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Hao B, Chen K, Zhai L, Liu M, Liu B, Tan M. Substrate and Functional Diversity of Protein Lysine Post-translational Modifications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae019. [PMID: 38862432 DOI: 10.1093/gpbjnl/qzae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/11/2023] [Accepted: 01/08/2024] [Indexed: 06/13/2024]
Abstract
Lysine post-translational modifications (PTMs) are widespread and versatile protein PTMs that are involved in diverse biological processes by regulating the fundamental functions of histone and non-histone proteins. Dysregulation of lysine PTMs is implicated in many diseases, and targeting lysine PTM regulatory factors, including writers, erasers, and readers, has become an effective strategy for disease therapy. The continuing development of mass spectrometry (MS) technologies coupled with antibody-based affinity enrichment technologies greatly promotes the discovery and decoding of PTMs. The global characterization of lysine PTMs is crucial for deciphering the regulatory networks, molecular functions, and mechanisms of action of lysine PTMs. In this review, we focus on lysine PTMs, and provide a summary of the regulatory enzymes of diverse lysine PTMs and the proteomics advances in lysine PTMs by MS technologies. We also discuss the types and biological functions of lysine PTM crosstalks on histone and non-histone proteins and current druggable targets of lysine PTM regulatory factors for disease therapy.
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Affiliation(s)
- Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Institute of Advanced Biomedical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kaifeng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Linhui Zhai
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, China
| | - Muyin Liu
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Bin Liu
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
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Sadri M, Wang H, Kuroishi T, Li Y, Zempleni J. Holocarboxylase synthetase knockout is embryonic lethal in mice. PLoS One 2022; 17:e0265539. [PMID: 35385533 PMCID: PMC8985998 DOI: 10.1371/journal.pone.0265539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/03/2022] [Indexed: 11/19/2022] Open
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the biotinylation of five distinct biotin-dependent carboxylases and perhaps chromatin proteins. HLCS deficiency causes multiple carboxylase deficiency which results in fatal consequences unless patients are diagnosed early and treated with pharmacological doses of biotin. The objective of this study was to develop an HLCS conditional knockout (KO) mouse and assess effects of HLCS knockout on embryo survival. In the mouse, exon 8 is flanked by LoxP sites, thereby removing a catalytically important region upon recombination by Cre. HLCS conditional KO mice were backcrossed for 14 generations with C57BL/6J mice to yield Hlcstm1Jze. Fertility and weight gain were normal and no frank disease phenotypes and abnormal feeding behavior were observed in the absence of Cre. HLCS knockout was embryonic lethal when dams homozygous for both the floxed Hlcs gene and tamoxifen-inducible Cre recombinase (denoted Hlcstm1.1Jze) were injected with tamoxifen on gestational days 2.5 and 10.5. This is the first report of an HLCS conditional KO mouse, which enables studies of the roles of HLCS and biotin in intermediary metabolism.
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Affiliation(s)
- Mahrou Sadri
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Haichuan Wang
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Toshinobu Kuroishi
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Yong Li
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
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Salazar-Anzures T, Pastén-Hidalgo K, Sicilia-Argumedo G, Riverón-Negrete L, Hernández-Vázquez ADJ, Fernanadez-Mejia C. Dietary biotin supplementation increases proliferation pathways in mice testes without affecting serum follicle-stimulating hormone levels and stem cell factor expression. Toxicol Appl Pharmacol 2021; 433:115774. [PMID: 34699867 DOI: 10.1016/j.taap.2021.115774] [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: 05/17/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 11/18/2022]
Abstract
Supplements containing pharmacological concentrations of biotin are commercially available. The mechanisms by which biotin at pharmacological concentrations exerts its action have been the subject of multiple investigations, particularly for biotin's medicinal potential and wide use for cosmetic purposes. Several studies have reported that biotin supplementation increases cell proliferation; however, the mechanisms involved in this effect have not yet been characterized. In a previous study, we found that a biotin-supplemented diet increased spermatogonia proliferation. The present study was focused on investigating the molecular mechanisms involved in biotin-induced testis cell proliferation. Male BALB/cAnNHsd mice were fed a control or a biotin-supplemented diet (1.76 or 97.7 mg biotin/kg diet) for eight weeks. Compared with the control group, the biotin-supplemented mice presented augmented protein abundance of the c-kit-receptor and pERK1/2Tyr204 and pAKTSer473, the active forms of ERK/AKT proliferation signaling pathways. No changes were observed in the testis expression of the stem cell factor and in the serum levels of the follicle-stimulating hormone. Analysis of mRNA abundance found an increase in cyclins Ccnd3, Ccne1, Ccna2; Kinases Cdk4, Cdk2; and E2F; and Sp1 & Sp3 transcription factors. Decreased expression of cyclin-dependent kinase inhibitor 1a (p21) was observed but not of Cdkn2a inhibitor (p16). The results of the present study identifies, for the first time, the mechanisms associated with biotin supplementation-induced cell proliferation, which raises concerns about the effects of biotin on male reproductive health because of its capacity to cause hyperplasia, especially because this vitamin is available in large amounts without regulation.
