Apoptosome and inflammasome are multimeric protein complexes that mediate the activation of specific caspases at the onset of apoptosis and inflammation. The central component of apoptosome or inflammasome is a tripartite scaffold protein, exemplified by Apaf-1 and NLRC4, which contains an amino-terminal homotypic interaction motif, a central nucleotide-binding oligomerization domain and a carboxyl-terminal ligand-sensing domain. In the absence of death cue or an inflammatory signal, Apaf-1 or NLRC4 exists in an auto-inhibited, monomeric state, which is stabilized by adenosine diphosphate (ADP). Binding to an apoptosis- or inflammation-inducing ligand, together with replacement of ADP by adenosine triphosphate (ATP), results in the formation of a multimeric apoptosome or inflammasome. The assembled apoptosome and inflammasome serve as dedicated machineries to facilitate the activation of specific caspases. In this review, we describe the structure and functional mechanisms of mammalian inflammasome and apoptosomes from three representative organisms. Emphasis is placed on the molecular mechanism of caspase activation and the shared features of apoptosomes and inflammasomes.

柴继杰    施一公    

National Science Review

2014

Programmed cell death in Caenorhabditis elegans requires activation of the caspase CED-3, which strictly depends on CED-4. CED-4 forms an octameric apoptosome, which binds the CED-3 zymogen and facilitates its autocatalytic maturation. Despite recent advances, major questions remain unanswered. Importantly, how CED-4 recognizes CED-3 and how such binding facilitates CED-3 activation remain completely unknown. Here we demonstrate that the L2′ loop of CED-3 directly binds CED-4 and plays a major role in the formation of an active CED-4-CED-3 holoenzyme. The crystal structure of the CED-4 apoptosome bound to the L2′ loop fragment of CED-3, determined at 3.2 Å resolution, reveals specific interactions between a stretch of five hydrophobic amino acids from CED-3 and a shallow surface pocket within the hutch of the funnel-shaped CED-4 apoptosome. Structure-guided biochemical analysis confirms the functional importance of the observed CED-4-CED-3 interface. Structural analysis together with published evidence strongly suggest a working model in which two molecules of CED-3 zymogen, through specific recognition, are forced into the hutch of the CED-4 apoptosome, consequently undergoing dimerization and autocatalytic maturation. The mechanism of CED-3 activation represents a major revision of the prevailing model for initiator caspase activation. © 2013, Published by Cold Spring Harbor Laboratory Press.

Huang Weijiao    Jiang Tianyu    Choi Wooyoung    Qi Shiqian    Pang Yuxuan    Qi Hu    徐艳辉    Xinqi Gong    Jeffrey Philip D.    王佳伟    施一公    

Genes and Development

2013

The MecA-ClpC complex is a bacterial type II AAA molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA rings and suggest that concerted actions of the two AAA rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA hexamers. © 2013 by The American Society for Biochemistry and Molecular Biology, Inc.

Liu Jing    Mei Ziqing    Li Ningning    Qi Yutao    Xu Yanji    施一公     王峰    雷建林    Ning Gao   

Journal of Biological Chemistry

2013

Environmental problems in China are urgent so that resource and environmental auditing is becoming more and more important. The objectives of this study are to introduce spatial and emerging information technologies and its applications in resource and environmental auditing. We synthesized characteristics and advantages of GIS applications and auditing application cases, implemented by National Audit Office of P. R. China, Nanjing Branch and Wuhan Branch, from the practice perspective. In the future, spatial information technology combining with emerging information technologies, including Big Data, Internet of Things, Cloud Computing, Augmented Reality (AR) Technique, large distributed and mobile network will improve the reliability of audit evidences and enhance the auditing conclusions and functions, especially resource and environmental auditing. © Springer-Verlag Berlin Heidelberg 2013.

Zhong Biao    Xia Xinyi    Hou Kunlei    施一公    

Communications in Computer and Information Science

2013

The Beclin 1 gene is a haplo-insufficient tumor suppressor and plays an essential role in autophagy. However, the molecular mechanism by which Beclin 1 functions remains largely unknown. Here we report the crystal structure of the evolutionarily conserved domain (ECD) of Beclin 1 at 1.6 Å resolution. Beclin 1 ECD exhibits a previously unreported fold, with three structural repeats arranged symmetrically around a central axis. Beclin 1 ECD defines a novel class of membrane-binding domain, with a strong preference for lipid membrane enriched with cardiolipin. The tip of a surface loop in Beclin 1 ECD, comprising three aromatic amino acids, acts as a hydrophobic finger to associate with lipid membrane, consequently resulting in the deformation of membrane and liposomes. Mutation of these aromatic residues rendered Beclin 1 unable to stably associate with lipid membrane in vitro and unable to fully rescue autophagy in Beclin 1-knockdown cells in vivo. These observations form an important framework for deciphering the biological functions of Beclin 1. © 2012 IBCB, SIBS, CAS All rights reserved.

