Novel insights through the integration of structural and functional genomics data with protein networks

In recent years, major advances in genomics, proteomics, macromolecular structure determination, and the computational resources capable of processing and disseminating the large volumes of data generated by each have played major roles in advancing a more systems-oriented appreciation of biological organization. One product of systems biology has been the delineation of graph models for describing genome-wide protein-protein interaction networks. The network organization and topology which emerges in such models may be used to address fundamental questions in an array of cellular processes, as well as biological features intrinsic to the constituent proteins (or "nodes") themselves. However, graph models alone constitute an abstraction which neglects the underlying biological and physical reality that the network's nodes and edges are highly heterogeneous entities. Here, we explore some of the advantages of introducing a protein structural dimension to such models, as the marriage of conventional network representations with macromolecular structural data helps to place static node and edge constructs in a biologically more meaningful context. We emphasize that 3D protein structures constitute a valuable conceptual and predictive framework by discussing examples of the insights provided, such as enabling in silico predictions of protein-protein interactions, providing rational and compelling classification schemes for network elements, as well as revealing interesting intrinsic differences between distinct node types, such as disorder and evolutionary features, which may then be rationalized in light of their respective functions within networks.     

Butterfly communities along an elevational gradient in the Tons valley,Western Himalayas: Implications of rapid assessment for insect conservation

As time and money is limited, explicit, cost-effective, quick, and appropriate methods are needed to assist conservation planners and managers for making quick decisions. Butterflies promise to be a good model for rapid assessment and habitat monitoring studies because they are widespread, conspicuous, and easily recognizable and they are effective indicators of forest health. We conducted a rapid assessment of butterflies at five disturbance gradient sites that varied in elevation from 900 m a.s.l. to 3500 m a.s.l. for 20 days during March–April 2010 and recorded 79 butterfly species and 1504 individuals in the Tons valley in Western Himalayas. We were able to sample approximately 77% (123 species) of the estimated species richness on continuing the sampling until July 2010. Species richness at the study site is estimated to be 159 (95% CI: 145–210) species. Diversity was highest in heterogeneous habitats and decreased towards homogeneous habitats. Unique species were highly restricted to lowest disturbed sites. Using Pearson's correlation analysis, the strongest vegetative predictors of butterfly richness were plant species richness, canopy cover, and herb and shrub density. Butterfly species richness and abundance were highly correlated with altitude, temperature, relative humidity, fire signs, and livestock abundance. We also found positive cross-taxon correlation among butterflies, moths, and beetles across sites, indicating that butterflies can be used as surrogate or indicator taxa for insect conservation. Short sampling periods providing comprehensive estimates of species richness were reliable for identifying habitats and sites with the most conservation value in the Tons valley landscape.     

Modeling and experimental analyses reveals signaling plasticity in a bi-modular assembly of CD40 receptor activated kinases

Depending on the strength of signal dose, CD40 receptor (CD40) controls ERK-1/2 and p38MAPK activation. At low signal dose, ERK-1/2 is maximally phosphorylated but p38MAPK is minimally phosphorylated; as the signal dose increases, ERK-1/2 phosphorylation is reduced whereas p38MAPK phosphorylation is reciprocally enhanced. The mechanism of reciprocal activation of these two MAPKs remains un-elucidated. Here, our computational model, coupled to experimental perturbations, shows that the observed reciprocity is a system-level behavior of an assembly of kinases arranged in two modules. Experimental perturbations with kinase inhibitors suggest that a minimum of two trans-modular negative feedback loops are required to reproduce the experimentally observed reciprocity. The bi-modular architecture of the signaling pathways endows the system with an inherent plasticity which is further expressed in the skewing of the CD40-induced productions of IL-10 and IL-12, the respective anti-inflammatory and pro-inflammatory cytokines. Targeting the plasticity of CD40 signaling significantly reduces Leishmania major infection in a susceptible mouse strain. Thus, for the first time, using CD40 signaling as a model, we show how a bi-modular assembly of kinases imposes reciprocity to a receptor signaling. The findings unravel that the signalling plasticity is inherent to a reciprocal system and that the principle can be used for designing a therapy.     

Linkers of Cell Polarity and Cell Cycle Regulation in the Fission Yeast Protein Interaction Network

The study of gene and protein interaction networks has improved our understanding of the multiple, systemic levels of regulation found in eukaryotic and prokaryotic organisms. Here we carry out a large-scale analysis of the protein-protein interaction (PPI) network of fission yeast (Schizosaccharomyces pombe) and establish a method to identify ‘linker’ proteins that bridge diverse cellular processes - integrating Gene Ontology and PPI data with network theory measures. We test the method on a highly characterized subset of the genome consisting of proteins controlling the cell cycle, cell polarity and cytokinesis and identify proteins likely to play a key role in controlling the temporal changes in the localization of the polarity machinery. Experimental inspection of one such factor, the polarity-regulating RNB protein Sts5, confirms the prediction that it has a cell cycle dependent regulation. Detailed bibliographic inspection of other predicted ‘linkers’ also confirms the predictive power of the method. As the method is robust to network perturbations and can successfully predict linker proteins, it provides a powerful tool to study the interplay between different cellular processes.     