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Affiliation(s)
- Tonatiuh Salazar-Anzures
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Pediatría, Avenida del Iman#1, 4th floor, Mexico City 04500, Mexico
| | - Karina Pastén-Hidalgo
- Cátedra CONACYT, Instituto Nacional de Pediatría, Avenida del Iman#1, 4th floor, Mexico City 04500, Mexico
| | - Gloria Sicilia-Argumedo
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Pediatría, Avenida del Iman#1, 4th floor, Mexico City 04500, Mexico
| | - Leticia Riverón-Negrete
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Pediatría, Avenida del Iman#1, 4th floor, Mexico City 04500, Mexico
| | - Alain de Jesús Hernández-Vázquez
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Pediatría, Avenida del Iman#1, 4th floor, Mexico City 04500, Mexico
| | - Cristina Fernanadez-Mejia
- Unidad de Genética de la Nutrición, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México/Instituto Nacional de Pediatría, Avenida del Iman#1, 4th floor, Mexico City 04500, Mexico.
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Biotin rescues mitochondrial dysfunction and neurotoxicity in a tauopathy model. Proc Natl Acad Sci U S A 2020; 117:33608-33618. [PMID: 33318181 DOI: 10.1073/pnas.1922392117] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Mitochondrial and metabolic dysfunction are often implicated in neurological disease, but effective mechanism-based therapies remain elusive. We performed a genome-scale forward genetic screen in a Drosophila model of tauopathy, a class of neurodegenerative disorders characterized by the accumulation of the protein tau, and identified manipulation of the B-vitamin biotin as a potential therapeutic approach in tauopathy. We show that tau transgenic flies have an innate biotin deficiency due to tau-mediated relaxation of chromatin and consequent aberrant expression of multiple biotin-related genes, disrupting both carboxylase and mitochondrial function. Biotin depletion alone causes mitochondrial pathology and neurodegeneration in both flies and human neurons, implicating mitochondrial dysfunction as a mechanism in biotin deficiency. Finally, carboxylase biotin levels are reduced in mammalian tauopathies, including brains of human Alzheimer's disease patients. These results provide insight into pathogenic mechanisms of human biotin deficiency, the resulting effects on neuronal health, and a potential therapeutic pathway in the treatment of tau-mediated neurotoxicity.
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Epigenetic modifications of gene expression by lifestyle and environment. Arch Pharm Res 2017; 40:1219-1237. [PMID: 29043603 DOI: 10.1007/s12272-017-0973-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/12/2017] [Indexed: 12/21/2022]
Abstract
Epigenetics oftenly described as the heritable changes in gene expression independent of changes in DNA sequence. Various environmental factors such as nutrition-dietary components, lifestyle, exercise, physical activity, toxins, and other contributing factors remodel the genome either in a constructive or detrimental way. Since epigenetic changes are reversible and nutrition is one of the many epigenetic regulators that modify gene expression without changing the DNA sequence, dietary nutrients and bioactive food components contribute to epigenetic phenomena either by directly suppressing DNA methylation or histone catalyzing enzymes or by changing the availability of substrates required for enzymatic reactions. Diets that contain catechol-dominant polyphenols are reported to suppress enzyme activity and activate epigenetically silenced genes. Furthermore, several dietary nutrients play a crucial role in one-carbon metabolism including folate, cobalamin, riboflavin, pyridoxine, and methionine by directly affecting S-adenosyl-L-methionine. Soy polyphenols block DNA methyltransferases and histone deacetylases to reverse aberrant CpG island methylation. Organosulfur rich compounds such as the sulforaphane found in broccoli appear to normalize DNA methylation and activate miR-140 expression, which represses SOX9 and ALDH1 and decreases tumor growth. The purpose of this short communication is to overview the epigenetic regulatory mechanisms of diet and other environmental factors. We discuss the epigenetic contributions of dietary components with a particular focus on nutritional polyphenols and flavonoids as epigenetic mediators that modify epigenetic tags and control gene expression. These mechanisms provide new insights to better understand the influence of dietary nutrients on epigenetic modifications and gene expression.
