Structural and functional analysis of two SHMT8 variants associated with soybean cyst nematode resistance

• Published in: The FEBS journal Vol. 291; no. 2; pp. 323 - 337
• Main Authors: Korasick, David A., Owuocha, Luckio F., Kandoth, Pramod K., Tanner, John J., Mitchum, Melissa G., Beamer, Lesa J.
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01.01.2024
• Subjects: Acid resistance; Amino acids; Animals; Catalytic activity; Crop production; crystal structure; Cultivars; Cysts; Economic impact; Enzymatic activity; Enzyme activity; enzyme mutation; enzyme structure; Enzymes; Folic Acid; Functional analysis; Glycine; Glycine Hydroxymethyltransferase - chemistry; Glycine max - genetics; Heterodera glycines; Nematoda - metabolism; Nematodes; parasite; Pest resistance; Plant Diseases; Serine; Soybeans; Structural analysis; structural biology; Structure-function relationships; Substrate inhibition; Tetrahydrofolic acid; crystal structure; parasite; structural biology; enzyme structure; enzyme mutation
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/febs.16971

Two amino acid variants in soybean serine hydroxymethyltransferase 8 (SHMT8) are associated with resistance to the soybean cyst nematode (SCN), a devastating agricultural pathogen with worldwide economic impacts on soybean production. SHMT8 is a cytoplasmic enzyme that catalyzes the pyridoxal 5‐phosphate‐dependent conversion of serine and tetrahydrofolate (THF) to glycine and 5,10‐methylenetetrahydrofolate. A previous study of the P130R/N358Y double variant of SHMT8, identified in the SCN‐resistant soybean cultivar (cv.) Forrest, showed profound impairment of folate binding affinity and reduced THF‐dependent enzyme activity, relative to the highly active SHMT8 in cv. Essex, which is susceptible to SCN. Given the importance of SCN‐resistance in soybean agriculture, we report here the biochemical and structural characterization of the P130R and N358Y single variants to elucidate their individual effects on soybean SHMT8. We find that both single variants have reduced THF‐dependent catalytic activity relative to Essex SHMT8 (10‐ to 50‐fold decrease in kcat/Km) but are significantly more active than the P130R/N368Y double variant. The kinetic data also show that the single variants lack THF‐substrate inhibition as found in Essex SHMT8, an observation with implications for regulation of the folate cycle. Five crystal structures of the P130R and N358Y variants in complex with various ligands (resolutions from 1.49 to 2.30 Å) reveal distinct structural impacts of the mutations and provide new insights into allosterism. Our results support the notion that the P130R/N358Y double variant in Forrest SHMT8 produces unique and unexpected effects on the enzyme, which cannot be easily predicted from the behavior of the individual variants. Amino acid variants in the soybean enzyme serine hydroxymethyltransferase 8 are associated with resistance to the agricultural pathogen soybean cyst nematode. Biochemical studies of the P130R and N38Y variants show distinct effects on the enzyme, including reduced catalytic activity and a loss of substrate inhibition. High‐resolution crystal structures reveal subtle asymmetry in the enzyme tetramer, with potential implications for understanding allosterism in the SHMT enzyme superfamily.