NMR assignments of cd-HO, a 24 kDa heme oxygenase from Corynebacterium diphtheria

We are employing a number of selective in vitro and in vivo methods including NMR to screen compounds that bind to heme oxygenases from pathogenic bacteria. We report the nearly complete HN, N, CO, Cα and Cβ chemical shift assignments of a 215-amino acid HO from Corynebacterium diphtheria in three forms, apo cd-HO-G135A, apo cd-HO and CO-bound ferrous holo cd-HO; these assignments will enable us to identify residues on cd-HO that are perturbed upon binding to selected compounds, and to help with the development of inhibitors specific to the bacterial proteins.     

Backbone and sidechain methyl Ile (δ1), Leu and Val resonance assignments of the catalytic domain of the yeast mRNA decapping enzyme, Dcp2

Eukaryotic mRNA decapping by Dcp2 is the penultimate step in several mRNA decay pathways. To understand regulation of Dcp2 by ligand interactions, we have assigned the backbone and sidechain methyl Ile (δ1), Leu and Val chemical shifts of the catalytic domain of the S. Cerevisiae enzyme.     

Microbial pathogen-induced necrotic cell death mediated by the inflammasome components CIAS1/cryopyrin/NLRP3 and ASC

Cryopyrin (CIAS1, NLRP3) and ASC are components of the inflammasome, a multiprotein complex required for caspase-1 activation and cytokine IL-1beta production. CIAS1 mutations underlie autoinflammation characterized by excessive IL-1beta secretion. Disease-associated cryopyrin also causes a program of necrosis-like cell death in macrophages, the mechanistic details of which are unknown. We find that patient monocytes carrying disease-associated CIAS1 mutations exhibit excessive necrosis-like death by a process dependent on ASC and cathepsin B, resulting in spillage of the proinflammatory mediator HMGB1. Shigella flexneri infection also causes cryopyrin-dependent macrophage necrosis with features similar to the death caused by mutant CIAS1. This necrotic death is independent of caspase-1 and IL-1beta, and thus independent of the inflammasome. Furthermore, necrosis of primary macrophages requires the presence of Shigella virulence genes. While similar proteins mediate pathogen-induced cell death in plants, this report identifies cryopyrin as an important host regulator of programmed pathogen-induced necrosis in animals, a process we term pyronecrosis.     

Two preferentially expressed proteins protect vascular endothelial cells from an attack by peptide-specific CTL

Vascular endothelial cells (EC) are an exposed tissue with intimate contact with circulating Ag-specific CTL. Experimental in vitro and clinical data suggested that endothelial cells present a different repertoire of MHC class I-restricted peptides compared with syngeneic leukocytes or epithelial cells. This endothelial-specific peptide repertoire might protect EC from CTL-mediated cell death. The HLA-A*02-restricted peptide profile of human EC and syngeneic B lymphoblastoid cells was biochemically analyzed and compared. For EC selective peptides, source protein expression, peptide binding affinity, and peptide-HLA-A*02 turnover were measured. The significance of abundant peptide presentation for target cell recognition by immunodominant CTL was tested by small interfering RNA treatment of EC to knock down the source proteins. High amounts of two peptides, PTRF(56-64) and CD59(106-114), were consistently detected in EC. This predominance of two endothelial peptides was explained by cell type-specific source protein expression that compensated for poor HLA-A*02 binding affinity and short half-live of peptide/HLA-A*02 complexes. Knocking down the source proteins containing the abundant endothelial peptide motifs led to a nearly 100-fold increase of surface expression of SMCY(311-319), an immunodominant minor histocompatibility Ag, as detected by cytotoxicity assays using SMCY(311-319)-specific CTL. We conclude that EC express and present preferentially two distinct HLA-A*02-restricted peptides at extraordinary high levels. These abundant self-peptides may protect EC from CTL-mediated lysis by competing for HLA-A*02 binding sites with immunodominant scarcely expressed antigenic peptides.     

Biotic stress resistance in agriculture through antimicrobial peptides

Antimicrobial peptides (AMPs) are the hosts' defense molecules against microbial pathogens and gaining extensive research attention worldwide. These have been reported to play vital role of host innate immunity in response to microbial challenges. AMPs can be used as a natural antibiotic as an alternative of their chemical counterpart for protection of plants/animals against diseases. There are a number of sources of AMPs including prokaryotic and eukaryotic organisms and are present, both in vertebrates and invertebrates. AMPs can be classified as cationic or anionic, based on net charges. Large number of databases and tools are available in the public domain which can be used for development of new genetically modified disease resistant varieties/breeds for agricultural production. The results of the biotechnological research as well as genetic engineering related to AMPs have shown high potential for reduction of economic losses of agricultural produce due to pathogens. In this article, an attempt has been made to introduce the role of AMPs in relation to plants and animals. Their functional and structural characteristics have been described in terms of its role in agriculture. Different sources of AMPs and importance of these sources has been reviewed in terms of its availability. This article also reviews the bioinformatics resources including different database tools and algorithms available in public domain. References of promising biotechnology research in relation to AMPs, prospects of AMPs for further development of genetically modified varieties/breeds are highlighted. AMPs are valuable resource for students, researchers, educators and medical and industrial personnel.     