Gene expression profiling through microarray analysis in Arabidopsis thaliana colonized by Pseudomonas putida MTCC5279, a plant growth promoting rhizobacterium

Plant growth promotion is a multigenic process under the influence of many factors; therefore an understanding of these processes and the functions regulated may have profound implications. Present study reports microarray analysis of Arabidopsis thaliana plants inoculated with Pseudomonas putida MTCC5279 (MTCC5279) which resulted in significant increase in growth traits as compared with non-inoculated control. The gene expression changes, represented by oligonucleotide array (24652 genes) have been studied to gain insight into MTCC5279 assisted plant growth promotion in Arabidopsis thaliana. MTCC5279 induced upregulated Arabidopsis thaliana genes were found to be involved in maintenance of genome integrity (At5g20850), growth hormone (At3g23890 and At4g36110), amino acid synthesis (At5g63890), abcissic acid (ABA) signaling and ethylene suppression (At2g29090, At5g17850), Ca⁺² dependent signaling (At3g57530) and induction of induced systemic resistance (At2g46370, At2g44840). The genes At3g32920 and At2g15890 which are suggested to act early in petal, stamen and embryonic development are among the downregulated genes. We report for the first time MTCC5279 assisted repression of At3g32920, a putative DNA repair protein involved in recombination and DNA strand transfer in a process of rapid meiotic and mitotic division.     

Small terminase couples viral DNA binding to genome-packaging ATPase activity

Packaging of viral genomes into empty procapsids is powered by a large DNA-packaging motor. In most viruses, this machine is composed of a large (L) and a small (S) terminase subunit complexed with a dodecamer of portal protein. Here we describe the 1.75?? crystal structure of the bacteriophage P22 S-terminase in a nonameric conformation. The structure presents a central channel ～23?? in diameter, sufficiently large to accommodate hydrated B-DNA. The last 23 residues of S-terminase are essential for binding to DNA and assembly to L-terminase. Upon binding to its own DNA, S-terminase functions as a specific activator of L-terminase ATPase activity. The DNA-dependent stimulation of ATPase activity thus rationalizes the exclusive specificity of genome-packaging motors for viral DNA in the crowd of host DNA, ensuring fidelity of packaging and avoiding wasteful ATP hydrolysis. This posits?a model for DNA-dependent activation of genome-packaging motors of general interest in virology.     

Involvement of secretory and endosomal compartments in presentation of an exogenous self-glycolipid to type II NKT cells

Natural Killer T (NKT) cells recognize both self and foreign lipid Ags presented by CD1 molecules. Although presentation of the marine sponge-derived lipid alphaGalCer to type I NKT cells has been well studied, little is known about self-glycolipid presentation to either type I or type II NKT cells. Here we have investigated presentation of the self-glycolipid sulfatide to a type II NKT cell that specifically recognizes a single species of sulfatide, namely lyso-sulfatide but not other sulfatides containing additional acyl chains. In comparison to other sulfatides or alphaGalCer, lyso-sulfatide binds with lower affinity to CD1d. Although plate-bound CD1d is inefficient in presenting lyso-sulfatide at neutral pH, it is efficiently presented at acidic pH and in the presence of saposin C. The lysosomal trafficking of mCD1d is required for alphaGalCer presentation to type I NKT cells, it is not important for presentation of lyso-sulfatide to type II NKT cells. Consistently, APCs deficient in a lysosomal lipid-transfer protein effectively present lyso-sulfatide. Presentation of lyso-sulfatide is inhibited in the presence of primaquine, concanamycin A, monensin, cycloheximide, and an inhibitor of microsomal triglyceride transfer protein but remains unchanged following treatment with brefeldin A. Wortmannin-mediated inhibition of lipid presentation indicates an important role for the PI-3kinase in mCD1d trafficking. Our data collectively suggest that weak CD1d-binding self-glycolipid ligands such as lyso-sulfatide can be presented via the secretory and endosomal compartments. Thus this study provides important insights into the exogenous self-glycolipid presentation to CD1d-restricted T cells.     

Structural and functional analyses of the severe acute respiratory syndrome coronavirus endoribonuclease Nsp15

The severe acute respiratory syndrome (SARS) coronavirus encodes several RNA-processing enzymes that are unusual for RNA viruses, including Nsp15 (nonstructural protein 15), a hexameric endoribonuclease that preferentially cleaves 3' of uridines. We solved the structure of a catalytically inactive mutant version of Nsp15, which was crystallized as a hexamer. The structure contains unreported flexibility in the active site of each subunit. Substitutions in the active site residues serine 293 and proline 343 allowed Nsp15 to cleave at cytidylate, whereas mutation of leucine 345 rendered Nsp15 able to cleave at purines as well as pyrimidines. Mutations that targeted the residues involved in subunit interactions generally resulted in the formation of catalytically inactive monomers. The RNA-binding residues were mapped by a method linking reversible cross-linking, RNA affinity purification, and peptide fingerprinting. Alanine substitution of several residues in the RNA-contacting portion of Nsp15 did not affect hexamer formation but decreased the affinity of RNA binding and reduced endonuclease activity. This suggests a model for Nsp15 hexamer interaction with RNA.