1
|
Zhang T, Guerra LF, Berlina Y, Wilson JR, Fierz B, Müller MM. Semisynthesis of Isomerized Histone H4 Reveals Robustness and Vulnerability of Chromatin toward Molecular Aging. J Am Chem Soc 2025; 147:4952-4961. [PMID: 39894946 PMCID: PMC11826994 DOI: 10.1021/jacs.4c14136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 01/13/2025] [Accepted: 01/14/2025] [Indexed: 02/04/2025]
Abstract
Proteins are subject to aging in the form of spontaneous, nonenzymatic post-translational modifications (PTMs). One such PTM is the formation of the β-linked isomer l-isoaspartic acid (isoAsp) from aspartic acid (Asp) or asparagine residues, which tends to occur in long-lived proteins. Histones can exhibit half-lives on the order of 100 days, and unsurprisingly, isoAsp formation has been observed in nearly every histone family. Delineating the molecular consequences of isoAsp formation in histones is challenging due to the multitude of processes that occur on such time scales. To isolate the effects of a specific isoAsp modification thus necessitates precise in vitro characterization with well-defined substrates. Here, we adapt a protein semisynthesis approach to generate full-length variants of histone H4 in which the canonical Asp at position 24 is replaced by its isoAsp isomer (H4isoD24). This variant was incorporated into chromatin templates, and the resulting constructs were used to interrogate key parameters of chromatin integrity and maintenance in vitro: compaction, nucleosome remodeling, and methylation of H4 lysine 20 (H4K20). Remarkably, despite its disruptive changes to the backbone's spacing and direction, isoD24 did not dramatically disrupt Mg2+-mediated chromatin self-association or nucleosome repositioning by the remodeler Chd1. In contrast, H4isoD24 significantly inhibited both Set8- and Suv4-20h1-catalyzed methylation at H4K20. These results suggest that H4isoD24 gives rise to a complex reorganization of the chromatin functional landscape, in which macroscopic processes show robustness and local mechanisms exhibit vulnerability to the presence of this mark.
Collapse
Affiliation(s)
- Tianze Zhang
- Department
of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Luis F. Guerra
- Department
of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| | - Yana Berlina
- École
Polytechnique Fédérale de Lausanne (EPFL), ISIC, Lausanne CH-1015, Switzerland
| | - Jon R. Wilson
- The
Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K.
| | - Beat Fierz
- École
Polytechnique Fédérale de Lausanne (EPFL), ISIC, Lausanne CH-1015, Switzerland
| | - Manuel M. Müller
- Department
of Chemistry, King’s College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K.
| |
Collapse
|
2
|
Nakagawa M, Nakagawa T. CUL4-Based Ubiquitin Ligases in Chromatin Regulation: An Evolutionary Perspective. Cells 2025; 14:63. [PMID: 39851492 PMCID: PMC11763709 DOI: 10.3390/cells14020063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2024] [Revised: 12/22/2024] [Accepted: 01/06/2025] [Indexed: 01/26/2025] Open
Abstract
Ubiquitylation is a post-translational modification that modulates protein function and stability. It is orchestrated by the concerted action of three types of enzymes, with substrate specificity governed by ubiquitin ligases (E3s), which may exist as single proteins or as part of multi-protein complexes. Although Cullin (CUL) proteins lack intrinsic enzymatic activity, they participate in the formation of active ubiquitin ligase complexes, known as Cullin-Ring ubiquitin Ligases (CRLs), through their association with ROC1 or ROC2, along with substrate adaptor and receptor proteins. Mammalian genomes encode several CUL proteins (CUL1-9), each contributing to distinct CRLs. Among these CUL proteins, CUL1, CUL3, and CUL4 are believed to be the most ancient and evolutionarily conserved from yeast to mammals, with CUL4 uniquely duplicated in vertebrates. Genetic evidence strongly implicates CUL4-based ubiquitin ligases (CRL4s) in chromatin regulation across various species and suggests that, in vertebrates, CRL4s have also acquired a cytosolic role, which is facilitated by a cytosol-localizing paralog of CUL4. Substrates identified through biochemical studies have elucidated the molecular mechanisms by which CRL4s regulate chromatin and cytosolic processes. The substantial body of knowledge on CUL4 biology amassed over the past two decades provides a unique opportunity to explore the functional evolution of CRL4. In this review, we synthesize the available structural, genetic, and biochemical data on CRL4 from various model organisms and discuss the conserved and novel functions of CRL4s.
