Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors

MOTIVATION: Characterizing the diversity of microbial communities and understanding the environmental factors that influence community diversity are central tenets of microbial ecology. The development and application of cultivation independent molecular tools has allowed for rapid surveying of microbial community composition at unprecedented resolutions and frequencies. There is a growing need to discern robust patterns and relationships within these datasets which provide insight into microbial ecology. Pearson correlation coefficient (PCC) analysis is commonly used for identifying the linear relationship between two species, or species and environmental factors. However, this approach may not be able to capture more complex interactions which occur in situ; thus, alternative analyses were explored. RESULTS: In this paper we introduced local similarity analysis (LSA), which is a technique that can identify more complex dependence associations among species as well as associations between species and environmental factors without requiring significant data reduction. To illustrate its capability of identifying relationships that may not otherwise be identified by PCC, we first applied LSA to simulated data. We then applied LSA to a marine microbial observatory dataset and identified unique, significant associations that were not detected by PCC analysis. LSA results, combined with results from PCC analysis were used to construct a theoretical ecological network which allows for easy visualization of the most significant associations. Biological implications of the significant associations detected by LSA were discussed. We also identified additional applications where LSA would be beneficial. AVAILABILITY: The algorithms are implemented in Splus/R and they are available upon request from the corresponding author.     

Prediction of glutathionylation sites in proteins using minimal sequence information and their experimental validation

S-glutathionylation of proteins plays an important role in various biological processes and is known to be protective modification during oxidative stress. Since, experimental detection of S-glutathionylation is labor intensive and time consuming, bioinformatics based approach is a viable alternative. Available methods require relatively longer sequence information, which may prevent prediction if sequence information is incomplete. Here, we present a model to predict glutathionylation sites from pentapeptide sequences. It is based upon differential association of amino acids with glutathionylated and non-glutathionylated cysteines from a database of experimentally verified sequences. This data was used to calculate position dependent F-scores, which measure how a particular amino acid at a particular position may affect the likelihood of glutathionylation event. Glutathionylation-score (G-score), indicating propensity of a sequence to undergo glutathionylation, was calculated using position-dependent F-scores for each amino-acid. Cut-off values were used for prediction. Our model returned an accuracy of 58% with Matthew’s correlation-coefficient (MCC) value of 0.165. On an independent dataset, our model outperformed the currently available model, in spite of needing much less sequence information. Pentapeptide motifs having high abundance among glutathionylated proteins were identified. A list of potential glutathionylation hotspot sequences were obtained by assigning G-scores and subsequent Protein-BLAST analysis revealed a total of 254 putative glutathionable proteins, a number of which were already known to be glutathionylated. Our model predicted glutathionylation sites in 93.93% of experimentally verified glutathionylated proteins. Outcome of this study may assist in discovering novel glutathionylation sites and finding candidate proteins for glutathionylation.     

Closed-Loop Control of Active Sensing Movements Regulates Sensory Slip

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Role of Polypyrimidine Tract Binding Protein in Mediating Internal Initiation of Translation of Interferon Regulatory Factor 2 RNA

Background

Earlier we have reported translational control of interferon regulatory factor 2 (IRF2) by internal initiation (Dhar et al, Nucleic Acids Res, 2007). The results implied possible role of IRF2 in controlling the intricate balance of cellular gene expression under stress conditions in general. Here we have investigated the secondary structure of the Internal Ribosome Entry Site of IRF2 RNA and demonstrated the role of PTB protein in ribosome assembly to facilitate internal initiation.

Methodology/Principal Findings

We have probed the putative secondary structure of the IRF2 5′UTR RNA using various enzymatic and chemical modification agents to constrain the secondary structure predicted from RNA folding algorithm Mfold. The IRES activity was found to be influenced by the interaction of trans-acting factor, polypyrimidine tract binding protein (PTB). Deletion of 25 nts from the 3′terminus of the 5′untranslated region resulted in reduced binding with PTB protein and also showed significant decrease in IRES activity compared to the wild type. We have also demonstrated putative contact points of PTB on the IRF2–5′UTR using primer extension inhibition assay. Majority of the PTB toe-prints were found to be restricted to the 3′end of the IRES. Additionally, Circular Dichroism (CD) spectra analysis suggested change in the conformation of the RNA upon PTB binding. Further, binding studies using S10 extract from HeLa cells, partially silenced for PTB gene expression, resulted in reduced binding by other trans-acting factors. Finally, we have demonstrated that addition of recombinant PTB enhances ribosome assembly on IRF2 IRES suggesting possible role of PTB in mediating internal initiation of translation of IRF2 RNA.

Conclusion/Significance

It appears that PTB binding to multiple sites within IRF2 5′UTR leads to a conformational change in the RNA that facilitate binding of other trans-acting factors to mediate internal initiation of translation.     

