PeptideMine - A webserver for the design of peptides for protein-peptide binding studies derived from protein-protein interactomes

Background  

Signal transduction events often involve transient, yet specific, interactions between structurally conserved protein domains and polypeptide sequences in target proteins. The identification and validation of these associating domains is crucial to understand signal transduction pathways that modulate different cellular or developmental processes. Bioinformatics strategies to extract and integrate information from diverse sources have been shown to facilitate the experimental design to understand complex biological events. These methods, primarily based on information from high-throughput experiments, have also led to the identification of new connections thus providing hypothetical models for cellular events. Such models, in turn, provide a framework for directing experimental efforts for validating the predicted molecular rationale for complex cellular processes. In this context, it is envisaged that the rational design of peptides for protein-peptide binding studies could substantially facilitate the experimental strategies to evaluate a predicted interaction. This rational design procedure involves the integration of protein-protein interaction data, gene ontology, physico-chemical calculations, domain-domain interaction data and information on functional sites or critical residues.     

Identification of specificity-defining amino acids of the wheat immune receptor Pm2 and powdery mildew effector AvrPm2

Plant nucleotide-binding leucine-rich repeat receptors (NLRs) act as intracellular sensors for pathogen-derived effector proteins and trigger an immune response, frequently resulting in the hypersensitive cell death response (HR) of the infected host cell. The wheat (Triticum aestivum) NLR Pm2 confers resistance against the fungal pathogen Blumeria graminis f. sp. tritici (Bgt) if the isolate contains the specific RNase-like effector AvrPm2. We identified and isolated seven new Pm2 alleles (Pm2e–i) in the wheat D-genome ancestor Aegilops tauschii and two new natural AvrPm2 haplotypes from Bgt. Upon transient co-expression in Nicotiana benthamiana, we observed a variant-specific HR of the Pm2 variants Pm2a and Pm2i towards AvrPm2 or its homolog from the AvrPm2 effector family, BgtE-5843, respectively. Through the introduction of naturally occurring non-synonymous single nucleotide polymorphisms and structure-guided mutations, we identified single amino acids in both the wheat NLR Pm2 and the fungal effector proteins AvrPm2 and BgtE-5843 responsible for the variant-specific HR of the Pm2 variants. Exchanging these amino acids led to a modified HR of the Pm2–AvrPm2 interaction and allowed the identification of the effector head epitope, a 20-amino-acid long unit of AvrPm2 involved in the HR. Swapping of the AvrPm2 head epitope to the non-HR-triggering AvrPm2 family member BgtE-5846 led to gain of a HR by Pm2a. Our study presents a molecular approach to identify crucial effector surface structures involved in the HR and demonstrates that natural and induced diversity in an immune receptor and its corresponding effectors can provide the basis for understanding and modifying NLR–effector specificity.     

Alternative Crassulacean Acid Metabolism Modes Provide Environment-Specific Water-Saving Benefits in a Leaf Metabolic Model

Crassulacean acid metabolism (CAM) evolved in arid environments as a water-saving alternative to C₃ photosynthesis. There is great interest in engineering more drought-resistant crops by introducing CAM into C₃ plants. However, it is unknown whether full CAM or alternative water-saving modes would be more productive in the environments typically experienced by C₃ crops. To study the effect of temperature and relative humidity on plant metabolism in the context of water saving, we coupled a time-resolved diel (based on a 24-h day-night cycle) model of leaf metabolism to an environment-dependent gas-exchange model. This combined model allowed us to study the emergence of CAM as a trade-off between leaf productivity and water saving. We show that vacuolar storage capacity in the leaf is a major determinant of the extent of CAM. Moreover, our model identified an alternative CAM cycle involving mitochondrial isocitrate dehydrogenase as a potential contributor to initial carbon fixation at night. Simulations across a range of environmental conditions show that the water-saving potential of CAM strongly depends on the daytime weather conditions and that the additional water-saving effect of carbon fixation by isocitrate dehydrogenase can reach 11% total water saving for the conditions tested.     

Risk Assessment for Natural Uranium in Subsurface Water of Punjab State,India

Traces of uranium were measured by laser fluorimeter in 235 subsurface water samples collected from four districts of Punjab state in India. The concentration of U in water samples ranged between <2–644 μg/L with a mean value of 73.1 μg/L. The radiological risk was observed to be in the range of 5.55 × 10^?6–1.78 × 10^?3 with a mean value of 2.03 × 10^?4, which is around 22% more than the maximum acceptable level (l.67 × 10^?4) as per guidelines of India's Atomic Energy Regulatory Board. The mean of chemical toxicity risk, expressed as life time average daily dose (LADD) was worked out to be 5.56 μg/kg/day with a range of 0.15–48 μg/kg/day by considering a bodyweight of 51.5 ± 8.5 kg, water ingestion rate of 4.05 L/d, and life expectancy of 63.7 yrs for an adult Indian reference man and compared with the reference dose (4.53 μg/kg/day). The average exposure level of U was comparatively high and the chemical toxicity was expected to be more. The mean of hazard quotient (LADD/ RfD) for all four districts was found to be greater than 1, indicating that groundwater may not be suitable for consumption from a chemical toxicity point of view.