Collapse
Affiliation(s)
- Makiko Nakagawa
- Institute of Gene Research, Yamaguchi University Science Research Center, Yamaguchi 755-8505, Japan;
- Advanced Technology Institute, Life Science Division, Yamaguchi University, Yamaguchi 755-8611, Japan
| | - Tadashi Nakagawa
- Division of Cell Proliferation, United Centers for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan
- Department of Clinical Pharmacology, Faculty of Pharmaceutical Sciences, Sanyo-Onoda City University, Sanyo-Onoda 756-0084, Japan
| |
Collapse
|
3
|
Kalailingam P, Mohd‐Kahliab K, Ngan SC, Iyappan R, Melekh E, Lu T, Zien GW, Sharma B, Guo T, MacNeil AJ, MacPherson REK, Tsiani EL, O'Leary DD, Lim KL, Su IH, Gao Y, Richards AM, Kalaria RN, Chen CP, McCarthy NE, Sze SK. Immunotherapy targeting isoDGR-protein damage extends lifespan in a mouse model of protein deamidation. EMBO Mol Med 2023; 15:e18526. [PMID: 37971164 PMCID: PMC10701600 DOI: 10.15252/emmm.202318526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/21/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
Aging results from the accumulation of molecular damage that impairs normal biochemical processes. We previously reported that age-linked damage to amino acid sequence NGR (Asn-Gly-Arg) results in "gain-of-function" conformational switching to isoDGR (isoAsp-Gly-Arg). This integrin-binding motif activates leukocytes and promotes chronic inflammation, which are characteristic features of age-linked cardiovascular disorders. We now report that anti-isoDGR immunotherapy mitigates lifespan reduction of Pcmt1-/- mouse. We observed extensive accumulation of isoDGR and inflammatory cytokine expression in multiple tissues from Pcmt1-/- and naturally aged WT animals, which could also be induced via injection of isoDGR-modified plasma proteins or synthetic peptides into young WT animals. However, weekly injection of anti-isoDGR mAb (1 mg/kg) was sufficient to significantly reduce isoDGR-protein levels in body tissues, decreased pro-inflammatory cytokine concentrations in blood plasma, improved cognition/coordination metrics, and extended the average lifespan of Pcmt1-/- mice. Mechanistically, isoDGR-mAb mediated immune clearance of damaged isoDGR-proteins via antibody-dependent cellular phagocytosis (ADCP). These results indicate that immunotherapy targeting age-linked protein damage may represent an effective intervention strategy in a range of human degenerative disorders.
Collapse
Affiliation(s)
| | | | - SoFong Cam Ngan
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Ranjith Iyappan
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Evelin Melekh
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Tian Lu
- iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life SciencesWestlake UniversityHangzhouChina
| | - Gan Wei Zien
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Bhargy Sharma
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Tiannan Guo
- iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life SciencesWestlake UniversityHangzhouChina
| | - Adam J MacNeil
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Rebecca EK MacPherson
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Evangelia Litsa Tsiani
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Deborah D O'Leary
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| | - Kah Leong Lim
- Lee Kong Chian School of MedicineNanyang Technological UniversitySingaporeSingapore
| | - I Hsin Su
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - Yong‐Gui Gao
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
| | - A Mark Richards
- Department of CardiologyNational University Heart CentreSingaporeSingapore
- Department of CardiologyUniversity of OtagoChristchurchNew Zealand
| | - Raj N Kalaria
- Institute of Neuroscience, Campus for Ageing and VitalityNewcastle UniversityNewcastle upon TyneUK
| | - Christopher P Chen
- Memory, Aging and Cognition CentreNational University Health SystemSingaporeSingapore
| | - Neil E McCarthy
- Centre for Immunobiology, The Blizard Institute, Bart's and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Siu Kwan Sze
- School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
- Department of Health Sciences, Faculty of Applied Health SciencesBrock UniversitySt. CatharinesONCanada
| |
Collapse
|
4
|
Zhong J, Yuan C, Liu L, Du Y, Hui Y, Chen Z, Diao C, Yang R, Liu G, Liu X. PCMT1 regulates the migration, invasion, and apoptosis of prostate cancer through modulating the PI3K/AKT/GSK-3β pathway. Aging (Albany NY) 2023; 15:11654-11671. [PMID: 37899170 PMCID: PMC10637816 DOI: 10.18632/aging.205152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023]
Abstract
Protein L-isoaspartate (D-aspartate) O-methyltransferase (PCMT1) is a repair enzyme that catalyzes the conversion of isomerized aspartic acid (iso-Asp) residues into their normal structure, thereby restoring the configuration and function of proteins. Studies have shown that PCMT1 is overexpressed in several tumors and affects patients' prognosis. However, there are few reports on the role of PCMT1 in prostate cancer (PCa). In the present research, with the assistance of The Cancer Genome Atlas Program (TCGA) database, we found that PCMT1 was overexpressed in PCa tissues. The results of quantitative reverse transcription-polymerase chain reaction (qRT-PCR), western blot and immunohistochemistry staining also showed that PCMT1 expression was significantly increased in PCa tissues and cell lines. In PCa clinical samples, PCMT1 expression was closely related to Gleason score, clinical stage, lymph node metastasis and bone metastasis. The experiments of overexpression and knockdown of PCMT1 in vitro or in vivo showed that PCMT1 can significantly promote the proliferation, migration and invasion of PCa cells, inhibit cell apoptosis, and promote the growth of PCa. We furthermore confirmed that PCMT1 regulated the migration, invasion and apoptosis of PCa cells by modulating the phosphatidylinositol 3-kinase/AKT kinase/glycogen-synthase kinase-3β (PI3K/AKT/GSK-3β) signaling pathway. Collectively, PCMT1 plays a cancer-facilitative role in PCa by promoting the proliferation, migration and invasion of PCa cells, and inhibiting apoptosis. Therefore, PCMT1 is considered to represent a novel target for treating PCa.
