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Peer-reviewedCC BY 4.0PLOS One

Evolutionary constraint on a core winter proteome across independently cold-adapted PACMAD grasses

  • Elad Oren1
  • Jingjing Zhai2
  • Travis E. Rooney3
  • Ruthie Angelovici4
  • Charles O. Hale5
  • Lara J. Brindisi6
  • Sheng-Kai Hsu7
  • Christine M. Gault8
  • Jian Hua
  • Thuy La
  • Nicholas Lepak
  • Qin Fu
2 more authors
  • Edward S. Buckler
  • Maria Cinta Romay
8 affiliations
  1. 1Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
  2. 2Newe Ya’ar Research Center, Institute of Plant Sciences, Agricultural Research Organization – Volcani Institute, Ramat Yishay, Israel
  3. 3Sesaco Corporation, Austin, Texas, United States of America
  4. 4Division of Biological Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, United States of America
  5. 5School of Integrative Plant Sciences, Plant Breeding and Genetics Section, Cornell University, Ithaca, New York, United States of America
  6. 6USDA-ARS, Ithaca, New York, United States of America
  7. 7School of Integrative Plant Science, Plant Biology Section, Cornell University, Ithaca, New York, United States of America
  8. 8Proteomics and Metabolomics Facility, Cornell University, Ithaca, New York, United States of America
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Abstract

Grasses in the Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, and Danthonioideae (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 poorly understood at the protein level. 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 (ρ = 0.80) than background proteins (ρ = 0.45), despite greater divergence in baseline abundance. This correlation advantage persisted (Δρ = 0.27) 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.

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Cite

BibTeXRIS
BibTeX
@article{oren2026evolutionary,
  title = {{Evolutionary constraint on a core winter proteome across independently cold-adapted PACMAD grasses}},
  author = {Elad Oren and Jingjing Zhai and Travis E. Rooney and Ruthie Angelovici and Charles O. Hale and Lara J. Brindisi and Sheng-Kai Hsu and Christine M. Gault and Jian Hua and Thuy La and Nicholas Lepak and Qin Fu and Edward S. Buckler and Maria Cinta Romay},
  journal = {PLOS One},
  year = {2026},
  month = oct,
  doi = {10.1371/journal.pone.0358458},
  url = {https://doi.org/10.1371/journal.pone.0358458},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Evolutionary constraint on a core winter proteome across independently cold-adapted PACMAD grasses
AU  - Elad Oren
AU  - Jingjing Zhai
AU  - Travis E. Rooney
AU  - Ruthie Angelovici
AU  - Charles O. Hale
AU  - Lara J. Brindisi
AU  - Sheng-Kai Hsu
AU  - Christine M. Gault
AU  - Jian Hua
AU  - Thuy La
AU  - Nicholas Lepak
AU  - Qin Fu
AU  - Edward S. Buckler
AU  - Maria Cinta Romay
PY  - 2026
DA  - 2026/10/14
JO  - PLOS One
DO  - 10.1371/journal.pone.0358458
UR  - https://doi.org/10.1371/journal.pone.0358458
AB  - Grasses in the Panicoideae, Aristidoideae, Chloridoideae, Micrairoideae, Arundinoideae, and Danthonioideae (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 poorly understood at the protein level. 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 (ρ = 0.80) than background proteins (ρ = 0.45), despite greater divergence in baseline abundance. This correlation advantage persisted (Δρ = 0.27) 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.
SN  - 1932-6203
ER  -