nitric oxide are involved in their mode of gastroprotective action. In the case of sargaol the gastroprotective activity was attenuated with indomethacin and N-ethylmaleimide, which suggests that prostaglandins and sulfhydryl groups are also involved in the mode of action using this model.

Adaptive responses of mitochondria to mild copper deprivation involve changes in morphology, OXPHOS remodeling and bioenergetics.

Copper is an essential cofactor of complex IV of the electron transfer chain, and it is directly involved in the generation of mitochondrial membrane potential. Its deficiency induces the formation of ROS, large mitochondria and anemia. Thus, there is a connection between copper metabolism and bioenergetics, mitochondrial dynamics and erythropoiesis. Copper depletion might end in cellular apoptosis or necrosis. However, before entering into those irreversible processes, mitochondria may execute a series of adaptive responses. Mitochondrial adaptive responses (MAR) may involve multiple and diverse mechanisms for preserving cell life, such as mitochondrial dynamics, OXPHOS remodeling and bioenergetics output. In this study, a mild copper deficiency was produced in an animal model through intraperitoneal injections of bathocuproine disulfonate in order to study the MAR. Under these conditions, a new type of mitochondrial morphology was discovered in the liver. Termed the "butternut squash" mitochondria, it coexisted with normal and swollen mitochondria. Western blot analyses of mitochondrial dynamics proteins showed an up-regulation of MFN-2 and OPA1 fusion proteins. Furthermore, isolated liver mitochondria displayed OXPHOS remodeling through a decrease in supercomplex activity with a concomitant increase at an individual level of complexes I and IV, higher respiratory rates at complex I and II levels, higher oligomycin-insensitive respiration, and lower respiratory control ratio values when compared to the control group. As expected, total ATP and ATP/ADP values were not significantly different, since animal's health was not compromised. As a whole, these results describe a compensatory and adaptive response of metabolism and bioenergetics under copper deprivation.

Introducing KICK-MEP: exploring potential energy surfaces in systems with significant non-covalent interactions.

CONTEXT: Exploring potential energy surfaces (PES) is fundamental in computational chemistry, as it provides insights into the relationship between molecular energy, geometry, and chemical reactivity. We introduce Kick-MEP, a hybrid method for exploring the PES of atomic and molecular clusters, particularly those dominated by non-covalent interactions. Kick-MEP computes the Coulomb integral between the maximum and minimum electrostatic potential values on a 0.001 a.u. electron density isosurface for two interacting fragments. This approach efficiently estimates interaction energies and selects low-energy configurations at reduced computational cost. Kick-MEP was evaluated on silicon-lithium clusters, water clusters, and thymol encapsulated within Cucurbit[7]uril, consistently identifying the lowest energy structures, including global minima and relevant local minima. METHODS: Kick-MEP generates an initial population of molecular structures using the stochastic Kick algorithm, which combines two molecular fragments (A and B). The molecular electrostatic potential (MEP) values on a 0.001 a.u. electron density isosurface for each fragment are used to compute the Coulomb integral between them. Structures with the lowest Coulomb integral are selected and refined through gradient-based optimization and DFT calculations at the PBE0-D3/Def2-TZVP level. Molecular docking simulations for the thymol-Cucurbit[7]uril complex using AutoDock Vina were performed for benchmarking. Kick-MEP was validated across different molecular systems, demonstrating its effectiveness in identifying the lowest energy structures, including global minima and relevant local minima, while maintaining a low computational cost.

Exploring aromatic rings with planar tetracoordinate group 13-15 atoms.

This study examines systems containing planar tetracoordinate group 13-15 atoms (E) within pentagonal C4H2E rings bridged by Si or Ge atoms. A detailed chemical bonding analysis of eleven candidates shows that true tetracoordination is achieved only in the C4H2NGe2+ system.

Translation initiation factor eIF1A rescues hygromycin B sensitivity caused by deleting the carboxy-terminal tail in the GPN-loop GTPase Npa3.

The essential yeast protein GPN-loop GTPase 1 (Npa3) plays a critical role in RNA polymerase II (RNAPII) assembly and subsequent nuclear import. We previously identified a synthetic lethal interaction between a mutant lacking the carboxy-terminal 106-amino acid tail of Npa3 (npa3ΔC) and a bud27Δ mutant. As the prefoldin-like Bud27 protein participates in ribosome biogenesis and translation, we hypothesized that Npa3 may also regulate these biological processes. We investigated this proposal by using Saccharomyces cerevisiae strains episomally expressing either wild-type Npa3 or hypomorphic mutants (Npa3ΔC, Npa3K16R, and Npa3G70A). The Npa3ΔC mutant fully supports RNAPII nuclear localization and activity. However, the Npa3K16R and Npa3G70A mutants only partially mediate RNAPII nuclear targeting and exhibit a higher reduction in Npa3 function. Cell proliferation in these strains displayed an increased sensitivity to protein synthesis inhibitors hygromycin B and geneticin/G418 (npa3G70A > npa3K16R > npa3ΔC > NPA3 cells) but not to transcriptional elongation inhibitors 6-azauracil, mycophenolic acid or 1,10-phenanthroline. In all three mutant strains, the increase in sensitivity to both aminoglycoside antibiotics was totally rescued by expressing NPA3. Protein synthesis, visualized by quantifying puromycin incorporation into nascent-polypeptide chains, was markedly more sensitive to hygromycin B inhibition in npa3ΔC, npa3K16R, and npa3G70A than NPA3 cells. Notably, high-copy expression of the TIF11 gene, that encodes the eukaryotic translation initiation factor 1A (eIF1A) protein, completely suppressed both phenotypes (of reduced basal cell growth and increased sensitivity to hygromycin B) in npa3ΔC cells but not npa3K16R or npa3G70A cells. We conclude that Npa3 plays a critical RNAPII-independent and previously unrecognized role in translation initiation.

Vasorelaxant Effect and Blood Pressure Reduction Potential of Pitaya Juice Concentrate (Stenocereus huastecorum) Associated with Calcium Channel Blockade.

Arterial hypertension is a highly prevalent chronic disease worldwide, with several etiologies and treatments that may eventually have side effects or result in patients developing tolerance. There is growing interest in traditional medicine and functional foods to isolate biomolecules that could be useful as coadjuvants for treating several aliments. Pitaya, a desert fruit endemic in Mexico, is a rich source of bioactive molecules (betalains and phenolic compounds). In this work, the vasorelaxation properties of pitaya juice concentrate and fraction one were investigated using aortic and mesenteric rings from rats. The incubation of rings with pitaya juice concentrate or fraction one induced significant vasorelaxation, independent of the endothelium, and showed resistance to potassium channel blockers. This vasorelaxation was associated with the transmembrane influx of extracellular calcium through the vascular smooth muscle cells, with an inhibitory effect on the voltage-dependent calcium channel currents. Also, 400 mg/mL of pitaya juice concentrate in spontaneous hypertensive rats reduced their blood pressure for 48 h. Phytochemical analyses showed that the primary compounds in F1 were glycosidic in nature, and could be a complex mixture of disaccharides, dimeric disaccharides, or even tetrasaccharides. The glycosidic compounds found in F1 primarily contributed to vasodilatation, establishing a voltage-dependent calcium channel inhibition as a possible molecular target.