{"doi":"10.1101/2025.05.15.654294","title":"Constrained evolution of a core winter proteome across independently cold-adapted PACMAD grasses","abstract":"Summary Grasses in the PACMAD clade independently colonized cold environments from warm-climate ancestors, but whether their molecular responses to freezing reflect shared evolutionary solutions or lineage-specific innovations remains unknown. We used comparative proteomics to test whether protein-level cold responses show stronger cross-species conservation than previously observed at the transcript level. We quantified seasonal rhizome proteomes (winter vs summer) from five PACMAD species grown in a common garden exposed to sustained sub-zero temperatures, identified differentially abundant proteins, and compared fold-change magnitudes across species using orthogroup-based correlation analyses. We further examined LEA3 protein structure through hydropathy profiling and motif analysis. Shared cold-responsive proteins showed higher cross-species fold-change correlation ( ρ = 0.80) than background proteins ( ρ = 0.45), despite greater divergence in baseline abundance. LEA3 was the only ortholog elevated across all five species. Cold-tolerant species contained more tandem 11-mer repeats than the cold-sensitive maize, and two species accumulated multiple LEA3 paralogs, increasing total LEA3 abundance. Independent evolution of freezing tolerance in PACMAD grasses is governed by evolutionary constraints on protein-level response magnitude, reflecting the retention of an ancestral protective capacity. Structural divergence of LEA3 in maize suggests that transcriptional induction alone does not ensure freezing tolerance; functional protection likely requires intact motif architecture.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":557959,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9415,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1325672,"name":"Jingjing Zhai","orcid":"0000-0002-1535-3103","position":1,"is_corresponding":false},{"id":1457978,"name":"Travis E. Rooney","orcid":"0000-0002-6301-1570","position":2,"is_corresponding":false},{"id":1457979,"name":"Ruthie Angelovici","orcid":"0000-0001-5150-0695","position":3,"is_corresponding":false},{"id":1436131,"name":"Charles O. Hale","orcid":"0000-0001-8119-5273","position":4,"is_corresponding":false},{"id":1457980,"name":"Lara Brindisi","orcid":"0000-0003-0325-5861","position":5,"is_corresponding":false},{"id":1452654,"name":"Sheng‐Kai Hsu","orcid":"0000-0002-6942-7163","position":6,"is_corresponding":false},{"id":1457981,"name":"Christine M. Gault","orcid":"0000-0002-8457-1702","position":7,"is_corresponding":false},{"id":1036774,"name":"Jian Hua","orcid":"0000-0002-3777-3344","position":8,"is_corresponding":false},{"id":832591,"name":"Thuy La","orcid":null,"position":9,"is_corresponding":false},{"id":1076280,"name":"Nicholas Lepak","orcid":null,"position":10,"is_corresponding":false},{"id":299431,"name":"Qin Fu","orcid":"0000-0003-4944-772X","position":11,"is_corresponding":false},{"id":19346,"name":"Edward S. Buckler","orcid":"0000-0002-3100-371X","position":12,"is_corresponding":false},{"id":1075793,"name":"M. Cinta Romay","orcid":"0000-0001-9309-1586","position":13,"is_corresponding":false},{"id":1457977,"name":"Elad Oren","orcid":"0000-0001-6821-4409","position":0,"is_corresponding":true}],"reference_count":62,"raw_metadata":null,"created_at":"2026-07-19T02:55:21.727661Z","pmid":"40661564","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":[]}