1
|
Xi Y, Xu R, Chen S, Fang J, Duan X, Zhang Y, Zhong G, He Z, Guo Y, Li X, Tao W, Li Y, Li Y, Fang L, Niikura Y. TSG101 depletion dysregulates mitochondria and PML NBs, triggering MAD2-overexpressing interphase cell death (MOID) through AIFM1-PML-DAXX pathway. Cell Death Dis 2024; 15:838. [PMID: 39551802 PMCID: PMC11570632 DOI: 10.1038/s41419-024-07229-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 10/30/2024] [Accepted: 11/06/2024] [Indexed: 11/19/2024]
Abstract
Overexpression of mitotic arrest deficiency 2 (MAD2/MAD2L1), a pivotal component of the spindle assembly checkpoint (SAC), resulted in many types of cancer. Here we show that the depletion of tumor susceptibility gene 101 (TSG101), causes synthetic dosage lethality (SDL) in MAD2-overexpressing cells, and we term this cell death MAD2-overexpressing interphase cell death (MOID). The induction of MOID depends on PML and DAXX mediating mitochondrial AIFM1-release. MAD2, TSG101, and AIF-PML-DAXX axis regulate mitochondria, PML nuclear bodies (NBs), and autophagy with close inter-dependent protein stability in survival cells. Loss of C-terminal phosphorylation(s) of TSG101 and closed (C-)MAD2-overexpression contribute to induce MOID. In survival cells, both MAD2 and TSG101 localize at PML NBs in interphase, and TSG101 Y390 phosphorylation is required for localization of TSG101 to PML NBs. PML release from PML NBs through PML deSUMOylation contributes to induce MOID. The post-transcriptional/translational cell death machinery and the non-canonical transcriptional regulation are intricately linked to MOID, and ER-MAM, may serve as a crucial intersection for MOID signaling.
Collapse
Affiliation(s)
- Yao Xi
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Rui Xu
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Shengnan Chen
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Jiezhu Fang
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Xiang Duan
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Yidan Zhang
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Guoli Zhong
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Zhifei He
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Yan Guo
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Xinyu Li
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Wenzhi Tao
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Yang Li
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Yan Li
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China.
| | - Yohei Niikura
- National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, Model Animal Research Center, Medical School of Nanjing University, Nanjing, 210061, China.
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, 210032, China.
| |
Collapse
|
2
|
Lin L, Guo H, Batool W, Lin L, Cao J, An Q, Aliyu SR, Bao J, Wang Z, Norvienyeku J. Translocon Subunits of the COP9 Signalosome Complex Are a Central Hub for Regulating Multiple Photoresponsive Processes and Autophagic Flux in Magnaporthe oryzae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:22015-22034. [PMID: 39319468 DOI: 10.1021/acs.jafc.4c03163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Photodependent processes, including circadian rhythm, autophagy, ubiquitination, neddylation/deneddylation, and metabolite biosynthesis, profoundly influence microbial pathogenesis. Although a photomorphogenesis signalosome (COP9/CSN) has been identified, the mechanism by which this large complex contributes to the pathophysiological processes in filamentous fungi remains unclear. Here, we identified eight CSN complex subunits in the rice blast fungus Magnaporthe oryzae and functionally characterized the translocon subunits containing a nuclear export or localization signal (NES/NLS). Targeted gene replacement of these CSN subunits, including MoCSN3, MoCSN5, MoCSN6, MoCSN7, and MoCSN12, attenuated vegetative growth and conidiation and rendered the deletion strains nonpathogenic. MoCSN7 deletion significantly suppressed arachidonic acid catabolism, and compromised cell wall integrity in M. oryzae. Surprisingly, we also discovered that MoCSN subunits, particularly MoCsn7, are required for the cAMP-dependent regulation of autophagic flux. Therefore, MoCSN significantly contributes to morphological, physiological, and pathogenic differentiation in M. oryzae by fostering cross-talk between multiple pathways.
Collapse
Affiliation(s)
- Lili Lin
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Hengyuan Guo
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan, China
| | - Wajjiha Batool
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Lianyu Lin
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jiaying Cao
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Qiuli An
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Sami Rukaiya Aliyu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Jiandong Bao
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- The Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Zonghua Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
- Institute of Oceanography, Minjiang University, Fuzhou 350108, Fujian, China
| | - Justice Norvienyeku
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, Hainan, China
| |
Collapse
|
3
|
Yu C, Novitsky E, Wang X, Echeverria I, Rychnovsky S, Huang L. Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.06.606913. [PMID: 39211111 PMCID: PMC11360931 DOI: 10.1101/2024.08.06.606913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Cross-linking mass spectrometry (XL-MS) is a powerful technology for mapping protein-protein interactions (PPIs) at the systems-level. By covalently connecting pairs of proximal residues, cross-linking reagents provide distance restraints to infer protein conformations and interaction interfaces. While binary cross-links have been remarkably informative, multimeric cross-links can offer enhanced spatial resolution to facilitate the characterization of dynamic and heterogeneous protein complexes. However, the identification of multimeric cross-links remains extremely challenging due to fragmentation complexity and the vast expansion of database search space. Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MS n analysis. Importantly, we have demonstrated that the TSTO-based XL-MS platform is effective for mapping PPIs of protein complexes and cellular networks. The trimeric interactions captured by TSTO have uncovered new structural details that cannot be easily revealed by existing reagents, allowing in-depth description of PPIs to facilitate structural modeling. This development not only advances XL-MS technologies for global PPI profiling from living cells, but also offers a new direction for creating multifunctional MS-cleavable cross-linkers to further push structural systems biology forward in the future.
Collapse
|
4
|
Bakti F, Stupperich H, Schmitt K, Valerius O, Köhler AM, Meister C, Strohdiek A, Harting R, Sasse C, Heimel K, Neumann P, Ficner R, Braus GH. Fungal COP9 signalosome assembly requires connection of two trimeric intermediates for integration of intrinsic deneddylase. Proc Natl Acad Sci U S A 2023; 120:e2305049120. [PMID: 37603767 PMCID: PMC10477865 DOI: 10.1073/pnas.2305049120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023] Open
Abstract
The conserved eight-subunit COP9 signalosome (CSN) is required for multicellular fungal development. The CSN deneddylase cooperates with the Cand1 exchange factor to control replacements of E3 ubiquitin cullin RING ligase receptors, providing specificity to eukaryotic protein degradation. Aspergillus nidulans CSN assembles through a heptameric pre-CSN, which is activated by integration of the catalytic CsnE deneddylase. Combined genetic and biochemical approaches provided the assembly choreography within a eukaryotic cell for native fungal CSN. Interactomes of functional GFP-Csn subunit fusions in pre-CSN deficient fungal strains were compared by affinity purifications and mass spectrometry. Two distinct heterotrimeric CSN subcomplexes were identified as pre-CSN assembly intermediates. CsnA-C-H and CsnD-F-G form independently of CsnB, which connects the heterotrimers to a heptamer and enables subsequent integration of CsnE to form the enzymatically active CSN complex. Surveillance mechanisms control accurate Csn subunit amounts and correct cellular localization for sequential assembly since deprivation of Csn subunits changes the abundance and location of remaining Csn subunits.
Collapse
Affiliation(s)
- Fruzsina Bakti
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Helena Stupperich
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Anna M. Köhler
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Cindy Meister
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Anja Strohdiek
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Rebekka Harting
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Christoph Sasse
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Kai Heimel
- Department of Microbial Cell Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute of Microbiology and Genetics, Goettingen Center for Molecular Biosciences, University of Goettingen, 37077Goettingen, Germany
| |
Collapse
|
5
|
Liu S, Wang H, Li X, Zhang F, Lee JKJ, Li Z, Yu C, Hu JJ, Zhao X, Suematsu T, Alvarez-Cabrera AL, Liu Q, Zhang L, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH. Structural basis of gRNA stabilization and mRNA recognition in trypanosomal RNA editing. Science 2023; 381:eadg4725. [PMID: 37410820 DOI: 10.1126/science.adg4725] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/17/2023] [Indexed: 07/08/2023]
Abstract
In Trypanosoma brucei, the editosome, composed of RNA-editing substrate-binding complex (RESC) and RNA-editing catalytic complex (RECC), orchestrates guide RNA (gRNA)-programmed editing to recode cryptic mitochondrial transcripts into messenger RNAs (mRNAs). The mechanism of information transfer from gRNA to mRNA is unclear owing to a lack of high-resolution structures for these complexes. With cryo-electron microscopy and functional studies, we have captured gRNA-stabilizing RESC-A and gRNA-mRNA-binding RESC-B and RESC-C particles. RESC-A sequesters gRNA termini, thus promoting hairpin formation and blocking mRNA access. The conversion of RESC-A into RESC-B or -C unfolds gRNA and allows mRNA selection. The ensuing gRNA-mRNA duplex protrudes from RESC-B, likely exposing editing sites to RECC-catalyzed cleavage, uridine insertion or deletion, and ligation. Our work reveals a remodeling event facilitating gRNA-mRNA hybridization and assembly of a macromolecular substrate for the editosome's catalytic modality.
