1
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Nagasawa CK, Bailey AO, Russell W, Garcia-Blanco MA. Inefficient recruitment of DDX39B impedes pre-spliceosome assembly on FOXP3 introns. RNA 2024:rna.079933.123. [PMID: 38575347 DOI: 10.1261/rna.079933.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/19/2024] [Indexed: 04/06/2024]
Abstract
Forkhead box P3 (FOXP3) is the master fate-determining transcription factor in regulatory T (Treg) cells and is essential for their development, function and homeostasis. Mutations in FOXP3 cause immunodysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome, and aberrant expression of FOXP3 has been implicated in other diseases such as multiple sclerosis and cancer. We previously demonstrated that pre-mRNA splicing of FOXP3 RNAs is highly sen-sitive to levels of DExD-box polypeptide 39B (DDX39B) and here we investigate the mechanism of this sensitivity. FOXP3 introns have cytidine (C)-rich/uridine (U)-poor polypyrimidine (py) tracts that are responsible for their inefficient splicing and confer sensitivity to DDX39B. We show that there is a deficiency in the assembly of commitment complexes (CCs) on FOXP3 introns, which is consistent with the lower affinity of U2AF2 for C-rich/U-poor py tracts. Our data indicate an even stronger effect on the conversion of CCs to pre-spliceosomes. We propose that this is due to an altered conformation that U2AF2 adopts when it binds to C-rich/U-poor py tracts and that this conformation has a lower affinity for DDX39B. As a consequence, CCs assembled on FOXP3 introns are defective in recruiting DDX39B and this leads to inefficient assembly of pre-spliceosome complexes.
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2
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Woodward A, Southard B, Chakraborty S, Bailey AO, Faria GNF, McKernan P, Razaq W, Harrison RG. Correction: annexin A5-DM1 protein-drug conjugate for the treatment of triple-negative breast cancer. Mol Biomed 2024; 5:16. [PMID: 38564119 PMCID: PMC10987452 DOI: 10.1186/s43556-024-00180-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Affiliation(s)
- Alexis Woodward
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | - Benjamin Southard
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | - Sampurna Chakraborty
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- AbCellera Biologics Inc, Vancouver, BC, Canada
| | - Gabriela N F Faria
- School of Sustainable Chemical, Biological, and Materials Engineering, University of Oklahoma, Norman, OK, USA
| | - Patrick McKernan
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | | | - Roger G Harrison
- School of Sustainable Chemical, Biological, and Materials Engineering, University of Oklahoma, Norman, OK, USA.
- Stephenson Cancer Center, Oklahoma City, OK, USA.
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Woodward A, Southard B, Chakraborty S, Bailey AO, Faria GNF, McKernan P, Razaq W, Harrison RG. Annexin A5-DM1 protein-drug conjugate for the treatment of triple-negative breast cancer. Mol Biomed 2024; 5:7. [PMID: 38369647 PMCID: PMC10874913 DOI: 10.1186/s43556-023-00167-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/19/2023] [Indexed: 02/20/2024] Open
Affiliation(s)
- Alexis Woodward
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | - Benjamin Southard
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | - Sampurna Chakraborty
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
- AbCellera Biologics Inc., Vancouver, BC, Canada
| | - Gabriela N F Faria
- School of Sustainable Chemical, Biological, and Materials Engineering, University of Oklahoma, Norman, OK, USA
| | - Patrick McKernan
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, OK, USA
| | | | - Roger G Harrison
- School of Sustainable Chemical, Biological, and Materials Engineering, University of Oklahoma, Norman, OK, USA.
- Stephenson Cancer Center, Oklahoma City, OK, USA.
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4
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Lee H, Chofflet N, Liu J, Fan S, Lu Z, Resua Rojas M, Penndorf P, Bailey AO, Russell WK, Machius M, Ren G, Takahashi H, Rudenko G. Designer molecules of the synaptic organizer MDGA1 reveal 3D conformational control of biological function. J Biol Chem 2023; 299:104586. [PMID: 36889589 PMCID: PMC10131064 DOI: 10.1016/j.jbc.2023.104586] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 03/08/2023] Open
Abstract
MDGAs (MAM domain-containing glycosylphosphatidylinositol anchors) are synaptic cell surface molecules that regulate the formation of trans-synaptic bridges between neurexins (NRXNs) and neuroligins (NLGNs), which promote synaptic development. Mutations in MDGAs are implicated in various neuropsychiatric diseases. MDGAs bind NLGNs in cis on the postsynaptic membrane and physically block NLGNs from binding to NRXNs. In crystal structures, the six immunoglobulin (Ig) and single fibronectin III domains of MDGA1 reveal a striking compact, triangular shape, both alone and in complex with NLGNs. Whether this unusual domain arrangement is required for biological function or other arrangements occur with different functional outcomes is unknown. Here, we show that WT MDGA1 can adopt both compact and extended 3D conformations that bind NLGN2. Designer mutants targeting strategic molecular elbows in MDGA1 alter the distribution of 3D conformations while leaving the binding affinity between soluble ectodomains of MDGA1 and NLGN2 intact. In contrast, in a cellular context, these mutants result in unique combinations of functional consequences, including altered binding to NLGN2, decreased capacity to conceal NLGN2 from NRXN1β, and/or suppressed NLGN2-mediated inhibitory presynaptic differentiation, despite the mutations being located far from the MDGA1-NLGN2 interaction site. Thus, the 3D conformation of the entire MDGA1 ectodomain appears critical for its function, and its NLGN-binding site on Ig1-Ig2 is not independent of the rest of the molecule. As a result, global 3D conformational changes to the MDGA1 ectodomain via strategic elbows may form a molecular mechanism to regulate MDGA1 action within the synaptic cleft.
