Structural basis for the negative regulation of bacterial stress response by RseB

The mitochondrial unfolded protein response (UPRmt) has emerged as a predominant mechanism that preserves mitochondrial function. Consequently, multiple pathways likely exist to modulate UPRmt. We unexpectedly discovered that the tRNA processing enzyme, homolog of ELAC2 (HOE-1), is central to UPRmt regulation in Caenorhabditis elegans. We find that nuclear HOE-1 is necessary and sufficient to robustly activate UPRmt. We show that HOE-1 acts via transcription factors ATFS-1 and DVE-1 that are crucial for UPRmt. Mechanistically, we show that HOE-1 likely mediates its effects via tRNAs, as blocking tRNA export prevents HOE-1-induced UPRmt. Interestingly, we find that HOE-1 does not act via the integrated stress response, which can be activated by uncharged tRNAs, pointing towards its reliance on a new mechanism. Finally, we show that the subcellular localization of HOE-1 is responsive to mitochondrial stress and is subject to negative regulation via ATFS-1. Together, we have discovered a novel RNA-based cellular pathway that modulates UPRmt.

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Structural basis for DNA-mediated allosteric regulation facilitated by the AAA+module of Lon protease

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s139900471302631x ◽

2014 ◽

Vol 70 (2) ◽

pp. 218-230 ◽

Cited By ~ 6

Author(s):

Alan Yueh-Luen Lee ◽

Yu-Da Chen ◽

Yu-Yung Chang ◽

Yu-Ching Lin ◽

Chi-Fon Chang ◽

...

Keyword(s):

Crystal Structure ◽

Dna Binding ◽

Electrostatic Interactions ◽

Allosteric Regulation ◽

Binding Mode ◽

Negative Regulation ◽

Enzymatic Activities ◽

Structural Basis ◽

Lon Protease ◽

Arginine Residues

Lon belongs to a unique group of AAA+proteases that bind DNA. However, the DNA-mediated regulation of Lon remains elusive. Here, the crystal structure of the α subdomain of the Lon protease fromBrevibacillus thermoruber(Bt-Lon) is presented, together with biochemical data, and the DNA-binding mode is delineated, showing that Arg518, Arg557 and Arg566 play a crucial role in DNA binding. Electrostatic interactions contributed by arginine residues in the AAA+module are suggested to be important to DNA binding and allosteric regulation of enzymatic activities. Intriguingly, Arg557, which directly binds DNA in the α subdomain, has a dual role in the negative regulation of ATPase stimulation by DNA and in the domain–domain communication in allosteric regulation of Bt-Lon by substrate. In conclusion, structural and biochemical evidence is provided to show that electrostatic interaction in the AAA+module is important for DNA binding by Lon and allosteric regulation of its enzymatic activities by DNA and substrate.

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The structural basis for the negative regulation of thioredoxin by thioredoxin-interacting protein

Nature Communications ◽

10.1038/ncomms3958 ◽

2014 ◽

Vol 5 (1) ◽

Cited By ~ 59

Author(s):

Jungwon Hwang ◽

Hyun-Woo Suh ◽

Young Ho Jeon ◽

Eunha Hwang ◽

Loi T. Nguyen ◽

...

Keyword(s):

Negative Regulation ◽

Structural Basis ◽

Interacting Protein ◽

Thioredoxin Interacting Protein

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Structural Basis for Negative Regulation of ABA Signaling by ROP11 GTPase

10.1101/2020.05.20.107185 ◽

2020 ◽

Author(s):

Chuankai Zhao ◽

Diwakar Shukla

Keyword(s):

Signal Transduction ◽

Large Scale ◽

Small Gtpases ◽

Free Energy Calculations ◽

Negative Regulation ◽

Coarse Grained ◽

Structural Basis ◽

Aba Signaling ◽

Aba Signal Transduction ◽

Critical Residue

Abscisic acid (ABA) is an essential plant hormone responsible for plant development and stress responses. Recent structural and biochemical studies have identified the key components involved in ABA signaling cascade, including PYR/PYL/RCAR receptors, protein phosphatases PP2C, and protein kinases SnRK2. The plant-specific, Roh-like (ROPs) small GTPases are negative regulators of ABA signal transduction by interacting with PP2C, which can shut off “leaky” ABA signal transduction caused by constitutive activity of monomeric PYR/PYL/RCAR receptors. However, the structural basis for negative regulation of ABA signaling by ROP GTPases remain elusive. In this study, we have utilized large-scale coarse-grained (10.05 milliseconds) and all-atom molecular dynamics simulations and standard protein-protein binding free energy calculations to predict the complex structure of AtROP11 and phosphatase AtABI1. In addition, we have elucidated the detailed complex association pathway and identified the critical residue pairs in AtROP11 and AtABI1 for complex stability. Overall, this study has established a powerful framework of using large-scale molecular simulations to predict unknown protein complex structures and elucidated the molecular mechanism of the negative regulation of ABA signal transduction by small GTPases.

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Genome-Wide Identification of Soybean U-Box E3 Ubiquitin Ligases and Roles of GmPUB8 in Negative Regulation of Drought Stress Response in Arabidopsis

Plant and Cell Physiology ◽

10.1093/pcp/pcw068 ◽

2016 ◽

Vol 57 (6) ◽

pp. 1189-1209 ◽

Cited By ~ 22

Author(s):

Ning Wang ◽

Yaping Liu ◽

Yahui Cong ◽

Tingting Wang ◽

Xiujuan Zhong ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Ubiquitin Ligases ◽

Negative Regulation ◽

E3 Ubiquitin Ligases ◽

Genome Wide

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Structural basis for negative regulation of hypoxia-inducible factor-1α by CITED2

Nature Structural & Molecular Biology ◽

10.1038/nsb936 ◽

2003 ◽

Vol 10 (7) ◽

pp. 504-512 ◽

Cited By ~ 129

Author(s):

Steven J Freedman ◽

Zhen-Yu J Sun ◽

Andrew L Kung ◽

Dennis S France ◽

Gerhard Wagner ◽

...

