Cyclic AMP-dependent protein lysine acylation in mycobacteria regulates fatty acid and propionate metabolism

Acetylation of lysine residues is a posttranslational modification that is used by both eukaryotes and prokaryotes to regulate a variety of biological processes. Here we identify multiple substrates for the cAMP-dependent protein lysine acetyltransferase from Mycobacterium tuberculosis (KATmt). We demonstrate that a catalytically important lysine residue in a number of FadD (fatty acyl CoA synthetase) enzymes is acetylated by KATmt in a cAMP-dependent manner and that acetylation inhibits the activity of FadD enzymes. A sirtuin-like enzyme can deacetylate multiple FadDs, thus completing the regulatory cycle. Using a strain deleted for the KATmt ortholog in Mycobacterium bovis Bacillus Calmette-Guerin (BCG), we show for the first time that acetylation is dependent on intracellular cAMP levels. KATmt can utilize propionyl CoA as a substrate and, therefore, plays a critical role in alleviating propionyl CoA toxicity in mycobacteria by inactivating acyl CoA synthetase (ACS). The precision by which mycobacteria can regulate the metabolism of fatty acids in a cAMP-dependent manner appears to be unparalleled in other biological organisms and is ideally suited to adapt to the complex environment that pathogenic mycobacteria experience in the host.

Tethering preferences of domain families co-occurring in multi-domain proteins

Genomic data of several organisms have revealed the presence of a vast repertoire of multi-domain proteins. The role played by individual domains in a multi-domain protein has a profound influence on the overall function of the protein. In the present analysis an attempt has been made to better understand the tethering preferences of domain families that occur in multi-domain proteins. The analysis has been carried out on an exhaustive dataset of 2 961 898 sequences of proteins from 930 organisms, where 741 274 proteins are comprised of at least two domain families. For every domain family, the number of other domain families with which it co-occurs within a protein in this dataset has been enumerated and is referred to as the tethering number of the domain family. It was found that, in the general dataset, the AAA ATPase family and the family of Ser/Thr kinases have the highest tethering numbers of 450 and 444 respectively. Further analysis reveals significant correlation between the number of members in a family and its tethering number. Positive correlation was also observed for the extent of a sequence and functional diversity within a family and the tethering numbers of domain families. Domain families that are present ubiquitously in diverse organisms tend to have large tethering numbers, while organism/kingdom-specific families have low tethering numbers. Thus, the analysis uncovers how domain families recombine and evolve to give rise to multi-domain proteins.

Heat and SDS insensitive NDK dimers are largely stabilised by hydrophobic interaction to form functional hexamer in Mycobacterium smegmatis

The primary structure and function of nucleoside diphosphate kinase (NDK), a substrate non-specific enzyme involved in the maintenance of nucleotide pools is also implicated to play pivotal roles in many other cellular processes. NDK is conserved from bacteria to human and forms a homotetramer or hexamer to exhibit its biological activity. However, the nature of the functional oligomeric form of the enzyme differs among different organisms. The functional form of NDKs from many bacterial systems, including that of the human pathogen, Mycobacterium tuberculosis (MtuNDK), is a hexamer, although some bacterial NDKs are tetrameric in nature. The present study addresses the oligomeric property of MsmNDK and how a dimer, the basic subunit of a functional hexamer, is stabilized by hydrogen bonds and hydrophobic interactions. Homology modeling was generated using the three-dimensional structure of MtuNDK as a template; the residues interacting at the monomer-monomer interface of MsmNDK were mapped. Using recombinant enzymes of wild type, catalytically inactive mutant, and monomer-monomer interactive mutants of MsmNDK, the stability of the dimer was verified under heat, SDS, low pH, and methanol. The predicted residues (Gln17, Ser24 and Glu27) were engaged in dimer formation, however the mutated proteins retained the ATPase and GTPase activity even after introducing single (MsmNDK- Q17A, MsmNDK-E27A, and MsmNDK-E27Q) and double (MsmNDK-E27A/Q17A) mutation. However, the monomer monomer interaction could be abolished using methanol, indicating the stabilization of the monomer-monomer interaction by hydrophobic interaction.