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León-Del-Río A, Valadez-Graham V, Gravel RA. Holocarboxylase Synthetase: A Moonlighting Transcriptional Coregulator of Gene Expression and a Cytosolic Regulator of Biotin Utilization. Annu Rev Nutr 2017; 37:207-223. [DOI: 10.1146/annurev-nutr-042617-104653] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alfonso León-Del-Río
- Programa de Investigación de Cáncer de Mama y Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de Mexico 04500, México
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62250, México
| | - Roy A. Gravel
- Department of Biochemistry & Molecular Biology, the University of Calgary and the Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, Alberta T2N 4N1, Canada
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Mock DM. Biotin: From Nutrition to Therapeutics. J Nutr 2017; 147:1487-1492. [PMID: 28701385 PMCID: PMC5525106 DOI: 10.3945/jn.116.238956] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/01/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022] Open
Abstract
Although frank symptomatic biotin deficiency is rare, some evidence suggests that marginal biotin deficiency occurs spontaneously in a substantial proportion of women during normal human pregnancy and might confer an increased risk of birth defects. Herein I review 1) advances in assessing biotin status, including the relation between acylcarnitine excretion and biotin status; 2) recent studies of biotin status in pregnancy; 3) advances in understanding the role of biotin in gene expression and the potential roles of biotinylated proteins that are neither histones nor carboxylases; and 4) novel large-dose biotin supplementation as therapy for multiple sclerosis. The review concludes with a summary of recent studies that have reported potentially dangerous erroneous results in individuals consuming large amounts of biotin for measurements of various plasma hormones for common clinical assays that use streptavidin-biotin technology.
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Affiliation(s)
- Donald M Mock
- University of Arkansas for Medical Sciences, Departments of Biochemistry and Molecular Biology and Pediatrics, Little Rock, AR
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Brewster RC, Gavins GC, Günthardt B, Farr S, Webb KM, Voigt P, Hulme AN. Chloromethyl-triazole: a new motif for site-selective pseudo-acylation of proteins. Chem Commun (Camb) 2016; 52:12230-12232. [PMID: 27722332 PMCID: PMC5656099 DOI: 10.1039/c6cc06801d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 09/13/2016] [Indexed: 11/21/2022]
Abstract
Rapid, site-selective modification of cysteine residues with chloromethyl-triazole derivatives generates pseudo-acyl sLys motifs, mimicking important post-translational modifications. Near-native biotinylation of peptide and protein substrates is shown to be site-selective and modified histone H4 retains functional activity.
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Affiliation(s)
- Richard C Brewster
- EaSTCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.
| | - Georgina C Gavins
- EaSTCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.
| | - Barbara Günthardt
- EaSTCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.
| | - Sarah Farr
- EaSTCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.
| | - Kimberly M Webb
- The Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Philipp Voigt
- The Wellcome Trust Centre for Cell Biology, The University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Alison N Hulme
- EaSTCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, UK.
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Sedel F, Bernard D, Mock DM, Tourbah A. Targeting demyelination and virtual hypoxia with high-dose biotin as a treatment for progressive multiple sclerosis. Neuropharmacology 2015; 110:644-653. [PMID: 26327679 DOI: 10.1016/j.neuropharm.2015.08.028] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/24/2015] [Accepted: 08/18/2015] [Indexed: 12/30/2022]
Abstract
Progressive multiple sclerosis (MS) is a severely disabling neurological condition, and an effective treatment is urgently needed. Recently, high-dose biotin has emerged as a promising therapy for affected individuals. Initial clinical data have shown that daily doses of biotin of up to 300 mg can improve objective measures of MS-related disability. In this article, we review the biology of biotin and explore the properties of this ubiquitous coenzyme that may explain the encouraging responses seen in patients with progressive MS. The gradual worsening of neurological disability in patients with progressive MS is caused by progressive axonal loss or damage. The triggers for axonal loss in MS likely include both inflammatory demyelination of the myelin sheath and primary neurodegeneration caused by a state of virtual hypoxia within the neuron. Accordingly, targeting both these pathological processes could be effective in the treatment of progressive MS. Biotin is an essential co-factor for five carboxylases involved in fatty acid synthesis and energy production. We hypothesize that high-dose biotin is exerting a therapeutic effect in patients with progressive MS through two different and complementary mechanisms: by promoting axonal remyelination by enhancing myelin production and by reducing axonal hypoxia through enhanced energy production. This article is part of the Special Issue entitled 'Oligodendrocytes in Health and Disease'.
