Predicted effects on herbicide binding of amino acid substitutions in the D1 protein of photosystem II

6-Ethoxy-4- N-(2-morpholin-4-ylethyl) -2-N-propan-2-yl-1,3, 5-triazine-2, 4-diamine endows herbicidal activity against Phalaris minor a weed of wheat crop field: An in -silico and experimental approaches of herbicide discovery

Phalaris minor is a major weed of wheat crop which has evolved resistance against herbicides. Isoproturon is the most accepted herbicide developed resistance in 1992. Later, introduced herbicides also developed resistance and cross-resistance to their respective binding sites. Isoproturon binds at the Q_B binding site of the D1 protein of photosystem-II (PS-II), which blocks the electron transfer in photosynthesis. In this work, we have carried out a series of computational studies to prioritize the promising herbicides against D1 protein of P. minor. Through the computational studies, twenty-four lead molecules are prioritized which have shown a higher binding affinity and inhibition constant than the reference ligand molecule. The binding and conformational stability of docked complexes was evaluated by molecular dynamics simulations and binding free energy calculations i.e., MM/PBSA. A list of amino acids such as Ala225, Ser226, Phe227, and Asn229 present in the binding site of protein is obtained to be playing an important role in the stability of the protein-lead complex via hydrogen bond and π-π interactions. Binding free energy calculation revealed that the selected lead molecule binding is energetically favorable and driven by electrostatic interactions. Among 24 leads, computational results have uncovered eight promising compounds as potential herbicides which have shown comparable physiochemical profile, better docking scores, system stability, H-bond occupancy, and binding free energy than terbutryn, a reference molecule. These prioritized molecules were custom synthesized and evaluated for their herbicidal activity and specificity through whole plant assay under laboratory-controlled conditions. The lead molecule ELC5 (6-ethoxy-4-N-(2-morpholin-4-ylethyl)-2-N-propan-2-yl-1,3,5-triazine-2,4-diamine) has shown comparable activity to the reference herbicide(isoproturon) against P. minor.

Implications of nighttime temperature on metamitron impacts on the photosynthetic machinery functioning of Malus x domestica Borkh

Metamitron (MET) is a fruitlet thinning compound for apple trees, needing better understanding of its action on leaf energy metabolism, depending on nighttime temperature. A trial under environmental controlled conditions was set with 'Golden Reinders' potted trees, under 25/7.5 and 25/15 °C (diurnal/nighttime temperature), with (MET, 247.5 ppm) or without (CTR) application, and considering the monitoring of photosynthetic and respiration components from day 1 (D1) to 14 (D14). Net photosynthesis (P_n) decline promoted by MET after D1 was not stomatal related. Instead, non-stomatal constraints, reflected on the photosynthetic capacity (A_max), included a clear photosystem (PS) II inhibition (but barely of PSI), as shown by severe reductions in thylakoid electron transport at PSII level, maximal (F_v/F_m) and actual (F_v'/F_m') PSII photochemical efficiencies, estimate of quantum yield of linear electron transport (Y_(II)), and the rise in PSII photoinhibition status (F_s/F_m' and PI_Chr) and uncontrolled energy dissipation (Y_(NO)). To P_n inhibition also contributed the impact in RuBisCO along the entire experiment, regardless of night temperature, here reported for the first time. Globally, MET impact on the photosynthetic parameters was usually greater under 7.5 °C, with maximal impacts between D4 and D7, probably associated to a less active metabolism at lower temperature. Cellular energy metabolism was further impaired under 7.5 °C, through moderate inhibition of NADH-dependent malate dehydrogenase (MDH) and pyruvate kinase (PK) enzymes involved in respiration, in contrast with the increase of dark respiration in MET 7.5 until D7. The lower impact on PK and MDH under 15 °C and a likely global higher active metabolism at that temperature would agree with the lowest sucrose levels in MET 15 at D4 and D7. Our findings showed that MET alters the cell energy machinery in a temperature dependent manner, affecting the sucrose balance mainly at 15 °C, justifying the observed greater thinning potential.

Biotechnological Advances in the Design of Algae-Based Biosensors

In addition to their use in biomass production and bioremediation, algae have been extensively exploited in biosensing applications. Algae-based biosensors have demonstrated potential for sensitive, sustainable, and multiplexed detection of analytes of agroenvironmental and security interest. Their advantages include the availability of different algal bioreceptors including whole cells and their photosynthetic subcomponents, their potential to be integrated into dual transduction miniaturized devices, and the opportunity for continuous environmental monitoring. Despite obstacles including limited stability and selectivity, algae-based biosensing is a realistic prospect that has some recent effective applications. Strategic exploitation of cutting-edge technologies including materials science, nanotechnology, microfluidics, and genome editing will help to achieve the full potential of algae-based sensors.