Keyword(s):

Hypoxia Inducible Factor ◽

Negative Regulation ◽

Structural Basis ◽

Hypoxia Inducible Factor 1Α

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Structural basis of eIF2B-catalyzed GDP exchange and phosphoregulation by the integrated stress response

10.1101/504654 ◽

2018 ◽

Author(s):

Aditya A Anand ◽

Lillian R Kenner ◽

Henry C Nguyen ◽

Alexander G Myasnikov ◽

Carolin J Klose ◽

...

Keyword(s):

Stress Response ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Structural Basis ◽

Integrated Stress Response ◽

Nucleotide Exchange ◽

Guanine Nucleotide Exchange ◽

Nucleotide Exchange Factor ◽

Initiation Factor Eif2 ◽

General Translation

The integrated stress response (ISR) tunes the rate of protein synthesis. Control is exerted by phosphorylation of the general translation initiation factor eIF2. eIF2 is a GTPase, that becomes activated by eIF2B, a large two-fold symmetric and heterodecameric complex that functions as eIF2's dedicated nucleotide exchange factor. Phosphorylation converts eIF2 from substrate into an inhibitor of eIF2B. We report cryoEM structures of eIF2 bound to eIF2B in the dephosphorylated state. The structures reveal that the eIF2B decamer is a static platform upon which one or two flexible eIF2 trimers bind and align with eIF2B's catalytic centers to catalyze guanine nucleotide exchange. Phosphorylation refolds eIF2, allowing it to contact eIF2B at a different interface and, we surmise, thereby sequesters it into a non-productive complex.

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Molecular and Structural Basis of Cross-Reactivity in M. tuberculosis Toxin–Antitoxin Systems

Toxins ◽

10.3390/toxins12080481 ◽

2020 ◽

Vol 12 (8) ◽

pp. 481 ◽

Cited By ~ 1

Author(s):

Himani Tandon ◽

Akhila Melarkode Vattekatte ◽

Narayanaswamy Srinivasan ◽

Sankaran Sandhya

Keyword(s):

Mycobacterium Tuberculosis ◽

Stress Response ◽

Structural Analysis ◽

Chemical Nature ◽

Structural Models ◽

Cross Reactivity ◽

Structural Basis ◽

Detailed Structural Analysis ◽

Response Network ◽

Computational Analyses

Mycobacterium tuberculosis genome encodes over 80 toxin–antitoxin (TA) systems. While each toxin interacts with its cognate antitoxin, the abundance of TA systems presents an opportunity for potential non-cognate interactions. TA systems mediate manifold interactions to manage pathogenicity and stress response network of the cell and non-cognate interactions may play vital roles as well. To address if non-cognate and heterologous interactions are feasible and to understand the structural basis of their interactions, we have performed comprehensive computational analyses on the available 3D structures and generated structural models of paralogous M. tuberculosis VapBC and MazEF TA systems. For a majority of the TA systems, we show that non-cognate toxin–antitoxin interactions are structurally incompatible except for complexes like VapBC15 and VapBC11, which show similar interfaces and potential for cross-reactivity. For TA systems which have been experimentally shown earlier to disfavor non-cognate interactions, we demonstrate that they are structurally and stereo-chemically incompatible. For selected TA systems, our detailed structural analysis identifies specificity conferring residues. Thus, our work improves the current understanding of TA interfaces and generates a hypothesis based on congenial binding site, geometric complementarity, and chemical nature of interfaces. Overall, our work offers a structure-based explanation for non-cognate toxin-antitoxin interactions in M. tuberculosis.

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Structural basis for eIF2B inhibition in integrated stress response

Science ◽

10.1126/science.aaw4104 ◽

2019 ◽

Vol 364 (6439) ◽

pp. 495-499 ◽

Cited By ~ 23

Author(s):

Kazuhiro Kashiwagi ◽

Takeshi Yokoyama ◽

Madoka Nishimoto ◽

Mari Takahashi ◽

Ayako Sakamoto ◽

...

Keyword(s):

Stress Response ◽

Translation Initiation Factor ◽

Initiation Factor ◽

Structural Basis ◽

Dependent Manner ◽

Integrated Stress Response ◽

Nucleotide Exchange ◽

Electron Microscopic ◽

Eukaryotic Translation ◽

Initiation Factor 2

A core event in the integrated stress response, an adaptive pathway common to all eukaryotic cells in response to various stress stimuli, is the phosphorylation of eukaryotic translation initiation factor 2 (eIF2). Normally, unphosphorylated eIF2 transfers the methionylated initiator tRNA to the ribosome in a guanosine 5′-triphosphate–dependent manner. By contrast, phosphorylated eIF2 inhibits its specific guanine nucleotide exchange factor, eIF2B. To elucidate how the eIF2 phosphorylation status regulates the eIF2B activity, we determined cryo–electron microscopic and crystallographic structures of eIF2B in complex with unphosphorylated or phosphorylated eIF2. The unphosphorylated and phosphorylated forms of eIF2 bind to eIF2B in completely different manners: the nucleotide exchange-active and -inactive modes, respectively. These structures explain how phosphorylated eIF2 dominantly inhibits the nucleotide exchange activity of eIF2B.

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