Collapse
Affiliation(s)
- Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Hong Wang
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Xiaorun Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Fan Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Jane K J Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Zihang Li
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Jason J Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Xiaojing Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Ana L Alvarez-Cabrera
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| | - Qiushi Liu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, USA
- Department of Biochemistry, Boston University Medical Campus, Boston, MA, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, CA, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, USA
| |
Collapse
|
6
|
Hu JJ, Lee JKJ, Liu YT, Yu C, Huang L, Aphasizheva I, Aphasizhev R, Zhou ZH. Discovery, structure, and function of filamentous 3-methylcrotonyl-CoA carboxylase. Structure 2023; 31:100-110.e4. [PMID: 36543169 PMCID: PMC9825669 DOI: 10.1016/j.str.2022.11.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/17/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
3-methylcrotonyl-CoA carboxylase (MCC) is a biotin-dependent mitochondrial enzyme necessary for leucine catabolism in most organisms. While the crystal structure of recombinant bacterial MCC has been characterized, the structure and potential polymerization of native MCC remain elusive. Here, we discovered that native MCC from Leishmania tarentolae (LtMCC) forms filaments, and determined the structures of different filament regions at 3.4, 3.9, and 7.3 Å resolution using cryoEM. α6β6 LtMCCs assemble in a twisted-stacks architecture, manifesting as supramolecular rods up to 400 nm. Filamentous LtMCCs bind biotin non-covalently and lack coenzyme A. Filaments elongate by stacking α6β6 LtMCCs onto the exterior α-trimer of the terminal LtMCC. This stacking immobilizes the biotin carboxylase domains, sequestering the enzyme in an inactive state. Our results support a new model for LtMCC catalysis, termed the dual-swinging-domains model, and cast new light on the function of polymerization in the carboxylase superfamily and beyond.
Collapse
Affiliation(s)
- Jason J Hu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Mathematics, UCLA, Los Angeles, CA 90095, USA
| | - Jane K J Lee
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA; Department of Psychology, UCLA, Los Angeles, CA 90095, USA
| | - Yun-Tao Liu
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus (BUMC), Boston, MA 02118, USA; Department of Biochemistry, BUMC, Boston, MA 02118, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA; California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA.
| |
Collapse
|
7
|
Leissing F, Misch NV, Wang X, Werner L, Huang L, Conrath U, Beckers GJM. Purification of MAP-kinase protein complexes and identification of candidate components by XL-TAP-MS. PLANT PHYSIOLOGY 2021; 187:2381-2392. [PMID: 34609515 PMCID: PMC8644975 DOI: 10.1093/plphys/kiab446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
The purification of low-abundance protein complexes and detection of in vivo protein-protein interactions in complex biological samples remains a challenging task. Here, we devised crosslinking and tandem affinity purification coupled to mass spectrometry (XL-TAP-MS), a quantitative proteomics approach for analyzing tandem affinity-purified, crosslinked protein complexes from plant tissues. We exemplarily applied XL-TAP-MS to study the MKK2-Mitogen-activated protein kinase (MPK4) signaling module in Arabidopsis thaliana. A tandem affinity tag consisting of an in vivo-biotinylated protein domain flanked by two hexahistidine sequences was adopted to allow for the affinity-based isolation of formaldehyde-crosslinked protein complexes under fully denaturing conditions. Combined with 15N stable isotopic labeling and tandem MS we captured and identified a total of 107 MKK2-MPK4 module-interacting proteins. Consistent with the role of the MPK signaling module in plant immunity, many of the module-interacting proteins are involved in the biotic and abiotic stress response of Arabidopsis. Validation of binary protein-protein interactions by in planta split-luciferase assays and in vitro kinase assays disclosed several direct phosphorylation targets of MPK4. Together, the XL-TAP-MS approach purifies low abundance protein complexes from biological samples and discovers previously unknown protein-protein interactions.
Collapse
Affiliation(s)
- Franz Leissing
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| | - Nicola V Misch
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| | - Xiaorong Wang
- Department of Physiology & Biophysics, University of California, Irvine, California 92697, USA
| | - Linda Werner
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, California 92697, USA
| | - Uwe Conrath
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| | - Gerold J M Beckers
- Department of Plant Physiology, RWTH Aachen University, Aachen 52056, Germany
| |
Collapse
|
8
|
Fang L, Chen D, Zhang J, Li H, Bradford B, Jin C. Potential functions of histone H3.3 lysine 56 acetylation in mammals. Epigenetics 2021; 17:498-517. [PMID: 33902396 DOI: 10.1080/15592294.2021.1922198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
H3K56 acetylation (H3K56Ac) was first identified in yeast and has recently been reported to play important roles in maintaining genomic stability, chromatin assembly, DNA replication, cell cycle progression and DNA repair. Although H3.1K56Ac has been relatively well studied, the function of H3.3K56Ac remains mostly unknown in mammals. In this study, we used H3.3K56Q and H3.3K56R mutants to study the possible function of H3.3K56 acetylation. The K-to-Q substitution mimics a constitutively acetylated lysine, while the K-to-R replacement mimics a constitutively unmodified lysine. We report that cell lines harbouring mutation of H3.3K56R exhibit increased cell death and dramatic morphology changes. Using a Tet-Off inducible system, we found an increased population of polyploid/aneuploid cells and decreased cell viability in H3.3K56R mutant cells. Consistent with these results, the H3.3K56R mutant had compromised H3.3 incorporation into several pericentric and centric heterochromatin regions we tested. Moreover, mass spectrometry analysis coupled with label-free quantification revealed that biological processes regulated by the H3.3-associating proteins, whose interaction with H3.3 was markedly increased by H3.3K56Q mutation but decreased by H3.3K56R mutation, include sister chromatid cohesion, mitotic nuclear division, and mitotic nuclear envelope disassembly. These results suggest that H3.3K56 acetylation is crucial for chromosome segregation and cell division in mammals.
Collapse
Affiliation(s)
- Lei Fang
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, USA.,Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Danqi Chen
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Jingzi Zhang
- Jiangsu Key Laboratory of Molecular Medicine, Chemistry and Biomedicine Innovation Center, Medical School of Nanjing University, Nanjing, Jiangsu, China
| | - Hongjie Li
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Beatrix Bradford
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Chunyuan Jin
- Department of Environmental Medicine, New York University Grossman School of Medicine, New York, NY, USA
| |
Collapse
|
9
|
Aphasizheva I, Yu T, Suematsu T, Liu Q, Mesitov MV, Yu C, Huang L, Zhang L, Aphasizhev R. Poly(A) binding KPAF4/5 complex stabilizes kinetoplast mRNAs in Trypanosoma brucei. Nucleic Acids Res 2020; 48:8645-8662. [PMID: 32614436 PMCID: PMC7470953 DOI: 10.1093/nar/gkaa575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 12/23/2022] Open
Abstract
In Trypanosoma brucei, mitochondrial pre-mRNAs undergo 3′-5′ exonucleolytic processing, 3′ adenylation and uridylation, 5′ pyrophosphate removal, and, often, U-insertion/deletion editing. The 3′ modifications are modulated by pentatricopeptide repeat (PPR) Kinetoplast Polyadenylation Factors (KPAFs). We have shown that KPAF3 binding to the 3′ region stabilizes properly trimmed transcripts and stimulates their A-tailing by KPAP1 poly(A) polymerase. Conversely, poly(A) binding KPAF4 shields the nascent A-tail from uridylation and decay thereby protecting pre-mRNA upon KPAF3 displacement by editing. While editing concludes in the 5′ region, KPAF1/2 dimer induces A/U-tailing to activate translation. Remarkably, 5′ end recognition and pyrophosphate hydrolysis by the PPsome complex also contribute to mRNA stabilization. Here, we demonstrate that KPAF4 functions as a heterodimer with KPAF5, a protein lacking discernable motifs. We show that KPAF5 stabilizes KPAF4 to enable poly(A) tail recognition, which likely leads to mRNA stabilization during the editing process and impedes spontaneous translational activation of partially-edited transcripts. Thus, KPAF4/5 represents a poly(A) binding element of the mitochondrial polyadenylation complex. We present evidence that RNA editing substrate binding complex bridges the 5′ end-bound PPsome and 3′ end-bound polyadenylation complexes. This interaction may enable mRNA circularization, an apparently critical element of mitochondrial mRNA stability and quality control.
Collapse
Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA
| | - Tian Yu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA
| | - Qiushi Liu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA
| | - Mikhail V Mesitov
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA.,Department of Biochemistry, Boston University Medical Campus, Boston, MA 02118, USA
| |
Collapse
|
10
|
Alkafeef SS, Lane S, Yu C, Zhou T, Solis NV, Filler SG, Huang L, Liu H. Proteomic profiling of the monothiol glutaredoxin Grx3 reveals its global role in the regulation of iron dependent processes. PLoS Genet 2020; 16:e1008881. [PMID: 32525871 PMCID: PMC7319344 DOI: 10.1371/journal.pgen.1008881] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/26/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
Iron is an essential nutrient required as a cofactor for many biological processes. As a fungal commensal-pathogen of humans, Candida albicans encounters a range of bioavailable iron levels in the human host and maintains homeostasis with a conserved regulatory circuit. How C. albicans senses and responds to iron availability is unknown. In model yeasts, regulation of the iron homeostasis circuit requires monothiol glutaredoxins (Grxs), but their functions beyond the regulatory circuit are unclear. Here, we show Grx3 is required for virulence and growth on low iron for C. albicans. To explore the global roles of Grx3, we applied a proteomic approach and performed in vivo cross-linked tandem affinity purification coupled with mass spectrometry. We identified a large number of Grx3 interacting proteins that function in diverse biological processes. This included Fra1 and Bol2/Fra2, which function with Grxs in intracellular iron trafficking in other organisms. Grx3 interacts with and regulates the activity of Sfu1 and Hap43, components of the C. albicans iron regulatory circuit. Unlike the regulatory circuit, which determines expression or repression of target genes in response to iron availability, Grx3 amplifies levels of gene expression or repression. Consistent with the proteomic data, the grx3 mutant is sensitive to heat shock, oxidative, nitrosative, and genotoxic stresses, and shows growth dependence on histidine, leucine, and tryptophan. We suggest Grx3 is a conserved global regulator of iron-dependent processes occurring within the cell. Mammalian pathogens occupy a diverse set of niches within the host organism. These niches vary in iron and oxygen availability. As a commensal and pathogen of humans, its ability to regulate iron uptake and utilization in response to bioavailable iron level is critical for its survival in different host environments encompassing a broad range of iron levels. This study aims to understand how C. albicans senses and responds to iron level to regulate multiple aspects of its biology. The cytosolic monothiol glutaredoxin Grx3 is a critical regulator of C. albicans iron homeostasis and virulence. Taking a proteomic approach, we identified a large list of Grx3 associated proteins of diverse functions, including iron-sulfur trafficking, iron homeostasis, metabolism redox homeostasis, protein translation, DNA maintenance and repair. In support of these protein associations, Grx3 is important for all these processes. Thus, Grx3 is a global regulator of iron homeostasis and other iron dependent cellular processes.
