The structural basis of the thermostability of SP1, a novel plant (Populus tremula) boiling stable protein

We previously reported on a new boiling stable protein isolated from aspen plants (Populus tremula), which we named SP1. SP1 is a stress-related protein with no significant sequence homology to other stress-related proteins. It is a 108-amino-acid hydrophilic polypeptide with a molecular mass of 12.4 kDa (Wang, W. X., Pelah, D., Alergand, T., Shoseyov, O., and Altman, A. (2002) Plant Physiol. 130, 865-875) and is found in an oligomeric form. Preliminary electron microscopy studies and matrix-assisted laser desorption ionization time-of-flight mass spectrometry experiments showed that SP1 is a dodecamer composed of two stacking hexamers. We performed a SDS-PAGE analysis, a differential scanning calorimetric study, and crystal structure determination to further characterize SP1. SDS-PAGE indicated a spontaneous assembly of SP1 to one stable oligomeric form, a dodecamer. Differential scanning calorimetric showed that SP1 has high thermostability i.e. Tm of 107 degrees C (at pH 7.8). The crystal structure of SP1 was initially determined to 2.4 A resolution by multi-wavelength anomalous dispersion method from a crystal belonging to the space group I422. The phases were extended to 1.8 A resolution using data from a different crystal form (P21). The final refined molecule includes 106 of the 108 residues and 132 water molecules (on average for each chain). The R-free is 20.1%. The crystal structure indicated that the SP1 molecule has a ferredoxin-like fold. Strong interactions between each two molecules create a stable dimer. Six dimers associate to form a ring-like-shaped dodecamer strongly resembling the particle visualized in the electron microscopy studies. No structural similarity was found between the crystal structure of SP1 and the crystal structure of other stress-related proteins such as small heat shock proteins, whose structure has been already determined. This structural study further supports our previous report that SP1 may represent a new family of stress-related proteins with high thermostability and oligomerization.     

Rare and localized events stabilize microbial community composition and patterns of spatial self-organization in a fluctuating environment

Spatial self-organization is a hallmark of surface-associated microbial communities that is governed by local environmental conditions and further modified by interspecific interactions. Here, we hypothesize that spatial patterns of microbial cell-types can stabilize the composition of cross-feeding microbial communities under fluctuating environmental conditions. We tested this hypothesis by studying the growth and spatial self-organization of microbial co-cultures consisting of two metabolically interacting strains of the bacterium Pseudomonas stutzeri. We inoculated the co-cultures onto agar surfaces and allowed them to expand (i.e. range expansion) while fluctuating environmental conditions that alter the dependency between the two strains. We alternated between anoxic conditions that induce a mutualistic interaction and oxic conditions that induce a competitive interaction. We observed co-occurrence of both strains in rare and highly localized clusters (referred to as “spatial jackpot events”) that persist during environmental fluctuations. To resolve the underlying mechanisms for the emergence of spatial jackpot events, we used a mechanistic agent-based mathematical model that resolves growth and dispersal at the scale relevant to individual cells. While co-culture composition varied with the strength of the mutualistic interaction and across environmental fluctuations, the model provides insights into the formation of spatially resolved substrate landscapes with localized niches that support the co-occurrence of the two strains and secure co-culture function. This study highlights that in addition to spatial patterns that emerge in response to environmental fluctuations, localized spatial jackpot events ensure persistence of strains across dynamic conditions.Subject terms: Microbial ecology, Biofilms     