Collapse
Affiliation(s)
- Jiacheng Zhong
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Chao Yuan
- Department of Urology, Jingzhou Central Hospital, Jingzhou 434020, China
| | - Lin Liu
- Department of Emergency, Renmin Hospital, Hubei University of Medicine, Shiyan 442000, China
| | - Yang Du
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yumin Hui
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhiyuan Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Changhui Diao
- Department of Urology, The First People’s Hospital of Shangqiu City, Shangqiu 476100, China
| | - Rui Yang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Guiyong Liu
- Department of Urology, Qianjiang Central Hospital, Qianjiang 433100, China
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| |
Collapse
|
5
|
Small EM, Osley MA. A screen for histone mutations that affect quiescence in S. cerevisiae. FEBS J 2023; 290:3539-3562. [PMID: 36871139 DOI: 10.1111/febs.16759] [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: 08/07/2022] [Revised: 12/15/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023]
Abstract
Quiescence or G0 is a reversible state in which cells cease division but retain the ability to resume proliferation. Quiescence occurs in all organisms and is essential for stem cell maintenance and tissue renewal. It is also related to chronological lifespan (CLS)-the survival of postmitotic quiescent cells (Q cells) over time-and thus contributes to longevity. Important questions remain regarding the mechanisms that control entry into quiescence, maintenance of quiescence and re-entry of Q cells into the cell cycle. S. cerevisiae has emerged as an excellent organism in which to address these questions because of the ease in which Q cells can be isolated. Following entry into G0, yeast cells remain viable for an extended period and can re-enter the cell cycle when exposed to growth-promoting signals. Histone acetylation is lost during the formation of Q cells and chromatin becomes highly condensed. This unique chromatin landscape regulates quiescence-specific transcriptional repression and has been linked to the formation and maintenance of Q cells. To ask whether other chromatin features regulate quiescence, we conducted two comprehensive screens of histone H3 and H4 mutants and identified mutants that show either altered quiescence entry or CLS. Examination of several quiescence entry mutants found that none of the mutants retain histone acetylation in Q cells but show differences in chromatin condensation. A comparison of H3 and H4 mutants with altered CLS to those with altered quiescence entry found that chromatin plays both overlapping and independent roles in the continuum of the quiescence program.
Collapse
Affiliation(s)
- Eric M Small
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Mary Ann Osley
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| |
Collapse
|
6
|
Zhang C, Guo ZF, Liu W, Kazama K, Hu L, Sun X, Wang L, Lee H, Lu L, Yang XF, Summer R, Sun J. PIMT is a novel and potent suppressor of endothelial activation. eLife 2023; 12:e85754. [PMID: 37070640 PMCID: PMC10112892 DOI: 10.7554/elife.85754] [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: 12/22/2022] [Accepted: 04/02/2023] [Indexed: 04/19/2023] Open
Abstract
Proinflammatory agonists provoke the expression of cell surface adhesion molecules on endothelium in order to facilitate leukocyte infiltration into tissues. Rigorous control over this process is important to prevent unwanted inflammation and organ damage. Protein L-isoaspartyl O-methyltransferase (PIMT) converts isoaspartyl residues to conventional methylated forms in cells undergoing stress-induced protein damage. The purpose of this study was to determine the role of PIMT in vascular homeostasis. PIMT is abundantly expressed in mouse lung endothelium and PIMT deficiency in mice exacerbated pulmonary inflammation and vascular leakage to LPS(lipopolysaccharide). Furthermore, we found that PIMT inhibited LPS-induced toll-like receptor signaling through its interaction with TNF receptor-associated factor 6 (TRAF6) and its ability to methylate asparagine residues in the coiled-coil domain. This interaction was found to inhibit TRAF6 oligomerization and autoubiquitination, which prevented NF-κB transactivation and subsequent expression of endothelial adhesion molecules. Separately, PIMT also suppressed ICAM-1 expression by inhibiting its N-glycosylation, causing effects on protein stability that ultimately translated into reduced EC(endothelial cell)-leukocyte interactions. Our study has identified PIMT as a novel and potent suppressor of endothelial activation. Taken together, these findings suggest that therapeutic targeting of PIMT may be effective in limiting organ injury in inflammatory vascular diseases.