Collapse
Affiliation(s)
- Selma S Alkafeef
- Department of Biological Chemistry, University of California, Irvine, California, United States of America.,Department of Biochemistry, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Shelley Lane
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
| | - Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, California, United States of America
| | - Tingting Zhou
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
| | - Norma V Solis
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Scott G Filler
- Division of Infectious Diseases, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America.,David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, California, United States of America
| | - Haoping Liu
- Department of Biological Chemistry, University of California, Irvine, California, United States of America
| |
Collapse
|
11
|
Niikura Y, Kitagawa R, Fang L, Kitagawa K. CENP-A Ubiquitylation Is Indispensable to Cell Viability. Dev Cell 2020; 50:683-689.e6. [PMID: 31550462 DOI: 10.1016/j.devcel.2019.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/30/2019] [Accepted: 07/14/2019] [Indexed: 01/10/2023]
Abstract
CENP-A is a centromere-specific histone H3 variant that epigenetically determines centromere identity, but how CENP-A is deposited at the centromere remains obscure. We previously reported that CENP-A K124 ubiquitylation, mediated by the CUL4A-RBX1-COPS8 complex, is essential for CENP-A deposition at the centromere. However, a recent report stated that CENP-A K124R mutants show no defects in centromere localization and cell viability. In the present study, we found that EYFP tagging induces additional ubiquitylation of EYFP-CENP-A K124R, which allows the mutant protein to bind to HJURP. Using a previously developed conditional CENP-A knockout system and our CENP-A K124R knockin mutant created by the CRISPR-Cas9 system, we show that the Flag-tagged or untagged CENP-A K124R mutant is lethal. This lethality is rescued by monoubiquitin fusion, indicating that CENP-A ubiquitylation is essential for viability.
Collapse
Affiliation(s)
- Yohei Niikura
- Greehey Children's Cancer Research Institute, Department of Molecular Medicine, UT Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229-3000, USA; MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, Jiangsu Province 210061, China.
| | - Risa Kitagawa
- Greehey Children's Cancer Research Institute, Department of Molecular Medicine, UT Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229-3000, USA
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, Jiangsu Province 210093, China
| | - Katsumi Kitagawa
- Greehey Children's Cancer Research Institute, Department of Molecular Medicine, UT Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX 78229-3000, USA.
| |
Collapse
|
12
|
Zhang J, Zhao R, Yu C, Bryant CLN, Wu K, Liu Z, Ding Y, Zhao Y, Xue B, Pan ZQ, Li C, Huang L, Fang L. IKK-Mediated Regulation of the COP9 Signalosome via Phosphorylation of CSN5. J Proteome Res 2020; 19:1119-1130. [PMID: 31950832 DOI: 10.1021/acs.jproteome.9b00626] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The COP9 signalosome (CSN) is an evolutionarily conserved multisubunit protein complex, which controls protein degradation through deneddylation and inactivation of cullin-RING ubiquitin E3 ligases (CRLs). Recently, the CSN complex has been linked to the NF-κB signaling pathway due to its association with the IKK complex. However, how the CSN complex is regulated in this signaling pathway remains unclear. Here, we have carried out biochemical experiments and confirmed the interaction between the CSN and IKK complexes. In addition, we have determined that overexpression of IKKα or IKKβ leads to enhanced phosphorylation of CSN5, the catalytic subunit for CSN deneddylase activity. Mutational analyses have revealed that phosphorylation at serine 201 and threonine 205 of CSN5 impairs CSN-mediated deneddylation activity in vitro. Interestingly, TNF-α treatment not only enhances the interaction between CSN and IKK but also induces an IKK-dependent phosphorylation of CSN5 at serine 201, linking CSN to TNF-α signaling through IKK. Moreover, TNF-α treatment affects the CSN interaction network globally, especially the associations of CSN with the proteasome complex, eukaryotic translation initiation factor complex, and CRL components. Collectively, our results provide new insights into IKK-mediated regulation of CSN associated with the NF-κB signaling pathway.
Collapse
Affiliation(s)
- Jingzi Zhang
- Medical School and Model Animal Research Center of Nanjing University, Nanjing 210093, China
| | - Ruoyu Zhao
- Medical School and Model Animal Research Center of Nanjing University, Nanjing 210093, China
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, Unites States
| | - Christine L N Bryant
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, Unites States
| | - Kenneth Wu
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York 10029, United States
| | - Zhihong Liu
- School of Life Science, Nanjing University, Nanjing 210023, China
| | - Yibing Ding
- Medical School and Model Animal Research Center of Nanjing University, Nanjing 210093, China
| | - Yue Zhao
- Medical School and Model Animal Research Center of Nanjing University, Nanjing 210093, China
| | - Bin Xue
- Medical School and Model Animal Research Center of Nanjing University, Nanjing 210093, China
| | - Zhen-Qiang Pan
- Department of Oncological Sciences, Mount Sinai School of Medicine, New York, New York 10029, United States
| | - Chaojun Li
- Medical School and Model Animal Research Center of Nanjing University, Nanjing 210093, China
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, Unites States
| | - Lei Fang
- Medical School and Model Animal Research Center of Nanjing University, Nanjing 210093, China.,Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210093, China
| |
Collapse
|
13
|
Wu Y, Zhang J, Fang L, Lee HC, Zhao YJ. A cytosolic chaperone complex controls folding and degradation of type III CD38. J Biol Chem 2019; 294:4247-4258. [PMID: 30670591 DOI: 10.1074/jbc.ra118.005844] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/11/2019] [Indexed: 11/06/2022] Open
Abstract
Cluster of differentiation 38 (CD38) is the best-studied enzyme catalyzing the synthesis of the Ca2+ messenger cyclic ADP-ribose. It is a single-pass transmembrane protein, but possesses dual orientations. We have documented the natural existence of type III CD38 in cells and shown that it is regulated by a cytosolic activator, calcium- and integrin-binding 1 (CIB1). However, how type III CD38 can be folded correctly in the reductive cytosol has not been addressed. Using the yeast two-hybrid technique with CD38's catalytic domain (sCD38) as bait, here we identified a chaperone, Hsp70-interacting protein (Hip), that specifically interacts with both the type III CD38 and sCD38. Immunoprecipitation coupled with MS identified a chaperone complex associated specifically with sCD38. Pharmacological and siRNA-mediated knockdown of Hsp90 chaperones decreased the expression levels of both sCD38 and type III CD38, suggesting that these chaperones facilitate their folding. Moreover, knockdown of Hsc70 or DNAJA2 increased the levels of both CD38 types, consistent with the roles of these proteins in mediating CD38 degradation. Notably, Hip knockdown decreased type III CD38 substantially, but only marginally affected sCD38, indicating that Hip was selective for the former. More remarkably, DNAJA1 knockdown decreased sCD38 but increased type III CD38 levels. Mechanistically, we show that Hsc70 mediates lysosomal degradation of type III CD38, requiring the lysosomal receptor Lamp2A and the C19-motif in the C terminus of CD38. Our results indicate that folding and degradation of type III CD38 is effectively controlled in cells, providing further strong support of its physiological relevance.
