Pan-genome dynamics of Pseudomonas gene complements enriched across hexachlorocyclohexane dumpsite

Background

Phylogenetic heterogeneity across Pseudomonas genus is complemented by its diverse genome architecture enriched by accessory genetic elements (plasmids, transposons, and integrons) conferring resistance across this genus. Here, we sequenced a stress tolerant genotype i.e. Pseudomonas sp. strain RL isolated from a hexachlorocyclohexane (HCH) contaminated pond (45 mg of total HCH g⁻¹ sediment) and further compared its gene repertoire with 17 reference ecotypes belonging to P. stutzeri, P. mendocina, P. aeruginosa, P. psychrotolerans and P. denitrificans, representing metabolically diverse ecosystems (i.e. marine, clinical, and soil/sludge). Metagenomic data from HCH contaminated pond sediment and similar HCH contaminated sites were further used to analyze the pan-genome dynamics of Pseudomonas genotypes enriched across increasing HCH gradient.

Results

Although strain RL demonstrated clear species demarcation (ANI ≤ 80.03%) from the rest of its phylogenetic relatives, it was found to be closest to P. stutzeri clade which was further complemented functionally. Comparative functional analysis elucidated strain specific enrichment of metabolic pathways like α-linoleic acid degradation and carbazole degradation in Pseudomonas sp. strain RL and P. stutzeri XLDN-R, respectively. Composition based methods (%codon bias and %G + C difference) further highlighted the significance of horizontal gene transfer (HGT) in evolution of nitrogen metabolism, two-component system (TCS) and methionine metabolism across the Pseudomonas genomes used in this study. An intact mobile class-I integron (3,552 bp) with a captured gene cassette encoding for dihydrofolate reductase (dhfra1) was detected in strain RL, distinctly demarcated from other integron harboring species (i.e. P. aeruginosa, P. stutzeri, and P. putida). Mobility of this integron was confirmed by its association with Tnp21-like transposon (95% identity) suggesting stress specific mobilization across HCH contaminated sites. Metagenomics data from pond sediment and recently surveyed HCH adulterated soils revealed the in situ enrichment of integron associated transposase gene (TnpA6100) across increasing HCH contamination (0.7 to 450 mg HCH g⁻¹ of soil).

Conclusions

Unlocking the potential of comparative genomics supplemented with metagenomics, we have attempted to resolve the environment and strain specific demarcations across 18 Pseudomonas gene complements. Pan-genome analyses of these strains indicate at astoundingly diverse metabolic strategies and provide genetic basis for the cosmopolitan existence of this taxon.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1488-2) contains supplementary material, which is available to authorized users.     

Different Modes of Retrovirus Restriction by Human APOBEC3A and APOBEC3G In Vivo

The apolipoprotein B editing complex 3 (A3) cytidine deaminases are among the most highly evolutionarily selected retroviral restriction factors, both in terms of gene copy number and sequence diversity. Primate genomes encode seven A3 genes, and while A3F and 3G are widely recognized as important in the restriction of HIV, the role of the other genes, particularly A3A, is not as clear. Indeed, since human cells can express multiple A3 genes, and because of the lack of an experimentally tractable model, it is difficult to dissect the individual contribution of each gene to virus restriction in vivo. To overcome this problem, we generated human A3A and A3G transgenic mice on a mouse A3 knockout background. Using these mice, we demonstrate that both A3A and A3G restrict infection by murine retroviruses but by different mechanisms: A3G was packaged into virions and caused extensive deamination of the retrovirus genomes while A3A was not packaged and instead restricted infection when expressed in target cells. Additionally, we show that a murine leukemia virus engineered to express HIV Vif overcame the A3G-mediated restriction, thereby creating a novel model for studying the interaction between these proteins. We have thus developed an in vivo system for understanding how human A3 proteins use different modes of restriction, as well as a means for testing therapies that disrupt HIV Vif-A3G interactions.     

Stress Protective Effect of Rhododendron arboreum Leaves (MEL) on Chromium-Treated Vigna radiata Plants

Oxidative stress due to hexavalent chromium [Cr(VI)] in Vigna radiata seedlings, and stress amelioration with treatment of methanol extract of Rhododendron arboreum leaves was observed in the present study by analyzing growth parameters, stomatal morphology, malondialdehyde (MDA) content, histological analysis, pigment contents, Cr metal uptake, elemental analysis, and antioxidant analysis. Chromium treatment resulted in the decline of root length, shoot length, fresh weight, and dry weight. Scanning electron microscopic studies revealed that Cr treatment altered the stomatal structure. As compared to control plants, MDA content increased by 80.1% in Cr-treated plants. Histological analysis with confocal microscope confirmed the nuclear damage, membrane damage, enhanced H₂O₂ accumulation, and decline in pigment concentration. Atomic absorption spectrometry analysis revealed an accumulation of 43.3% Chromium in the plant tissues and decreased concentration of essential elements as consequences of Cr treatment. The methanol extract of R. arboreum leaves (MEL) alleviated Cr stress in Vigna radiata seedlings by restoring normal growth, stomatal structure, and pigment contents, as well as essential elements. Reduction in H₂O₂ accumulation, reduced MDA content by 29.2%, and decline in Cr accumulation to 32.8% was observed after MEL supplementation to Cr-stressed plants. Decreased nuclear and membrane damage along with increased lipid-soluble as well as water-soluble antioxidants after MEL application in Cr-stressed plants are further symptoms of stress amelioration properties of Rhododendron leaves.