Experimental Studies on the Kinematics of Cutting in Granular Materials

Slow flow in granular materials is characterized by high solid fraction and sustained inter-particle interaction. The kinematics of trawling or cutting is encountered in processes such as locomotion of organisms in sand; trawl gear movement on a soil deposit; plow movement; movement of rovers, earth moving equipment etc. Additionally, this configuration is very akin to shallow drilling configuration encountered in the mining and petroleum industries. An experimental study has been made in order to understand velocity and deformation fields in cutting of a model rounded sand. Under nominal plane strain conditions, sand is subjected to orthogonal cutting at different tool-rake angles. High-resolution optical images of the region of cutting were obtained during the flow of the granular ensemble around the tool. Interesting kinematics underlying the formation of a chip and the evolution of the deformation field is seen in these experiments. These images are also analyzed using a PIV algorithm and detailed information of the deformation parameters such as velocity, strain rate and volume change is obtained.

Penetrative phototactic bioconvection in an isotropic scattering suspension

Phototaxis is a directed swimming response dependent upon the light intensity sensed by micro-organisms. Positive (negative) phototaxis denotes the motion directed towards (away from) the source of light. Using the phototaxis model of Ghorai, Panda, and Hill ''Bioconvection in a suspension of isotropically scattering phototactic algae,'' Phys. Fluids 22, 071901 (2010)], we investigate two-dimensional phototactic bioconvection in an absorbing and isotropic scattering suspension in the nonlinear regime. The suspension is confined by a rigid bottom boundary, and stress-free top and lateral boundaries. The governing equations for phototactic bioconvection consist of Navier-Stokes equations for an incompressible fluid coupled with a conservation equation for micro-organisms and the radiative transfer equation for light transport. The governing system is solved efficiently using a semi-implicit second-order accurate conservative finite-difference method. The radiative transfer equation is solved by the finite volume method using a suitable step scheme. The resulting bioconvective patterns differ qualitatively from those found by Ghorai and Hill ''Penetrative phototactic bioconvection,'' Phys. Fluids 17, 074101 (2005)] at a higher critical wavelength due to the effects of scattering. The solutions show transition from steady state to periodic oscillations as the governing parameters are varied. Also, we notice the accumulation of micro-organisms in two horizontal layers at two different depths via their mean swimming orientation profile for some governing parameters at a higher scattering albedo. (C) 2013 AIP Publishing LLC.

Coral diseases are major contributors to coral mortality in Shingle Island, Gulf of Mannar, southeastern India

The present study reports coral mortality, driven primarily by coral diseases, around Shingle Island, Gulf of Mannar (GOM), Indian Ocean. In total, 2910 colonies were permanently monitored to assess the incidence of coral diseases and consequent mortality for 2 yr. Four types of lesions consistent with white band disease (WBD), black disease (BD), white plaque disease (WPD), and pink spot disease (PSD) were recorded from 4 coral genera: Montipora, Pocillopora, Acropora, and Porites. Porites were affected by 2 disease types, while the other 3 genera were affected by only 1 disease type. Overall disease prevalence increased from 8% (n = 233 colonies) to 41.9% (n = 1219) over the 2 yr study period. BD caused an unprecedented 100% mortality in Pocillopora, followed by 20.4 and 13.1% mortality from WBD in Montipora and Acropora, respectively. Mean disease progression rates of 0.8 +/- 1.0 and 0.6 +/- 0.5 cm mo(-1) over live coral colonies were observed for BD and WBD. Significant correlations between temperature and disease progression were observed for BD (r = 0.86, R-2 = 0.75, p < 0.001) and WBD (R-2 = 0.76, p < 0.001). This study revealed the increasing trend of disease prevalence and progression of disease over live coral in a relatively limited study area; further study should investigate the status of the entire coral reef in the GOM and the role of diseases in reef dynamics.