Collapse
Affiliation(s)
- Chen Zhang
- Center for Translational Medicine, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Zhi-Fu Guo
- Center for Translational Medicine, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Wennan Liu
- Center for Translational Medicine, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Kyosuke Kazama
- Center for Translational Medicine, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Louis Hu
- Center for Translational Medicine, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Xiaobo Sun
- Center for Translational Medicine, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Lu Wang
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Hyoungjoo Lee
- Quantitative Proteomics Resource Center, University of PennsylvaniaPhiladelphiaUnited States
| | - Lin Lu
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiao-Feng Yang
- Center for Metabolic Disease Research, Lewis Katz School of Medicine, Temple UniversityPhiladelphiaUnited States
| | - Ross Summer
- Center for Translational Medicine, Thomas Jefferson UniversityPhiladelphiaUnited States
| | - Jianxin Sun
- Center for Translational Medicine, Thomas Jefferson UniversityPhiladelphiaUnited States
| |
Collapse
|
7
|
Chen Y, Wang J, Yao L, Li B, Ma X, Si E, Yang K, Li C, Shang X, Meng Y, Wang H. Combined Proteomic and Metabolomic Analysis of the Molecular Mechanism Underlying the Response to Salt Stress during Seed Germination in Barley. Int J Mol Sci 2022; 23:ijms231810515. [PMID: 36142428 PMCID: PMC9499682 DOI: 10.3390/ijms231810515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/18/2022] Open
Abstract
Salt stress is a major abiotic stress factor affecting crop production, and understanding of the response mechanisms of seed germination to salt stress can help to improve crop tolerance and yield. The differences in regulatory pathways during germination in different salt-tolerant barley seeds are not clear. Therefore, this study investigated the responses of different salt-tolerant barley seeds during germination to salt stress at the proteomic and metabolic levels. To do so, the proteomics and metabolomics of two barley seeds with different salt tolerances were comprehensively examined. Through comparative proteomic analysis, 778 differentially expressed proteins were identified, of which 335 were upregulated and 443 were downregulated. These proteins, were mainly involved in signal transduction, propanoate metabolism, phenylpropanoid biosynthesis, plant hormones and cell wall stress. In addition, a total of 187 salt-regulated metabolites were identified in this research, which were mainly related to ABC transporters, amino acid metabolism, carbohydrate metabolism and lipid metabolism; 72 were increased and 112 were decreased. Compared with salt-sensitive materials, salt-tolerant materials responded more positively to salt stress at the protein and metabolic levels. Taken together, these results suggest that salt-tolerant germplasm may enhance resilience by repairing intracellular structures, promoting lipid metabolism and increasing osmotic metabolites. These data not only provide new ideas for how seeds respond to salt stress but also provide new directions for studying the molecular mechanisms and the metabolic homeostasis of seeds in the early stages of germination under abiotic stresses.
Collapse
Affiliation(s)
- Yiyou Chen
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Juncheng Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Lirong Yao
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Baochun Li
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- Department of Botany, College of Life Sciences and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaole Ma
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Erjing Si
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Ke Yang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
| | - Chengdao Li
- Western Barley Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Xunwu Shang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yaxiong Meng
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- Correspondence: (Y.M.); (H.W.)
| | - Huajun Wang
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, China
- Correspondence: (Y.M.); (H.W.)
| |
Collapse
|
8
|
Cantone N, Cummings RT, Trojer P. Screening for Small-Molecule Inhibitors of Histone Methyltransferases. Methods Mol Biol 2022; 2529:477-490. [PMID: 35733027 DOI: 10.1007/978-1-0716-2481-4_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Potent and highly selective small-molecule inhibitors are needed to unravel the biological complexities of histone methyltransferases and to reveal their therapeutic potential. A prerequisite to developing these inhibitors is the identification of validated chemical matter for initiating a medicinal chemistry campaign. For the most part, finding these initial starting points occurs through screening of large, unbiased compound libraries. The size and nature of these libraries, coupled with the complexities of the bisubstrate utilizing histone methyltransferases, necessitates that the primary screen and subsequent hit triage be carefully considered.In this chapter, using EZH2 as a representative example, we describe a screening and hit triage campaign that identified validated chemical matter allowing initiation of medicinal chemistry studies. Moreover, we discuss a cell-based assay to support lead identification and optimization. The approach described here entailing a mixture of biochemical, biophysical and cell-based assays should be applicable to identifying validated starting points for other histone methyltransferases.
