Recent advances in genome-scale modeling of proteome allocation. Issue 26 (June 2021)

• Record Type: Journal Article
• Authors: Dahal, Sanjeev; Zhao, Jiao; Yang, Laurence
• Is Part Of: Current opinion in systems biology. Issue 26(2021)
• Page Start: 39
• Page End: 45
• Publication Date: 2021-06
• Subjects: Proteome allocation -- Stress response -- Genome-scale modeling -- Cell metabolism -- Multiscale modeling -- Protein expression; Systems biology -- Periodicals; 570
• DOI: 10.1016/j.coisb.2021.04.002
• Languages: English
• ISSNs: 2452-3100

Abstract

Abstract: Genome-scale models (GEMs) have been expanded to compute both the metabolic and proteomic states of a cell in different conditions. These multiscale models called GEMs of metabolism and macromolecular expression (ME-models) expand the scope of GEMs and provide greater predictive abilities and therefore are being increasingly used in system understanding of microbial biology. In this review, we describe ME-models, their advantages, and computational advances. We then describe extensions of ME-models to model stress response and a related human red blood cell model that integrates metabolism and macromolecular mechanisms. Finally, we discuss how ME-models were recently used to explain resource allocation trade-offs for microbial growth in adaptively evolved strains, in synthetic communities, and under stress.