     

Altering host resistance to infections through microbial transplantation

Host resistance to bacterial infections is thought to be dictated by host genetic factors. Infections by the natural murine enteric pathogen Citrobacter rodentium (used as a model of human enteropathogenic and enterohaemorrhagic E. coli infections) vary between mice strains, from mild self-resolving colonization in NIH Swiss mice to lethality in C3H/HeJ mice. However, no clear genetic component had been shown to be responsible for the differences observed with C. rodentium infections. Because the intestinal microbiota is important in regulating resistance to infection, and microbial composition is dependent on host genotype, it was tested whether variations in microbial composition between mouse strains contributed to differences in "host" susceptibility by transferring the microbiota of resistant mice to lethally susceptible mice prior to infection. Successful transfer of the microbiota from resistant to susceptible mice resulted in delayed pathogen colonization and mortality. Delayed mortality was associated with increased IL-22 mediated innate defense including antimicrobial peptides Reg3γ and Reg3β, and immunono-neutralization of IL-22 abrogated the beneficial effect of microbiota transfer. Conversely, depletion of the native microbiota in resistant mice by antibiotics and transfer of the susceptible mouse microbiota resulted in reduced innate defenses and greater pathology upon infection. This work demonstrates the importance of the microbiota and how it regulates mucosal immunity, providing an important factor in susceptibility to enteric infection. Transfer of resistance through microbial transplantation (bacteriotherapy) provides additional mechanisms to alter "host" resistance, and a novel means to alter enteric infection and to study host-pathogen interactions.     

The phytohormone crosstalk paradigm takes center stage in understanding how plants respond to abiotic stresses

The highly coordinated, dynamic nature of growth requires plants to perceive and react to various environmental signals in an interactive manner. Elaborate signaling networks mediate this plasticity in growth and the ability to adapt to changing environmental conditions. The fluctuations of stress-responsive hormones help alter the cellular dynamics and hence play a central role in coordinately regulating the growth responses under stress. Recent experimental data unequivocally demonstrated that interactions among various phytohormones are the rule rather than exception in integrating the diverse input signals and readjusting growth as well as acquiring stress tolerance. The presence of multiple and often redundant signaling intermediates for each phytohormone appears to help in such crosstalk. Furthermore, there are several examples of similar developmental changes occurring in response to distinct abiotic stress signals, which can be explained by the crosstalk in phytohormone signaling. Therefore, in this brief review, we have highlighted the major phytohormone crosstalks with a focus on the response of plants to abiotic stresses. The recent findings have made it increasingly apparent that such crosstalk will also explain the extreme pleiotropic responses elicited by various phytohormones. Indeed, it would not be presumptuous to expect that in the coming years this paradigm will take a central role in explaining developmental regulation.     

Design and evaluation of novel 8-oxo-pyridopyrimidine Jak1/2 inhibitors

A highly ligand efficient, novel 8-oxo-pyridopyrimidine containing inhibitor of Jak1 and Jak2 isoforms with a pyridone moiety as the hinge-binding motif was discovered. Structure-based design strategies were applied to significantly improve enzyme potency and the polarity of the molecule was adjusted to gain cellular activity. The crystal structures of two representative inhibitors bound to Jak1 were obtained to enable SAR exploration.     

Characterization of alkalotolerant bacterial community by 16S rDNA-based denaturing gradient gel electrophoresis method for degradation of dibenzofuran in soil microcosm

An alkalotolerant bacterial community was developed by continuous enrichment in the chemostat in presence of dibenzofuran (DF) as sole carbon source. Six different types of bacterial isolates were cultured on nutrient broth agar plates together with six operational taxonomic units (OTUs) at pH 7.0 and pH 8.0 by 16S rDNA-DGGE method. However, isolates of microbial community was declined from three OTUs (pH 9.0) to two at pH 10.0 after enrichment in alkaline condition. Among the six isolates tested for degradation of DF, Pseudomonas sp. and Bacillus sp. the members of alkalotolerant bacterial community had better potency to degrade dibenzofuran. Alkalotolerant bacterial community introduced in soil microcosm for evaluation of survival of most suitable isolates and degradation of dioxin-like compound indicated more than 90% degradation of dibenzofuran after 45 days by the bacterial community enriched for 180 days in the chemostat at pH 10, however, microbial community was not competent to utilize even 50% DF after day 30, not enriched in the chemostat. The survival of competent bacteria monitored by DGGE method in soil microcosm indicated presence of two major alkalotolerant isolates for utilization of dibenzofuran, substantiated the results and significance of alkalotolerant bacteria for in situ bioremediation of dioxin-like compounds in the environment.     

Comparative analysis of human matrix metalloproteinases: Emerging therapeutic targets in diseases

The identification of specific target proteins for any diseased condition involves extensive characterization of the potentially involved proteins. Members of a protein family demonstrating comparable features may show certain unusual features when implicated in a pathological condition. Advancements in the field of computational biology and the use of various bioinformatics tools for analysis can aid researchers to comprehend their system of work in primary stages of research. This initial screening can help to reduce time and cost of testing and experimentation in laboratory. Human matrix metalloproteinase (MMP) family of endopeptidases is one such family of 23 members responsible for the remodeling of extracellular matrix (ECM) by degradation of the ECM proteins. Though their role has been implicated in various pathological conditions such as arthritis, atherosclerosis, cancer, liver fibrosis, cardio-vascular and neurodegenerative disorders, little is known about the specific involvement of members of the large MMP family in diseases. A comparative in silico characterization of the MMP protein family has been carried out to analyze their physico-chemical, secondary structural and functional properties. Based on the observed patterns of occurrence of atypical features, we hypothesize that cysteine rich and highly thermostable MMPs might be key players in diseased conditions. Thus, a plausible grouping of disease responsive MMPs that might be considered as promising clinical targets may be done. This study can be used as a fundamental approach to characterize, analyze and screen large protein families for the identification of signature patterns.