Modeling the quinone-B binding site of the photosystem-II reaction center using notions of complementarity and contact-surface between atoms

Functional identity and significant similarities in cofactors and sequence exist between the L and M reaction center proteins of the photosynthetic bacteria and the D1 and D2 photosystem-II reaction center proteins of cyanobacteria, algae, and plants. A model of the quinone (QB) binding site of the D1 protein is presented based upon the resolved structure of the QB binding pocket of the L subunit, and introducing novel quantitative notions of complementarity and contact surface between atoms. This model, built without using traditional methods of molecular mechanics and restricted to residues in direct contact with QB, accounts for the experimentally derived functional state of mutants of the D1 protein in the region of QB. It predicts the binding of both the classical and phenol-type PSII herbicides and rationalizes the relative levels of tolerance of mutant phenotypes.

Thermoluminescence and flash-induced oxygen yield in herbicide resistant mutants of the D1 protein in Synechococcus PCC7942

Several strains of Synechococcus PCC7942 carrying point mutations in the gene psbA were studied by thermoluminescence and polarographic measurement of flash-induced oxygen yield. The following results were obtained: (a) Replacement of Ser-264 in D1 by Ala (mutant Di1) or Gly (mutant G264) resulting in DCMU and atrazine resistance leads to a downshift of the thermoluminescence (TL) B-band peak temperature from 40 degrees C in wild-type thylakoids to about 30 degrees C. In dark adapted samples of both mutants the TL and oxygen yield pattern induced by a train of single turnover flashes were strongly damped indicative of a high miss factor. (b) In contrast to Ser-264 mutants, replacement of Phe-255 in D1 by Tyr (mutant Tyr5) induced strong resistance to atrazine but not to DCMU and did not affect the peak termperature of the B-band and the flash-induced TL and oxygen yield patterns. In this respect mutant Tyr5 resembles the wild type. (c) No significant differences have been found between strains with single site mutations in psbAI and normal psbAII/psbAIII genes, and strains with same mutations in psbAI but additional deletion of psbAII and psbAIII. Obviously in strains were psbAI is present, PS II complexes containing gene products of psbAII and psbAIII are not assembled in detectable amounts. (d) Strains with double mutations at positions 264 and 255 display a downshift of the B-band peak temperature. Their oscillatory patterns of B-band intensity and oxygen yield are highly damped. This behaviour is similar to strains D1 and G264 which are modified at position 264 only. We extend reports on additivity of mutation effects on herbicide binding to binding of QB. (e) Mutations at the QB site not only influence the binding of QB and herbicides but also change the thermoluminescence quantum yield and the lifetimes of the redox states S2 and S3 of the water oxidase. This finding might indicate long ranging effects on Photosystem II exerted by structural modifications of the QB site. From these data we conclude that Ser-264 is essential for binding of atrazine, DCMU and QB, whereas Phe-255 is involved in atrazine binding and its substitution by Tyr does not markedly affect QB or DCMU binding in Synechococcus PCC7942.

Binding affinity of bicarbonate and formate in herbicide-resistant D1 mutants of Synechococcus sp. PCC 7942

We examined the effects of mutations at amino acid residues S264 and F255 in the D1 protein on the binding affinity of the stimulatory anion bicarbonate and inhibitory anion formate in Photosystem II (PS II) in Synechococcus sp. PCC 7942. Measurements on the rates of oxygen evolution in the wild type and mutant cells in the presence of different concentrations of formate with a fixed bicarbonate concentration and vice versa, analyzed in terms of an equilibrium activator-inhibitor model, led to the conclusion that the equilibrium dissociation constant for bicarbonate is increased in the mutants, while that of the formate remains unchanged (11±0.5 mM). The hierarchy of the equilibrium dissociation constant for bicarbonate (highest to lowest, ±2 μM) was: D1-F255L/S264A (46 μM)>D1-F255Y/ S264A (31 μM)≈D1-S264A (34 μM)≈D1-F255Y (33 μM)>wild type (25 μM). The data suggest the importance of D1-S264 and D1-F255 in the bicarbonate binding niche. A possible involvement of bicarbonate and these two residues in the protonation of QB (-), the reduced secondary plastoquinone of PS II, in the D1 protein is discussed.

Analysis of a herbicide resistant mutant obtained by transformation of the Chlamydomonas chloroplast

A herbicide resistant Chlamydomonas double mutant (I219A264) has been obtained by transforming the psbA deletion mutant FuD7 with a cloned psbA gene fragment containing mutations in codons 219 and 264. Copies from both the recipient (FuD7) genome and the genome carrying the mutated psbA gene persist in the transformant. This stable heteroplasmic state appears to be required for photoautotrophic growth. Comparison of resistance profiles for classical and phenol-type inhibitors of the double mutant and the corresponding single mutants demonstrates independent, additive contributions of both amino acids to herbicide binding. The approach chosen here to modify the psbA gene should be useful in those cases where consequences of psbA gene manipulations are not predictable with respect to inhibitor resistance.