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Affiliation(s)
- Hubert Lee
- Deptartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Nicolas Chofflet
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Quebec, Canada; Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shanghua Fan
- Deptartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Zhuoyang Lu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Martin Resua Rojas
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Quebec, Canada
| | - Patrick Penndorf
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Quebec, Canada
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mischa Machius
- Deptartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Hideto Takahashi
- Synapse Development and Plasticity Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Quebec, Canada; Integrated Program in Neuroscience, McGill University, Montreal, Quebec, Canada; Department of Medicine, Université de Montréal, Montréal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montréal, Quebec, Canada.
| | - Gabby Rudenko
- Deptartment of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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5
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Wu W, Kim JS, Bailey AO, Russell WK, Richards SJ, Chen T, Chen T, Chen Z, Liang B, Yamauchi M, Guo H. Comparative genomic and biochemical analyses identify a collagen galactosylhydroxylysyl glucosyltransferase from Acanthamoeba polyphaga mimivirus. Sci Rep 2022; 12:16806. [PMID: 36207453 PMCID: PMC9546862 DOI: 10.1038/s41598-022-21197-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 09/23/2022] [Indexed: 11/10/2022] Open
Abstract
Humans and Acanthamoeba polyphaga mimivirus share numerous homologous genes, including collagens and collagen-modifying enzymes. To explore this homology, we performed a genome-wide comparison between human and mimivirus using DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST) and identified 52 new putative mimiviral proteins that are homologous with human proteins. To gain functional insights into mimiviral proteins, their human protein homologs were organized into Gene Ontology (GO) and REACTOME pathways to build a functional network. Collagen and collagen-modifying enzymes form the largest subnetwork with most nodes. Further analysis of this subnetwork identified a putative collagen glycosyltransferase R699. Protein expression test suggested that R699 is highly expressed in Escherichia coli, unlike the human collagen-modifying enzymes. Enzymatic activity assay and mass spectrometric analyses showed that R699 catalyzes the glucosylation of galactosylhydroxylysine to glucosylgalactosylhydroxylysine on collagen using uridine diphosphate glucose (UDP-glucose) but no other UDP-sugars as a sugar donor, suggesting R699 is a mimiviral collagen galactosylhydroxylysyl glucosyltransferase (GGT). To facilitate further analysis of human and mimiviral homologous proteins, we presented an interactive and searchable genome-wide comparison website for quickly browsing human and Acanthamoeba polyphaga mimivirus homologs, which is available at RRID Resource ID: SCR_022140 or https://guolab.shinyapps.io/app-mimivirus-publication/ .
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Affiliation(s)
- Wenhui Wu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Arvinas, LLC, 5 Science Park, New Haven, CT, USA
| | - Jeong Seon Kim
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Stephen J Richards
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Tiantian Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Tingfei Chen
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Zhenhang Chen
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Mitsuo Yamauchi
- Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Houfu Guo
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA. .,Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
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6
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Wang X, Mayorga-Flores M, Bien KG, Bailey AO, Iwahara J. DNA-mediated proteolysis by neutrophil elastase enhances binding activities of the HMGB1 protein. J Biol Chem 2022; 298:102577. [DOI: 10.1016/j.jbc.2022.102577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/01/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
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7
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Kumar A, Aglyamova G, Yim Y, Bailey AO, Lynch H, Powell R, Nguyen N, Rosenthal Z, Zhao WN, Li Y, Chen J, Fan S, Lee H, Russell W, Stephan C, Robison A, Haggarty S, Nestler E, Zhou J, Machius M, Rudenko G. Chemically targeting the redox switch in AP1 transcription factor ΔFOSB. Nucleic Acids Res 2022; 50:9548-9567. [PMID: 36039764 PMCID: PMC9458432 DOI: 10.1093/nar/gkac710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/24/2022] Open
Abstract
The AP1 transcription factor ΔFOSB, a splice variant of FOSB, accumulates in the brain in response to chronic insults such as exposure to drugs of abuse, depression, Alzheimer's disease and tardive dyskinesias, and mediates subsequent long-term neuroadaptations. ΔFOSB forms heterodimers with other AP1 transcription factors, e.g. JUND, that bind DNA under control of a putative cysteine-based redox switch. Here, we reveal the structural basis of the redox switch by determining a key missing crystal structure in a trio, the ΔFOSB/JUND bZIP domains in the reduced, DNA-free form. Screening a cysteine-focused library containing 3200 thiol-reactive compounds, we identify specific compounds that target the redox switch, validate their activity biochemically and in cell-based assays, and show that they are well tolerated in different cell lines despite their general potential to bind to cysteines covalently. A crystal structure of the ΔFOSB/JUND bZIP domains in complex with a redox-switch-targeting compound reveals a deep compound-binding pocket near the DNA-binding site. We demonstrate that ΔFOSB, and potentially other, related AP1 transcription factors, can be targeted specifically and discriminately by exploiting unique structural features such as the redox switch and the binding partner to modulate biological function despite these proteins previously being thought to be undruggable.