Collapse
Affiliation(s)
- Nico Cantone
- Constellation, A MorphoSys Company, Cambridge, MA, USA
| | | | | |
Collapse
|
9
|
Acedo JZ, Bothwell IR, An L, Trouth A, Frazier C, van der Donk WA. O-Methyltransferase-Mediated Incorporation of a β-Amino Acid in Lanthipeptides. J Am Chem Soc 2019; 141:16790-16801. [PMID: 31568727 DOI: 10.1021/jacs.9b07396] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lanthipeptides represent a large class of cyclic natural products defined by the presence of lanthionine (Lan) and methyllanthionine (MeLan) cross-links. With the advances in DNA sequencing technologies and genome mining tools, new biosynthetic enzymes capable of installing unusual structural features are continuously being discovered. In this study, we investigated an O-methyltransferase that is a member of the most prominent auxiliary enzyme family associated with class I lanthipeptide biosynthetic gene clusters. Despite the prevalence of these enzymes, their function has not been established. Herein, we demonstrate that the O-methyltransferase OlvSA encoded in the olv gene cluster from Streptomyces olivaceus NRRL B-3009 catalyzes the rearrangement of a highly conserved aspartate residue to a β-amino acid, isoaspartate, in the lanthipeptide OlvA(BCSA). We elucidated the NMR solution structure of the GluC-digested peptide, OlvA(BCSA)GluC, which revealed a unique ring topology comprising four interlocking rings and positions the isoaspartate residue in a solvent exposed loop that is stabilized by a MeLan ring. Gas chromatography-mass spectrometry analysis further indicated that OlvA(BCSA) contains two dl-MeLan rings and two Lan rings with an unusual ll-stereochemistry. Lastly, in vitro reconstitution of OlvSA activity showed that it is a leader peptide-independent and S-adenosyl methionine-dependent O-methyltransferase that mediates the conversion of a highly conserved aspartate residue in a cyclic substrate into a succinimide, which is hydrolyzed to generate an Asp or isoAsp containing peptide. This overall transformation converts an α-amino acid into a β-amino acid in a ribosomally synthesized peptide, via an electrophilic intermediate that may be the intended product.
Collapse
Affiliation(s)
- Jeella Z Acedo
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ian R Bothwell
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Linna An
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Abby Trouth
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Clara Frazier
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Wilfred A van der Donk
- Department of Chemistry and Howard Hughes Medical Institute , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| |
Collapse
|
10
|
Liu J, Murali T, Yu T, Liu C, Sivakumaran TA, Moseley HNB, Zhulin IB, Weiss HL, Durbin EB, Ellingson SR, Liu J, Huang B, Hallahan BJ, Horbinski CM, Hodges K, Napier DL, Bocklage T, Mueller J, Vanderford NL, Fardo DW, Wang C, Arnold SM. Characterization of Squamous Cell Lung Cancers from Appalachian Kentucky. Cancer Epidemiol Biomarkers Prev 2018; 28:348-356. [PMID: 30377206 DOI: 10.1158/1055-9965.epi-17-0984] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/08/2018] [Accepted: 10/25/2018] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Lung cancer is the leading cause of cancer mortality in the United States (U.S.). Squamous cell carcinoma (SQCC) represents 22.6% of all lung cancers nationally, and 26.4% in Appalachian Kentucky (AppKY), where death from lung cancer is exceptionally high. The Cancer Genome Atlas (TCGA) characterized genetic alterations in lung SQCC, but this cohort did not focus on AppKY residents. METHODS Whole-exome sequencing was performed on tumor and normal DNA samples from 51 lung SQCC subjects from AppKY. Somatic genomic alterations were compared between the AppKY and TCGA SQCC cohorts. RESULTS From this AppKY cohort, we identified an average of 237 nonsilent mutations per patient and, in comparison with TCGA, we found that PCMTD1 (18%) and IDH1 (12%) were more commonly altered in AppKY versus TCGA. Using IDH1 as a starting point, we identified a mutually exclusive mutational pattern (IDH1, KDM6A, KDM4E, JMJD1C) involving functionally related genes. We also found actionable mutations (10%) and/or intermediate or high-tumor mutation burden (65%), indicating potential therapeutic targets in 65% of subjects. CONCLUSIONS This study has identified an increased percentage of IDH1 and PCMTD1 mutations in SQCC arising in the AppKY residents versus TCGA, with population-specific implications for the personalized treatment of this disease. IMPACT Our study is the first report to characterize genomic alterations in lung SQCC from AppKY. These findings suggest population differences in the genetics of lung SQCC between AppKY and U.S. populations, highlighting the importance of the relevant population when developing personalized treatment approaches for this disease.