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Affiliation(s)
- Frédéric Sedel
- MedDay Pharmaceuticals, ICM-Brain and Spine Institute-IPEPs, Groupe Hospitalier Pitié Salpêtrière, 47 Boulevard de l'Hopital, 75013 Paris, France.
| | - Delphine Bernard
- MedDay Pharmaceuticals, ICM-Brain and Spine Institute-IPEPs, Groupe Hospitalier Pitié Salpêtrière, 47 Boulevard de l'Hopital, 75013 Paris, France.
| | - Donald M Mock
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, 4301 W Markham Street, Little Rock, AR 72205, USA.
| | - Ayman Tourbah
- Department of Neurology and Faculté de Médecine de Reims, CHU de Reims, URCA, 45 Rue Cognacq Jay, 51092 Reims Cedex, France.
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Perry CA, West AA, Gayle A, Lucas LK, Yan J, Jiang X, Malysheva O, Caudill MA. Pregnancy and lactation alter biomarkers of biotin metabolism in women consuming a controlled diet. J Nutr 2014; 144:1977-84. [PMID: 25122647 PMCID: PMC4230210 DOI: 10.3945/jn.114.194472] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Biotin functions as a cofactor for several carboxylase enzymes with key roles in metabolism. At present, the dietary requirement for biotin is unknown and intake recommendations are provided as Adequate Intakes (AIs). The biotin AI for adults and pregnant women is 30 μg/d, whereas 35 μg/d is recommended for lactating women. However, pregnant and lactating women may require more biotin to meet the demands of these reproductive states. OBJECTIVE The current study sought to quantify the impact of reproductive state on biotin status response to a known dietary intake of biotin. METHODS To achieve this aim, we measured a panel of biotin biomarkers among pregnant (gestational week 27 at study entry; n = 26), lactating (postnatal week 5 at study entry; n = 28), and control (n = 21) women who participated in a 10- to 12-wk feeding study providing 57 μg of dietary biotin/d as part of a mixed diet. RESULTS Over the course of the study, pregnant women excreted 69% more (vs. control; P < 0.001) 3-hydroxyisovaleric acid (3-HIA), a metabolite that accumulates during the catabolism of leucine when the activity of biotin-dependent methylcrotonyl-coenzyme A carboxylase is impaired. Interestingly, urinary excretion of 3-hydroxyisovaleryl-carnitine (3-HIA-carnitine), a downstream metabolite of 3-HIA, was 27% lower (P = 0.05) among pregnant (vs. control) women, a finding that may arise from carnitine inadequacy during gestation. No differences (P > 0.05) were detected in plasma biotin, urinary biotin, or urinary bisnorbiotin between pregnant and control women. Lactating women excreted 76% more (vs. control; P = 0.001) of the biotin catabolite bisnorbiotin, indicating that lactation accelerates biotin turnover and loss. Notably, with respect to control women, lactating women excreted 23% less (P = 0.04) urinary 3-HIA and 26% less (P = 0.05) urinary 3-HIA-carnitine, suggesting that lactation reduces leucine catabolism and that these metabolites may not be useful indicators of biotin status during lactation. CONCLUSIONS Overall, these data demonstrate significant alterations in markers of biotin metabolism during pregnancy and lactation and suggest that biotin intakes exceeding current recommendations are needed to meet the demands of these reproductive states. This trial was registered at clinicaltrials.gov as NCT01127022.