Collapse
Affiliation(s)
- Yang Wu
- From the State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, 518055 and
| | - Jingzi Zhang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, Jiangsu Province, China, 210093
| | - Lei Fang
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, Jiangsu Province, China, 210093
| | - Hon Cheung Lee
- From the State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, 518055 and
| | - Yong Juan Zhao
- From the State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, 518055 and
| |
Collapse
|
14
|
Mesitov MV, Yu T, Suematsu T, Sement FM, Zhang L, Yu C, Huang L, Aphasizheva I. Pentatricopeptide repeat poly(A) binding protein KPAF4 stabilizes mitochondrial mRNAs in Trypanosoma brucei. Nat Commun 2019; 10:146. [PMID: 30635574 PMCID: PMC6329795 DOI: 10.1038/s41467-018-08137-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 12/19/2018] [Indexed: 01/25/2023] Open
Abstract
In Trypanosoma brucei, most mitochondrial mRNAs undergo editing, and 3′ adenylation and uridylation. The internal sequence changes and terminal extensions are coordinated: pre-editing addition of the short (A) tail protects the edited transcript against 3′-5′ degradation, while post-editing A/U-tailing renders mRNA competent for translation. Participation of a poly(A) binding protein (PABP) in coupling of editing and 3′ modification processes has been inferred, but its identity and mechanism of action remained elusive. We report identification of KPAF4, a pentatricopeptide repeat-containing PABP which sequesters the A-tail and impedes mRNA degradation. Conversely, KPAF4 inhibits uridylation of A-tailed transcripts and, therefore, premature A/U-tailing of partially-edited mRNAs. This quality check point likely prevents translation of incompletely edited mRNAs. We also find that RNA editing substrate binding complex (RESC) mediates the interaction between the 5′ end-bound pyrophosphohydrolase MERS1 and 3′ end-associated KPAF4 to enable mRNA circularization. This event appears to be critical for edited mRNA stability. Polyadenylation stabilizes edited mitochondrial mRNAs in Trypanosoma brucei, but the involved poly(A) binding protein is unknown. Here, Mesitov et al. show that a pentatricopeptide repeat factor KPAF4 binds to A-tail and prevents exonucleolytic degradation as well as translation of incompletely edited mRNAs.
Collapse
Affiliation(s)
- Mikhail V Mesitov
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, 02118, USA
| | - Tian Yu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, 02118, USA.,Bioinformatics Program, Boston University, Boston, MA, 02215, USA
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, 02118, USA
| | - Francois M Sement
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, 02118, USA
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTechUniversity, 201210, Shanghai, China
| | - Clinton Yu
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA, 02118, USA.
| |
Collapse
|
15
|
Wang Y, Zhou Z, Wang X, Zhang X, Chen Y, Bai J, Di W. TRIM59 Is a Novel Marker of Poor Prognosis and Promotes Malignant Progression of Ovarian Cancer by Inducing Annexin A2 Expression. Int J Biol Sci 2018; 14:2073-2082. [PMID: 30585270 PMCID: PMC6299375 DOI: 10.7150/ijbs.28757] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/26/2018] [Indexed: 12/30/2022] Open
Abstract
Ovarian cancer is the fifth common cause of death in woman worldwide. The tripartite motif-containing (TRIM) proteins consist of more than 70 known protein members. Studies have showed that TRIM proteins are involved in cancer and play important roles in cancer cell proliferation, migration, adhesion and metastasis. Recent studies have indicated that TRIM59, as a putative ubiquitin ligase, is up-regulated in some cancers and associated with poor prognosis of gastric cancer. However, the exact roles of TRIM59 in ovarian cancer are still unknown. In this study, we found that TRIM59 expression was increased and positively associated with histological grades (P = 0.000), FIGO stages (P = 0.016), and metastasis (P = 0.027) in ovarian cancer. A integrative data analysis tool revealed that ovarian cancer patients with high TRIM59 expression were correlated with more unfavorable overall and progression-free survival than the rest patients with low TRIM59 expression (P = 0.0024 and P = 7.5×10-6, respectively). Based on the finding in the clinical data, we performed a series of cell line and animal experiments, and found that TRIM59 knockdown could significantly inhibit the ovarian cancer cell proliferation, clone formation, and invasion in vitro and the ovarian cancer growth of the subcutaneous and orthotopic implantation in vivo. Furthermore, TRIM59 was found to interact with Annexin A2 and induce Annexin A2 expression. Our data imply that TRIM59 can serve as a promising prognostic marker and a potential therapeutic target.
Collapse
Affiliation(s)
- You Wang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China.,Shanghai Key Laboratory of Gynecologic Oncology, Focus Construction Subject of Shanghai Education Department, Shanghai
| | - Zhicheng Zhou
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinran Wang
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China.,Shanghai Key Laboratory of Gynecologic Oncology, Focus Construction Subject of Shanghai Education Department, Shanghai
| | - Xuping Zhang
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Yansu Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China
| | - Wen Di
- Department of Obstetrics and Gynecology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, China
| |
Collapse
|
16
|
Minic Z, Dahms TES, Babu M. Chromatographic separation strategies for precision mass spectrometry to study protein-protein interactions and protein phosphorylation. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:96-108. [PMID: 30380468 DOI: 10.1016/j.jchromb.2018.10.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 11/30/2022]
Abstract
Investigating protein-protein interactions and protein phosphorylation can be of great significance when studying biological processes and human diseases at the molecular level. However, sample complexity, presence of low abundance proteins, and dynamic nature of the proteins often impede in achieving sufficient analytical depth in proteomics research. In this regard, chromatographic separation methodologies have played a vital role in the identification and quantification of proteins in complex sample mixtures. The combination of peptide and protein fractionation techniques with advanced high-performance mass spectrometry has allowed the researchers to successfully study the protein-protein interactions and protein phosphorylation. Several new fractionation strategies for large scale analysis of proteins and peptides have been developed to study protein-protein interactions and protein phosphorylation. These emerging chromatography methodologies have enabled the identification of several hundred protein complexes and even thousands of phosphorylation sites in a single study. In this review, we focus on current workflow strategies and chromatographic tools, highlighting their advantages and disadvantages, and examining their associated challenges and future potential.
Collapse
Affiliation(s)
- Zoran Minic
- Department of Chemistry and Biomolecular Science, University of Ottawa, John L. Holmes, Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, Room 02, Ottawa, ON K1N 1A2, Canada.
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| | - Mohan Babu
- Department of Chemistry and Biochemistry, University of Regina, 3737 Wascana Parkway, Regina, SK S4S 0A2, Canada
| |
Collapse
|
17
|
Yu C, Huang L. Cross-Linking Mass Spectrometry: An Emerging Technology for Interactomics and Structural Biology. Anal Chem 2018; 90:144-165. [PMID: 29160693 PMCID: PMC6022837 DOI: 10.1021/acs.analchem.7b04431] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Clinton Yu
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
| | - Lan Huang
- Department of Physiology & Biophysics, University of California, Irvine, Irvine, CA 92697
| |
Collapse
|
18
|
Wang X, Huang L. Dissecting Dynamic and Heterogeneous Proteasome Complexes Using In Vivo Cross-Linking-Assisted Affinity Purification and Mass Spectrometry. Methods Mol Biol 2018; 1844:401-410. [PMID: 30242723 DOI: 10.1007/978-1-4939-8706-1_25] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein-protein interactions are essential for protein complex formation and function. Affinity purification coupled with mass spectrometry (AP-MS) is the method of choice for studying protein-protein interactions at the systems level under different physiological conditions. Although effective in capturing stable protein interactions, transient, weak, and/or dynamic interactors are often lost due to extended procedures during conventional AP-MS experiments. To circumvent this problem, we have recently developed XAP (in vivo cross-linking (X)-assisted affinity purification)-MS strategy to better preserve dynamic protein complexes under native lysis conditions. In addition, we have developed XBAP (in vivo cross-linking (X)-assisted bimolecular tandem affinity purification)-MS method by incorporating XAP with bimolecular affinity purification to define dynamic and heterogeneous protein subcomplexes. Here we describe general experimental protocols of XAP- and XBAP-MS to study dynamic protein complexes and their subcomplexes, respectively. Specifically, we present their applications in capturing and identifying proteasome dynamic interactors and ubiquitin receptor (UbR)-proteasome subcomplexes.
Collapse
Affiliation(s)
- Xiaorong Wang
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA.
| |
Collapse
|
19
|
Najor NA, Fitz GN, Koetsier JL, Godsel LM, Albrecht LV, Harmon R, Green KJ. Epidermal Growth Factor Receptor neddylation is regulated by a desmosomal-COP9 (Constitutive Photomorphogenesis 9) signalosome complex. eLife 2017; 6:22599. [PMID: 28891468 PMCID: PMC5663478 DOI: 10.7554/elife.22599] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 09/08/2017] [Indexed: 12/12/2022] Open
Abstract
Cell junctions are scaffolds that integrate mechanical and chemical signaling. We previously showed that a desmosomal cadherin promotes keratinocyte differentiation in an adhesion-independent manner by dampening Epidermal Growth Factor Receptor (EGFR) activity. Here we identify a potential mechanism by which desmosomes assist the de-neddylating COP9 signalosome (CSN) in attenuating EGFR through an association between the Cops3 subunit of the CSN and desmosomal components, Desmoglein1 (Dsg1) and Desmoplakin (Dp), to promote epidermal differentiation. Silencing CSN or desmosome components shifts the balance of EGFR modifications from ubiquitination to neddylation, inhibiting EGFR dynamics in response to an acute ligand stimulus. A reciprocal relationship between loss of Dsg1 and neddylated EGFR was observed in a carcinoma model, consistent with a role in sustaining EGFR activity during tumor progression. Identification of this previously unrecognized function of the CSN in regulating EGFR neddylation has broad-reaching implications for understanding how homeostasis is achieved in regenerating epithelia. The outer layer of skin – the epidermis – forms a critical barrier against a range of stresses from the environment. The epidermis itself consists of multiple layers of cells that are constantly being renewed. New cells are made in the deepest layer and move upwards until they eventually reach the skin’s surface. During this journey, the cells change the molecules they make in a process called epidermal differentiation. To maintain an effective barrier, the epidermis must balance the division of cells in the deepest layer with the differentiation of cells in the layers above. When activated, a protein called the Epidermal Growth Factor Receptor (or EGFR for short) encourages cells in the deepest layer to divide. However, it remains poorly understood how the balance between cells dividing and cells differentiating is achieved. The desmosome is a structure that can link together cells within the epidermis. Najor et al. now report a new interaction between the desmosome and a very large protein complex called the COP9- signalosome known to remove protein-based tags from other proteins. The experiments show that the COP9-signalosome results in the removal of these tags from EGFR. The status of the tags on EGFR regulates whether or not it is found at the cell surface. Najor et al. propose that that the desmosome acts as a scaffold and holds the COP9 signalosome close to EGFR. The enzyme in the COP9 signalosome then removes protein-based tags from EGFR, which triggers a series of events that remove EGFR from the cell surface. This dampens down the signals EGFR would normally send to make cells divide, and allows differentiation to proceed. The balance between cell division and differentiation is a fundamental process that is affected in many skin conditions, including psoriasis and atopic dermatitis. EGFR is also commonly overactive in cancers. As such, understanding how epidermal differentiation and cell division are controlled will shed light on a variety of disorders, allowing for the potential development of new treatments for these diseases.