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Affiliation(s)
| | | | - Yun Young Yim
- Nash Family Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Haley M Lynch
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Reid T Powell
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Nghi D Nguyen
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Zachary Rosenthal
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Wen-Ning Zhao
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Yi Li
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jianping Chen
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Shanghua Fan
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Hubert Lee
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Clifford Stephan
- HTS Screening Core, Texas A&M University School of Medicine, Institute of Biosciences and Technology, Center for Translational Cancer Research, Houston, TX 77030, USA
| | - Alfred J Robison
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Stephen J Haggarty
- Chemical Neurobiology Laboratory, Center for Genomic Medicine, Massachusetts General Hospital, Departments of Psychiatry & Neurology, Harvard Medical School, Boston, MA 02114, USA
| | - Eric J Nestler
- Nash Family Department of Neuroscience and the Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Mischa Machius
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gabby Rudenko
- To whom correspondence should be addressed. Tel: +1 409 772 6292; Fax: +1 409 772 9642;
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8
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Smith CA, Ebrahimpour A, Novikova L, Farina D, Bailey AO, Russell WK, Jain A, Saltzman AB, Malovannaya A, Prasad BV, Hu L, Ghebre YT. Esomeprazole covalently interacts with the cardiovascular enzyme dimethylarginine dimethylaminohydrolase: Insights into the cardiovascular risk of proton pump inhibitors. Biochim Biophys Acta Gen Subj 2022; 1866:130149. [DOI: 10.1016/j.bbagen.2022.130149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/31/2022] [Accepted: 04/07/2022] [Indexed: 11/28/2022]
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9
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Bailey AO, Huguet R, Mullen C, Syka JEP, Russell WK. Ion-Ion Charge Reduction Addresses Multiple Challenges Common to Denaturing Intact Mass Analysis. Anal Chem 2022; 94:3930-3938. [PMID: 35189062 DOI: 10.1021/acs.analchem.1c04973] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Complete LC-MS-based protein primary sequence characterization requires measurement of intact protein profiles under denaturing and/or reducing conditions. To address issues of protein overcharging of unstructured proteins under acidic, denaturing conditions and sample heterogeneity (macro- and micro-scales) which often confound denaturing intact mass analysis of a wide variety of protein samples, we propose the use of broadband isolation of entire charge state distributions of intact proteins followed by ion-ion proton transfer charge reduction, which we have termed "full scan PTCR" (fsPTCR). Using rapid denaturing size exclusion chromatography coupled to fsPTCR-Orbitrap MS and time-resolved deconvolution data analysis, we demonstrate a strategy for method optimization, leading to significant analytical advantages over conventional MS1. Denaturing analysis of the flexible bacterial translation initiation factor 2 (91 kDa) using fsPTCR reduced overcharging and showed an 11-fold gain in S/N compared to conventional MS1. Analysis by fsPTCR-MS of the microheterogeneous glycoprotein fetuin revealed twice as many proteoforms as MS1 (112 vs 56). In a macroheterogeneous mixture of proteins ranging from 14 to 148 kDa, fsPTCR provided more than 10-fold increased sensitivity and quantitative accuracy for diluted bovine serum albumin (66 kDa). Finally, our analysis shows that collisional gas pressure is a key parameter which can be utilized during fsPTCR to retain or remove larger proteins from acquired spectra.
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Affiliation(s)
- Aaron O Bailey
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
| | - Romain Huguet
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - Christopher Mullen
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - John E P Syka
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, California 95134, United States
| | - William K Russell
- University of Texas Medical Branch, 301 University Drive, Galveston, Texas 77551, United States
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10
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Hogan AK, Sathyan KM, Willis AB, Khurana S, Srivastava S, Zasadzińska E, Lee AS, Bailey AO, Gaynes MN, Huang J, Bodner J, Rosencrance CD, Wong KA, Morgan MA, Eagen KP, Shilatifard A, Foltz DR. UBR7 acts as a histone chaperone for post-nucleosomal histone H3. EMBO J 2021; 40:e108307. [PMID: 34786730 PMCID: PMC8672181 DOI: 10.15252/embj.2021108307] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/24/2021] [Accepted: 10/22/2021] [Indexed: 12/13/2022] Open
Abstract
Histone chaperones modulate the stability of histones beginning from histone synthesis, through incorporation into DNA, and during recycling during transcription and replication. Following histone removal from DNA, chaperones regulate histone storage and degradation. Here, we demonstrate that UBR7 is a histone H3.1 chaperone that modulates the supply of pre-existing post-nucleosomal histone complexes. We demonstrate that UBR7 binds to post-nucleosomal H3K4me3 and H3K9me3 histones via its UBR box and PHD. UBR7 binds to the non-nucleosomal histone chaperone NASP. In the absence of UBR7, the pool of NASP-bound post-nucleosomal histones accumulate and chromatin is depleted of H3K4me3-modified histones. We propose that the interaction of UBR7 with NASP and histones opposes the histone storage functions of NASP and that UBR7 promotes reincorporation of post-nucleosomal H3 complexes.