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Affiliation(s)
- Cydne A Perry
- Shepherd University, Shepherdstown, WV; and,Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Allyson A West
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Antoinette Gayle
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Lauren K Lucas
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Jian Yan
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Xinyin Jiang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Olga Malysheva
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
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Zempleni J, Liu D, Camara DT, Cordonier EL. Novel roles of holocarboxylase synthetase in gene regulation and intermediary metabolism. Nutr Rev 2014; 72:369-76. [PMID: 24684412 DOI: 10.1111/nure.12103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The role of holocarboxylase synthetase (HLCS) in catalyzing the covalent binding of biotin to the five biotin-dependent carboxylases in humans is well established, as are the essential roles of these carboxylases in the metabolism of fatty acids, the catabolism of leucine, and gluconeogenesis. This review examines recent discoveries regarding the roles of HLCS in assembling a multiprotein gene repression complex in chromatin. In addition, emerging evidence suggests that the number of biotinylated proteins is far larger than previously assumed and includes members of the heat-shock superfamily of proteins and proteins coded by the ENO1 gene. Evidence is presented linking biotinylation of heat-shock proteins HSP60 and HSP72 with redox biology and immune function, respectively, and biotinylation of the two ENO1 gene products MBP-1 and ENO1 with tumor suppression and glycolysis, respectively.
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Affiliation(s)
- Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Gravel RA. Holocarboxylase synthetase: a multitalented protein with roles in biotin transfer, gene regulation and chromatin dynamics. Mol Genet Metab 2014; 111:305-306. [PMID: 24361214 DOI: 10.1016/j.ymgme.2013.11.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 11/16/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Roy A Gravel
- Departments of Biochemistry & Molecular Biology and of Medical Genetics and the Alberta Children's Hospital Research Institute for Child and Maternal Health, Faculties of Medicine and Kinesiology, University of Calgary, Room 250 Heritage Medical Research Building, 3330 Hospital Drive N.W., Calgary, Alberta, Canada T3H-1C1.
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Trujillo-Gonzalez I, Cervantes-Roldan R, Gonzalez-Noriega A, Michalak C, Reyes-Carmona S, Barrios-Garcia T, Meneses-Morales I, Leon-Del-Rio A. Holocarboxylase synthetase acts as a biotin-independent transcriptional repressor interacting with HDAC1, HDAC2 and HDAC7. Mol Genet Metab 2014; 111:321-330. [PMID: 24239178 DOI: 10.1016/j.ymgme.2013.10.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 10/25/2013] [Accepted: 10/25/2013] [Indexed: 10/26/2022]
Abstract
In human cells, HCS catalyzes the biotinylation of biotin-dependent carboxylases and mediates the transcriptional control of genes involved in biotin metabolism through the activation of a cGMP-dependent signal transduction pathway. HCS also targets to the cell nucleus in association with lamin-B suggesting additional gene regulatory functions. Studies from our laboratory in Drosophila melanogaster showed that nuclear HCS is associated with heterochromatin bands enriched with the transcriptionally repressive mark histone 3 trimethylated at lysine 9. Further, HCS was shown to be recruited to the core promoter of the transcriptionally inactive hsp70 gene suggesting that it may participate in the repression of gene expression, although the mechanism involved remained elusive. In this work, we expressed HCS as a fusion protein with the DNA-binding domain of GAL4 to evaluate its effect on the transcription of a luciferase reporter gene. We show that HCS possesses transcriptional repressor activity in HepG2 cells. The transcriptional function of HCS was shown by in vitro pull down and in vivo co-immunoprecipitation assays to depend on its interaction with the histone deacetylases HDAC1, HDAC2 and HDAC7. We show further that HCS interaction with HDACs and its function in transcriptional repression is not affected by mutations impairing its biotin-ligase activity. We propose that nuclear HCS mediates events of transcriptional repression through a biotin-independent mechanism that involves its interaction with chromatin-modifying protein complexes that include histone deacetylases.
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Affiliation(s)
- Isis Trujillo-Gonzalez
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | - Rafael Cervantes-Roldan
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | - Alfonso Gonzalez-Noriega
- Departamento de Biología Celular, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | - Colette Michalak
- Departamento de Biología Celular, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | - Sandra Reyes-Carmona
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | - Tonatiuh Barrios-Garcia
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | - Ivan Meneses-Morales
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico
| | - Alfonso Leon-Del-Rio
- Programa de Investigación de Cáncer de Mama, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México D.F. 04510, Mexico.