Collapse
Affiliation(s)
- Jinpeng Liu
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - Thilakam Murali
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky
| | - Tianxin Yu
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky
| | - Chunming Liu
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky
| | - Theru A Sivakumaran
- Department of Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, Arizona
| | - Hunter N B Moseley
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, Kentucky
| | - Igor B Zhulin
- Department of Microbiology, The Ohio State University, Columbus, Ohio.,Center for Bioinformatics, Pavlov First Saint Petersburg State Medical University, Saint Petersburg, Russia
| | - Heidi L Weiss
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - Eric B Durbin
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky.,Division of Biomedical Informatics, University of Kentucky, Lexington, Kentucky
| | - Sally R Ellingson
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky.,Division of Biomedical Informatics, University of Kentucky, Lexington, Kentucky
| | - Jinze Liu
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky.,Department of Computer Science, University of Kentucky, Lexington, Kentucky
| | - Bin Huang
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky.,Department of Biostatistics, University of Kentucky, Lexington, Kentucky
| | - Brent J Hallahan
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - Craig M Horbinski
- Department of Pathology and Neurosurgery, Northwestern University, Chicago, Illinois
| | - Kurt Hodges
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Dana L Napier
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - Thèrése Bocklage
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, Kentucky
| | - Joseph Mueller
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - Nathan L Vanderford
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, Kentucky
| | - David W Fardo
- Department of Biostatistics, University of Kentucky, Lexington, Kentucky
| | - Chi Wang
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. .,Department of Biostatistics, University of Kentucky, Lexington, Kentucky
| | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky. .,Department of Medicine, University of Kentucky, Lexington, Kentucky
| |
Collapse
|
11
|
Boehm D, Ott M. Host Methyltransferases and Demethylases: Potential New Epigenetic Targets for HIV Cure Strategies and Beyond. AIDS Res Hum Retroviruses 2017; 33:S8-S22. [PMID: 29140109 DOI: 10.1089/aid.2017.0180] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A successful HIV cure strategy may require reversing HIV latency to purge hidden viral reservoirs or enhancing HIV latency to permanently silence HIV transcription. Epigenetic modifying agents show promise as antilatency therapeutics in vitro and ex vivo, but also affect other steps in the viral life cycle. In this review, we summarize what we know about cellular DNA and protein methyltransferases (PMTs) as well as demethylases involved in HIV infection. We describe the biology and function of DNA methyltransferases, and their controversial role in HIV infection. We further explain the biology of PMTs and their effects on lysine and arginine methylation of histone and nonhistone proteins. We end with a focus on protein demethylases, their unique modes of action and their emerging influence on HIV infection. An outlook on the use of methylation-modifying agents in investigational HIV cure strategies is provided.
Collapse
Affiliation(s)
- Daniela Boehm
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California
- Department of Medicine, University of California, San Francisco, California
| |
Collapse
|
12
|
Tidwell TR, Søreide K, Hagland HR. Aging, Metabolism, and Cancer Development: from Peto's Paradox to the Warburg Effect. Aging Dis 2017; 8:662-676. [PMID: 28966808 PMCID: PMC5614328 DOI: 10.14336/ad.2017.0713] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 06/13/2017] [Indexed: 12/15/2022] Open
Abstract
Medical advances made over the last century have increased our lifespan, but age-related diseases are a fundamental health burden worldwide. Aging is therefore a major risk factor for cardiovascular disease, cancer, diabetes, obesity, and neurodegenerative diseases, all increasing in prevalence. However, huge inter-individual variations in aging and disease risk exist, which cannot be explained by chronological age, but rather physiological age decline initiated even at young age due to lifestyle. At the heart of this lies the metabolic system and how this is regulated in each individual. Metabolic turnover of food to energy leads to accumulation of co-factors, byproducts, and certain proteins, which all influence gene expression through epigenetic regulation. How these epigenetic markers accumulate over time is now being investigated as the possible link between aging and many diseases, such as cancer. The relationship between metabolism and cancer was described as early as the late 1950s by Dr. Otto Warburg, before the identification of DNA and much earlier than our knowledge of epigenetics. However, when the stepwise gene mutation theory of cancer was presented, Warburg's theories garnered little attention. Only in the last decade, with epigenetic discoveries, have Warburg's data on the metabolic shift in cancers been brought back to life. The stepwise gene mutation theory fails to explain why large animals with more cells, do not have a greater cancer incidence than humans, known as Peto's paradox. The resurgence of research into the Warburg effect has given us insight to what may explain Peto's paradox. In this review, we discuss these connections and how age-related changes in metabolism are tightly linked to cancer development, which is further affected by lifestyle choices modulating the risk of aging and cancer through epigenetic control.
Collapse
Affiliation(s)
- Tia R. Tidwell
- Department of Mathematics and Natural Sciences, Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
| | - Kjetil Søreide
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hanne R. Hagland
- Department of Mathematics and Natural Sciences, Centre for Organelle Research, University of Stavanger, Stavanger, Norway
- Gastrointestinal Translational Research Unit, Molecular Laboratory, Hillevaåg, Stavanger University Hospital, Stavanger, Norway
| |
Collapse
|
13
|
Andrews FH, Strahl BD, Kutateladze TG. Insights into newly discovered marks and readers of epigenetic information. Nat Chem Biol 2017; 12:662-8. [PMID: 27538025 DOI: 10.1038/nchembio.2149] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023]
Abstract
The field of chromatin biology has been advancing at an accelerated pace. Recent discoveries of previously uncharacterized sites and types of post-translational modifications (PTMs) and the identification of new sets of proteins responsible for the deposition, removal, and reading of these marks continue raising the complexity of an already exceedingly complicated biological phenomenon. In this Perspective article we examine the biological importance of new types and sites of histone PTMs and summarize the molecular mechanisms of chromatin engagement by newly discovered epigenetic readers. We also highlight the imperative role of structural insights in understanding PTM-reader interactions and discuss future directions to enhance the knowledge of PTM readout.