Cyanamide mediated syntheses under plausible primitive earth conditions

Summary A mixture of ammonium palmitate,¹⁴C-sn-glycero-1(3)-phosphate, cyanimide and imidazole when heated for several hours formed significant quantities of phospholipids. These reaction products were shown by chromatographic, chemical and enzymatic procedures to be monopalmitoylglycerophosphate (MPGP), dipalmitoylglycerophosphate (DPGP) and monopalmitoyl cyclic glycerophosphate (cMPGP). A portion of the MPGP and DPGP possessed the same steric configuration as naturally occurring lysophosphatidic acid and phosphatidic acid. The yield of total phospholipid was maximal at temperatures between 60° and 90° after 8 h. When ratios of reactants were varied, up to 45% of radioactive glycerophosphate was converted into phospholipids. The average proportions of individual phosphatidic acids were: 60% MPGP, 27% DPGP and 13% cMPGP. Evidence was obtained for a synergistic relationship between cyanamide and imidazole in promoting the formation of phosphatidic acids. These results suggest that phosphatidic acids, which are essential precursors for the biochemical synthesis of more complex membrane phospholipids, could have been produced on the primitive Earth.The following abbreviations are employed: for phospholipid standards with designated steric configuration LPA lysophosphatidic acid (1-acyl-sn-glycero-3-phosphate) - PA phosphatidic acid (1, 2-di-acyl-sn-glycero-3-phosphate) - MPGP monopalmitoylglycerophosphate - cMPGP monopalmitoyl cyclic glycerophosphate (1(3)-acyl-sn-glycero-2,3 (1,2)-cyclic phosphate) - DPGP dipalmitoylglycerophosphate - GP glycerophosphate - cGP cyclic glycerophosphate (sn-glycero-2,3 (1,2)-cyclic phosphate) - TLC thin layer chromatography To whom reprint requests should be addressed.     

Plant traits shape the effects of tidal flooding on soil and plant communities in saltmarshes

Saltmarshes are recognised worldwide to be among the most complex ecosystems, where several environmental factors concur to sustain their fragile functioning. Among them, soil–plant interactions are pivotal but often overlooked. The aim of this work was to use a structural equation modelling (SEM) approach to get new insight into soil–plant interactions, focusing on the effect of plant traits and abundance on soil, and test the effect of soil and/or plants on the entire community, monitoring changes in plant richness. The target halophytes Limonium narbonense and Sarcocornia fruticosa were sampled in the Marano and Grado lagoon (northern Adriatic Sea). Basal leaves of L. narbonense and green shoots of S. fruticosa were used to estimate plant growth, while the abundance of both species was used as a proxy of species competition. SEM was applied to test relationships between predictors and response variables in a single causal network. The flooding period (hydroperiod) negatively affected plant growth and soil properties, whereas plants decreased the intensity of soil reduction. Flooding did not directly affect species abundance or diversity, whose changes were instead driven by plant traits. The direct relationships between plant traits and species richness highlighted that species competition could be even more important than environmental stresses in defining plant diversity and zonation.     

Hyphomycetes fungi in rainwater failling from building roofs

The presence of 33 Hyphomycetes species was noted in rainwater falling from six roof types. The following fungi were recorded for the first time from Poland:Dactylaria lunata, Hyaloscypha zalewskii, Scolecobasidium flagelliferum andWiesneriomyces laurinus.     

SARS-CoV-2 receptor binding domain fusion protein efficiently neutralizes virus infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. Currently, as dangerous mutations emerge, there is an increased demand for specific treatments for SARS-CoV-2 infected patients. The spike glycoprotein on the virus envelope binds to the angiotensin converting enzyme 2 (ACE2) on host cells through its receptor binding domain (RBD) to mediate virus entry. Thus, blocking this interaction may inhibit viral entry and consequently stop infection. Here, we generated fusion proteins composed of the extracellular portions of ACE2 and RBD fused to the Fc portion of human IgG1 (ACE2-Ig and RBD-Ig, respectively). We demonstrate that ACE2-Ig is enzymatically active and that it can be recognized by the SARS-CoV-2 RBD, independently of its enzymatic activity. We further show that RBD-Ig efficiently inhibits in-vivo SARS-CoV-2 infection better than ACE2-Ig. Mechanistically, we show that anti-spike antibody generation, ACE2 enzymatic activity, and ACE2 surface expression were not affected by RBD-Ig. Finally, we show that RBD-Ig is more efficient than ACE2-Ig at neutralizing high virus titers. We thus propose that RBD-Ig physically blocks virus infection by binding to ACE2 and that RBD-Ig should be used for the treatment of SARS-CoV-2-infected patients.     

