Pfam domain adaptation profiles reflect plant species’ evolutionary history

Authors: JENSEN, SARAH - Sygenta Seeds; Buckler, Edward - Ed

Submitted to: bioRxiv
Publication Type: Pre-print Publication
Publication Acceptance Date: 7/14/2021
Publication Date: 7/14/2021
Citation: Jensen, S.E., Buckler IV, E.S. 2021. Pfam domain adaptation profiles reflect plant species’ evolutionary history. bioRxiv. https://doi.org/10.1101/2021.07.13.452250.
DOI: https://doi.org/10.1101/2021.07.13.452250

Interpretive Summary: High temperatures affect plant growth and development and often reduce crop yields. They are also becoming more prevalent due to global climate change. Understanding how and why plants are affected by heat stress will be important for developing heat-tolerant crops for the future. Some crops are more heat tolerant than others, but we don’t yet understand why that is at a molecular level. In this project we compared the heat tolerance of plant proteins across three species: maize, poplar, and Arabidopsis. We found that protein temperature sensitivity varies, both across species and across plant organs (e.g. root, leaf) within each species. This project offers a first look at how plant proteins are differently adapted to high temperatures and suggests that protein temperature adaptation may vary even within different plant organs and organelles. Future studies can build upon this research to identify which proteins are unstable at high temperatures and therefore likely to reduce plant growth and crop yield in extreme temperature conditions. Identifying such proteins will be an key step in developing heat-tolerant crops for the future.

Technical Abstract: The increase in global temperatures predicted by climate change models presents a serious problem for agriculture because high temperatures reduce crop yields. Protein biochemistry is at the core of plant heat stress response, and understanding the interactions between protein biochemistry and temperature will be key to developing heat-tolerant crop varieties. Current experimental studies of proteome-wide plant thermostability are limited by the complexity of plant proteomes: evaluating function for thousands of proteins across a variety of temperatures is simply not feasible with existing technologies. In this paper, we use homologous prokaryote sequences to predict plant Pfam temperature adaptation and gain insights into how thermostability varies across the proteome for three species: maize, Arabidopsis, and poplar. We find that patterns of Pfam domain adaptation across organelles are consistent and highly significant between species, with cytosolic proteins having the largest range of predicted Pfam stabilities and a long tail of highly-stable ribosomal proteins. Pfam adaptation in leaf and root organs varies between species, and maize root proteins have more low-temperature Pfam domains than do Arabidopsis or poplar root proteins. Both poplar and maize populations have an excess of low-temperature mutations in Pfam domains, but only the mutations identified in poplar accessions have a negative effect on Pfam temperature adaptation overall. These Pfam domain adaptation profiles provide insight into how different plant structures adapt to their surrounding environment and can help inform breeding or protein editing strategies to produce heat-tolerant crops.