{"doi":"10.1016/j.celrep.2023.113087","title":"Maximizing microbial bioproduction from sustainable carbon sources using iterative systems engineering","abstract":"Maximizing the production of heterologous biomolecules is a complex problem that can be addressed with a systems-level understanding of cellular metabolism and regulation. Specifically, growth-coupling approaches can increase product titers and yields and also enhance production rates. However, implementing these methods for non-canonical carbon streams is challenging due to gaps in metabolic models. Over four design-build-test-learn cycles, we rewire Pseudomonas putida KT2440 for growth-coupled production of indigoidine from para-coumarate. We explore 4,114 potential growth-coupling solutions and refine one design through laboratory evolution and ensemble data-driven methods. The final growth-coupled strain produces 7.3 g/L indigoidine at 77% maximum theoretical yield in para-coumarate minimal medium. The iterative use of growth-coupling designs and functional genomics with experimental validation was highly effective and agnostic to specific hosts, carbon streams, and final products and thus generalizable across many systems.","journal":"Cell Reports","year":2023,"id":322250,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":41,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9525,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1035719,"name":"Deepanwita Banerjee","orcid":"0000-0002-0083-0608","position":1,"is_corresponding":false},{"id":1035720,"name":"Javier Menasalvas","orcid":"0000-0002-4003-4999","position":2,"is_corresponding":false},{"id":913562,"name":"Yan Chen","orcid":"0009-0009-1387-4165","position":3,"is_corresponding":false},{"id":335307,"name":"Jennifer Gin","orcid":"0000-0001-5636-7563","position":4,"is_corresponding":false},{"id":1035721,"name":"Hemant Choudhary","orcid":"0000-0003-2847-3080","position":5,"is_corresponding":false},{"id":416294,"name":"Edward E. K. Baidoo","orcid":"0000-0001-5787-1219","position":6,"is_corresponding":false},{"id":321656,"name":"Jian-Hua Chen","orcid":"0000-0002-7998-0878","position":7,"is_corresponding":false},{"id":321657,"name":"Axel Ekman","orcid":"0000-0002-4210-2617","position":8,"is_corresponding":false},{"id":1025265,"name":"Ramu Kakumanu","orcid":"0000-0003-4984-7766","position":9,"is_corresponding":false},{"id":1036458,"name":"Yuzhong Liu Diercks","orcid":null,"position":10,"is_corresponding":false},{"id":1035722,"name":"Alex Codik","orcid":"0009-0000-7094-4443","position":11,"is_corresponding":false},{"id":79422,"name":"Carolyn A. Larabell","orcid":"0000-0002-6262-4789","position":12,"is_corresponding":false},{"id":840151,"name":"John M. Gladden","orcid":"0000-0002-6985-2485","position":13,"is_corresponding":false},{"id":1035723,"name":"Blake A. Simmons","orcid":"0000-0002-1332-1810","position":14,"is_corresponding":false},{"id":271245,"name":"Jay D. Keasling","orcid":"0000-0003-4170-6088","position":15,"is_corresponding":false},{"id":335308,"name":"Christopher J. Petzold","orcid":"0000-0002-8270-5228","position":16,"is_corresponding":false},{"id":560171,"name":"Aindrila Mukhopadhyay","orcid":"0000-0002-6513-7425","position":17,"is_corresponding":false},{"id":45099,"name":"Thomas Eng","orcid":"0000-0002-4974-3863","position":0,"is_corresponding":true}],"reference_count":101,"raw_metadata":null,"created_at":"2026-07-19T01:07:42.497873Z","pmid":"37665664","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}