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Affiliation(s)
- Ann K Hogan
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Kizhakke M Sathyan
- R. D. Berlin Center for Cell Analysis and ModelingThe University of Connecticut School of MedicineFarmingtonCTUSA
| | - Alexander B Willis
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Sakshi Khurana
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Shashank Srivastava
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Ewelina Zasadzińska
- Drug Substance TechnologiesProcess Development, Amgen Inc.Thousand OaksCAUSA
| | - Alexander S Lee
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Aaron O Bailey
- Department of Biochemistry and Molecular BiologyUniversity of Texas Medical BranchGalvestonTXUSA
| | - Matthew N Gaynes
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Jiehuan Huang
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Justin Bodner
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Celeste D Rosencrance
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Kelvin A Wong
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Marc A Morgan
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Kyle P Eagen
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular GeneticsNorthwestern University Feinberg School of MedicineChicagoILUSA
- Robert H. Lurie Comprehensive Cancer CenterNorthwestern University Feinberg School of MedicineChicagoILUSA
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11
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Ren C, Bailey AO, VanderPorten E, Oh A, Phung W, Mulvihill MM, Harris SF, Liu Y, Han G, Sandoval W. Quantitative Determination of Protein–Ligand Affinity by Size Exclusion Chromatography Directly Coupled to High-Resolution Native Mass Spectrometry. Anal Chem 2018; 91:903-911. [DOI: 10.1021/acs.analchem.8b03829] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Aaron O. Bailey
- Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States
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12
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Zasadzińska E, Huang J, Bailey AO, Guo LY, Lee NS, Srivastava S, Wong KA, French BT, Black BE, Foltz DR. Inheritance of CENP-A Nucleosomes during DNA Replication Requires HJURP. Dev Cell 2018; 47:348-362.e7. [PMID: 30293838 PMCID: PMC6219920 DOI: 10.1016/j.devcel.2018.09.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/26/2018] [Accepted: 09/06/2018] [Indexed: 12/17/2022]
Abstract
Centromeric chromatin defines the site of kinetochore formation and ensures faithful chromosome segregation. Centromeric identity is epigenetically specified by the incorporation of CENP-A nucleosomes. DNA replication presents a challenge for inheritance of centromeric identity because nucleosomes are removed to allow for replication fork progression. Despite this challenge, CENP-A nucleosomes are stably retained through S phase. We used BioID to identify proteins transiently associated with CENP-A during DNA replication. We found that during S phase, HJURP transiently associates with centromeres and binds to pre-existing CENP-A, suggesting a distinct role for HJURP in CENP-A retention. We demonstrate that HJURP is required for centromeric nucleosome inheritance during S phase. HJURP co-purifies with the MCM2-7 helicase complex and, together with the MCM2 subunit, binds CENP-A simultaneously. Therefore, pre-existing CENP-A nucleosomes require an S phase function of the HJURP chaperone and interaction with MCM2 to ensure faithful inheritance of centromere identity through DNA replication.
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Affiliation(s)
- Ewelina Zasadzińska
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Jiehuan Huang
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Lucie Y Guo
- Department of Biochemistry and Biophysics and Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy S Lee
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Shashank Srivastava
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kelvin A Wong
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bradley T French
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Ben E Black
- Department of Biochemistry and Biophysics and Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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13
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Bailey AO, Han G, Phung W, Gazis P, Sutton J, Josephs JL, Sandoval W. Charge variant native mass spectrometry benefits mass precision and dynamic range of monoclonal antibody intact mass analysis. MAbs 2018; 10:1214-1225. [PMID: 30339478 PMCID: PMC6284562 DOI: 10.1080/19420862.2018.1521131] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The preponderance and diversity of charge variants in therapeutic monoclonal antibodies has implications for antibody efficacy and degradation. Understanding the extent and impact of minor antibody variants is of great interest, and it is also a critical regulatory requirement. Traditionally, a combination of approaches is used to characterize antibody charge heterogeneity, including ion exchange chromatography and independent mass spectrometric variant site mapping after proteolytic digestion. Here, we describe charge variant native mass spectrometry (CVMS), an integrated native ion exchange mass spectrometry-based charge variant analytical approach that delivers detailed molecular information in a single, semi-automated analysis. We utilized pure volatile salt mobile phases over a pH gradient that effectively separated variants based on minimal differences in isoelectric point. Characterization of variants such as deamidation, which are traditionally unattainable by intact mass due to their minimal molecular weight differences, were measured unambiguously by mass and retention time to allow confident MS1 identification. We demonstrate that efficient chromatographic separation allows introduction of the purified forms of the charge variant isoforms into the Orbitrap mass spectrometer. Our CVMS method allows confident assignment of intact monoclonal antibody isoforms of similar mass and relative abundance measurements across three orders of magnitude dynamic range.
