Structural Basis for the Discriminative Recognition of N6-Methyladenosine RNA by the Human YT521-B Homology Domain Family of Proteins

N⁶-Methyladenosine (m⁶A) is the most abundant internal modification in RNA and is specifically recognized by YT521-B homology (YTH) domain-containing proteins. Recently we reported that YTHDC1 prefers guanosine and disfavors adenosine at the position preceding the m⁶A nucleotide in RNA and preferentially binds to the GG(m⁶A)C sequence. Now we systematically characterized the binding affinities of the YTH domains of three other human proteins and yeast YTH domain protein Pho92 and determined the crystal structures of the YTH domains of human YTHDF1 and yeast Pho92 in complex with a 5-mer m⁶A RNA, respectively. Our binding and structural data revealed that the YTH domain used a conserved aromatic cage to recognize m⁶A. Nevertheless, none of these YTH domains, except YTHDC1, display sequence selectivity at the position preceding the m⁶A modification. Structural comparison of these different YTH domains revealed that among those, only YTHDC1 harbors a distinctly selective binding pocket for the nucleotide preceding the m⁶A nucleotide.     

MiaB protein is a bifunctional radical-S-adenosylmethionine enzyme involved in thiolation and methylation of tRNA

The last biosynthetic step for 2-methylthio-N(6)-isopentenyl-adenosine (ms(2)i(6)A), present at position 37 in some tRNAs, consists of the methylthiolation of the isopentenyl-adenosine (i(6)A) precursor. In this work we have reconstituted in vitro the conversion of i(6)A to ms(2)i(6)A within a tRNA substrate using the iron-sulfur MiaB protein, S-adenosylmethionine (AdoMet), and a reducing agent. We show that a synthetic i(6)A-containing RNA corresponding to the anticodon stem loop of tRNA(Phe) is also a substrate. This study demonstrates that MiaB protein is a bifunctional system, involved in both thiolation and methylation of i(6)A. In this process, one molecule of AdoMet is converted to 5'-deoxyadenosine, probably through reductive cleavage and intermediate formation ofa5'-deoxyadenosyl radical as observed in other "Radical-AdoMet" enzymes, and a second molecule of AdoMet is used as a methyl donor as shown by labeling experiments. The origin of the sulfur atom is discussed.     

Drought-induced modifications of photosynthetic electron transport in intact leaves: Analysis and use of neural networks as a tool for a rapid non-invasive estimation

Water deficit is one of the most important environmental factors limiting sustainable crop yields and it requires a reliable tool for fast and precise quantification. In this work we use simultaneously recorded signals of photoinduced prompt fluorescence (PF) and delayed fluorescence (DF) as well as modulated reflection (MR) of light at 820nm for analysis of the changes in the photosynthetic activity in detached bean leaves during drying. Depending on the severity of the water deficit we identify different changes in the primary photosynthetic processes. When the relative water content (RWC) is decreased to 60% there is a parallel decrease in the ratio between the rate of excitation trapping in the Photosystem (PS) II reaction center and the rate of reoxidation of reduced PSII acceptors. A further decrease of RWC to 20% suppresses the electron transfer from the reduced plastoquinone pool to the PSI reaction center. At RWC below values 15%, the reoxidation of the photoreduced primary quinone acceptor of PSII, Q(A)(-), is inhibited and at less than 5%, the primary photochemical reactions in PSI and II are inactivated. Using the collected sets of PF, DF and MR signals, we construct and train an artificial neural network, capable of recognizing the RWC in a series of "unknown" samples with a correlation between calculated and gravimetrically determined RWC values of about R(2)≈0.98. Our results demonstrate that this is a reliable method for determination of RWC in detached leaves and after further development it could be used for quantifying of drought stress of crop plants in situ. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.     