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14
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Hasim S, Tati S, Madayiputhiya N, Nandakumar R, Nickerson KW. Histone biotinylation inCandida albicans. FEMS Yeast Res 2013; 13:529-39. [DOI: 10.1111/1567-1364.12056] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 05/16/2013] [Accepted: 05/16/2013] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sahar Hasim
- School of Biological Sciences; University of Nebraska; Lincoln; NE; USA
| | - Swetha Tati
- School of Biological Sciences; University of Nebraska; Lincoln; NE; USA
| | | | - Renu Nandakumar
- Department of Biochemistry; Redox Biology Center; University of Nebraska; Lincoln; NE; USA
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15
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Chen X, Chou HH, Wurtele ES. Holocarboxylase synthetase 1 physically interacts with histone h3 in Arabidopsis. SCIENTIFICA 2013; 2013:983501. [PMID: 24278788 PMCID: PMC3820309 DOI: 10.1155/2013/983501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 12/30/2012] [Indexed: 05/22/2023]
Abstract
Biotin is a water-soluble vitamin required by all organisms, but only synthesized by plants and some bacterial and fungal species. As a cofactor, biotin is responsible for carbon dioxide transfer in all biotin-dependent carboxylases, including acetyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, and pyruvate carboxylase. Adding biotin to carboxylases is catalyzed by the enzyme holocarboxylase synthetase (HCS). Biotin is also involved in gene regulation, and there is some indication that histones can be biotinylated in humans. Histone proteins and most histone modifications are highly conserved among eukaryotes. HCS1 is the only functional biotin ligase in Arabidopsis and has a high homology with human HCS. Therefore, we hypothesized that HCS1 also biotinylates histone proteins in Arabidopsis. A comparison of the catalytic domain of HCS proteins was performed among eukaryotes, prokaryotes, and archaea, and this domain is highly conserved across the selected organisms. Biotinylated histones could not be identified in vivo by using avidin precipitation or two-dimensional gel analysis. However, HCS1 physically interacts with Arabidopsis histone H3 in vitro, indicating the possibility of the role of this enzyme in the regulation of gene expression.
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Affiliation(s)
- Xi Chen
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Hui-Hsien Chou
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- Department of Computer Science, Iowa State University, Ames, IA 50011, USA
| | - Eve Syrkin Wurtele
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- *Eve Syrkin Wurtele:
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16
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Biotinylation of lysine 16 in histone H4 contributes toward nucleosome condensation. Arch Biochem Biophys 2012; 529:105-11. [PMID: 23219734 DOI: 10.1016/j.abb.2012.11.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Revised: 11/07/2012] [Accepted: 11/08/2012] [Indexed: 02/02/2023]
Abstract
Holocarboxylase synthetase (HLCS) is part of a multiprotein gene repression complex and catalyzes the covalent binding of biotin to lysines (K) in histones H3 and H4, thereby creating rare gene repression marks such as K16-biotinylated histone H4 (H4K16bio). We tested the hypothesis that H4K16bio contributes toward nucleosome condensation and gene repression by HLCS. We used recombinant histone H4 in which K16 was mutated to a cysteine (H4K16C) for subsequent chemical biotinylation of the sulfhydryl group to create H4K16Cbio. Nucleosomes were assembled by using H4K16Cbio and the 'Widom 601' nucleosomal DNA position sequence; biotin-free histone H4 and H4K16C were used as controls. Nucleosomal compaction was analyzed using atomic force microscopy (AFM). The length of DNA per nucleosome was ∼30% greater in H4K16Cbio-containing histone octamers (61.14±10.92nm) compared with native H4 (46.89±12.6nm) and H4K16C (47.26±10.32nm), suggesting biotin-dependent chromatin condensation (P<0.001). Likewise, the number of DNA turns around histone core octamers was ∼17.2% greater in in H4K16Cbio-containing octamers (1.78±0.16) compared with native H4 (1.52±0.21) and H4K16C (1.52±0.17), judged by the rotation angle (P<0.001; N=150). We conclude that biotinylation of K16 in histone H4 contributes toward chromatin condensation.
