Pfam domain adaptation profiles reflect plant species’ evolutionary history

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.

An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

“…The coding sequence fragment that encodes the flap lid domain and the corresponding amino acids are shown in magenta. Residues in bold showed significant associations with prokaryote optimal growth temperature (55; 56). (B) Optimal prokaryote growth temperature (OGT) test of different amino acids at the residue equivalent to the polymorphic residue 211 in HPC1.…”

“…4A). The flap lid domain is important for phospholipase activity and is located in a lipase class 3 domain (PFAM domain PF01764) that is highly conserved across the tree of life (52). We recovered 982 observations of the lipase class 3 PFAM domain from 719 prokaryotic species using PfamScan (62; 63) and estimated optimal growth temperatures from their tRNA sequences (64).…”

“…Adaptive loss-of-function mutations can be an effective way to gain new metabolic functions in new environmental conditions (79). Taking advantage of the conserved lipase domain of HPC1 in bacteria, we used a new method that can identify how genetic variation in DNA regions encoding protein domains is correlated with optimal growth temperature of bacteria (55; 56). The probable causal SNP in HPC1 changed an amino acid in the flap-lid domain of HPC1 (Fig.…”

An adaptive teosintemexicanaintrogression modulates phosphatidylcholine levels and is associated with maize flowering time

“…4 A ). The flap-lid domain is important for phospholipase activity and is located in a lipase class 3 domain (Protein Families (PFAM) database domain PF01764) that is highly conserved across the tree of life ( 55 ). We recovered 982 observations of the lipase class 3 PFAM domain from 719 prokaryotic species using PfamScan ( 56 , 57 ) and estimated optimal growth temperatures from their tRNA sequences ( 58 ).…”

“…The coding sequence fragment that encodes the flap-lid domain and the corresponding amino acids are shown in magenta. Residues in boldface type showed significant associations with prokaryote optimal growth temperature ( 55 , 59 ). ( B ) Optimal prokaryote growth temperature (OGT) test of different amino acids at the residue equivalent to the polymorphic residue 211 in HPC1.…”