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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 experiment 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 (\n                    <jats:italic>\u03c1<\/jats:italic>\n                    \u2009=\u20090.80) than background proteins (\n                    <jats:italic>\u03c1<\/jats:italic>\n                    \u2009=\u20090.45), despite greater divergence in baseline abundance. This correlation advantage persisted (\u0394\n                    <jats:italic>\u03c1<\/jats:italic>\n                    \u2009=\u20090.27) after controlling for effect-size selection by comparing shared cold-responsive proteins against magnitude-matched single-species responses. LEA3 was the only ortholog elevated across all five species, with cold-tolerant species containing more tandem 11-mer repeats than the cold-sensitive maize. Two species accumulated multiple LEA3 paralogs, increasing total LEA3 abundance. Independent evolution of freezing tolerance in PACMAD grasses is consistent with 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.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0358458","type":"journal-article","created":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T17:23:37Z","timestamp":1791998617000},"page":"e0358458","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Evolutionary constraint on a core winter proteome across independently cold-adapted PACMAD grasses"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6821-4409","authenticated-orcid":true,"given":"Elad","family":"Oren","sequence":"first","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University","place":["Ithaca, New York, United States of America"]},{"name":"Newe Ya\u2019ar Research Center, Institute of Plant Sciences, Agricultural Research Organization \u2013 Volcani Institute","place":["Ramat Yishay, Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingjing","family":"Zhai","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Travis E.","family":"Rooney","sequence":"additional","affiliation":[{"name":"Sesaco Corporation","place":["Austin, Texas, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruthie","family":"Angelovici","sequence":"additional","affiliation":[{"name":"University of Missouri","place":["Columbia, Missouri, United States of America"],"department":["Division of Biological Sciences and Interdisciplinary Plant Group"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Charles O.","family":"Hale","sequence":"additional","affiliation":[{"name":"School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0325-5861","authenticated-orcid":true,"given":"Lara J.","family":"Brindisi","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University","place":["Ithaca, New York, United States of America"]},{"name":"USDA-ARS","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6942-7163","authenticated-orcid":true,"given":"Sheng-Kai","family":"Hsu","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine M.","family":"Gault","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Hua","sequence":"additional","affiliation":[{"name":"School of Integrative Plant Science, Plant Biology Section, Cornell University","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thuy","family":"La","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas","family":"Lepak","sequence":"additional","affiliation":[{"name":"USDA-ARS","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Fu","sequence":"additional","affiliation":[{"name":"Proteomics and Metabolomics Facility, Cornell University","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3100-371X","authenticated-orcid":true,"given":"Edward S.","family":"Buckler","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University","place":["Ithaca, New York, United States of America"]},{"name":"USDA-ARS","place":["Ithaca, New York, United States of America"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Cinta","family":"Romay","sequence":"additional","affiliation":[{"name":"Institute for Genomic Diversity, Cornell University","place":["Ithaca, New York, United States of 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