Collapse
Affiliation(s)
- Nicole Ann Najor
- Department of Biology, College of Engineering and Science, University of Detroit Mercy, Detroit, United States.,Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Gillian Nicole Fitz
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Jennifer Leigh Koetsier
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Lisa Marie Godsel
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, United States.,Department of Dermatology Chicago, Feinberg School of Medicine, Northwestern University, Evanston, United States
| | - Lauren Veronica Albrecht
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Robert Harmon
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, United States
| | - Kathleen Janee Green
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, United States.,Department of Dermatology Chicago, Feinberg School of Medicine, Northwestern University, Evanston, United States
| |
Collapse
|
20
|
Zhang L, Sement FM, Suematsu T, Yu T, Monti S, Huang L, Aphasizhev R, Aphasizheva I. PPR polyadenylation factor defines mitochondrial mRNA identity and stability in trypanosomes. EMBO J 2017; 36:2435-2454. [PMID: 28684539 DOI: 10.15252/embj.201796808] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 05/10/2017] [Accepted: 05/22/2017] [Indexed: 11/09/2022] Open
Abstract
In Trypanosoma brucei, most mitochondrial mRNAs undergo internal changes by RNA editing and 3' end modifications. The temporally separated and functionally distinct modifications are manifested by adenylation prior to editing, and by post-editing extension of a short A-tail into a long A/U-heteropolymer. The A-tail stabilizes partially and fully edited mRNAs, while the A/U-tail enables mRNA binding to the ribosome. Here, we identify an essential pentatricopeptide repeat-containing RNA binding protein, kinetoplast polyadenylation factor 3 (KPAF3), and demonstrate its role in protecting pre-mRNA against degradation by the processome. We show that KPAF3 recruits KPAP1 poly(A) polymerase to the 3' terminus, thus leading to pre-mRNA stabilization, or decay depending on the occurrence and extent of editing. In vitro, KPAF3 stimulates KPAP1 activity and inhibits mRNA uridylation by RET1 TUTase. Our findings indicate that KPAF3 selectively directs pre-mRNA toward adenylation rather than uridylation, which is a default post-trimming modification characteristic of ribosomal and guide RNAs. As a quality control mechanism, KPAF3 binding ensures that mRNAs entering the editing pathway are adenylated and, therefore, competent for post-editing A/U-tailing and translational activation.
Collapse
Affiliation(s)
- Liye Zhang
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA.,Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Francois M Sement
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| | - Tian Yu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA.,Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| |
Collapse
|
21
|
Wang X, Cimermancic P, Yu C, Schweitzer A, Chopra N, Engel JL, Greenberg C, Huszagh AS, Beck F, Sakata E, Yang Y, Novitsky EJ, Leitner A, Nanni P, Kahraman A, Guo X, Dixon JE, Rychnovsky SD, Aebersold R, Baumeister W, Sali A, Huang L. Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome. Mol Cell Proteomics 2017; 16:840-854. [PMID: 28292943 PMCID: PMC5417825 DOI: 10.1074/mcp.m116.065326] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/13/2017] [Indexed: 12/28/2022] Open
Abstract
The 26S proteasome is the macromolecular machine responsible for ATP/ubiquitin dependent degradation. As aberration in proteasomal degradation has been implicated in many human diseases, structural analysis of the human 26S proteasome complex is essential to advance our understanding of its action and regulation mechanisms. In recent years, cross-linking mass spectrometry (XL-MS) has emerged as a powerful tool for elucidating structural topologies of large protein assemblies, with its unique capability of studying protein complexes in cells. To facilitate the identification of cross-linked peptides, we have previously developed a robust amine reactive sulfoxide-containing MS-cleavable cross-linker, disuccinimidyl sulfoxide (DSSO). To better understand the structure and regulation of the human 26S proteasome, we have established new DSSO-based in vivo and in vitro XL-MS workflows by coupling with HB-tag based affinity purification to comprehensively examine protein-protein interactions within the 26S proteasome. In total, we have identified 447 unique lysine-to-lysine linkages delineating 67 interprotein and 26 intraprotein interactions, representing the largest cross-link dataset for proteasome complexes. In combination with EM maps and computational modeling, the architecture of the 26S proteasome was determined to infer its structural dynamics. In particular, three proteasome subunits Rpn1, Rpn6, and Rpt6 displayed multiple conformations that have not been previously reported. Additionally, cross-links between proteasome subunits and 15 proteasome interacting proteins including 9 known and 6 novel ones have been determined to demonstrate their physical interactions at the amino acid level. Our results have provided new insights on the dynamics of the 26S human proteasome and the methodologies presented here can be applied to study other protein complexes.
Collapse
Affiliation(s)
- Xiaorong Wang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, Irvine, California 92697
| | - Peter Cimermancic
- §Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94143
| | - Clinton Yu
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, Irvine, California 92697
| | - Andreas Schweitzer
- ¶Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Nikita Chopra
- §Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94143
| | - James L Engel
- ‖Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093
| | - Charles Greenberg
- §Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94143
| | - Alexander S Huszagh
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, Irvine, California 92697
| | - Florian Beck
- ¶Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Eri Sakata
- ¶Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Yingying Yang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, Irvine, California 92697
| | - Eric J Novitsky
- **Department of Chemistry, University of California, Irvine, Irvine, California 92697
| | - Alexander Leitner
- ‡‡Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
| | - Paolo Nanni
- §§Functional Genomics Center Zurich (FGCZ), University of Zurich, ETH Zurich, CH-8057 Zurich, Switzerland
| | - Abdullah Kahraman
- ¶¶Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | - Xing Guo
- ‖Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093
| | - Jack E Dixon
- ‖Department of Pharmacology, University of California, San Diego, La Jolla, California, 92093
| | - Scott D Rychnovsky
- **Department of Chemistry, University of California, Irvine, Irvine, California 92697
| | - Ruedi Aebersold
- ‡‡Department of Biology, Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Wolfgang Baumeister
- ¶Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried 82152, Germany
| | - Andrej Sali
- §Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California 94143
| | - Lan Huang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, Irvine, California 92697;
| |
Collapse
|
22
|
Yu C, Yang Y, Wang X, Guan S, Fang L, Liu F, Walters KJ, Kaiser P, Huang L. Characterization of Dynamic UbR-Proteasome Subcomplexes by In vivo Cross-linking (X) Assisted Bimolecular Tandem Affinity Purification (XBAP) and Label-free Quantitation. Mol Cell Proteomics 2016; 15:2279-92. [PMID: 27114451 DOI: 10.1074/mcp.m116.058271] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Indexed: 12/14/2022] Open
Abstract
Proteasomes are protein degradation machines that exist in cells as heterogeneous and dynamic populations. A group of proteins function as ubiquitin receptors (UbRs) that can recognize and deliver ubiquitinated substrates to proteasome complexes for degradation. Defining composition of proteasome complexes engaged with UbRs is critical to understand proteasome function. However, because of the dynamic nature of UbR interactions with the proteasome, it remains technically challenging to capture and isolate UbR-proteasome subcomplexes using conventional purification strategies. As a result, distinguishing the molecular differences among these subcomplexes remains elusive. We have developed a novel affinity purification strategy, in vivo cross-linking (X) assisted bimolecular tandem affinity purification strategy (XBAP), to effectively isolate dynamic UbR-proteasome subcomplexes and define their subunit compositions using label-free quantitative mass spectrometry. In this work, we have analyzed seven distinctive UbR-proteasome complexes and found that all of them contain the same type of the 26S holocomplex. However, selected UbRs interact with a group of proteasome interacting proteins that may link each UbR to specific cellular pathways. The compositional similarities and differences among the seven UbR-proteasome subcomplexes have provided new insights on functional entities of proteasomal degradation machineries. The strategy described here represents a general and useful proteomic tool for isolating and studying dynamic and heterogeneous protein subcomplexes in cells that have not been fully characterized.