Developments in Biotechnology for Environmentally Benign Iron Ore Beneficiation

Biomineralization and biogenesis of iron ore deposits are illustrated in relation to indigenous microorganisms inhabiting iron ore mines. Aerobic and anaerobic microorganisms indigenous to iron oxide mineralization are analyzed. Microbially-induced flotation and flocculation of iron ore minerals such as hematite, alumina, calcite and quartz are discussed with respect to use of four types of microorganisms, namely, Paenibacillus polymyxa, Bacillus subtilis, Saccharomyces cerevisiae and Desulfovibrio desulfuricans. The role of the above organisms in the removal of silica, alumina, clays and apatite from hematite is illustrated with respect to mineral-specific bioreagents, surface chemical changes and microbe-mineral interaction mechanisms. Silica and alumina removal from real iron ores through biobeneficiation is outlined. Environmental benefits of biobeneficiation are demonstrated with respect to biodegradation of toxic reagents and environmentally-safe waste disposal and processing.

An automated approach to network features of protein structure ensembles

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone-efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user-friendly, standalone program package named PSN-Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X-ray structures. The novelty in network construction lies in the explicit consideration of side-chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long-range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross-correlation/interaction energy in PSN-Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN-Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin-conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN-Ensemble for single-static structures of active/inactive states of 2-adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN-Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN-Ensemble/psn_index.html.

Regulation of transcription initiation in mycobacteria

The success of Mycobacterium tuberculosis as a deadly pathogen lies in its ability to survive under adverse conditions during pre- and post-infectious stages. The transcription process and the regulation of gene expression are central to the survival of the pathogen through the harsh conditions. Multiple sigma factors, transcription regulators, diverse two-component systems contribute in tailoring the events to meet the challenges faced by the pathogen. Although the machinery is conserved, many aspects of transcription and its regulation seem to be different in mycobacteria when compared to the other well-studied organisms. Here, we discuss salient aspects of transcription and its regulation in the context of distinct physiology of mycobacteria.

Studies on Groundnut Fermentation

The nature and the density of population of micro-organisms associated with groundnut fermentation have been established by adopting suitable microbioIogical procedures. Evidence has been drawn to show that the microflora ofthe fermenting liquors are responsible for the decomposition of the fatty cbmponents of the groundnut during its fermentation

Differential Action of Glycoprotein Hormones: Significance in Cancer Progression

Growth of multicellular organisms depends on maintenance of proper balance between proliferation and differentiation. Any disturbance in this balance in animal cells can lead to cancer. Experimental evidence is provided to conclude with special reference to the action of follicle-stimulating hormone (FSH) on Sertoli cells, and luteinizing hormone (LH) on Leydig cells that these hormones exert a differential action on their target cells, i.e., stimulate proliferation when the cells are in an undifferentiated state which is the situation with cancer cells and promote only functional parameters when the cell are fully differentiated. Hormones and growth factors play a key role in cell proliferation, differentiation, and apoptosis. There is a growing body of evidence that various tumors express some hormones at high levels as well as their cognate receptors indicating the possibility of a role in progression of cancer. Hormones such as LH, FSH, and thyroid-stimulating hormone have been reported to stimulate cell proliferation and act as tumor promoter in a variety of hormone-dependent cancers including gonads, lung, thyroid, uterus, breast, prostate, etc. This review summarizes evidence to conclude that these hormones are produced by some cancer tissues to promote their own growth. Also an attempt is made to explain the significance of the differential action of hormones in progression of cancer with special reference to prostate cancer.

Interspecies and intraspecies interactions in social amoebae

The stable co-existence of individuals of different genotypes and reproductive division of labour within heterogeneous groups are issues of fundamental interest from the viewpoint of evolution. Cellular slime moulds are convenient organisms in which to address both issues. Strains of a species co-occur, as do different species; social groups are often genetically heterogeneous. Intra- and interspecies 1:1 mixes of wild isolates of Dictyostelium giganteum and D.purpureum form chimaeric aggregates, following which they segregate to varying extents. Intraspecies aggregates develop in concert and give rise to chimaeric fruiting bodies that usually contain more spores (reproductives) of one component than the other. Reproductive skew and variance in the proportion of reproductives are positively correlated. Interspecies aggregates exhibit almost complete sorting; most spores in a fruiting body come from a single species. Between strains, somatic compatibility correlates weakly with sexual compatibility. It is highest within clones, lower between strains of a species and lowest between strains of different species. Trade-offs among fitness-related traits (between compatible strains), sorting out (between incompatible strains) and avoidance (between species) appear to lie behind coexistence.

