Nascentome Analysis Uncovers Futile Protein Synthesis in Escherichia coli

Although co-translational biological processes attract much attention, no general and easy method has been available to detect cellular nascent polypeptide chains, which we propose to call collectively a “nascentome.” We developed a method to selectively detect polypeptide portions of cellular polypeptidyl-tRNAs and used it to study the generality of the quality control reactions that rescue dead-end translation complexes. To detect nascent polypeptides, having their growing ends covalently attached to a tRNA, cellular extracts are separated by SDS-PAGE in two dimensions, first with the peptidyl-tRNA ester bonds preserved and subsequently after their in-gel cleavage. Pulse-labeled nascent polypeptides of Escherichia coli form a characteristic line below the main diagonal line, because each of them had contained a tRNA of nearly uniform size in the first-dimension electrophoresis but not in the second-dimension. The detection of nascent polypeptides, separately from any translation-completed polypeptides or degradation products thereof, allows us to follow their fates to gain deeper insights into protein biogenesis and quality control pathways. It was revealed that polypeptidyl-tRNAs were significantly stabilized in E. coli upon dysfunction of the tmRNA-ArfA ribosome-rescuing system, whose function had only been studied previously using model constructs. Our results suggest that E. coli cells are intrinsically producing aberrant translation products, which are normally eliminated by the ribosome-rescuing mechanisms

Soil-water and solute movement under precision irrigation: knowledge gaps for managing sustainable root zones

Precision irrigation involves the accurate and precise application of water to meet the specific requirements of individual plants or management units and minimize adverse environmental impact. Under precision irrigation applications, water and associated solute movement will vary spatially within the root zone and excess water application will not necessarily result in deep drainage and leaching of salt below the root zone. This paper estimates that 10% of the irrigated land area (producing as much as 40% of the total annual revenue from irrigated land) could be adversely affected by root zone salinity resulting from the adoption of precision irrigation within Australia. The cost of increases in root zone salinisation due to inappropriate irrigation management in the Murray and Murrumbidgee irrigation areas was estimated at AUD 245 million (in 2000/01) or 13.5% of the revenue from these cropping systems. A review of soil–water and solute movement under precision irrigation systems highlights the gaps in current knowledge including the mismatch between the data required by complex, process-based soil–water or solute simulation models and the data that is easily available from soil survey and routine soil analyses. Other major knowledge gaps identified include: (a) effect of root distribution, surface evaporation and plant transpiration on soil wetted patterns, (b) accuracy and adequacy of using simple mean values of root zone soil salinity levels to estimate the effect of salt on the plant, (c) fate of solutes during a single irrigation and during multiple irrigation cycles, and (d) effect of soil heterogeneity on the distribution of water and solutes in relation to placement of water. Opportunities for research investment are identified across a broad range of areas including: (a) requirements for soil characterisation, (b) irrigation management effects, (c) agronomic responses to variable water and salt distributions in the root zone, (d) potential to scale or evaluate impacts at various scales, (e) requirements for simplified soil–water and solute modelling tools, and (f) the need to build skills and capacity in soil–water and solute modelling