Collapse
Affiliation(s)
- Clinton Yu
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Yingying Yang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Xiaorong Wang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Shenheng Guan
- §Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Lei Fang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Fen Liu
- ¶Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Kylie J Walters
- ¶Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702
| | - Peter Kaiser
- ‖Department of Biological Chemistry, University of California, Irvine, California 92697
| | - Lan Huang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697;
| |
Collapse
|
23
|
Suematsu T, Zhang L, Aphasizheva I, Monti S, Huang L, Wang Q, Costello CE, Aphasizhev R. Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3' Processome to Generate Guide RNAs. Mol Cell 2016; 61:364-378. [PMID: 26833087 PMCID: PMC4744118 DOI: 10.1016/j.molcel.2016.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/16/2015] [Accepted: 12/24/2015] [Indexed: 12/21/2022]
Abstract
Small, noncoding RNA biogenesis typically involves cleavage of structured precursor by RNase III-like endonucleases. However, guide RNAs (gRNAs) that direct U-insertion/deletion mRNA editing in mitochondria of trypanosomes maintain 5' triphosphate characteristic of the transcription initiation and possess a U-tail indicative of 3' processing and uridylation. Here, we identified a protein complex composed of RET1 TUTase, DSS1 3'-5' exonuclease, and three additional subunits. This complex, termed mitochondrial 3' processome (MPsome), is responsible for primary uridylation of ∼800 nt gRNA precursors, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. Both strands of the gRNA gene are transcribed into sense and antisense precursors of similar lengths. Head-to-head hybridization of these transcripts blocks symmetrical 3'-5' degradation at a fixed distance from the double-stranded region. Together, our findings suggest a model in which gRNA is derived from the 5' extremity of a primary molecule by uridylation-induced, antisense transcription-controlled 3'-5' exonucleolytic degradation.
Collapse
Affiliation(s)
- Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Lan Huang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Qi Wang
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Catherine E Costello
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA.
| |
Collapse
|
24
|
Aphasizheva I, Maslov DA, Qian Y, Huang L, Wang Q, Costello CE, Aphasizhev R. Ribosome-associated pentatricopeptide repeat proteins function as translational activators in mitochondria of trypanosomes. Mol Microbiol 2016; 99:1043-58. [PMID: 26713541 DOI: 10.1111/mmi.13287] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2015] [Indexed: 12/20/2022]
Abstract
Mitochondrial ribosomes of Trypanosoma brucei are composed of 9S and 12S rRNAs, eubacterial-type ribosomal proteins, polypeptides lacking discernible motifs and approximately 20 pentatricopeptide repeat (PPR) RNA binding proteins. Several PPRs also populate the polyadenylation complex; among these, KPAF1 and KPAF2 function as general mRNA 3' adenylation/uridylation factors. The A/U-tail enables mRNA binding to the small ribosomal subunit and is essential for translation. The presence of A/U-tail also correlates with requirement for translation of certain mRNAs in mammalian and insect parasite stages. Here, we inquired whether additional PPRs activate translation of individual mRNAs. Proteomic analysis identified KRIPP1 and KRIPP8 as components of the small ribosomal subunit in mammalian and insect forms, but also revealed their association with the polyadenylation complex in the latter. RNAi knockdowns demonstrated essential functions of KRIPP1 and KRIPP8 in the actively respiring insect stage, but not in the mammalian stage. In the KRIPP1 knockdown, A/U-tailed mRNA encoding cytochrome c oxidase subunit 1 declined concomitantly with the de novo synthesis of this subunit whereas polyadenylation and translation of cyb mRNA were unaffected. In contrast, the KRIPP8 knockdown inhibited A/U-tailing and translation of both CO1 and cyb mRNAs. Our findings indicate that ribosome-associated PPRs may selectively activate mRNAs for translation.
Collapse
Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA, 02118, USA
| | - Dmitri A Maslov
- Department of Biology, University of California, Riverside, CA, 92521, USA
| | - Yu Qian
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA, 02118, USA
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Qi Wang
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Catherine E Costello
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, MA, 02118, USA.,Department of Biochemistry, Boston University School of Medicine, Boston, MA, 02118, USA
| |
Collapse
|
25
|
Meyer K, Selbach M. Quantitative affinity purification mass spectrometry: a versatile technology to study protein-protein interactions. Front Genet 2015; 6:237. [PMID: 26236332 PMCID: PMC4500955 DOI: 10.3389/fgene.2015.00237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/25/2015] [Indexed: 01/11/2023] Open
Abstract
While the genomic revolution has dramatically accelerated the discovery of disease-associated genes, the functional characterization of the corresponding proteins lags behind. Most proteins fulfill their tasks in complexes with other proteins, and analysis of protein–protein interactions (PPIs) can therefore provide insights into protein function. Several methods can be used to generate large-scale protein interaction networks. However, most of these approaches are not quantitative and therefore cannot reveal how perturbations affect the network. Here, we illustrate how a clever combination of quantitative mass spectrometry with different biochemical methods provides a rich toolkit to study different aspects of PPIs including topology, subunit stoichiometry, and dynamic behavior.
Collapse
Affiliation(s)
- Katrina Meyer
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine , Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine , Berlin, Germany
| |
Collapse
|
26
|
Li Q, Li Y, Gu B, Fang L, Zhou P, Bao S, Huang L, Dai X. Akt Phosphorylates Wnt Coactivator and Chromatin Effector Pygo2 at Serine 48 to Antagonize Its Ubiquitin/Proteasome-mediated Degradation. J Biol Chem 2015; 290:21553-67. [PMID: 26170450 DOI: 10.1074/jbc.m115.639419] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Indexed: 01/16/2023] Open
Abstract
Pygopus 2 (Pygo2/PYGO2) is an evolutionarily conserved coactivator and chromatin effector in the Wnt/β-catenin signaling pathway that regulates cell growth and differentiation in various normal and malignant tissues. Although PYGO2 is highly overexpressed in a number of human cancers, the molecular mechanism underlying its deregulation is largely unknown. Here we report that Pygo2 protein is degraded through the ubiquitin/proteasome pathway and is posttranslationally stabilized through phosphorylation by activated phosphatidylinositol 3-kinase/Akt signaling. Specifically, Pygo2 is stabilized upon inhibition of the proteasome, and its intracellular level is regulated by Cullin 4 (Cul4) and DNA damage-binding protein 1 (DDB1), components of the Cul4-DDB1 E3 ubiquitin ligase complex. Furthermore, Pygo2 is phosphorylated at multiple residues, and Akt-mediated phosphorylation at serine 48 leads to its decreased ubiquitylation and increased stability. Finally, we provide evidence that Akt and its upstream growth factors act in parallel with Wnt to stabilize Pygo2. Taken together, our findings highlight chromatin regulator Pygo2 as a common node downstream of oncogenic Wnt and Akt signaling pathways and underscore posttranslational modification, particularly phosphorylation and ubiquitylation, as a significant mode of regulation of Pygo2 protein expression.
Collapse
Affiliation(s)
- Qiuling Li
- From the Department of Biological Chemistry, the State Key Laboratory of Molecular and Developmental Biology, Center for Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China, and
| | - Yuewei Li
- the Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065
| | - Bingnan Gu
- From the Department of Biological Chemistry
| | - Lei Fang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California 92697
| | - Pengbo Zhou
- the Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York 10065
| | - Shilai Bao
- the State Key Laboratory of Molecular and Developmental Biology, Center for Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China, and
| | - Lan Huang
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California 92697,
| | - Xing Dai
- From the Department of Biological Chemistry,
| |
Collapse
|
27
|
Kaake RM, Kao A, Yu C, Huang L. Characterizing the dynamics of proteasome complexes by proteomics approaches. Antioxid Redox Signal 2014; 21:2444-56. [PMID: 24423446 PMCID: PMC4241863 DOI: 10.1089/ars.2013.5815] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
SIGNIFICANCE The proteasome is the degradation machine of the ubiquitin-proteasome system, which is critical in controlling many essential biological processes. Aberrant regulation of proteasome-dependent protein degradation can lead to various human diseases, and general proteasome inhibitors have shown efficacy for cancer treatments. Though clinically effective, current proteasome inhibitors have detrimental side effects and, thus, better therapeutic strategies targeting proteasomes are needed. Therefore, a comprehensive characterization of proteasome complexes will provide the molecular details that are essential for developing new and improved drugs. RECENT ADVANCES New mass spectrometry (MS)-based proteomics approaches have been developed to study protein interaction networks and structural topologies of proteasome complexes. The results have helped define the dynamic proteomes of proteasome complexes, thus providing new insights into the mechanisms underlying proteasome function and regulation. CRITICAL ISSUES The proteasome exists as heterogeneous populations in tissues/cells, and its proteome is highly dynamic and complex. In addition, proteasome complexes are regulated by various mechanisms under different physiological conditions. Consequently, complete proteomic profiling of proteasome complexes remains a major challenge for the field. FUTURE DIRECTIONS We expect that proteomic methodologies enabling full characterization of proteasome complexes will continue to evolve. Further advances in MS instrumentation and protein separation techniques will be needed to facilitate the detailed proteomic analysis of low-abundance components and subpopulations of proteasome complexes. The results will help us understand proteasome biology as well as provide new therapeutic targets for disease diagnostics and treatment.
