Modeling metabolic adjustment in <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> upon treatment with isoniazid

Complex biological systems exhibit a property of robustness at all levels of organization. Through different mechanisms, the system tries to sustain stress such as due to starvation or drug exposure. To explore whether reconfiguration of the metabolic networks is used as a means to achieve robustness, we have studied possible metabolic adjustments in Mtb upon exposure to isoniazid (INH), a front-line clinical drug. The redundancy in the genome of M. tuberculosis (Mtb) makes it an attractive system to explore if alternate routes of metabolism exist in the bacterium. While the mechanism of action of INH is well studied, its effect on the overall metabolism is not well characterized. Using flux balance analysis, inhibiting the fluxes flowing through the reactions catalyzed by Rv1484, the target of INH, significantly changes the overall flux profiles. At the pathway level, activation or inactivation of certain pathways distant from the target pathway, are seen. Metabolites such as NADPH are shown to reduce drastically, while fatty acids tend to accumulate. The overall biomass also decreases with increasing inhibition levels. Inhibition studies, pathway level clustering and comparison of the flux profiles with the gene expression data indicate the activation of folate metabolism, ubiquinone metabolism, and metabolism of certain amino acids. This analysis provides insights useful for target identification and designing strategies for combination therapy. Insights gained about the role of individual components of a system and their interactions will also provide a basis for reconstruction of whole systems through synthetic biology approaches.     

Synthesis, crystal structures and magnetic properties of two bis(μ-phenoxido)dicopper(II) complexes derived from reduced Schiff base ligands

Two phenoxido bridged dinuclear Cu(II) complexes, [Cu₂(L¹)₂(NCNCN)₂] (1) and [Cu₂(L²)₂(NCNCN)₂]·2H₂O (2) have been synthesized using the tridentate reduced Schiff-base ligands 2-[1-(2-dimethylamino-ethylamino)-ethyl]-phenol (HL¹) and 2-[1-(3-methylamino-propylamino)-ethyl]-phenol (HL²), respectively. The complexes have been characterized by X-ray structural analyses and variable-temperature magnetic susceptibility measurements. Both the complexes present a diphenoxido bridging Cu₂O₂ core. The geometries around metal atoms are intermediate between trigonal bipyramid and square pyramid with the Addison parameters (τ) = 0.57 and 0.49 for 1 and 2, respectively. Within the core the Cu–O–Cu angles are 99.15° and 103.51° and average Cu–O bond distances are 2.036 and 1.978 Å for compounds 1 and 2, respectively. These differences have marked effect on the magnetic properties of two compounds. Although both are antiferromagnetically coupled, the coupling constants (J = −184.3 and −478.4 cm⁻¹ for 1 and 2, respectively) differ appreciably.     

Trinuclear and tetranuclear adduct formation between sodium perchlorate and copper(II) complexes of salicylaldimine type ligands: Structural characterization and theoretical investigation

The synthesis of two new sodium perchlorate adducts (1:2 and 1:3) with copper(II) “ligand-complexes” is reported. One adduct is trinuclear [(CuL¹)₂NaClO₄] (1) and the other is tetranuclear [(CuL²)₃Na]ClO₄·EtOH (2). The ligands are the tetradentate di-Schiff base of 1,3-propanediamines and salicylaldehyde (H₂L¹) or 2-hydroxyacetophenone (H₂L²). Both complexes have been characterized by X-ray single crystal structure analyses. In both structures, the sodium cation has a six-coordinate distorted octahedral environment being bonded to four oxygen atoms from two Schiff-base complexes in addition to a chelated perchlorate anion in 1 and to six oxygen atoms from three Schiff-base complexes in 2. We have carried out a DFT theoretical study (RI-B97-D/def2-SVP level of theory) to compute and compare the formation energies of 1:2 and 1:3 adducts. The DFT study reveals that the latter is more stabilized than the former. The X-ray crystal structure of 1 shows that the packing of the trinuclear unit is controlled by unconventional C-H···O H-bonds and Cu²⁺-π non-covalent interactions. These interactions explain the formation of 1 which is a priori disfavored with respect to 2.     