Collapse
Affiliation(s)
- Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, the University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
| |
Collapse
|
14
|
Janetzko J, Walker S. Aspartate Glycosylation Triggers Isomerization to Isoaspartate. J Am Chem Soc 2017; 139:3332-3335. [PMID: 28207246 DOI: 10.1021/jacs.6b12866] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
O-Linked β-N-acetylglucosamine transferase (OGT) is an essential human enzyme that glycosylates numerous nuclear and cytoplasmic proteins on serine and threonine. It also cleaves Host cell factor 1 (HCF-1) by a mechanism in which the first step involves glycosylation on glutamate. Replacing glutamate with aspartate in an HCF-1 proteolytic repeat was shown to prevent peptide backbone cleavage, but whether aspartate glycosylation occurred was not examined. We report here that OGT glycosylates aspartate much faster than it glycosylates glutamate in an otherwise identical model peptide substrate; moreover, once formed, the glycosyl aspartate reacts further to form a succinimide intermediate that hydrolyzes to produce the corresponding isoaspartyl peptide. Aspartate-to-isoaspartate isomerization in proteins occurs in cells but was previously thought to be exclusively non-enzymatic. Our findings suggest it may also be enzyme-catalyzed. In addition to OGT, enzymes that may catalyze aspartate to isoaspartate isomerization include PARPs, enzymes known to ribosylate aspartate residues in the process of poly(ADP-ribosyl)ation.
Collapse
Affiliation(s)
- John Janetzko
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States.,Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| |
Collapse
|
15
|
Unraveling proteome changes of Holstein beef M. semitendinosus and its relationship to meat discoloration during post-mortem storage analyzed by label-free mass spectrometry. J Proteomics 2017; 154:85-93. [DOI: 10.1016/j.jprot.2016.12.012] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/25/2016] [Accepted: 12/22/2016] [Indexed: 01/27/2023]
|
16
|
Ogasawara M, Otani M, Takano M, Shudou M, Inaba Y, Nirasawa S, Takahashi S, Kiyoi T, Tanaka Y, Kameda K, Kunugita N, Maeyama K, Sano K, Yamashita M, Yamauchi K. The protective role of protein L-isoaspartyl (D-aspartate) O-methyltransferase for maintenance of mitochondrial morphology in A549 cell. Exp Lung Res 2016; 42:245-62. [PMID: 27327778 DOI: 10.1080/01902148.2016.1197984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE The increasing amounts of evidence with abnormal aging process have been involved in the pathogenesis of chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Mice with deficient protein L-isoaspartate (D-aspartate) O-methyl transferase 1 (PCMT1) expression reveal acceleration of aging and result in the increased proportion of D-aspartate (D-Asp) residues and dysfunction in proteins. Furthermore, mitochondrial morphology and functions are associated with COPD and IPF pathogenesis. The purpose of the current study was to investigate the role of PCMT1 on mitochondrial morphology using A549 cells. MATERIALS AND METHODS We investigated PCMT1, prohibitin1 (PHB1), mitochondrial membrane proteins expression, mitochondrial morphology, and the proportion of D-Asp residues in PHB1 in A549 cells with (PCMT1-KD) and without the context of decreased PCMT1 expression (PCMT1-Cont) using electron microscopy, fluorescence staining, Western blot analysis, and the ATP content per cells. To investigate the effects of the PCMT1-KD cells, we developed double-transfected cell lines containing either the cytosolic or the endoplasmic isoform of PCMT1. RESULTS We found a significantly higher proportion of D-Asp residues in PHB1 in PCMT1-KD cells than that in PCMT1-Cont cells. The PCMT1-KD cells without cigarette smoke extract exposure were characterized by a significantly increased proportion of the D-Asp residues in PHB1, damaged mitochondrial ultrastructure, and a tendency toward the fission direction of the mitochondrial dynamics followed by a significant decrease in the cellular ATP content. CONCLUSIONS The increased proportion of the D-Asp residues may contribute to COPD pathogenesis, via irreversible protein conformational changes, followed by mitochondrial dysfunction.
