{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T04:23:40Z","timestamp":1771561420132,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008596","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,1,29]],"date-time":"2021-01-29T00:00:00Z","timestamp":1611878400000}}],"reference-count":82,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2021,1,19]],"date-time":"2021-01-19T00:00:00Z","timestamp":1611014400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Novo Nordisk Foundation \/ Center for Biosustainability at the Technical University of Denmark","award":["NNF10CC1016517"],"award-info":[{"award-number":["NNF10CC1016517"]}]},{"DOI":"10.13039\/100000057","name":"NIH National Institute of General Medical Sciences","doi-asserted-by":"crossref","award":["NIH R01 GM057089"],"award-info":[{"award-number":["NIH R01 GM057089"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>The fitness landscape is a concept commonly used to describe evolution towards optimal phenotypes. It can be reduced to mechanistic detail using genome-scale models (GEMs) from systems biology. We use recently developed GEMs of Metabolism and protein Expression (ME-models) to study the distribution of<jats:italic>Escherichia coli<\/jats:italic>phenotypes on the rate-yield plane. We found that the measured phenotypes distribute non-uniformly to form a highly stratified fitness landscape. Systems analysis of the ME-model simulations suggest that this stratification results from discrete ATP generation strategies. Accordingly, we define \u201caero-types\u201d, a phenotypic trait that characterizes how a balanced proteome can achieve a given growth rate by modulating 1) the relative utilization of oxidative phosphorylation, glycolysis, and fermentation pathways; and 2) the differential employment of electron-transport-chain enzymes. This global, quantitative, and mechanistic systems biology interpretation of fitness landscape formed upon proteome allocation offers a fundamental understanding of bacterial physiology and evolution dynamics.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1008596","type":"journal-article","created":{"date-parts":[[2021,1,19]],"date-time":"2021-01-19T18:49:57Z","timestamp":1611082197000},"page":"e1008596","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":18,"title":["Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2089-1288","authenticated-orcid":true,"given":"Ke","family":"Chen","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3720-4301","authenticated-orcid":true,"given":"Amitesh","family":"Anand","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3681-0446","authenticated-orcid":true,"given":"Connor","family":"Olson","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3240-3659","authenticated-orcid":true,"given":"Troy E.","family":"Sandberg","sequence":"additional","affiliation":[]},{"given":"Ye","family":"Gao","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4302-9052","authenticated-orcid":true,"given":"Nathan","family":"Mih","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2357-6785","authenticated-orcid":true,"given":"Bernhard 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