Diacerein modulates TLR4/ NF-κB/IL-1β and TRPC1/CHOP signalling pathways in gentamicin-induced parotid toxicity in rats

The present study aimed to identify the possible protective effect of diacerein (DIA) on gentamicin (GNT)-induced parotid toxicity in rats. DIA was administered in the presence and absence of GNT. Thirty-two Wistar adult male rats were randomly arranged into four groups: control, DIA (50 mg/kg/day), GNT (100 mg/kg) and GNT+DIA groups for 8 days. Parotid oxidative stress parameters, besides inflammatory and apoptotic biomarkers, were evaluated. Salivary flow rate, transient receptor potential canonical 1 (TRCP1), and C/EBP homologous protein (CHOP) in parotid tissue were measured. A parotid histopathological examination and an interleukin-1 beta (IL-1β) immunohistochemical study were also performed. GNT significantly increased parotid oxidative stress, inflammatory, apoptotic and CHOP biomarkers with decreased salivary flow rate and TRCP1 level. A histopathological picture of parotid damage and high IL-1β immunoexpression were detected. DIA significantly normalized the distributed oxidative, inflammatory and apoptotic indicators, CHOP and TRCP1, with a prompt improvement in the histopathological picture and a decrease in IL-1β immunoexpression. These results reported that DIA protects against GNT-induced parotid toxicity via modulation of TLR4/NF-κB/IL-1β and TRPC1/CHOP signalling pathways.     

Chlorophyll fluorescence as a tool for nutrient status identification in rapeseed plants

In natural conditions, plants growth and development depends on environmental conditions, including the availability of micro- and macroelements in the soil. Nutrient status should thus be examined not by establishing the effects of single nutrient deficiencies on the physiological state of the plant but by combinations of them. Differences in the nutrient content significantly affect the photochemical process of photosynthesis therefore playing a crucial role in plants growth and development. In this work, an attempt was made to find a connection between element content in (i) different soils, (ii) plant leaves, grown on these soils and (iii) changes in selected chlorophyll a fluorescence parameters, in order to find a method for early detection of plant stress resulting from the combination of nutrient status in natural conditions. To achieve this goal, a mathematical procedure was used which combines principal component analysis (a tool for the reduction of data complexity), hierarchical k-means (a classification method) and a machine-learning method—super-organising maps. Differences in the mineral content of soil and plant leaves resulted in functional changes in the photosynthetic machinery that can be measured by chlorophyll a fluorescent signals. Five groups of patterns in the chlorophyll fluorescent parameters were established: the ‘no deficiency’, Fe-specific deficiency, slight, moderate and strong deficiency. Unfavourable development in groups with nutrient deficiency of any kind was reflected by a strong increase in F _o and ΔV/Δt ₀ and decline in φ _Po, φ _Eo δ _Ro and φ _Ro. The strong deficiency group showed the suboptimal development of the photosynthetic machinery, which affects both PSII and PSI. The nutrient-deficient groups also differed in antenna complex organisation. Thus, our work suggests that the chlorophyll fluorescent method combined with machine-learning methods can be highly informative and in some cases, it can replace much more expensive and time-consuming procedures such as chemometric analyses.     

Improving water quality in polluated drains with free water surface constructed wetlands

In Egypt, disposing of partially treated or untreated domestic and industrial wastewater into agricultural drains deteriorates their water quality. A growing interest in effective low-cost treatment of polluted water and wastewater has resulted in many studies on constructed wetlands.This study evaluates free water surface constructed wetlands (by far the largest application project is named “Lake Manzala Engineered Wetland [Egypt]”) utilized to improve the water quality in Bahr El Baqar drain, which is located at the northeastern edge of the Nile Delta. This drain discharges its water into Manzala Lake, which in turn has many fishing activities and is connected to the Mediterranean Sea. The full capacity of the constructed wetland system is 25,000 m³/day. Three various flow rate wetlands were investigated; five wetland beds of high flow rate of 0.344 m³/m²-day, five wetland beds of low flow rate of 0.048 m³/m²-day and reciprocated cells of flow of 500 m³/day.The concentrations of different contaminants along the constructed wetlands system were measured to determine the treatment efficiency. The effluent was compared with the Egyptian standards of water quality in agricultural drains (Law 48/1982). Due to the high percentage of the agricultural water drain, the concentrations of contaminants in the influent were relatively low. The percentages of removal for the different contaminants were BOD₅: 52%, COD: 50%, TSS: 87%, TDS: 32%, NH₄-N: 66%, PO₄: 52%, Fe: 51%, Cu: 36%, Zn: 47% and Pb: 52%. The natural vegetation considerably increased the value of dissolved oxygen in the treated effluent. There were little differences in the removal efficiency between the high and low flow rates beds in the system.