Natural variation of submergence tolerance among Arabidopsis thaliana accessions

? The exploitation of natural variation in Arabidopsis thaliana (Arabidopsis) provides a huge potential for the identification of the molecular mechanisms underlying this variation as a result of the availability of a vast array of genetic and genomic resources for this species. Eighty-six Arabidopsis accessions were screened for natural variation in flooding tolerance. This forms the first step towards the identification and characterization of the role of candidate genes contributing to flooding tolerance. ? Arabidopsis accessions at the 10-leaf stage were subjected to complete submergence in the dark. Survival curves were plotted to estimate median lethal times as a measure of tolerance. Flooding-associated survival parameters, such as root and shoot oxygen content, initial carbohydrate content and petiole elongation under water, were also measured. ? There was a significant variation in submergence tolerance among Arabidopsis accessions. However, the order of tolerance did not correlate with root and shoot oxygen content or initial amounts of shoot starch and total soluble sugars. A negative correlation was observed between submergence tolerance and underwater petiole elongation. ? Arabidopsis accessions show considerable variation in the ability to tolerate complete submergence, making it a good species in which to identify and characterize genes and to study mechanisms that contribute to survival under water.     

DNA repair and global sumoylation are regulated by distinct Ubc9 noncovalent complexes

Global sumoylation, SUMO chain formation, and genome stabilization are all outputs generated by a limited repertoire of enzymes. Mechanisms driving selectivity for each of these processes are largely uncharacterized. Here, through crystallographic analyses we show that the SUMO E2 Ubc9 forms a noncovalent complex with a SUMO-like domain of Rad60 (SLD2). Ubc9:SLD2 and Ubc9:SUMO noncovalent complexes are structurally analogous, suggesting that differential recruitment of Ubc9 by SUMO or Rad60 provides a novel means for such selectivity. Indeed, deconvoluting Ubc9 function by disrupting either the Ubc9:SLD2 or Ubc9:SUMO noncovalent complex reveals distinct roles in facilitating sumoylation. Ubc9:SLD2 acts in the Nse2 SUMO E3 ligase-dependent pathway for DNA repair, whereas Ubc9:SUMO instead promotes global sumoylation and chain formation, via the Pli1 E3 SUMO ligase. Moreover, this Pli1-dependent SUMO chain formation causes the genome instability phenotypes of SUMO-targeted ubiquitin ligase (STUbL) mutants. Overall, we determine that, unexpectedly, Ubc9 noncovalent partner choice dictates the role of sumoylation in distinct cellular pathways.     

Extraction and characterization of essential oil components based on geraniol and citronellol from Java citronella (Cymbopogon winterianus Jowitt)

Citronella oil is the main product of Java citronella grass (Cymbopogon winterianus Jowitt) rich in geraniol and citronellol, widely used in mosquito repellents and perfumeries. The age of the plant plays a key role in oil composition and its yield such that young leaves have lesser oil content than the mature leaves. Also, a remarkable difference between fresh and dried leaves regarding oil yield is observed. The various methods of extracting essential oils from citronella grass with respect to yield (%) were studied. Average percent yield in the manual extraction and hydro-distillation procedure was 0.8 and 1 % respectively, which was better as compared to steam distilled oil (0.7 %). The chromatographic analysis of essential oils with respect to standards geraniol and citronellol were studied by high performance thin layer chromatography (HPTLC) with n-hexane and ethyl acetate (3:2) as mobile phase followed by its separation on plates. The developed plates showed geraniol, citronellol and citronellal as major bands. The analysis of all extracted oil samples by means of electrospray ionization-mass spectrometry (ESI-MS) in the positive ion mode showed rapid mass fingerprints of constituents present in the samples according to the observed mass of standards. Furthermore, the analysis of vibrational spectra was accomplished with Fourier transform infra-red spectroscopy (FTIR) specifying all the functional groups as major peaks confirming all of them as monoterpene alcohols with conjugated double bonds. Thus, HPTLC, ESI-MS and FTIR studies evidenced that the two essential oil components were majorly present in the methanol extract suggesting methanol as a good extractant in the manual extraction process.     