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Affiliation(s)
- Aaron O Bailey
- a Chromatography and Mass Spectrometry Division , Thermo Fisher Scientific , San Jose , CA , USA
| | - Guanghui Han
- b Department of Microchemistry, Proteomics and Lipidomics , Genentech, Inc , South San Francisco , CA , USA
| | - Wilson Phung
- b Department of Microchemistry, Proteomics and Lipidomics , Genentech, Inc , South San Francisco , CA , USA
| | - Paul Gazis
- a Chromatography and Mass Spectrometry Division , Thermo Fisher Scientific , San Jose , CA , USA
| | - Jennifer Sutton
- a Chromatography and Mass Spectrometry Division , Thermo Fisher Scientific , San Jose , CA , USA
| | - Jonathan L Josephs
- a Chromatography and Mass Spectrometry Division , Thermo Fisher Scientific , San Jose , CA , USA
| | - Wendy Sandoval
- b Department of Microchemistry, Proteomics and Lipidomics , Genentech, Inc , South San Francisco , CA , USA
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14
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Bailey AO, Panchenko T, Shabanowitz J, Lehman SM, Bai DL, Hunt DF, Black BE, Foltz DR. Identification of the Post-translational Modifications Present in Centromeric Chromatin. Mol Cell Proteomics 2015; 15:918-31. [PMID: 26685127 DOI: 10.1074/mcp.m115.053710] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Indexed: 01/15/2023] Open
Abstract
The centromere is the locus on the chromosome that acts as the essential connection point between the chromosome and the mitotic spindle. A histone H3 variant, CENP-A, defines the location of the centromere, but centromeric chromatin consists of a mixture of both CENP-A-containing and H3-containing nucleosomes. We report a surprisingly uniform pattern of primarily monomethylation on lysine 20 of histone H4 present in short polynucleosomes mixtures of CENP-A and H3 nucleosomes isolated from functional centromeres. Canonical H3 is not a component of CENP-A-containing nucleosomes at centromeres, so the H3 we copurify from these preparations comes exclusively from adjacent nucleosomes. We find that CENP-A-proximal H3 nucleosomes are not uniformly modified but contain a complex set of PTMs. Dually modified K9me2-K27me2 H3 nucleosomes are observed at the centromere. Side-chain acetylation of both histone H3 and histone H4 is low at the centromere. Prior to assembly at centromeres, newly expressed CENP-A is sequestered for a large portion of the cell cycle (late S-phase, G2, and most of mitosis) in a complex that contains its partner, H4, and its chaperone, HJURP. In contrast to chromatin associated centromeric histone H4, we show that prenucleosomal CENP-A-associated histone H4 lacks K20 methylation and contains side-chain and α-amino acetylation. We show HJURP displays a complex set of serine phosphorylation that may potentially regulate the deposition of CENP-A. Taken together, our findings provide key information regarding some of the key components of functional centromeric chromatin.
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Affiliation(s)
- Aaron O Bailey
- From the ‡Department of Cell Biology, University of Virginia, Charlottesville, Virginia, 22908
| | - Tanya Panchenko
- §Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6059
| | - Jeffrey Shabanowitz
- ¶Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22908
| | - Stephanie M Lehman
- ¶Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22908
| | - Dina L Bai
- ¶Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22908
| | - Donald F Hunt
- ¶Department of Chemistry, University of Virginia, Charlottesville, Virginia, 22908
| | - Ben E Black
- §Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104-6059;
| | - Daniel R Foltz
- From the ‡Department of Cell Biology, University of Virginia, Charlottesville, Virginia, 22908; ‖Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, 22908; **Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago Illinois 60611
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15
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Abstract
The centromere is the chromosomal region that directs kinetochore assembly during mitosis in order to facilitate the faithful segregation of sister chromatids. The location of the human centromere is epigenetically specified. The presence of nucleosomes that contain the histone H3 variant, CENP-A, are thought to be the epigenetic mark that indicates active centromeres. Maintenance of centromeric identity requires the deposition of new CENP-A nucleosomes with each cell cycle. During S-phase, existing CENP-A nucleosomes are divided among the daughter chromosomes, while new CENP-A nucleosomes are deposited during early G1. The specific assembly of CENP-A nucleosomes at centromeres requires the Mis18 complex, which recruits the CENP-A assembly factor, HJURP. We will review the unique features of centromeric chromatin as well as the mechanism of CENP-A nucleosome deposition. We will also highlight a few recent discoveries that begin to elucidate the factors that temporally and spatially control CENP-A deposition.
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Affiliation(s)
- Madison E Stellfox
- Department of Biochemistry and Molecular Genetics, University of Virginia Medical School, PO Box 800733, Charlottesville, VA 22908, USA
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16
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Foltz DR, Jansen LE, Bailey AO, Yates JR, Bassett EA, Wood S, Black BE, Cleveland DW. Centromere-specific assembly of CENP-a nucleosomes is mediated by HJURP. Cell 2009; 137:472-84. [PMID: 19410544 PMCID: PMC2747366 DOI: 10.1016/j.cell.2009.02.039] [Citation(s) in RCA: 506] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 11/18/2008] [Accepted: 02/20/2009] [Indexed: 12/11/2022]
Abstract
The centromere is responsible for accurate chromosome segregation. Mammalian centromeres are specified epigenetically, with all active centromeres containing centromere-specific chromatin in which CENP-A replaces histone H3 within the nucleosome. The proteins responsible for assembly of human CENP-A into centromeric nucleosomes during the G1 phase of the cell cycle are shown here to be distinct from the chromatin assembly factors previously shown to load other histone H3 variants. Here we demonstrate that prenucleosomal CENP-A is complexed with histone H4, nucleophosmin 1, and HJURP. Recruitment of new CENP-A into nucleosomes at replicated centromeres is dependent on HJURP. Recognition by HJURP is mediated through the centromere targeting domain (CATD) of CENP-A, a region that we demonstrated previously to induce a unique conformational rigidity to both the subnucleosomal CENP-A heterotetramer and the corresponding assembled nucleosome. We propose HJURP to be a cell-cycle-regulated CENP-A-specific histone chaperone required for centromeric chromatin assembly.
