Co-crystalization reveals the interaction between AtYchF1 and ppGpp
AtYchF1 is an unconventional G-protein in Arabidopsis thaliana that exhibits relaxed nucleotide-binding specificity. The bindings between AtYchF1 and biomolecules including GTP, ATP, and 26S rRNA have been reported. In this study, we demonstrated the binding of AtYchF1 to ppGpp in addition to the ab...
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Frontiers Media S.A.
2022-11-01
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2022.1061350/full |
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| author | Ming-Yan Cheung Xiaorong Li Yee-Shan Ku Zhongzhou Chen Hon-Ming Lam |
| author_facet | Ming-Yan Cheung Xiaorong Li Yee-Shan Ku Zhongzhou Chen Hon-Ming Lam |
| author_sort | Ming-Yan Cheung |
| collection | DOAJ |
| description | AtYchF1 is an unconventional G-protein in Arabidopsis thaliana that exhibits relaxed nucleotide-binding specificity. The bindings between AtYchF1 and biomolecules including GTP, ATP, and 26S rRNA have been reported. In this study, we demonstrated the binding of AtYchF1 to ppGpp in addition to the above molecules. AtYchF1 is a cytosolic protein previously reported as a negative regulator of both biotic and abiotic stresses while the accumulation of ppGpp in the cytoplasm induces retarded plant growth and development. By co-crystallization, in vitro pull-down experiments, and hydrolytic biochemical assays, we demonstrated the binding and hydrolysis of ppGpp by AtYchF1. ppGpp inhibits the binding of AtYchF1 to ATP, GTP, and 26S rRNA. The ppGpp hydrolyzing activity of AtYchF1 failed to be activated by AtGAP1. The AtYchF1-ppGpp co-crystal structure suggests that ppGpp might prevent His136 from executing nucleotide hydrolysis. In addition, upon the binding of ppGpp, the conformation between the TGS and helical domains of AtYchF1 changes. Such structural changes probably influence the binding between AtYchF1 and other molecules such as 26S rRNA. Since YchF proteins are conserved among different kingdoms of life, the findings advance the knowledge on the role of AtYchF1 in regulating nucleotide signaling as well as hint at the possible involvement of YchF proteins in regulating ppGpp level in other species. |
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| last_indexed | 2024-04-11T15:46:04Z |
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| series | Frontiers in Molecular Biosciences |
| spelling | doaj.art-c1b572df8bee446fa6a7fd26913f01e22022-12-22T04:15:35ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2022-11-01910.3389/fmolb.2022.10613501061350Co-crystalization reveals the interaction between AtYchF1 and ppGppMing-Yan Cheung0Xiaorong Li1Yee-Shan Ku2Zhongzhou Chen3Hon-Ming Lam4Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, ChinaState Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, ChinaCenter for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, ChinaState Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, ChinaCenter for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, ChinaAtYchF1 is an unconventional G-protein in Arabidopsis thaliana that exhibits relaxed nucleotide-binding specificity. The bindings between AtYchF1 and biomolecules including GTP, ATP, and 26S rRNA have been reported. In this study, we demonstrated the binding of AtYchF1 to ppGpp in addition to the above molecules. AtYchF1 is a cytosolic protein previously reported as a negative regulator of both biotic and abiotic stresses while the accumulation of ppGpp in the cytoplasm induces retarded plant growth and development. By co-crystallization, in vitro pull-down experiments, and hydrolytic biochemical assays, we demonstrated the binding and hydrolysis of ppGpp by AtYchF1. ppGpp inhibits the binding of AtYchF1 to ATP, GTP, and 26S rRNA. The ppGpp hydrolyzing activity of AtYchF1 failed to be activated by AtGAP1. The AtYchF1-ppGpp co-crystal structure suggests that ppGpp might prevent His136 from executing nucleotide hydrolysis. In addition, upon the binding of ppGpp, the conformation between the TGS and helical domains of AtYchF1 changes. Such structural changes probably influence the binding between AtYchF1 and other molecules such as 26S rRNA. Since YchF proteins are conserved among different kingdoms of life, the findings advance the knowledge on the role of AtYchF1 in regulating nucleotide signaling as well as hint at the possible involvement of YchF proteins in regulating ppGpp level in other species.https://www.frontiersin.org/articles/10.3389/fmolb.2022.1061350/fullArabidopsisprotein crystallographyG-proteinGTPaseppGppRelA/SpoT homolog |
| spellingShingle | Ming-Yan Cheung Xiaorong Li Yee-Shan Ku Zhongzhou Chen Hon-Ming Lam Co-crystalization reveals the interaction between AtYchF1 and ppGpp Frontiers in Molecular Biosciences Arabidopsis protein crystallography G-protein GTPase ppGpp RelA/SpoT homolog |
| title | Co-crystalization reveals the interaction between AtYchF1 and ppGpp |
| title_full | Co-crystalization reveals the interaction between AtYchF1 and ppGpp |
| title_fullStr | Co-crystalization reveals the interaction between AtYchF1 and ppGpp |
| title_full_unstemmed | Co-crystalization reveals the interaction between AtYchF1 and ppGpp |
| title_short | Co-crystalization reveals the interaction between AtYchF1 and ppGpp |
| title_sort | co crystalization reveals the interaction between atychf1 and ppgpp |
| topic | Arabidopsis protein crystallography G-protein GTPase ppGpp RelA/SpoT homolog |
| url | https://www.frontiersin.org/articles/10.3389/fmolb.2022.1061350/full |
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