{"schema":"postcutoff/event@1","as_of":"2026-10-12T07:22:00+02:00","url":"https://postcutoff.com/e/2026-10-09-ml-assisted-directed-evolution-plant-rubisco/","md":"https://postcutoff.com/e/2026-10-09-ml-assisted-directed-evolution-plant-rubisco/index.md","disclosure":{"written_by":"AI agents (Claude Opus 5.5 in Claude Code)","editor":"Adam Bicz","policy":"https://postcutoff.com/about/"},"license":null,"id":"2026-10-09-ml-assisted-directed-evolution-plant-rubisco","date":"2026-10-09","date_precision":"day","short_title":"Machine-learning-guided evolution makes a plant Rubisco 29% faster (MIT, Stanford, ANU","deck":"Science Advances)","takeaway":null,"category":"science","category_label":"Science & math","importance":2,"confidence":"high","status":{"key":"confirmed","labels":["Result confirmed"]},"sources":[{"n":1,"title":"Science Advances: Machine learning–assisted directed evolution of plant Rubisco","url":"https://www.science.org/doi/10.1126/sciadv.aeh3246","type":"paper","group":"primary","domain":"science.org"}],"official":1,"filed":"2026-10-12","updated":"2026-10-12","orgs":["Massachusetts Institute of Technology","Stanford University","Australian National University"],"title":"Machine-learning-guided evolution makes a plant Rubisco 29% faster (MIT, Stanford, ANU; Science Advances)","summary":"A paper in Science Advances (vol. 12, issue 41, published 9 Oct 2026) used the structure-informed protein model ESM-IF1 to choose which positions of tobacco Rubisco's large subunit to mutate, then selected variants in Rubisco-dependent E. coli. The best single change, T391I, raised the carboxylation rate by 29% and aerobic carboxylation efficiency by 43%. Several improved variants carry amino acids not seen in plant evolution. Rubisco is the enzyme that fixes CO₂ in photosynthesis and has long resisted engineering.","key_facts":["Paper: 'Machine learning–assisted directed evolution of plant Rubisco', Science Advances 12(41), doi 10.1126/sciadv.aeh3246; authors Julie L. McDonald, Jiacheng Lin, Yunlong Zhao, Brian L. Hie, Rosemary Birch, Mary Gehring, Bryan D. Bryson, Spencer M. Whitney, Matthew D. Shoulders, Robert H. Wilson (MIT; Stanford; Australian National University)","Method (abstract): 'We applied the structure-informed machine learning (ML) model ESM-IF1 to identify plausible amino acid sites in the large subunit of Nicotiana tabacum Rubisco to target for directed evolution', followed by selection in Rubisco-dependent Escherichia coli","Result (abstract): 'the T391I substitution improved carboxylation rate by 29% and aerobic carboxylation efficiency by 43%'","Abstract: several improved variants 'carried amino acid changes not found in the evolutionary lineage of plants, despite being assembly competent in plant chloroplasts'","Limits: the abstract reports enzyme kinetics, not crop yield; it speaks of 'potential for enhancing crop productivity'. Written from the abstract (Crossref); the full text was not read"],"key_numbers":[],"tags":["biology","protein-engineering","rubisco","photosynthesis","directed-evolution","esm-if1","peer-reviewed"],"science":{"field":"biology","subfield":"protein engineering / photosynthesis","problem":"Engineering a more efficient Rubisco, the slow CO₂-fixing enzyme of photosynthesis","result":"ML-chosen mutation sites plus directed evolution gave tobacco Rubisco variants with higher catalytic efficiency; T391I: +29% carboxylation rate, +43% aerobic carboxylation efficiency.","open_since":"","ai_system":["ESM-IF1"],"human_role":"Human-led with AI tools: the model proposed sites for the mutant library; laboratory selection and measurement did the rest","verification":{"key":"peer-review","label":"Peer-reviewed","text":"Peer-reviewed in Science Advances; lab-validated"},"status":"confirmed","shock":"","short":"Faster plant Rubisco by ML-guided evolution"},"body_md":"## What happened\n\nRubisco catalyses the step of photosynthesis that captures CO₂. It is slow and inefficient and, in the words of the abstract, \"has proven challenging to engineer\".\nThe MIT-led team used ESM-IF1, an inverse-folding protein model, to pick positions in the tobacco enzyme\nwhere changes were plausible, built libraries at those positions and let bacteria that depend on Rubisco select the better\nvariants. Some winning mutations do not occur in any plant lineage.\n\n## Why it matters\n\n\"A better Rubisco\" is on the list of grand challenges for biology (see the related entry). This is a peer-reviewed, lab-validated\nstep on a plant enzyme, using a small specialised model as a guide for experiments. It is an enzyme-level gain, not yet a\ndemonstrated gain in crop yield.","disputed":[],"related":[{"id":"2026-10-05-deepmind-alphaprotein-novo-enzyme-design","url":"https://postcutoff.com/e/2026-10-05-deepmind-alphaprotein-novo-enzyme-design/","date":"2026-10-05","date_precision":"day","short_title":"Google DeepMind's AlphaProtein Novo designs new-to-nature enzymes from scratch (piperidine synthesis, DEHP degradation), with Frances Arnold's lab","deck":null,"takeaway":"Most industrial enzymes start from natural proteins and are improved by mutation.","category":"science","category_label":"Science & math","importance":4,"confidence":"high","status":{"key":"pending","labels":["Event confirmed","Awaiting review"]},"sources":5,"official":4,"filed":"2026-10-06","updated":"2026-10-07","orgs":["Google DeepMind","Caltech","University of Pittsburgh"]},{"id":"2026-09-19-millennium-problems-for-biology","url":"https://postcutoff.com/e/2026-09-19-millennium-problems-for-biology/","date":"2026-09-19","date_precision":"day","short_title":"FutureHouse and Edison Scientific publish twelve 'Millennium Problems for Biology', pitched as the 'last reasonable eval' for AI in biology","deck":null,"takeaway":"Rodriques called them \"the 'last reasonable eval' for AI in biology\"; the launch post had ~508k views on X, and cash prizes and a judging panel were promised.","category":"science","category_label":"Science & math","importance":3,"confidence":"high","status":{"key":"pending","labels":["Event confirmed","Awaiting review"]},"sources":7,"official":5,"filed":"2026-10-03","updated":"2026-10-03","orgs":["FutureHouse","Edison Scientific"]}],"people":[],"posts":[],"videos":[],"models":[],"changes":[{"date":"2026-10-12","type":"filed","text":"Created from the Science Advances table of contents and the Crossref abstract"}],"provenance":{"agents":[{"model":"Claude Opus 5.5","maker":"Anthropic","tool":"Claude Code"}],"filed":"2026-10-12","run":null,"sources_read":"The Science Advances table of contents and the Crossref abstract","updated":"2026-10-12","human_review":null,"version":null},"gaps":[{"model_id":"gpt-6-astra","name":"GPT-6 Astra","cutoff":"2026-04","days_after":162,"in_training_data":false},{"model_id":"claude-opus-5-5","name":"Claude Opus 5.5","cutoff":"2026-06","days_after":101,"in_training_data":false},{"model_id":"gemini-3-8-flash","name":"Gemini 3.8 Flash","cutoff":"2026-03","days_after":192,"in_training_data":false},{"model_id":"grok-4-7","name":"Grok 4.7","cutoff":"2026-05","days_after":131,"in_training_data":false}],"short_url":null}