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Affiliation(s)
- Daniel R. Foltz
- Ludwig Institute for Cancer Research, San Diego CA 92093-0670, U.S.A
- Department of Cell and Molecular Medicine, University of California at San Diego, La Jolla, CA 93093-0670, U.S.A
- Present Address: Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville VA 22908, U.S.A
| | - Lars E.T. Jansen
- Ludwig Institute for Cancer Research, San Diego CA 92093-0670, U.S.A
- Department of Cell and Molecular Medicine, University of California at San Diego, La Jolla, CA 93093-0670, U.S.A
- Present Address: Instituto Gulbenkian de Ciência, 2770-186 Oeiras, Portugal
| | | | - John R. Yates
- The Scripps Research Institute, La Jolla, CA 92037, U.S.A
| | - Emily A. Bassett
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059, U.S.A
| | - Stacey Wood
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059, U.S.A
| | - Ben E. Black
- Ludwig Institute for Cancer Research, San Diego CA 92093-0670, U.S.A
- Department of Cell and Molecular Medicine, University of California at San Diego, La Jolla, CA 93093-0670, U.S.A
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104-6059, U.S.A
| | - Don W. Cleveland
- Ludwig Institute for Cancer Research, San Diego CA 92093-0670, U.S.A
- Department of Cell and Molecular Medicine, University of California at San Diego, La Jolla, CA 93093-0670, U.S.A
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17
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Wong CCL, Xu T, Rai R, Bailey AO, Yates JR, Wolf YI, Zebroski H, Kashina A. Global analysis of posttranslational protein arginylation. PLoS Biol 2007; 5:e258. [PMID: 17896865 PMCID: PMC1988855 DOI: 10.1371/journal.pbio.0050258] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Accepted: 07/30/2007] [Indexed: 11/27/2022] Open
Abstract
Posttranslational arginylation is critical for embryogenesis, cardiovascular development, and angiogenesis, but its molecular effects and the identity of proteins arginylated in vivo are largely unknown. Here we report a global analysis of this modification on the protein level and identification of 43 proteins arginylated in vivo on highly specific sites. Our data demonstrate that unlike previously believed, arginylation can occur on any N-terminally exposed residue likely defined by a structural recognition motif on the protein surface, and that it preferentially affects a number of physiological systems, including cytoskeleton and primary metabolic pathways. The results of our study suggest that protein arginylation is a general mechanism for regulation of protein structure and function and outline the potential role of protein arginylation in cell metabolism and embryonic development. A common cellular mechanism for the regulation of proteins, once they have been translated from mRNA, is the addition and removal of chemical groups via enzymatic reactions. The posttranslational addition of arginyl groups is critical for the embryonic development and survival of an organism, but the molecular effects and the identity of proteins arginylated in vivo are largely unknown. We developed a technique to screen large numbers of proteins for this modification and identified 43 proteins arginylated in vivo on highly specific sites. Arginylation can occur on any exposed residue at the N-terminus of a protein and appears to require a specific structural recognition motif on the protein surface. It preferentially affects a number of physiological systems, including cytoskeleton and primary metabolic pathways and seems to be a general mechanism for regulation of protein structure and function. Our data provide insights into the previously unknown arginylation-dependent mechanisms of the regulation of embryonic development. A comprehensive study indicates that protein arginylation may be a general mechanism for regulation of protein structure and function, similar to other major posttranslational modifications.
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Affiliation(s)
- Catherine C. L Wong
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Tao Xu
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Reena Rai
- Department of Animal Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Aaron O Bailey
- The Scripps Research Institute, LaJolla, California, United States of America
| | - John R Yates
- The Scripps Research Institute, LaJolla, California, United States of America
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Henry Zebroski
- Rockefeller University, New York, NewYork, United States of America
| | - Anna Kashina
- Department of Animal Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * To whom correspondence should be addressed. E-mail:
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18
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Abstract
This proteomic protocol purifies and identifies palmitoylated proteins (i.e., S-acylated proteins) from complex protein extracts. The method relies on an acyl-biotinyl exchange chemistry in which biotin moieties are substituted for the thioester-linked protein acyl-modifications through a sequence of three in vitro chemical steps: (i) blockade of free thiols with N-ethylmaleimide; (ii) cleavage of the Cys-palmitoyl thioester linkages with hydroxylamine; and (iii) labeling of thiols, newly exposed by the hydroxylamine, with biotin-HPDP (Biotin-HPDP-N-[6-(Biotinamido)hexyl]-3'-(2'-pyridyldithio)propionamide. The biotinylated proteins are then affinity-purified using streptavidin-agarose and identified by multi-dimensional protein identification technology (MuDPIT), a high-throughput, tandem mass spectrometry (MS/MS)-based proteomic technology. MuDPIT also affords a semi-quantitative analysis that may be used to assess the gross changes induced to the global palmitoylation profile by mutation or drugs. Typically, 2-3 weeks are required for this analysis.
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Affiliation(s)
- Junmei Wan
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA
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19
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Bailey AO, Miller TM, Dong MQ, Velde CV, Cleveland DW, Yates JR. RCADiA: simple automation platform for comparative multidimensional protein identification technology. Anal Chem 2007; 79:6410-8. [PMID: 17616168 PMCID: PMC2528021 DOI: 10.1021/ac070585g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Multidimensional liquid chromatography in combination with tandem mass spectrometry has been used to analyze a variety of biological structures including protein complexes. Incorporating this approach with autosampling devices presents a number of problems including decreased sensitivity due to exposure to extra surfaces, carryover from run to run, and increased dead volume. We developed a device, termed Radial Column Array for Distribution and Automation (RCADiA), to automate multiple MuDPIT experiments while eliminating many of these problems and maintaining a high resolution and sensitive analysis. The design, which places each sample downstream of any common fluid path, presents a low risk of carryover between successive analyses. Beyond the convenience of automation, the RCADiA platform also produces data of similar quality to the standard method of performing individual MuDPIT experiments. We demonstrate this device by performing a comparative analysis of mitochondria enriched from rat liver and spinal cord.