Selecting Populations for Non-Analogous Climate Conditions Using Universal Response Functions: The Case of Douglas-Fir in Central Europe

Identifying populations within tree species potentially adapted to future climatic conditions is an important requirement for reforestation and assisted migration programmes. Such populations can be identified either by empirical response functions based on correlations of quantitative traits with climate variables or by climate envelope models that compare the climate of seed sources and potential growing areas. In the present study, we analyzed the intraspecific variation in climate growth response of Douglas-fir planted within the non-analogous climate conditions of Central and continental Europe. With data from 50 common garden trials, we developed Universal Response Functions (URF) for tree height and mean basal area and compared the growth performance of the selected best performing populations with that of populations identified through a climate envelope approach. Climate variables of the trial location were found to be stronger predictors of growth performance than climate variables of the population origin. Although the precipitation regime of the population sources varied strongly none of the precipitation related climate variables of population origin was found to be significant within the models. Overall, the URFs explained more than 88% of variation in growth performance. Populations identified by the URF models originate from western Cascades and coastal areas of Washington and Oregon and show significantly higher growth performance than populations identified by the climate envelope approach under both current and climate change scenarios. The URFs predict decreasing growth performance at low and middle elevations of the case study area, but increasing growth performance on high elevation sites. Our analysis suggests that population recommendations based on empirical approaches should be preferred and population selections by climate envelope models without considering climatic constrains of growth performance should be carefully appraised before transferring populations to planting locations with novel or dissimilar climate.     

Remarkable photocytotoxicity in hypoxic HeLa cells by a dipyridophenazine copper(II) Schiff base thiolate

Copper(II) complexes [Cu(satp)(L)] (1-3) of a Schiff base thiolate (salicylidene-2-aminothiophenol, H₂satp) and phenanthroline bases (L), viz. 1,10-phenanthroline (phen in 1), dipyrido[3,2-d:2′,3′-f]quinoxaline (dpq in 2) and dipyrido[3,2-a:2′,3′-c]phenazine (dppz in 3), were prepared, characterized and their anaerobic DNA photocleavage activity and hypoxic photocytotoxicity studied. The redox active complexes show the Cu(II)-Cu(I) couple near − 0.5 V for 1 and near 0.0 V vs. SCE (saturated calomel electrode) for 2 and 3. The one-electron paramagnetic complexes (~ 1.85 μ_B) are avid DNA binders giving K_b values within 1.0 × 10⁵ − 8.0 × 10⁵ M^− 1. Thermal melting and viscosity data along with molecular docking calculations suggest DNA groove and/or partial intercalative binding of the complexes. The complexes show anaerobic DNA cleavage activity in red light under argon via type-I pathway, while DNA photocleavage in air proceeds via hydroxyl radical pathway. The DFT (density functional theory) calculations reveal a thyil radical pathway for the anaerobic DNA photocleavage activity and suggest the possibility of generation of a transient copper(I) species due to bond breakage between the copper and sulfur to generate the thyil radical. An oxidation of the copper(I) species is likely by oxygen in an aerobic medium or by the buffer medium in an anaerobic condition. Complex 3 exhibits significant photocytotoxicity in HeLa cells (IC₅₀ = 8.3(± 1.0) μM) in visible light, while showing lower dark toxicity (IC₅₀ = 17.2(± 1.0) μM). A significant reduction in the dark toxicity is observed under hypoxic cellular conditions (IC₅₀ = 30.0(± 1.0) μM in dark), while retaining its photocytotoxicity (IC₅₀ = 8.0(± 1.0) μM).     

NMR evidence against covalent attachment of an aldehyde ‘transition-state’ analogue to α-chymotrypsin

Proton NMR studies on the binding of trans-cinnamaldehyde to α-chymotrypsin indicates that the free aldehyde form of the “transition-state” analogue is complexed to the enzyme. Specifically, the aldehyde porton chemical shift does not change in the presence of enzyme, ruling out binding as the hydrate or hemiacetal. However, line broadening effects are observed, confirming fast to intermediate chemical exchange.     

Conserved functions of MATE transporters and their potential to enhance plant tolerance to aluminium toxicity

Almost half of the world’s arable land has acidic pH. Aluminum salts present in acid soils dissociate to release Al³⁺ ions in the soil solution that inhibit root growth causing severe loss in crop yields. Aluminium toxicity accounts for the second highest loss in plant productivity after drought. Aluminium in high doses causes damage to the plant cell wall, cytoskeleton and DNA. One of the ways by which plants alleviate aluminium toxicity is by the exudation of citrate from the roots that chelates the free Al³⁺ and prevents its entry into the plant. In several crop plants Multidrug and Toxic Compound Extrusion (MATE) transporters regulate citrate exudation from the roots. The MATE proteins are ubiquitously present in bacteria, archaea, fungi, animals and plants. The origin and evolution of these membrane transporters in plants is not well known. Here, using protein sequence information we identify MATE transporters in major groups of land plants and their algal ancestors. Our study indicates that the MATE family members expanded in number and functionally diverse among the land plants. We also identify motifs present across the streptophyte clade and a conserved aspartate residue that might regulate citrate exudation. This study can provide leads to engineer MATE transporters to confer enhanced tolerance in acid soils.

     

Iron (Fe3+)-mediated redox responses and amelioration of oxidative stress in cadmium (Cd2+) stressed mung bean seedlings: a biochemical and computational analysis

Journal of Plant Biochemistry and Biotechnology - The present investigation aims to evaluate the possible ameliorative role of iron (Fe3+) on cadmium (Cd2+)-induced oxidative stress in mung bean...