Subcellular Proteomics as a Unified Approach of Experimental Localizations and Computed Prediction Data for Arabidopsis and Crop Plants

In eukaryotic organisms, subcellular protein location is critical in defining protein function and understanding sub-functionalization of gene families. Some proteins have defined locations, whereas others have low specificity targeting and complex accumulation patterns. There is no single approach that can be considered entirely adequate for defining the in vivo location of all proteins. By combining evidence from different approaches, the strengths and weaknesses of different technologies can be estimated, and a location consensus can be built. The Subcellular Location of Proteins in Arabidopsis database ( http://suba.live/ ) combines experimental data sets that have been reported in the literature and is analyzing these data to provide useful tools for biologists to interpret their own data. Foremost among these tools is a consensus classifier (SUBAcon) that computes a proposed location for all proteins based on balancing the experimental evidence and predictions. Further tools analyze sets of proteins to define the abundance of cellular structures. Extending these types of resources to plant crop species has been complex due to polyploidy, gene family expansion and contraction, and the movement of pathways and processes within cells across the plant kingdom. The Crop Proteins of Annotated Location database ( http://crop-pal.org/ ) has developed a range of subcellular location resources including a species-specific voting consensus for 12 plant crop species that offers collated evidence and filters for current crop proteomes akin to SUBA. Comprehensive cross-species comparison of these data shows that the sub-cellular proteomes (subcellulomes) depend only to some degree on phylogenetic relationship and are more conserved in major biosynthesis than in metabolic pathways. Together SUBA and cropPAL created reference subcellulomes for plants as well as species-specific subcellulomes for cross-species data mining. These data collections are increasingly used by the research community to provide a subcellular protein location layer, inform models of compartmented cell function and protein-protein interaction network, guide future molecular crop breeding strategies, or simply answer a specific question-where is my protein of interest inside the cell?

CropPAL for discovering divergence in protein subcellular location in crops to support strategies for molecular crop breeding

Agriculture faces increasing demand for yield, higher plant-derived protein content and diversity while facing pressure to achieve sustainability. Although the genomes of many of the important crops have been sequenced, the subcellular locations of most of the encoded proteins remain unknown or are only predicted. Protein subcellular location is crucial in determining protein function and accumulation patterns in plants, and is critical for targeted improvements in yield and resilience. Integrating location data from over 800 studies for 12 major crop species into the cropPAL2020 data collection showed that while >80% of proteins in most species are not localised by experimental data, combining species data or integrating predictions can help bridge gaps at similar accuracy. The collation and integration of over 61 505 experimental localisations and more than 6 million predictions showed that the relative sizes of the protein catalogues located in different subcellular compartments are comparable between crops and Arabidopsis. A comprehensive cross-species comparison showed that between 50% and 80% of the subcellulomes are conserved across species and that conservation only depends to some degree on the phylogenetic relationship of the species. Protein subcellular locations in major biosynthesis pathways are more often conserved than in metabolic pathways. Underlying this conservation is a clear potential for subcellular diversity in protein location between species by means of gene duplication and alternative splicing. Our cropPAL data set and search platform (https://crop-pal.org) provide a comprehensive subcellular proteomics resource to drive compartmentation-based approaches for improving yield, protein composition and resilience in future crop varieties.

Disparity in the effects of two N-methyl nicotinamides on poly(ADP-ribose) synthetase and macromolecular synthesis in hepatomas

The inhibitory effects of nicotinamide analogs on the activity of poly(ADP-ribose)) synthetase were compared to effects on precursor incorporation into macromolecules in three lines of hepatoma cells (Morris hepatomas 5123C, 7777 and HTC). N'-methylnicotinamide was a less effective inhibitor of poly (ADP-ribose) synthetase than was 1-methylnicotinamide while both these compounds had smaller inhibitory effects on the enzyme than were seen with nicotinamide or 3-aminobenzamide. On the other hand, the incorporation of [3H]thymidine into DNA and of [3H]uridine into RNA were inhibited by N'-methylnicotinamide in the concentration range 2-20 mM but not by 1-methylnicotinamide. Under the conditions examined there were no significant effects on the incorporation of [14C]lysine and [3H]leucine in hepatoma cells. The data indicated that the inhibitory effect of N'-methylnicotinamide on nucleic acid synthesis may be unrelated to action on poly (ADP-ribose) synthetase.

Factors affecting the assay of histone H1 and polylysine by binding of Coomassie blue G

Although a mixture of calf thymus histones or the H2B and H4 fractions gave values in the Bradford assay that were similar to those for bovine serum albumin, low values were obtained with histone H1 and polylysine. The assay was found to be more sensitive for histone H1 and polylysine if the phosphoric acid concentration in the reagent was decreased or the polypeptide solutions contained low concentrations of nonionic detergents. Substitution of perchloric acid or hydrochloric acid for phosphoric acid and alcohol in the Coomassie blue G reagent provided an assay that was similar in sensitivity for histone H1 and a total histone mixture. It was suggested that the degree of metachromasia with Coomassie blue G may serve as a probe of conformational changes in histone H1.