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Affiliation(s)
- Aaron O. Bailey
- The Scripps Research Institute, 10550 North Torrey Pines Rd., SR11, Department of Cell Biology, La Jolla, CA 92037
| | - Timothy M. Miller
- University of California at San Diego, Ludwig Institute for Cancer Research, Mail Code 0670, CMM-East 9072, 9500 Gilman Dr., La Jolla, CA 92093-0670
| | - Meng-Qiu Dong
- The Scripps Research Institute, 10550 North Torrey Pines Rd., SR11, Department of Cell Biology, La Jolla, CA 92037
| | - Christine Vande Velde
- University of California at San Diego, Ludwig Institute for Cancer Research, Mail Code 0670, CMM-East 9072, 9500 Gilman Dr., La Jolla, CA 92093-0670
| | - Don W. Cleveland
- University of California at San Diego, Ludwig Institute for Cancer Research, Mail Code 0670, CMM-East 9072, 9500 Gilman Dr., La Jolla, CA 92093-0670
| | - John R. Yates
- The Scripps Research Institute, 10550 North Torrey Pines Rd., SR11, Department of Cell Biology, La Jolla, CA 92037
- To whom correspondence should be addressed.
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20
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O'Neill BM, Szyjka SJ, Lis ET, Bailey AO, Yates JR, Aparicio OM, Romesberg FE. Pph3-Psy2 is a phosphatase complex required for Rad53 dephosphorylation and replication fork restart during recovery from DNA damage. Proc Natl Acad Sci U S A 2007; 104:9290-5. [PMID: 17517611 PMCID: PMC1890487 DOI: 10.1073/pnas.0703252104] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Activation of the checkpoint kinase Rad53 is a critical response to DNA damage that results in stabilization of stalled replication forks, inhibition of late-origin initiation, up-regulation of dNTP levels, and delayed entry to mitosis. Activation of Rad53 is well understood and involves phosphorylation by the protein kinases Mec1 and Tel1 as well as in trans autophosphorylation by Rad53 itself. However, deactivation of Rad53, which must occur to allow the cell to recover from checkpoint arrest, is not well understood. Here, we present genetic and biochemical evidence that the type 2A-like protein phosphatase Pph3 forms a complex with Psy2 (Pph3-Psy2) that binds and dephosphorylates activated Rad53 during treatment with, and recovery from, methylmethane sulfonate-mediated DNA damage. In the absence of Pph3-Psy2, Rad53 dephosphorylation and the resumption of DNA synthesis are delayed during recovery from DNA damage. This delay in DNA synthesis reflects a failure to restart stalled replication forks, whereas, remarkably, genome replication is eventually completed by initiating late origins of replication despite the presence of hyperphosphorylated Rad53. These findings suggest that Rad53 regulates replication fork restart and initiation of late firing origins independently and that regulation of these processes is mediated by specific Rad53 phosphatases.
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Affiliation(s)
| | - Shawn J. Szyjka
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | | | - Aaron O. Bailey
- Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; and
| | - John R. Yates
- Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037; and
| | - Oscar M. Aparicio
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089
| | - Floyd E. Romesberg
- Departments of Chemistry and
- To whom correspondence should be addressed at:
Department of Chemistry, The Scripps Research Institute, CB262R, 10550 North Torrey Pines Road, La Jolla, CA 92037. E-mail:
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21
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Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN, Phinney BS, Yates JR, Davis NG. Global analysis of protein palmitoylation in yeast. Cell 2006; 125:1003-13. [PMID: 16751107 PMCID: PMC2246083 DOI: 10.1016/j.cell.2006.03.042] [Citation(s) in RCA: 421] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2005] [Revised: 02/23/2006] [Accepted: 03/23/2006] [Indexed: 11/20/2022]
Abstract
Protein palmitoylation is a reversible lipid modification that regulates membrane tethering for key proteins in cell signaling, cancer, neuronal transmission, and membrane trafficking. Palmitoylation has proven to be a difficult study: Specifying consensuses for predicting palmitoylation remain unavailable, and first-example palmitoylation enzymes--i.e., protein acyltransferases (PATs)--were identified only recently. Here, we use a new proteomic methodology that purifies and identifies palmitoylated proteins to characterize the palmitoyl proteome of the yeast Saccharomyces cerevisiae. Thirty-five new palmitoyl proteins are identified, including many SNARE proteins and amino acid permeases as well as many other participants in cellular signaling and membrane trafficking. Analysis of mutant yeast strains defective for members of the DHHC protein family, a putative PAT family, allows a matching of substrate palmitoyl proteins to modifying PATs and reveals the DHHC family to be a family of diverse PAT specificities responsible for most of the palmitoylation within the cell.
