Biology subjects

Ray, A.

Publications and source records attributed to Ray, A..

3 recordsLinked to original sources

bioRxiv2018

Taxa-driven functional shifts associated with stormflow in an urban stream microbial community

Urban streams are susceptible to stormwater and sewage inputs that can impact their ecological health and water quality. Microbial communities in streams play important functional roles and their composition and metabolic potential can help assess ecological state and water quality. Although these environments are highly heterogenous, little is known about the influence of isolated perturbations, such as those resulting from rain events on urban stream microbiota. Here, we examined the microbial community composition and diversity in an urban stream during dry and wet weather conditions with both 16S rRNA gene sequencing across multiple years and shotgun metagenomics to more deeply analyze a single stormflow event. Metagenomics was used to assess population-level dynamics as well as shifts in the microbial community taxonomic profile and functional potential before and after a substantial rainfall. Results demonstrated general trends present in the stream under stormflow vs. baseflow conditions across years and seasons and also highlighted the significant influence of increased effluent flow following rain in shifting the stream microbial community from abundant freshwater taxa to those more associated with urban/anthropogenic settings. Shifts in the taxonomic composition were also linked to changes in functional gene content, particularly for transmembrane transport and organic substance biosynthesis. We also observed an increase in relative abundance of genes encoding degradation of organic pollutants and antibiotic resistance after rain. Overall, this study provided evidence of stormflow impacts on an urban stream microbiome from an environmental and public health perspective.\n\nImportanceUrban streams in various parts of the world are facing increased anthropogenic pressure on their water quality, and stormflow events represent one such source of complex physical, chemical and biological perturbations. Microorganisms are important components of these streams from both ecological and public-health perspectives, and analyzing the effect of such perturbations on the stream microbial community can help improve current knowledge on the impact such chronic disturbances can have on these water resources. This study examines microbial community dynamics during rain-induced stormflow conditions in an urban stream of the Chicago Area Waterway System. Additionally, using shotgun metagenomics we identified significant shifts in the microbial community composition and functional gene content following a high rainfall event, with potential environment and public health implications. Previous work in this area has been limited to specific genes/organisms or has not assessed immediate stormflow impact.

microbiology↗

bioRxiv2017

Specific cholesterol binding drives drastic structural alterations in apolipoprotein A1

Protein adopts multitude of flexible and rapidly interconverting conformers, many which are governed by specific protein-interaction domains. ApoA1, a key player involved in high-density lipoprotein (HDL) regulation exists in structurally diverse forms with varying degree of cholesterol association, and each state is associated with different functional properties. While disc-shaped HDL and its oligomeric ApoA1 protein components have been the focus of several investigations, structural properties of monomeric ApoA1 are poorly understood. Here, we undertook large-scale structural analysis of ApoA1 in apo and cholesterol-bound forms using tens of independent simulations with total computing time exceeding 50 s. Examination of multiple lipid-free trajectories of monomeric ApoA1 revealed a common conformation, with distinct spatial proximity between N- and C-terminal domains. With incorporation of physiologically known cholesterol concentration ({approx}100 cholesterol molecules) in ApoA1 simulations, the monomeric protein spontaneously formed an open circular topology. Remarkably, these drastic structural perturbations are driven by specific binding site at C-terminal and a novel cholesterol binding site at the N-terminal. We proposed a mechanism of stage-wise opening of ApoA1 and demonstrated that less cholesterol concentration around interaction sites or mutation within N-terminal binding sites does not lead to open bell-shaped topology. The kinetic barriers between open and closed-states also showed an ensemble of loosely packed helix bundle (H1-H7; H4-H7) that posed as a slow-intermediate step. Lastly we performed complementary experiments, including ITC and CD measurements to confirm that structural changes are induced by ligand association and not driven by random hydrophobic effect. Collectively, our study suggests a previously unknown mechanism of cholesterol sequestering by ApoA1 that could directly aid in developing modulators for cholesterol efflux with chronic cardiovascular diseases.

biophysics↗

bioRxiv2017

Atypical domain communication and domain functions of a Hsp110 chaperone

Hsp110s are well recognized nucleotide exchange factors (NEFs) of Hsp70s, in addition they are implicated in various aspects of cellular proteostasis as discrete chaperones with yet enigmatic molecular mechanism. Stark similarity in domain organization and structure between Hsp110s and Hsp70s, is easily discernible although the nature of domain communication and domain functions of Hsp110s are still puzzling. Here, we report atypical domain communication of yeast Hsp110, Sse1 using single molecule FRET, small angle X-ray scattering measurements (SAXS) and Molecular Dynamic simulations. Our data show that Sse1 lacks typical domain movements as exhibited by Hsp70s, albeit it undergoes unique structural alteration upon nucleotide and substrate binding. Hsp70-like domain-movements can be artificially salvaged in chimeric constructs of Hsp110-Hsp70 although such salvaging proves detrimental for the NEF activity of the protein. Furthermore, we show that substrate binding domain (SBD) of Hsp110, chaperones self, as well as foreign nucleotide binding domains (NBD). Interestingly, the substrate binding specificity of Hsp110 is largely determined by its NBD rather than SBD, the latter being the foremost substrate binding region for Hsp70s.

biochemistry↗