DNA STRUCTURAL FEATURES AND ARCHITECTURE OF PROMOTER REGIONS PLAY A ROLE IN GENE RESPONSIVENESS OF S. CEREVISIAE

Gene expression is the most fundamental biological process, which is essential for phenotypic variation. It is regulated by various external (environment and evolution) and internal (genetic) factors. The level of gene expression depends on promoter architecture, along with other external factors. Presence of sequence motifs, such as transcription factor binding sites (TFBSs) and TATA-box, or DNA methylation in vertebrates has been implicated in the regulation of expression of some genes in eukaryotes, but a large number of genes lack these sequences. On the other hand, several experimental and computational studies have shown that promoter sequences possess some special structural properties, such as low stability, less bendability, low nucleosome occupancy, and more curvature, which are prevalent across all organisms. These structural features may play role in transcription initiation and regulation of gene expression. We have studied the relationship between the structural features of promoter DNA, promoter directionality and gene expression variability in S. cerevisiae. This relationship has been analyzed for seven different measures of gene expression variability, along with two different regulatory effect measures. We find that a few of the variability measures of gene expression are linked to DNA structural properties, nucleosome occupancy, TATA-box presence, and bidirectionality of promoter regions. Interestingly, gene responsiveness is most intimately correlated with DNA structural features and promoter architecture.

Molecular Dynamics Perspective on the Protein Thermal Stability: A Case Study Using SAICAR Synthetase

The enzyme SAICAR synthetase ligates aspartate with CAIR (5'-phosphoribosyl-4-carboxy-5-aminoimidazole) forming SAICAR (5-amino-4-imidazole-N-succinocarboxamide ribonucleotide) in the presence of ATP. In continuation with our previous study on the thermostability of this enzyme in hyper-/thermophiles based on the structural aspects, here, we present the dynamic aspects that differentiate the mesophilic (E. coli, E. chaffeensis), thermophilic (G. kaustophilus), and hyperthermophilic (M. jannaschii, P. horikoshii) SAICAR synthetases by carrying out a total of 11 simulations. The five functional dimers from the above organisms were simulated using molecular dynamics for a period of 50 ns each at 300 K, 363 K, and an additional simulation at 333 K for the thermophilic protein. The basic features like root-mean-square deviations, root-mean-square fluctuations, surface accessibility, and radius of gyration revealed the instability of mesophiles at 363 K. Mean square displacements establish the reduced flexibility of hyper-/thermophiles at all temperatures. At the simulations time scale considered here, the long-distance networks are considerably affected in mesophilic structures at 363 K. In mesophiles, a comparatively higher number of short-lived (having less percent existence time) C alpha, hydrogen bonds, hydrophobic interactions are formed, and long-lived (with higher percentage existence time) contacts are lost. The number of time-averaged salt-bridges is at least 2-fold higher in hyperthermophiles at 363 K. The change in surface accessibility of salt-bridges at 363 K from 300 K is nearly doubled in mesophilic protein compared to proteins from other temperature classes.

Phylogeography unplugged: comparative surveys in the genomic era

In March 2012, the authors met at the National Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, USA, to discuss approaches and cooperative ventures in Indo-Pacific phylogeography. The group emerged with a series of findings: (1) Marine population structure is complex, but single locus mtDNA studies continue to provide powerful first assessment of phylogeographic patterns. (2) These patterns gain greater significance/power when resolved in a diversity of taxa. New analytical tools are emerging to address these analyses with multi-taxon approaches. (3) Genome-wide analyses are warranted if selection is indicated by surveys of standard markers. Such indicators can include discordance between genetic loci, or between genetic loci and morphology. Phylogeographic information provides a valuable context for studies of selection and adaptation. (4) Phylogeographic inferences are greatly enhanced by an understanding of the biology and ecology of study organisms. (5) Thorough, range-wide sampling of taxa is the foundation for robust phylogeographic inference. (6) Congruent geographic and taxonomic sampling by the Indo-Pacific community of scientists would facilitate better comparative analyses. The group concluded that at this stage of technology and software development, judicious rather than wholesale application of genomics appears to be the most robust course for marine phylogeographic studies. Therefore, our group intends to affirm the value of traditional (''unplugged'') approaches, such as those based on mtDNA sequencing and microsatellites, along with essential field studies, in an era with increasing emphasis on genomic approaches.