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1. EXO70D isoforms mediate selective autophagic degradation of type-A ARR proteins to regulate cytokinin sensitivity

   https://doi.org/10.1073/pnas.2013161117  

   Acheampong, Atiako Kwame; Shanks, Carly; Cheng, Chia-Yi; Schaller, G. Eric; Dagdas, Yasin; Kieber, Joseph J. (October 2020, Proceedings of the National Academy of Sciences)

   The phytohormone cytokinin influences many aspects of plant growth and development, several of which also involve the cellular process of autophagy, including leaf senescence, nutrient remobilization, and developmental transitions. TheArabidopsistype-A response regulators (type-A ARR) are negative regulators of cytokinin signaling that are transcriptionally induced in response to cytokinin. Here, we describe a mechanistic link between cytokinin signaling and autophagy, demonstrating that plants modulate cytokinin sensitivity through autophagic regulation of type-A ARR proteins. Type-A ARR proteins were degraded by autophagy in an AUTOPHAGY-RELATED (ATG)5-dependent manner, and this degradation is promoted by phosphorylation on a conserved aspartate in the receiver domain of the type-A ARRs. EXO70D family members interacted with type-A ARR proteins, likely in a phosphorylation-dependent manner, and recruited them to autophagosomes via interaction of the EXO70D AIM with the core autophagy protein, ATG8. Consistently, loss-of-functionexo70D1,2,3mutants exhibited compromised targeting of type-A ARRs to autophagic vesicles, have elevated levels of type-A ARR proteins, and are hyposensitive to cytokinin. Disruption of both type-AARRsandEXO70D1,2,3compromised survival in carbon-deficient conditions, suggesting interaction between autophagy and cytokinin responsiveness in response to stress. These results indicate that the EXO70D proteins act as selective autophagy receptors to target type-A ARR cargos for autophagic degradation, demonstrating modulation of cytokinin signaling by selective autophagy. 

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2. Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE

   https://doi.org/DOI: 10.1038/s41598-020-62847-6  

   Fellner, M; Huizenga, KG; Hausinger, RP; Hu, J. (April 2020, Scientific reports)

   Abstract Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca2+, Mn2+, Fe2+/Fe3+, Co2+, Ni2+, Cu2+, Zn2+, and Cd2+, but not monovalent metal ions, Cr3+, Mg2+, Y3+, Sr2+ or Ba2+. Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization. 

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3. The primary structural photoresponse of phytochrome proteins captured by a femtosecond X-ray laser

   https://doi.org/10.7554/elife.53514  

   Claesson, Elin; Wahlgren, Weixiao Yuan; Takala, Heikki; Pandey, Suraj; Castillon, Leticia; Kuznetsova, Valentyna; Henry, Léocadie; Panman, Matthijs; Carrillo, Melissa; Kübel, Joachim; et al (March 2020, eLife)

   Phytochrome proteins control the growth, reproduction, and photosynthesis of plants, fungi, and bacteria. Light is detected by a bilin cofactor, but it remains elusive how this leads to activation of the protein through structural changes. We present serial femtosecond X-ray crystallographic data of the chromophore-binding domains of a bacterial phytochrome at delay times of 1 ps and 10 ps after photoexcitation. The data reveal a twist of the D-ring, which leads to partial detachment of the chromophore from the protein. Unexpectedly, the conserved so-called pyrrole water is photodissociated from the chromophore, concomitant with movement of the A-ring and a key signaling aspartate. The changes are wired together by ultrafast backbone and water movements around the chromophore, channeling them into signal transduction towards the output domains. We suggest that the observed collective changes are important for the phytochrome photoresponse, explaining the earliest steps of how plants, fungi and bacteria sense red light. 

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4. Kinetic Characterization and Identification of Key Active Site Residues of the L‐Aspartate N ‐Hydroxylase, CreE

   https://doi.org/10.1002/cbic.202400350  

   Johnson, Sydney_B; Valentino, Hannah; Sobrado, Pablo (July 2024, ChemBioChem)

   Abstract CreE is a flavin‐dependent monooxygenase (FMO) that catalyzes three sequential nitrogen oxidation reactions of L‐aspartate to produce nitrosuccinate, contributing to the biosynthesis of the antimicrobial and antiproliferative nautral product, cremeomycin. This compound contains a highly reactive diazo functional group for which the reaction of CreE is essential to its formation. Nitro and diazo functional groups can serve as potent electrophiles, important in some challenging nucleophilic addition reactions. Formation of these reactive groups positions CreE as a promising candidate for biomedical and synthetic applications. Here, we present the catalytic mechanism of CreE and the identification of active site residues critical to binding L‐aspartate, aiding in future enzyme engineering efforts. Steady‐state analysis demonstrated that CreE is very specific for NADPH over NADH and performs a highly coupled reaction with L‐aspartate. Analysis of the rapid‐reaction kinetics showed that flavin reduction is very fast, along with the formation of the oxygenating species, the C4a−hydroperoxyflavin. The slowest step observed was the dehydration of the flavin. Structural analysis and site‐directed mutagenesis implicated T65, R291, and R440 in the binding L‐aspartate. The data presented describes the catalytic mechanism and the active site architecture of this unique FMO. 

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5. Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins

   https://doi.org/10.1093/nar/gkad045  

   Wang, Xi; Bigman, Lavi S.; Greenblatt, Harry M.; Yu, Binhan; Levy, Yaakov; Iwahara, Junji (February 2023, Nucleic Acids Research)

   Abstract In eukaryotes, many DNA/RNA-binding proteins possess intrinsically disordered regions (IDRs) with large negative charge, some of which involve a consecutive sequence of aspartate (D) or glutamate (E) residues. We refer to them as D/E repeats. The functional role of D/E repeats is not well understood, though some of them are known to cause autoinhibition through intramolecular electrostatic interaction with functional domains. In this work, we investigated the impacts of D/E repeats on the target DNA search kinetics for the high-mobility group box 1 (HMGB1) protein and the artificial protein constructs of the Antp homeodomain fused with D/E repeats of varied lengths. Our experimental data showed that D/E repeats of particular lengths can accelerate the target association in the overwhelming presence of non-functional high-affinity ligands (‘decoys’). Our coarse-grained molecular dynamics (CGMD) simulations showed that the autoinhibited proteins can bind to DNA and transition into the uninhibited complex with DNA through an electrostatically driven induced-fit process. In conjunction with the CGMD simulations, our kinetic model can explain how D/E repeats can accelerate the target association process in the presence of decoys. This study illuminates an unprecedented role of the negatively charged IDRs in the target search process. 

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