Lactobacillus protected bone damage and maintained the antioxidant status of liver and kidney homogenates in female wistar rats

The aim of the study was to evaluate protective property of Lactobacillus casei and Lactobacillus acidophilus in minimizing oxidative stress associated with arthritis from liver and kidney. Subsequently, protective property of Lactobacillus against the bone damage was also taken into consideration. Arthritis was induced by injecting freund's complete adjuvant (100 μl) into sub plantar surface of hind paw. Oral administration of culture, vehicle, and drug started after induction of arthritis (i.e. on day 9th). Indomethacin was used as a standard drug. Radiographic analysis of the hind paw knee joint was also done at the end of the 21st day. Oxidative stress parameters were studied from liver and kidney homogenate. Histopathology of liver and kidney was also performed. Lactobacillus treatment significantly rescued the enzymatic level of catalase, superoxide dismutase, reduced glutathione, and glutathione peroxidase in both liver and kidney homogenates, whereas it has decreased the malonaldehyde accumulation. Oral administration of Lactobacillus also significantly decreased the serum ceruloplasmin level. Radiographic analysis also corroborated these findings. Lactobacillus treatment maintained the normal histopathology of liver and kidney. Results of this study clearly suggest that L. casei and L. acidophilus, alone or in combination, decreased the bone damaged and effectively restored antioxidant status of liver and kidney. Lactobacillus has a significant antiarthritic and antioxidant activity against freund's complete adjuvant induced arthritis in rats.     

Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [<Emphasis Type="Italic">Setaria italica</Emphasis> (L.) P. Beauv.]

The unavailability of microsatellite markers and saturated genetic linkage map has restricted the genetic improvement of foxtail millet [Setaria italica (L.) P. Beauv.], despite the fact that in recent times it has been documented as a new model species for biofuel grasses. With the objective to generate a good number of microsatellite markers in foxtail millet cultivar ‘Prasad’, 690 clones were sequenced which generated 112.95 kb high quality sequences obtained from three genomic libraries each enriched with different microsatellite repeat motifs. Microsatellites were identified in 512 (74.2%) of the 690 positive clones and 172 primer pairs (pp) were successfully designed from 249 (48.6%) unique SSR-containing clones. The efficacies of the microsatellite containing genomic sequences were established by superior primer designing ability (69%), PCR amplification efficiency (85.5%) and polymorphic potential (52%) in the parents of F₂ mapping population. Out of 172 pp, functional 147 markers showed high level of cross-species amplification (~74%) in six grass species. Higher polymorphism rate and broad range of genetic diversity (0.30–0.69 averaging 0.58) obtained in constructed phylogenetic tree using 52 microsatellite markers, demonstrated the utility of markers in germplasm characterizations. In silico comparative mapping of 147 foxtail millet microsatellite containing sequences against the mapping data of sorghum (~18%), maize (~16%) and rice (~5%) indicated the presence of orthologous sequences of the foxtail millet in the respective species. The result thus demonstrates the applicability of microsatellite markers in various genotyping applications, determining phylogenetic relationships and comparative mapping in several important grass species.     

Waterlogging induced oxidative stress and antioxidant activity in pigeonpea genotypes

The objective of this study was to examine the role of antioxidant enzymes in waterlogging tolerance of pigeonpea (Cajanus cajan L. Halls) genotypes ICP 301 (tolerant) and Pusa 207 (susceptible). Waterlogging resulted in visible yellowing and senescence of leaves, decrease in leaf area, dry matter, relative water content and chlorophyll content in leaves, and membrane stability index in roots and leaves. The decline in all parameters was greater in Pusa 207 than ICP 301. Oxidative stress in the form of superoxide radical, hydrogen peroxide and thiobarbituric acid reactive substances (TBARS) contents initially decreased, however at 4 and 6 d of waterlogging it increased over control plants, probably due to activation of DPI-sensitive NADPH-oxidase. Antioxidant enzymes such as superoxide dismutase, ascorbate peroxidase, glutathione reductase and catalase also increased under waterlogging. The comparatively greater antioxidant enzyme activities resulting in less oxidative stress in ICP 301 could be one of the factor determining its higher tolerance to flooding as compared to Pusa 207. This study is the first to conclusively prove that waterlogging induced increase in ROS is via NADPH oxidase.     

Isolation and characterization of microcystin producing Microcystis from a Central Indian water bloom

Microcystis aeruginosa Kütz, a well-known microcystin (hepatotoxin) producing cyanobacterium was the dominant bloom-forming organism in a mesotrophic lake at Nagpur in Central India, which was isolated and characterized for morphospecies and microcystin content. Compact spherical colonies, formation of daughter colonies, and clathration of older colonies leading to release of solitary cells, were characteristics of laboratory grown M. aeruginosa. Its growth, monitored as increase in optical density (OD) measured at 678 nm (the wavelength selected using dilution curve technique), exhibited a maximum specific growth rate (μ_max) of 0.34 day⁻¹ which, was attained on the 5th day of the experiment with a doubling time of 3.25 days. Though the morphological characters of the M. aeruginosa under field conditions were not retained under laboratory conditions, the microcystin content and type of variants did match with bloom samples. Reverse phase high performance liquid chromatography (RP-HPLC) analyses revealed that the laboratory grown isolate of Microcystis produced microcystin-RR (732 μg g⁻¹ dry weight biomass) and demethylated microcystin-RR (165 μg g⁻¹ dry weight biomass) variants, which are reported to be less toxic when compared to microcystin-LR. LC/ESI/MS further confirmed the presence of these two variants. Geographical distribution of microcystin variants and their prevailing concentrations need to be considered during formulation of guideline values for drinking and recreational waters.