Visual account of protein investment in cellular functions

Abstract

Proteomics techniques generate an avalanche of data and promise to satisfy biologists' long-held desire to measure absolute protein abundances on a genome-wide scale. However, can this knowledge be translated into a clearer picture of how cells invest their protein resources? This article aims to give a broad perspective on the composition of proteomes as gleaned from recent quantitative proteomics studies. We describe proteomaps, an approach for visualizing the composition of proteomes with a focus on protein abundances and functions. In proteomaps, each protein is shown as a polygon-shaped tile, with an area representing protein abundance. Functionally related proteins appear in adjacent regions. General trends in proteomes, such as the dominance of metabolism and protein production, become easily visible. We make interactive visualizations of published proteome datasets accessible at www.proteomaps.net. We suggest that evaluating the way protein resources are allocated by various organisms and cell types in different conditions will sharpen our understanding of how and why cells regulate the composition of their proteomes.Voronoi treemap | functional classification | mass spectrometry | cell resource allocation | cellular economy

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitro k cat measurements

“…To achieve good coverage in other organisms, a parallel essential effort is a more comprehensive mapping between enzymes and their associated metabolic reactions. Although in E. coli most of the proteome has been characterized (46), limited gene annotations in other organisms may lead to biased predictions of k app , as one must know which enzymes support flux through a given metabolic reaction to infer the rate of the enzymes.…”

CTP:phosphocholine cytidylyltransferase: Function, regulation, and structure of an amphitropic enzyme required for membrane biogenesis

“…The isoforms encode proteins with highly conserved central catalytic and M-domains, but differ in length and sequence of the N and C-terminal regions. Quantitative proteomics has revealed that CCT enzymes are minor cellular constituents accounting for $0.005 percent of the total proteomes of cells from Homo sapiens, S. cerevisiae, and Arabidopsis thaliana [82].…”

Beyond Computational Genomics towards Systems Metabolomics for Precision Oncology

“…This capability depends upon the fact that metabolism plays a central role in living cells by supporting different relevant activities: utilization of nutrients to provide energy and building blocks for growth and proliferation, protection against external stress by generating appropriate homeostatic response. While in microbial cells about the 50% of proteome is allocated to metabolism, with 25% dedicated to glycolysis alone, in human cells, in which there is an average increase of about 100 fold of cellular protein content as compared to microbial cells, the aliquot of proteome dedicated to central carbon metabolism, energy metabolism, biosynthetic metabolism and other enzymes, still account for about 20% of the proteome, being very conspicuous the aliquot dedicated to transcription, translation, folding, sorting and degradation, and to cytoskeleton, while much smaller is the quantitative relevance of signaling, of course observing differences in the comparison of various types of human cells (56).…”