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17
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Rios-Avila L, Pestinger V, Zempleni J. K16-biotinylated histone H4 is overrepresented in repeat regions and participates in the repression of transcriptionally competent genes in human Jurkat lymphoid cells. J Nutr Biochem 2011; 23:1559-64. [PMID: 22192339 DOI: 10.1016/j.jnutbio.2011.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 12/11/2022]
Abstract
Holocarboxylase synthetase (HCS) catalyzes the binding of biotin to lysine (K) residues in histones H3 and H4. Histone biotinylation marks are enriched in repressed loci, including retrotransposons. Preliminary studies suggested that K16 in histone H4 is a target for biotinylation by HCS. Here we tested the hypotheses that H4K16bio is a real histone mark in human chromatin and that H4K16bio is overrepresented in repressed gene loci and repeat regions. Polyclonal rabbit anti-human H4K16bio was generated and affinity purified. An extensive series of testing with synthetic and natural targets confirmed that this new antibody is specific for H4K16bio. Using anti-H4K16bio and chromatin immunoprecipitation assays, we demonstrated that H4K16bio is overrepresented in repeat regions [pericentromeric alpha satellite repeats and long terminal repeats (LTR)] compared with euchromatin promoters. H4K16bio was also enriched in the repressed interleukin-2 gene promoter in human lymphoid cells; transcriptional activation of the interleukin-2 gene by mitogens and phorbol esters coincided with a depletion of the H4K16bio mark at the gene promoter. The enrichment of H4K16bio depended on biotin supply; the enrichment at LTR22 and promoter 1 of the sodium-dependent multivitamin transporter (SMVT) was greater in biotin-supplemented cells compared with biotin-normal and biotin-deficient cells. The enrichment of H4K16bio at LTR15 and SMVT promoter 1 was significantly lower in fibroblasts from an HCS-deficient patient compared with an HCS wild-type control. We conclude that H4K16bio is a real phenomenon and that this mark, like other biotinylation marks, is overrepresented in repressed loci where it marks HCS docking sites.
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Affiliation(s)
- Luisa Rios-Avila
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583-0806, USA
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18
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Kuroishi T, Rios-Avila L, Pestinger V, Wijeratne SSK, Zempleni J. Biotinylation is a natural, albeit rare, modification of human histones. Mol Genet Metab 2011; 104:537-45. [PMID: 21930408 PMCID: PMC3224183 DOI: 10.1016/j.ymgme.2011.08.030] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 08/29/2011] [Accepted: 08/30/2011] [Indexed: 01/08/2023]
Abstract
Previous studies suggest that histones H3 and H4 are posttranslationally modified by binding of the vitamin biotin, catalyzed by holocarboxylase synthetase (HCS). Albeit a rare epigenetic mark, biotinylated histones were repeatedly shown to be enriched in repeat regions and repressed loci, participating in the maintenance of genome stability and gene regulation. Recently, a team of investigators failed to detect biotinylated histones and proposed that biotinylation is not a natural modification of histones, but rather an assay artifact. Here, we describe the results of experiments, including the comparison of various analytical protocols, antibodies, cell lines, classes of histones, and radiotracers. These studies provide unambiguous evidence that biotinylation is a natural, albeit rare, histone modification. Less than 0.001% of human histones H3 and H4 are biotinylated, raising concerns that the abundance might too low to elicit biological effects in vivo. We integrated information from this study, previous studies, and ongoing research efforts to present a new working model in which biological effects are caused by a role of HCS in multiprotein complexes in chromatin. In this model, docking of HCS in chromatin causes the occasional binding of biotin to histones as a tracer for HCS binding sites.
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19
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Bao B, Rodriguez-Melendez R, Zempleni J. Cytosine methylation in miR-153 gene promoters increases the expression of holocarboxylase synthetase, thereby increasing the abundance of histone H4 biotinylation marks in HEK-293 human kidney cells. J Nutr Biochem 2011; 23:635-9. [PMID: 21764280 DOI: 10.1016/j.jnutbio.2011.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 02/27/2011] [Accepted: 03/08/2011] [Indexed: 12/11/2022]
Abstract
Holocarboxylase synthetase (HCS) plays an essential role in catalyzing the biotinylation of carboxylases and histones. Biotinylated carboxylases are important for the metabolism of glucose, lipids and leucine; biotinylation of histones plays important roles in gene regulation and genome stability. Recently, we reported that HCS activity is partly regulated by subcellular translocation events and by miR-539. Here we tested the hypothesis that the HCS 3'-untranslated region (3'-UTR) contains binding sites for miR other than miR-539. A binding site for miR-153 was predicted to reside in the HCS 3'-UTR by using in silico analyses. When miR-153 site was overexpressed in transgenic HEK-293 human embryonic kidney cells, the abundance of HCS mRNA decreased by 77% compared with controls. In silico analyses also predicted three putative cytosine methylation sites in two miR-153 genes; the existence of these sites was confirmed by methylation-sensitive polymerase chain reaction. When cytosines were demethylated by treatment with 5-aza-2'-deoxycytidine, the abundance of miR-153 increased by more than 25 times compared with untreated controls, and this increase coincided with low levels of HCS and histone biotinylation. Together, this study provides novel insights into the mechanisms of novel epigenetic synergies among folate-dependent methylation events, miR and histone biotinylation.