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective

Proteins in thermophilic organisms remain stable and function optimally at high temperatures. Owing to their important applicability in many industrial processes, such thermostable proteins have been studied extensively, and several structural factors attributed to their enhanced stability. How these factors render the emergent property of thermostability to proteins, even in situations where no significant changes occur in their three-dimensional structures in comparison to their mesophilic counter-parts, has remained an intriguing question. In this study we treat Lipase A from Bacillus subtilis and its six thermostable mutants in a unified manner and address the problem with a combined complex network-based analysis and molecular dynamic studies to find commonality in their properties. The Protein Contact Networks (PCN) of the wild-type and six mutant Lipase A structures developed at a mesoscopic scale were analyzed at global network and local node (residue) level using network parameters and community structure analysis. The comparative PCN analysis of all proteins pointed towards important role of specific residues in the enhanced thermostability. Network analysis results were corroborated with finer-scale molecular dynamics simulations at both room and high temperatures. Our results show that this combined approach at two scales can uncover small but important changes in the local conformations that add up to stabilize the protein structure in thermostable mutants, even when overall conformation differences among them are negligible. Our analysis not only supports the experimentally determined stabilizing factors, but also unveils the important role of contacts, distributed throughout the protein, that lead to thermostability. We propose that this combined mesoscopic-network and fine-grained molecular dynamics approach is a convenient and useful scheme not only to study allosteric changes leading to protein stability in the face of negligible over-all conformational changes due to mutations, but also in other molecular networks where change in function does not accompany significant change in the network structure.     

Seasonal variation in expression pattern of genes under HSP70

Heat shock protein 70 (HSP70) is one of the most abundant and best characterized heat shock protein family that consists of highly conserved stress proteins, expressed in response to stress, and plays crucial roles in environmental stress tolerance and adaptation. The present study was conducted to identify major types of genes under the HSP70 family and to quantify their expression pattern in heat- and cold-adapted Indian goats (Capra hircus) with respect to different seasons. Five HSP70 gene homologues to HSPA8, HSPA6, HSPA1A, HSPA1L, and HSPA2 were identified by gene-specific primers. The cDNA sequences showed high similarity to other mammals, and proteins have an estimated molecular weight of around 70 kDa. The expression of HSP70 genes was observed during summer and winter. During summer, the higher expression of HSPA8, HSPA6, and HSPA1A was observed, whereas the expression levels of HSPA1L and HSPA2 were found to be lower. It was also observed that the expression of HSPA1A and HSPA8 was higher during winter in both heat- and cold-adapted goats but downregulates in case of other HSPs. Therefore, both heat and cold stress induced the overexpression of HSP70 genes. An interesting finding that emerged from the study is the higher expression of HSP70 genes in cold-adapted goats during summer and in heat-adapted goats during winter. Altogether, the results indicate that the expression pattern of HSP70 genes is species- and breed-specific, most likely due to variations in thermal tolerance and adaptation to different climatic conditions.     

Development of a novel spatiotemporal depletion system for cellular cholesterol

Cholesterol is an essential component of mammalian cell membranes whose subcellular concentration and function are tightly regulated by de novo biosynthesis, transport, and storage. Although recent reports have suggested diverse functions of cellular cholesterol in different subcellular membranes, systematic investigation of its site-specific roles has been hampered by the lack of a methodology for spatiotemporal manipulation of cellular cholesterol levels. Here, we report the development of a new cholesterol depletion system that allows for spatiotemporal manipulation of intracellular cholesterol levels. This system utilizes a genetically encoded cholesterol oxidase whose intrinsic membrane binding activity is engineered in such a way that its membrane targeting can be controlled in a spatiotemporally specific manner via chemically induced dimerization. In combination with in situ quantitative imaging of cholesterol and signaling activity measurements, this system allows for unambiguous determination of site-specific functions of cholesterol in different membranes, including the plasma membrane and the lysosomal membrane.     

Topoisomerase II poisoning by indazole and imidazole complexes of ruthenium

Trans-imidazolium (bis imidazole) tetrachloro ruthenate (RuIm) and trans-indazolium (bis indazole) tetrachloro ruthenate (RuInd) are ruthenium coordination complexes, which were first synthesized and exploited for their anticancer activity. These molecules constitute two of the few most effective anticancer ruthenium compounds. The clinical use of these compounds however was hindered due to toxic side effects on the human body. Our present study on topoisomerase II poisoning by these compounds shows that they effectively poison the activity of topoisomerase II by forming a ternary cleavage complex of DNA, drug and topoisomerase II. The thymidine incorporation assays show that the inhibition of cancer cell proliferation correlates with topoisomerase II poisoning. The present study on topoisomerase II poisoning by these two compounds opens a new avenue for renewing further research on these compounds. This is because they could be effective lead candidates for the development of more potent and less toxic ruthenium containing topoisomerase II poisons. Specificity of action on this molecular target may reduce the toxic effects of these ruthenium-containing molecules and thus improve their therapeutic index.