Understanding the Positional Binding and Substrate Interaction of a Highly Thermostable GH10 Xylanase from Thermotoga maritima by Molecular Docking

Glycoside hydrolase family 10 (GH10) xylanases are responsible for enzymatic cleavage of the internal glycosidic linkages of the xylan backbone, to generate xylooligosaccharides (XOS) and xyloses. The topologies of active-site cleft determine the substrate preferences and product profiles of xylanases. In this study, positional bindings and substrate interactions of TmxB, one of the most thermostable xylanases characterized from Thermotoga maritima to date, was investigated by docking simulations. XOS with backbone lengths of two to five (X2–X5) were docked into the active-site cleft of TmxB by AutoDock The modeled complex structures provided a series of snapshots of the interactions between XOS and TmxB. Changes in binding energy with the length of the XOS backbone indicated the existence of four effective subsites in TmxB. The interaction patterns at subsites −2 to +1 in TmxB were conserved among GH10 xylanases whereas those at distal aglycone subsite +2, consisting of the hydrogen bond network, was unique for TmxB. This work helps in obtaining an in-depth understanding of the substrate-binding property of TmxB and provides a basis for rational design of mutants with desired product profiles

Effect of hydrogen sulfide (H2S) on the growth and development of tobacco seedlings in absence of stress

Abstract Background Hydrogen sulfide (H2S) is a novel signaling molecule involved in the growth and development of plants and their response to stress. However, the involvement of H2S in promoting the growth and development of tobacco plants is still unclear. Results In this study, we explored the effect of pre-soaking or irrigating the roots of tobacco plants with 0.0, 2.0, 4.0, 6.0, and 8.0 mM of sodium hydrosulfide (NaHS) on endogenous H2S production, antioxidant enzymatic and cysteine desulfhydrase activities, seed germination, agronomic traits, photosynthetic pigments contents, and root vigor. The results revealed that exogenous NaHS treatment could significantly promote endogenous H2S production by inducing gene expression of D/L-CD and the activities of D/L-CD enzymes. Additionally, a significant increase in the agronomic traits and the contents of photosynthetic pigments, and no significant difference in carotenoid content among tobacco plants treated with 0.0 to 8.0 mM of NaHS was observed. Additionally, a significant increase in the germination speed, dry weight, and vigor of tobacco seeds, whereas no significant effect on the percentage of seed germination was observed on NaHS treatment. Furthermore, NaHS treatment could significantly increase the activity of superoxide dismutase (SOD) and peroxidase (POD) enzymes, which reduces damage due to oxidative stress by maintaining reactive oxygen species homeostasis. Conclusions These results would aid in enhancing our understanding of the involvement of H2S, a novel signaling molecule to promote the growth and development of tobacco plants

Toward Understanding the Dynamics of Microbial Communities in an Estuarine System

<div><p>Community assembly theories such as species sorting theory provide a framework for understanding the structures and dynamics of local communities. The effect of theoretical mechanisms can vary with the scales of observation and effects of specific environmental factors. Based on 16S rRNA gene tag pyrosequencing, different structures and temporal succession patterns were discovered between the surface sediments and bottom water microbial communities in the Pearl River Estuary (PRE). The microbial communities in the surface sediment samples were more diverse than those in the bottom water samples, and several genera were specific for the water or sediment communities. Moreover, water temperature was identified as the main variable driving community dynamics and the microbial communities in the sediment showed a greater temporal change. We speculate that nutrient-based species sorting and bacterial plasticity to the temperature contribute to the variations observed between sediment and water communities in the PRE. This study provides a more comprehensive understanding of the microbial community structures in a highly dynamic estuarine system and sheds light on the applicability of ecological theoretical mechanisms.</p></div

Summary of RDA.

<p>RDA was performed for each of the 4 factors (sample type, season, station, and physicochemical parameters) and for all factors to study the variance in the microbial data. Only the first and second axes are shown. Permutation test was performed to assess the significance of the relationship between the environmental factors and the variance.</p

Maps showing the sampling stations.

<p>The surface sediment and its overlying bottom water were collected from 6 stations (E1, S4, S9, S16, S19 and S21) along a transect from the Pearl River Estuary (PRE) to the South China Sea.</p

Taxonomic classification of qualified bacterial reads retrieved from samples of the surface sediment and its overlying bottom water at different stations in (a) summer and (b) winter.

<p>Qualified reads were assigned to different phyla using the RDP classifier in the QIIME pipeline with a confidence threshold of 80%. “W” represents water samples, “S” represents sediment samples, “09” represents samples collected in the summer of 2009, and “10” represents samples collected in the winter of 2010.</p

Environmental parameters measured from the overlying water.

<p>(a) Depth, (b) salinity, (c) temperature, (d) pH, and (e) dissolved oxygen were measured using a YSI. Nutrients, including (f) PO₄, (h) SiO₄, (i) NH₄, and (j) NO₃+NO₂, were measured using a nutrient autoanalyzer. (g) Chlorophyll a (Chl a) content was determined with a fluorometer.</p

Microbial diversity in bottom water and surface sediments from the Pearl River Estuary in summer and winter.

<p>OTUs were determined at a similarity level of 97%. Values are based on data normalized to the smallest library size (ie, 7841 reads).</p