Collapse
Affiliation(s)
- Masahito Ogasawara
- a Department of Pharmacology , Ehime University Graduate School of Medicine , Toon City , Japan
| | - Mieko Otani
- b Laboratory of Molecular Cell Biology , Department of Life Sciences Pharmacy , School of Pharmaceutical Sciences, Kobe Gakuin University , Chuo-ku, Kobe City , Japan
| | - Masaoki Takano
- b Laboratory of Molecular Cell Biology , Department of Life Sciences Pharmacy , School of Pharmaceutical Sciences, Kobe Gakuin University , Chuo-ku, Kobe City , Japan
| | - Masachika Shudou
- c Integrated Center for Science , Shigenobu Station, Ehime University Graduate School of Medicine , Toon City , Japan
| | - Yohei Inaba
- d Department of Environment Health , National Institute of Public Health , Minami, Wako City , Saitama , Japan
| | - Satoru Nirasawa
- e Biological Resources and Post-Harvest Division , Japan International Research Center for Agricultural Sciences , Tsukuba City , Ibaraki , Japan
| | - Saori Takahashi
- f Akita Research Institute of Food and Brewing , Akita City , Japan
| | - Takeshi Kiyoi
- c Integrated Center for Science , Shigenobu Station, Ehime University Graduate School of Medicine , Toon City , Japan
| | - Yuki Tanaka
- c Integrated Center for Science , Shigenobu Station, Ehime University Graduate School of Medicine , Toon City , Japan
| | - Kenji Kameda
- c Integrated Center for Science , Shigenobu Station, Ehime University Graduate School of Medicine , Toon City , Japan
| | - Naoki Kunugita
- d Department of Environment Health , National Institute of Public Health , Minami, Wako City , Saitama , Japan
| | - Kazutaka Maeyama
- a Department of Pharmacology , Ehime University Graduate School of Medicine , Toon City , Japan
| | - Keiji Sano
- b Laboratory of Molecular Cell Biology , Department of Life Sciences Pharmacy , School of Pharmaceutical Sciences, Kobe Gakuin University , Chuo-ku, Kobe City , Japan
| | - Masahiro Yamashita
- g Department of Respiratory Medicine , Iwate Medical University School of Medicine , Morioka City , Japan
| | - Kohei Yamauchi
- g Department of Respiratory Medicine , Iwate Medical University School of Medicine , Morioka City , Japan
| |
Collapse
|
17
|
|
18
|
Joshi AD, Mustafa MG, Lichti CF, Elferink CJ. Homocitrullination Is a Novel Histone H1 Epigenetic Mark Dependent on Aryl Hydrocarbon Receptor Recruitment of Carbamoyl Phosphate Synthase 1. J Biol Chem 2015; 290:27767-78. [PMID: 26424795 DOI: 10.1074/jbc.m115.678144] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Indexed: 11/06/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR), a regulator of xenobiotic toxicity, is a member of the eukaryotic Per-Arnt-Sim domain protein family of transcription factors. Recent evidence identified a novel AhR DNA recognition sequence called the nonconsensus xenobiotic response element (NC-XRE). AhR binding to the NC-XRE in response to activation by the canonical ligand 2,3,7,8-tetrachlorodibenzo-p-dioxin resulted in concomitant recruitment of carbamoyl phosphate synthase 1 (CPS1) to the NC-XRE. Studies presented here demonstrate that CPS1 is a bona fide nuclear protein involved in homocitrullination (hcit), including a key lysine residue on histone H1 (H1K34hcit). H1K34hcit represents a hitherto unknown epigenetic mark implicated in enhanced gene expression of the peptidylarginine deiminase 2 gene, itself a chromatin-modifying protein. Collectively, our data suggest that AhR activation promotes CPS1 recruitment to DNA enhancer sites in the genome, resulting in a specific enzyme-independent post-translational modification of the linker histone H1 protein (H1K34hcit), pivotal in altering local chromatin structure and transcriptional activation.
Collapse
Affiliation(s)
- Aditya D Joshi
- From the Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555 and
| | | | - Cheryl F Lichti
- From the Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555 and
| | - Cornelis J Elferink
- From the Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas 77555 and
| |
Collapse
|
19
|
Analysis of differentially expressed novel post-translational modifications of plasma apolipoprotein E in Taiwanese females with breast cancer. J Proteomics 2015; 126:252-62. [PMID: 26079612 DOI: 10.1016/j.jprot.2015.05.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 05/07/2015] [Accepted: 05/24/2015] [Indexed: 12/22/2022]
Abstract
APOE ε2 or ε4 alleles being used as indicators of breast cancer risk are controversial in Taiwanese females. We provide a concept for relative comparisons of post-translational modifications (PTMs) of plasma apolipoprotein E (ApoE) between normal controls and breast cancer patients to investigate the association of ApoE with breast cancer risk. APOE polymorphisms (ApoE isoforms) were not assessed in this study. The relative modification ratio (%) of 15 targeted and 21 modified peptides were evaluated by 1D SDS-PAGE, in-gel digestion, and label-free nano-LC/MS to compare normal controls with breast cancer patients. Plasma levels of the ApoE protein did not significantly differ between normal controls and breast cancer patients. Eleven sites with novel PTMs were identified from 7 pairs of differentially expressed targeted and modified peptides according to the relative modification ratio including methylation at the E3 (↑1.45-fold), E7 (↑1.45-fold), E11 (↑1.19-fold), E77 (↑2.02-fold), E87 (↑2.02-fold), and Q98 (↑1.62-fold) residues; dimethylation at the Q187 (↑1.44-fold) residue; dihydroxylation at the R92 (↑1.25-fold), K95 (↑1.25-fold), and R103 (↑1.25-fold) residues; and glycosylation at the S129 (↑1.14-fold) residue. The clustered methylation and dihydroxylation of plasma ApoE proteins may play a role in breast cancer.
Collapse
|