Raza, M. M. | Search bioRxiv

bioRxiv2022

Climate change, biotic yield gaps and disease pressure in cereal crops

Plant diseases are major causes of crop yield losses and exert a financial burden via expenditure on disease control. The magnitude of these burdens depends on biological, environmental and management factors, but this variation is poorly understood. Here we model the effects of weather on potential yield losses due to fungal plant pathogens (the biotic yield gap, Ygb) using experimental trials of fungicide-treated and untreated cereal crops in the UK, and project future Ygb under climate change. We find that Ygb varies between 10 and 20 % of fungicide-treated yields depending on crop, and increases under warmer winter and wetter spring conditions. Ygb will increase for winter wheat and winter barley under climate change, while declining for spring crops because drier summers offset the effects of warmer winters. Potential disease impacts are comparable in magnitude to the effects of suboptimal weather and crop varieties.

ecology↗

bioRxiv2021

An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor, to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.

biophysics↗