Epigenome Microarray Platform for Proteome-Wide Dissection of Chromatin-Signaling Networks

Knowledge of protein domains that function as the biological effectors for diverse post-translational modifications of histones is critical for understanding how nuclear and epigenetic programs are established. Indeed, mutations of chromatin effector domains found within several proteins are associated with multiple human pathologies, including cancer and immunodeficiency syndromes. To date, relatively few effector domains have been identified in comparison to the number of modifications present on histone and non-histone proteins. Here we describe the generation and application of human modified peptide microarrays as a platform for high-throughput discovery of chromatin effectors and for epitope-specificity analysis of antibodies commonly utilized in chromatin research. Screening with a library containing a majority of the Royal Family domains present in the human proteome led to the discovery of TDRD7, JMJ2C, and MPP8 as three new modified histone-binding proteins. Thus, we propose that peptide microarray methodologies are a powerful new tool for elucidating molecular interactions at chromatin.     

A transfer function method for the continuous assessment of baroreflex control of renal sympathetic nerve activity in rats

The present study examined whether the gain of the transfer function relating cardiac-related rhythm of renal sympathetic nerve activity (RSNA) to arterial pressure (AP) pulse might serve as a spontaneous index of sympathetic baroreflex sensitivity (BRS). AP and RSNA were simultaneously recorded in conscious rats, either baroreceptor-intact (control, n = 11) or with partial denervation of baroreflex afferents [aortic baroreceptor denervated (ABD; n = 10)] during 1-h periods of spontaneous activity. Transfer gain was calculated over 58 adjacent 61.4-s periods (segmented into 10.2-s periods). Coherence between AP and RSNA was statistically (P < 0.05) significant in 90 +/- 3% and 56 +/- 10% of cases in control and ABD rats, respectively. Transfer gain was higher (P = 0.0049) in control [2.39 +/- 0.13 normalized units (NU)/mmHg] than in ABD (1.48 +/- 0.22 NU/mmHg) rats. In the pooled study sample, transfer gain correlated with sympathetic BRS estimated by the vasoactive drug injection technique (R = 0.75; P < 0.0001) and was inversely related to both time- (standard deviation; R = -0.74; P = 0.0001) and frequency-domain [total spectral power (0.00028-2.5 Hz); R = -0.82; P < 0.0001] indices of AP variability. In control rats, transfer gain exhibited large fluctuations (coefficient of variation: 34 +/- 3%) that were not consistently related to changes in the mean level of AP, heart rate, or RSNA. In conclusion, the transfer function method provides a continuous, functionally relevant index of sympathetic BRS and reveals that the latter fluctuates widely over time.     

Wide vessels sustain marginal transpiration flux and do not optimize inefficient gas exchange activity under impaired hydraulic control and salinity

Plants optimize water use and carbon assimilation via transient regulation of stomata resistance and by limiting hydraulic conductivity in a long-term response of xylem anatomy. We postulated that without effective hydraulic regulation plants would permanently restrain water loss and photosynthetic productivity under salt stress conditions. We compared wild-type tomatoes to a transgenic type (TT) with impaired stomatal control. Gas exchange activity, biomass, starch content, leaf area and root traits, mineral composition and main stems xylem anatomy and hydraulic conductivity were analyzed in plants exposed to salinities of 1 and 4 dS m⁻¹ over 60 days. As the xylem cannot easily readjust to different environmental conditions, shifts in its anatomy and the permanent effect on plant hydraulic conductivity kept transpiration at lower levels under unstressed conditions and maintained it under salt-stress, while sustaining higher but inefficient assimilation rates, leading to starch accumulation and decreased plant biomass, leaf and root area and root length. Narrow conduits in unstressed TT plants were related to permanent restrain of hydraulic conductivity and plant transpiration. Under salinity, TT plants followed the atmospheric water demand, sustained similar transpiration rate from unstressed to salt-stressed conditions and possibly maintained hydraulic integrity, due to likely impaired hydraulic regulation, wider conduits and higher hydraulic conductivity. The accumulation of salts and starch in the TT plants was a strong evidence of salinity tolerance via osmotic regulation, also thought to help to maintain the assimilation rates and transpiration flux under salinity, although it was not translated into higher growth.