Collapse
Affiliation(s)
- Robyn M Kaake
- Department of Physiology and Biophysics, University of California , Irvine, Irvine, California
| | | | | | | |
Collapse
|
28
|
Aphasizheva I, Zhang L, Wang X, Kaake RM, Huang L, Monti S, Aphasizhev R. RNA binding and core complexes constitute the U-insertion/deletion editosome. Mol Cell Biol 2014; 34:4329-42. [PMID: 25225332 PMCID: PMC4248751 DOI: 10.1128/mcb.01075-14] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/02/2014] [Accepted: 09/11/2014] [Indexed: 12/19/2022] Open
Abstract
Enzymes embedded into the RNA editing core complex (RECC) catalyze the U-insertion/deletion editing cascade to generate open reading frames in trypanosomal mitochondrial mRNAs. The sequential reactions of mRNA cleavage, U-addition or removal, and ligation are directed by guide RNAs (gRNAs). We combined proteomic, genetic, and functional studies with sequencing of total and complex-bound RNAs to define a protein particle responsible for the recognition of gRNAs and pre-mRNA substrates, editing intermediates, and products. This approximately 23-polypeptide tripartite assembly, termed the RNA editing substrate binding complex (RESC), also functions as the interface between mRNA editing, polyadenylation, and translation. Furthermore, we found that gRNAs represent only a subset of small mitochondrial RNAs, and yet an inexplicably high fraction of them possess 3' U-tails, which correlates with gRNA's enrichment in the RESC. Although both gRNAs and mRNAs are associated with the RESC, their metabolic fates are distinct: gRNAs are degraded in an editing-dependent process, whereas edited mRNAs undergo 3' adenylation/uridylation prior to translation. Our results demonstrate that the well-characterized editing core complex (RECC) and the RNA binding particle defined in this study (RESC) typify enzymatic and substrate binding macromolecular constituents, respectively, of the ∼40S RNA editing holoenzyme, the editosome.
Collapse
MESH Headings
- Base Sequence
- Mitochondria/genetics
- Open Reading Frames/genetics
- Peptide Chain Elongation, Translational/genetics
- Polyadenylation/genetics
- Protozoan Proteins/metabolism
- RNA/genetics
- RNA Editing/genetics
- RNA Interference
- RNA, Catalytic/genetics
- RNA, Guide, Kinetoplastida/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Mitochondrial
- RNA, Protozoan/genetics
- RNA, Small Interfering
- RNA-Binding Proteins/genetics
- Sequence Analysis, RNA
- Trypanosoma brucei brucei/genetics
Collapse
Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, USA
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xiaorong Wang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Robyn M Kaake
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Lan Huang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, USA Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
| |
Collapse
|
29
|
Kaake RM, Wang X, Burke A, Yu C, Kandur W, Yang Y, Novtisky EJ, Second T, Duan J, Kao A, Guan S, Vellucci D, Rychnovsky SD, Huang L. A new in vivo cross-linking mass spectrometry platform to define protein-protein interactions in living cells. Mol Cell Proteomics 2014; 13:3533-43. [PMID: 25253489 DOI: 10.1074/mcp.m114.042630] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Protein-protein interactions (PPIs) are fundamental to the structure and function of protein complexes. Resolving the physical contacts between proteins as they occur in cells is critical to uncovering the molecular details underlying various cellular activities. To advance the study of PPIs in living cells, we have developed a new in vivo cross-linking mass spectrometry platform that couples a novel membrane-permeable, enrichable, and MS-cleavable cross-linker with multistage tandem mass spectrometry. This strategy permits the effective capture, enrichment, and identification of in vivo cross-linked products from mammalian cells and thus enables the determination of protein interaction interfaces. The utility of the developed method has been demonstrated by profiling PPIs in mammalian cells at the proteome scale and the targeted protein complex level. Our work represents a general approach for studying in vivo PPIs and provides a solid foundation for future studies toward the complete mapping of PPI networks in living systems.
Collapse
Affiliation(s)
- Robyn M Kaake
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Xiaorong Wang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Anthony Burke
- ¶Department of Chemistry, University of California, Irvine, California 92697
| | - Clinton Yu
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Wynne Kandur
- ¶Department of Chemistry, University of California, Irvine, California 92697
| | - Yingying Yang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Eric J Novtisky
- ¶Department of Chemistry, University of California, Irvine, California 92697
| | - Tonya Second
- ‖Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134
| | - Jicheng Duan
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Athit Kao
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697
| | - Shenheng Guan
- **Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143
| | - Danielle Vellucci
- ¶Department of Chemistry, University of California, Irvine, California 92697
| | - Scott D Rychnovsky
- ¶Department of Chemistry, University of California, Irvine, California 92697
| | - Lan Huang
- From the ‡Department of Physiology & Biophysics, University of California, Irvine, California 92697;
| |
Collapse
|
30
|
Subbotin RI, Chait BT. A pipeline for determining protein-protein interactions and proximities in the cellular milieu. Mol Cell Proteomics 2014; 13:2824-35. [PMID: 25172955 DOI: 10.1074/mcp.m114.041095] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
It remains extraordinarily challenging to elucidate endogenous protein-protein interactions and proximities within the cellular milieu. The dynamic nature and the large range of affinities of these interactions augment the difficulty of this undertaking. Among the most useful tools for extracting such information are those based on affinity capture of target bait proteins in combination with mass spectrometric readout of the co-isolated species. Although highly enabling, the utility of affinity-based methods is generally limited by difficulties in distinguishing specific from nonspecific interactors, preserving and isolating all unique interactions including those that are weak, transient, or rapidly exchanging, and differentiating proximal interactions from those that are more distal. Here, we have devised and optimized a set of methods to address these challenges. The resulting pipeline involves flash-freezing cells in liquid nitrogen to preserve the cellular environment at the moment of freezing; cryomilling to fracture the frozen cells into intact micron chunks to allow for rapid access of a chemical reagent and to stabilize the intact endogenous subcellular assemblies and interactors upon thawing; and utilizing the high reactivity of glutaraldehyde to achieve sufficiently rapid stabilization at low temperatures to preserve native cellular interactions. In the course of this work, we determined that relatively low molar ratios of glutaraldehyde to reactive amines within the cellular milieu were sufficient to preserve even labile and transient interactions. This mild treatment enables efficient and rapid affinity capture of the protein assemblies of interest under nondenaturing conditions, followed by bottom-up MS to identify and quantify the protein constituents. For convenience, we have termed this approach Stabilized Affinity Capture Mass Spectrometry. Here, we demonstrate that Stabilized Affinity Capture Mass Spectrometry allows us to stabilize and elucidate local, distant, and transient protein interactions within complex cellular milieux, many of which are not observed in the absence of chemical stabilization.
Collapse
Affiliation(s)
- Roman I Subbotin
- From the ‡The Rockefeller University 1230 York Ave, New York, New York
| | - Brian T Chait
- From the ‡The Rockefeller University 1230 York Ave, New York, New York
| |
Collapse
|
31
|
Singer R, Atar S, Atias O, Oron E, Segal D, Hirsch JA, Tuller T, Orian A, Chamovitz DA. Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development. Nucleic Acids Res 2014; 42:9761-70. [PMID: 25106867 PMCID: PMC4150811 DOI: 10.1093/nar/gku723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The COP9 signalosome protein complex has a central role in the regulation of development of multicellular organisms. While the function of this complex in ubiquitin-mediated protein degradation is well established, results over the past few years have hinted that the COP9 signalosome may function more broadly in the regulation of gene expression. Here, using DamID technology, we show that COP9 signalosome subunit 7 functionally associates with a large number of genomic loci in the Drosophila genome, and show that the expression of many genes within these loci is COP9 signalosome-dependent. This association is likely direct as we show CSN7 binds DNA in vitro. The genes targeted by CSN7 are preferentially enriched for transcriptionally active regions of the genome, and are involved in the regulation of distinct gene ontology groupings including imaginal disc development and cell-cycle control. In accord, loss of CSN7 function leads to cell-cycle delay and altered wing development. These results indicate that CSN7, and by extension the entire COP9 signalosome, functions directly in transcriptional control. While the COP9 signalosome protein complex has long been known to regulate protein degradation, here we expand the role of this complex by showing that subunit 7 binds DNA in vitro and functions directly in vivo in transcriptional control of developmentally important pathways that are relevant for human health.
Collapse
Affiliation(s)
- Ruth Singer
- Department of Molecular Biology and Ecology of Plants
| | | | - Osnat Atias
- Department of Molecular Biology and Ecology of Plants
| | - Efrat Oron
- Department of Molecular Biology and Ecology of Plants
| | - Daniel Segal
- Department of Molecular Microbiology and Biotechnology
| | - Joel A Hirsch
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
| | | | - Amir Orian
- Cancer and Vascular Biology Research Center, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | | |
Collapse
|
32
|
Jia C, Yu Q, Wang J, Li L. Qualitative and quantitative top-down mass spectral analysis of crustacean hyperglycemic hormones in response to feeding. Proteomics 2014; 14:1185-94. [PMID: 24532205 DOI: 10.1002/pmic.201300331] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/07/2013] [Accepted: 02/10/2014] [Indexed: 12/13/2022]
Abstract
An efficient pipeline for peptide discovery accelerates peptidomic analysis and facilitates a better understanding of the functional roles of neuropeptides. However, qualitative and quantitative analysis of large neuropeptides is challenging due to the bigger molecular sizes, multiple PTMs, and interference by homologous isoforms. Herein, we refined two methodologies in the pipeline for highly confident and efficient MS-based peptide discovery. For the qualitative analysis, the so-called "high resolution/accurate mass" measurement on Orbitrap mass spectrometers was integrated with computer-assisted homology search, which was successfully applied to decipher the substituted amino acid residues in large neuropeptides by referring to homologous sequences. For the quantitative analysis, a new isotopic labeling-assisted top-down MS strategy was developed, which enabled direct monitoring of the abundance changes of endogenous large neuropeptides. By using the refined peptide discovery pipeline, one novel crustacean hyperglycemic hormone (CHH) from the Dungeness crab sinus glands was confidently identified and de novo sequenced, and its relative abundance was quantified. Comparative analysis of CHHs in unfed and fed crabs revealed that the peptide abundance in the sinus glands was significantly increased after food intake, suggesting that the release of CHHs might be altered by feeding behavior.