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Affiliation(s)
- Amy F. Roth
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Junmei Wan
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Aaron O. Bailey
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Beimeng Sun
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Jason A. Kuchar
- Department of Biochemistry, Michigan State University, East Lansing, MI 48824, USA
| | - William N. Green
- Department of Neurobiology, Pharmacology and Physiology, University of Chicago, Chicago, IL 60637, USA
| | - Brett S. Phinney
- Department of Biochemistry, Michigan State University, East Lansing, MI 48824, USA
| | - John R. Yates
- Department of Cell Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas G. Davis
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- *Contact:
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22
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Karakozova M, Kozak M, Wong CCL, Bailey AO, Yates JR, Mogilner A, Zebroski H, Kashina A. Arginylation of beta-actin regulates actin cytoskeleton and cell motility. Science 2006; 313:192-6. [PMID: 16794040 DOI: 10.1126/science.1129344] [Citation(s) in RCA: 205] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Posttranslational arginylation is critical for mouse embryogenesis, cardiovascular development, and angiogenesis, but its molecular effects and the identity of proteins arginylated in vivo are unknown. We found that beta-actin was arginylated in vivo to regulate actin filament properties, beta-actin localization, and lamella formation in motile cells. Arginylation of beta-actin apparently represents a critical step in the actin N-terminal processing needed for actin functioning in vivo. Thus, posttranslational arginylation of a single protein target can regulate its intracellular function, inducing global changes on the cellular level, and may contribute to cardiovascular development and angiogenesis.
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Affiliation(s)
- Marina Karakozova
- Department of Animal Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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23
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Green EM, Antczak AJ, Bailey AO, Franco AA, Wu KJ, Yates JR, Kaufman PD. Replication-independent histone deposition by the HIR complex and Asf1. Curr Biol 2006; 15:2044-9. [PMID: 16303565 PMCID: PMC2819815 DOI: 10.1016/j.cub.2005.10.053] [Citation(s) in RCA: 169] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Revised: 10/05/2005] [Accepted: 10/07/2005] [Indexed: 01/08/2023]
Abstract
The orderly deposition of histones onto DNA is mediated by conserved assembly complexes, including chromatin assembly factor-1 (CAF-1) and the Hir proteins . CAF-1 and the Hir proteins operate in distinct but functionally overlapping histone deposition pathways in vivo . The Hir proteins and CAF-1 share a common partner, the highly conserved histone H3/H4 binding protein Asf1, which binds the middle subunit of CAF-1 as well as to Hir proteins . Asf1 binds to newly synthesized histones H3/H4 , and this complex stimulates histone deposition by CAF-1 . In yeast, Asf1 is required for the contribution of the Hir proteins to gene silencing . Here, we demonstrate that Hir1, Hir2, Hir3, and Hpc2 comprise the HIR complex, which copurifies with the histone deposition protein Asf1. Together, the HIR complex and Asf1 deposit histones onto DNA in a replication-independent manner. Histone deposition by the HIR complex and Asf1 is impaired by a mutation in Asf1 that inhibits HIR binding. These data indicate that the HIR complex and Asf1 proteins function together as a conserved eukaryotic pathway for histone replacement throughout the cell cycle.
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Affiliation(s)
- Erin M. Green
- Lawrence Berkeley National Laboratory and Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA 94720
| | - Andrew J. Antczak
- Lawrence Berkeley National Laboratory and Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA 94720
| | - Aaron O. Bailey
- Department of Cell Biology The Scripps Research Institute La Jolla, CA 92037
| | - Alexa A. Franco
- Lawrence Berkeley National Laboratory and Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA 94720
| | - Kevin J. Wu
- Lawrence Berkeley National Laboratory and Department of Molecular and Cell Biology, University of California, Berkeley Berkeley, CA 94720
| | - John R. Yates
- Department of Cell Biology The Scripps Research Institute La Jolla, CA 92037
| | - Paul D. Kaufman
- Program in Gene Function and Expression University of Massachusetts Medical School Worcester, MA 01605-2324
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24
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Foltz DR, Jansen LET, Black BE, Bailey AO, Yates JR, Cleveland DW. The human CENP-A centromeric nucleosome-associated complex. Nat Cell Biol 2006; 8:458-69. [PMID: 16622419 DOI: 10.1038/ncb1397] [Citation(s) in RCA: 537] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Accepted: 04/03/2006] [Indexed: 11/09/2022]
Abstract
The basic element for chromosome inheritance, the centromere, is epigenetically determined in mammals. The prime candidate for specifying centromere identity is the array of nucleosomes assembled with CENP-A, the centromere-specific histone H3 variant. Here, we show that CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of three new human centromere proteins (CENP-M, CENP-N and CENP-T), along with CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Facilitates chromatin transcription (FACT) and nucleophosmin-1 (previously implicated in transcriptional chromatin remodelling and as a multifunctional nuclear chaperone, respectively) are absent from histone H3-containing nucleosomes, but are stably recruited to CENP-A nucleosomes independent of CENP-A NAC. Seven new CENP-A-nucleosome distal (CAD) centromere components (CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S) are identified as assembling on the CENP-A NAC. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling.
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Affiliation(s)
- Daniel R Foltz
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093-0670, USA
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Zumbro GL, Tillman L, Bailey AO, Treasure RL. A comparison between propranolol and hypothermia in preventing ischemic contracture of the left ventricle (stone heart). Ann Thorac Surg 1978; 25:541-50. [PMID: 148874 DOI: 10.1016/s0003-4975(10)63606-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ischemic contracture of the left ventricle ("stone heart") was studied utilizing a previously described stone heart model. Our studies suggest that beta-adrenergic blockade is not quantitatively as important as hypothermia in protecting ischemic myocardium. On the basis of reduced fibrillatory activity and a slight protective effect shown by electron microscopy, it would appear that combining propranolol with hypothermia may be superior to either used singly.
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