Huang Weijiao    Choi Wooyoung    Hu Wanqiu    Mi Na    Guo Qiang    Ma Meisheng    Mei Liu    Yuan Tian    卢培龙    Wang Feng-Liang    Deng Haiteng    刘磊    Ning Gao    俞立    施一公    

Cell Research

2012

The CED-4 homo-oligomer or apoptosome is required for initiation of programmed cell death in Caenorhabditis elegans by facilitating autocatalytic activation of the CED-3 caspase zymogen. How the CED-4 apoptosome assembles and activates CED-3 remains enigmatic. Here we report the crystal structure of the complete CED-4 apoptosome and show that it consists of eight CED-4 molecules, organized as a tetramer of an asymmetric dimer via a previously unreported interface among AAA ATPases. These eight CED-4 molecules form a funnel-shaped structure. The mature CED-3 protease is monomeric in solution and forms an active holoenzyme with the CED-4 apoptosome, within which the protease activity of CED-3 is markedly stimulated. Unexpectedly, the octameric CED-4 apoptosome appears to bind only two, not eight, molecules of mature CED-3. The structure of the CED-4 apoptosome reveals shared principles for the NB-ARC family of AAA ATPases and suggests a mechanism for the activation of CED-3. © 2010 Elsevier Inc.

Qi Shiqian    Pang Yuxuan    Qi Hu    Liu Qun    Hua Li    Zhou Yulian    He Tianxi    Qionglin Liang    Liu Yexing    Yuan Xiaoqiu    Guoan Luo    Huilin Li    王佳伟    颜宁    施一公    

Cell

2010

The specific molecular events that characterize the intrinsic apoptosis pathway have been the subject of intense research due to the pathway's fundamental role in development, homeostasis, and cancer. This pathway is defined by the release of cytochrome c from mitochondria into the cytosol and subsequent binding of cytochrome c to the caspase activator Apaf-1. Here, we report that both mitochondrial and cytosolic transfer RNA (tRNA) bind to cytochrome c. This binding prevents cytochrome c interaction with Apaf-1, blocking Apaf-1 oligomerization and caspase activation. tRNA hydrolysis in living cells and cell lysates enhances apoptosis and caspase activation, whereas microinjection of tRNA into living cells blocks apoptosis. These findings suggest that tRNA, in addition to its well-established role in gene expression, may determine cellular responsiveness to apoptotic stimuli. © 2010 Elsevier Inc. All rights reserved.

梅一德    Yong Jeongsik    Liu Hongtu    施一公     Meinkoth Judy    Gideon Dreyfuss    Xiaolu Yang   

Molecular Cell

2010

A cell's decision to growth arrest, apoptose, or differentiate in response to transforming growth factor β (TGF-β) superfamily ligands depends on the ligand concentration. How cells sense the concentration of extracellular bioavailable TGF-β remains poorly understood. We therefore undertook a systematic quantitative analysis of how TGF-β ligand concentration is transduced into downstream phospho-Smad2 kinetics, and we found that the rate of TGF-β ligand depletion is the principal determinant of Smad signal duration. TGF-β depletion is caused by two mechanisms: (i) cellular uptake of TGF-β by a TGF-β type II receptor-dependent mechanism and (ii) reversible binding of TGF-β to the cell surface. Our results indicate that cells sense TGF-β dose by depleting TGF-β via constitutive TGF-β type II receptor trafficking processes. Our results also have implications for the role of the TGF-β type II receptor in disease, as tumor cells harboring TGF-β type II receptor mutations exhibit impaired TGF-β depletion, which may contribute to the overproduction of TGF-β and a consequently poor prognosis in cancer. Copyright © 2009, American Society for Microbiology.

Clarke David C.    Brown Meredith L.    Erickson Richard A.    施一公     刘学东   

Molecular and Cellular Biology

2009

施一公    

Science in China. Series C, Life sciences / Chinese Academy of Sciences

2009

The reversible phosphorylation of proteins is accomplished by opposing activities of kinases and phosphatases. Relatively few protein serine/threonine phosphatases (PSPs) control the specific dephosphorylation of thousands of phosphoprotein substrates. Many PSPs, exemplified by protein phosphatase 1 (PP1) and PP2A, achieve substrate specificity and regulation through combinatorial interactions between conserved catalytic subunits and a large number of regulatory subunits. Other PSPs, represented by PP2C and FCP/SCP, contain both catalytic and regulatory domains within the same polypeptide chain. Here, we discuss biochemical and structural investigations that advance the mechanistic understanding of the three major classes of PSPs, with a focus on PP2A. © 2009 Elsevier Inc. All rights reserved.

施一公    

Cell

2009