Collapse
Affiliation(s)
- Chenxi Jia
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, WI, USA
| | | | | | | |
Collapse
|
33
|
Sane S, Abdullah A, Boudreau DA, Autenried RK, Gupta BK, Wang X, Wang H, Schlenker EH, Zhang D, Telleria C, Huang L, Chauhan SC, Rezvani K. Ubiquitin-like (UBX)-domain-containing protein, UBXN2A, promotes cell death by interfering with the p53-Mortalin interactions in colon cancer cells. Cell Death Dis 2014; 5:e1118. [PMID: 24625977 PMCID: PMC3973214 DOI: 10.1038/cddis.2014.100] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/02/2014] [Accepted: 02/07/2014] [Indexed: 02/08/2023]
Abstract
Mortalin (mot-2) induces inactivation of the tumor suppressor p53's transcriptional and apoptotic functions by cytoplasmic sequestration of p53 in select cancers. The mot-2-dependent cytoprotective function enables cancer cells to support malignant transformation. Abrogating the p53-mot-2 interaction can control or slow down the growth of cancer cells. In this study, we report the discovery of a ubiquitin-like (UBX)-domain-containing protein, UBXN2A, which binds to mot-2 and consequently inhibits the binding between mot-2 and p53. Genetic analysis showed that UBXN2A binds to mot-2's substrate binding domain, and it partly overlaps p53's binding site indicating UBXN2A and p53 likely bind to mot-2 competitively. By binding to mot-2, UBXN2A releases p53 from cytosolic sequestration, rescuing the tumor suppressor functions of p53. Biochemical analysis and functional assays showed that the overexpression of UBXN2A and the functional consequences of unsequestered p53 trigger p53-dependent apoptosis. Cells expressing shRNA against UBXN2A showed the opposite effect of that seen with UBXN2A overexpression. The expression of UBXN2A and its apoptotic effects were not observed in normal colonic epithelial cells and p53-/- colon cancer cells. Finally, significant reduction in tumor volume in a xenograft mouse model in response to UBXN2A expression was verified in vivo. Our results introduce UBXN2A as a home defense response protein, which can reconstitute inactive p53-dependent apoptotic pathways. Inhibition of mot-2-p53 interaction by UBXN2A is an attractive therapeutic strategy in mot-2-elevated tumors.
Collapse
Affiliation(s)
- S Sane
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| | - A Abdullah
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| | - D A Boudreau
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| | - R K Autenried
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| | - B K Gupta
- Department of Pharmaceutical Sciences, Cancer Research Center, University of Tennessee Health Science Center, 19S Manassas Avenue, Memphis, TN, USA
| | - X Wang
- Departments of Physiology & Biophysics, University of California, Irvine, CA, USA
| | - H Wang
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| | - E H Schlenker
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| | - D Zhang
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| | - C Telleria
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| | - L Huang
- Departments of Physiology & Biophysics, University of California, Irvine, CA, USA
| | - S C Chauhan
- Department of Pharmaceutical Sciences, Cancer Research Center, University of Tennessee Health Science Center, 19S Manassas Avenue, Memphis, TN, USA
| | - K Rezvani
- Division of Basic Biomedical Sciences, Sanford School of Medicine, The University of South Dakota, 414 E. Clark Street, Lee Medical Building, Vermillion, SD, USA
| |
Collapse
|
34
|
Yu C, Kandur W, Kao A, Rychnovsky S, Huang L. Developing new isotope-coded mass spectrometry-cleavable cross-linkers for elucidating protein structures. Anal Chem 2014; 86:2099-106. [PMID: 24471733 PMCID: PMC3985771 DOI: 10.1021/ac403636b] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structural characterization of protein complexes is essential for the understanding of their function and regulation. However, it remains challenging due to limitations in existing tools. With recent technological improvements, cross-linking mass spectrometry (XL-MS) has become a powerful strategy to define protein-protein interactions and elucidate structural topologies of protein complexes. To further advance XL-MS studies, we present here the development of new isotope-coded MS-cleavable homobifunctional cross-linkers: d0- and d10-labeled dimethyl disuccinimidyl sulfoxide (DMDSSO). Detailed characterization of DMDSSO cross-linked peptides further demonstrates that sulfoxide-containing MS-cleavable cross-linkers offer robust and predictable MS2 fragmentation of cross-linked peptides, permitting subsequent MS3 analysis for simplified, unambiguous identification. Concurrent usage of these reagents provides a characteristic doublet pattern of DMDSSO cross-linked peptides, thus aiding in the confidence of cross-link identification by MS(n) analysis. More importantly, the unique isotopic profile permits quantitative analysis of cross-linked peptides and therefore expands the capability of XL-MS strategies to analyze both static and dynamic protein interactions. Together, our work has established a new XL-MS workflow for future studies toward the understanding of structural dynamics of protein complexes.
Collapse
Affiliation(s)
- Clinton Yu
- Department of Physiology and Biophysics, University of California , Medical Science I, D233, Irvine, California 92697, United States
| | | | | | | | | |
Collapse
|
35
|
Marcilla M, Albar JP. Quantitative proteomics: A strategic ally to map protein interaction networks. IUBMB Life 2013; 65:9-16. [PMID: 23281033 DOI: 10.1002/iub.1081] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 07/27/2012] [Indexed: 12/12/2022]
Abstract
Many physiological processes are regulated by dynamic protein interaction networks whose characterization provides valuable information on cell biology. Several strategies can be used to analyze protein-protein interactions. Among them, affinity purification combined with mass spectrometry (AP-MS) is arguably the most widely employed technique, not only owing to its high throughput and sensitivity but also because it can answer critical questions such as where, when, and how protein-protein interactions occur. In AP-MS workflows, both the target protein and its interacting partners are isolated before being identified by MS. The main challenge of this approach is to distinguish bona fide binders from background contaminants. This review focuses on the different strategies designed to circumvent this limitation. In this regard, the combination of quantitative proteomics and affinity purification emerges as one of the most powerful, yet relatively simple, strategies to characterize protein-protein interactions.
Collapse
Affiliation(s)
- Miguel Marcilla
- Proteomics Unit, Centro Nacional de Biotecnología, CSIC, Madrid, Spain.
| | | |
Collapse
|
36
|
Eckey M, Kraft F, Kob R, Escher N, Asim M, Fischer H, Fritsche MK, Melle C, Baniahmad A. The corepressor activity of Alien is controlled by CREB-binding protein/p300. FEBS J 2013; 280:1861-8. [DOI: 10.1111/febs.12211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 02/13/2013] [Accepted: 02/14/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Maren Eckey
- Institute for Human Genetics; Jena University Hospital; Germany
| | - Florian Kraft
- Institute for Human Genetics; Jena University Hospital; Germany
| | - Robert Kob
- Institute for Human Genetics; Jena University Hospital; Germany
| | - Niko Escher
- Institute for Human Genetics; Jena University Hospital; Germany
| | - Mohammad Asim
- Institute for Human Genetics; Jena University Hospital; Germany
| | - Heike Fischer
- Institute for Human Genetics; Jena University Hospital; Germany
| | | | - Christian Melle
- Biomolecular Photonics Group; Jena University Hospital; Germany
| | - Aria Baniahmad
- Institute for Human Genetics; Jena University Hospital; Germany
| |
Collapse
|
37
|
Jia C, Hui L, Cao W, Lietz CB, Jiang X, Chen R, Catherman AD, Thomas PM, Ge Y, Kelleher NL, Li L. High-definition de novo sequencing of crustacean hyperglycemic hormone (CHH)-family neuropeptides. Mol Cell Proteomics 2012; 11:1951-64. [PMID: 23028060 DOI: 10.1074/mcp.m112.020537] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A complete understanding of the biological functions of large signaling peptides (>4 kDa) requires comprehensive characterization of their amino acid sequences and post-translational modifications, which presents significant analytical challenges. In the past decade, there has been great success with mass spectrometry-based de novo sequencing of small neuropeptides. However, these approaches are less applicable to larger neuropeptides because of the inefficient fragmentation of peptides larger than 4 kDa and their lower endogenous abundance. The conventional proteomics approach focuses on large-scale determination of protein identities via database searching, lacking the ability for in-depth elucidation of individual amino acid residues. Here, we present a multifaceted MS approach for identification and characterization of large crustacean hyperglycemic hormone (CHH)-family neuropeptides, a class of peptide hormones that play central roles in the regulation of many important physiological processes of crustaceans. Six crustacean CHH-family neuropeptides (8-9.5 kDa), including two novel peptides with extensive disulfide linkages and PTMs, were fully sequenced without reference to genomic databases. High-definition de novo sequencing was achieved by a combination of bottom-up, off-line top-down, and on-line top-down tandem MS methods. Statistical evaluation indicated that these methods provided complementary information for sequence interpretation and increased the local identification confidence of each amino acid. Further investigations by MALDI imaging MS mapped the spatial distribution and colocalization patterns of various CHH-family neuropeptides in the neuroendocrine organs, revealing that two CHH-subfamilies are involved in distinct signaling pathways.
Collapse
Affiliation(s)
- Chenxi Jia
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53705, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|