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Affiliation(s)
- Baolong Bao
- Department of Nutrition and Health Sciences, University of Nebraska at Lincoln, Lincoln, NE 68583, USA
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20
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Zempleni J, Li Y, Xue J, Cordonier EL. The role of holocarboxylase synthetase in genome stability is mediated partly by epigenomic synergies between methylation and biotinylation events. Epigenetics 2011; 6:892-4. [PMID: 21555910 DOI: 10.4161/epi.6.7.15544] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Holocarboxylase synthetase (HLCS) catalyzes the covalent binding of biotin to histones. Biotinylated histones are gene repression marks and are particularly enriched in long terminal repeats, telomeres, and other repeat regions. The effects of HLCS in gene regulation are mediated by its physical interactions with chromatin proteins such as histone H3, DNMT1, MeCP2, and EHMT-1. It appears that histone biotinylation depends on prior methylation of cytosines. De-repression of long terminal repeats in biotin- or HLCS-deficient cell cultures and organisms is associated with genome instability.
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Affiliation(s)
- Janos Zempleni
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA.
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21
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Reyes-Carmona S, Valadéz-Graham V, Aguilar-Fuentes J, Zurita M, León-Del-Río A. Trafficking and chromatin dynamics of holocarboxylase synthetase during development of Drosophila melanogaster. Mol Genet Metab 2011; 103:240-8. [PMID: 21463962 DOI: 10.1016/j.ymgme.2011.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 03/05/2011] [Accepted: 03/05/2011] [Indexed: 11/26/2022]
Abstract
This work examines the cellular localization of holocarboxylase synthetase (HCS) and its association to chromatin during different stages of development of Drosophila melanogaster. While HCS is well known for its role in the attachment of biotin to biotin-dependent carboxylase, it also regulates the transcription of HCS and carboxylases genes by triggering a cGMP-dependent signal transduction cascade. Further, its presence in the nucleus of cells suggests additional regulatory roles, but the mechanism involved has remained elusive. In this study, we show in D. melanogaster that HCS migrates to the nucleus at the gastrulation stage. In polytene chromosomes, it is associated to heterochromatin bands where it co-localizes with histone 3 trimethylated at lysine 9 (H3K9met3) but not with the euchromatin mark histone 3 acetylated at lysine 9 (H3K9ac). Further, we demonstrate the association of HCS with the hsp70 promoter by immunofluorescence and chromatin immuno-precipitation (ChIP) of associated DNA sequences. We demonstrate the occupancy of HCS to the core promoter region of the transcriptionally inactive hsp70 gene. On heat-shock activation of the hsp70 promoter, HCS is displaced and the promoter region becomes enriched with the TFIIH subunits XPD and XPB and elongating RNA pol II, the latter also demonstrated using ChIP assays. We suggest that HCS may have a role in the repression of gene expression through a mechanism involving its trafficking to the nucleus and interaction with heterochromatic sites coincident with H3K9met3.
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Affiliation(s)
- Sandra Reyes-Carmona
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México DF 04510, Mexico.
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22
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Zhang J, Zhou J, Liu J, Chen K, Liu L, Chen J. Development of chemically defined media supporting high cell density growth of Ketogulonicigenium vulgare and Bacillus megaterium. BIORESOURCE TECHNOLOGY 2011; 102:4807-4814. [PMID: 21296571 DOI: 10.1016/j.biortech.2010.10.124] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 10/24/2010] [Accepted: 10/25/2010] [Indexed: 05/30/2023]
Abstract
The immediate precursor of L-ascorbic acid, or vitamin C, is 2-keto-L-gulonic acid (2-KLG). This is commonly produced commercially by Ketogulonicigenium vulgare and Bacillus megaterium, using corn steep liquor powder (CSLP) as an organic nitrogen source. In this study, the effects of the individual CSLP components (amino acids, vitamins, and metal elements) on 2-KLG production were evaluated, with the aim of developing a complete, chemically defined medium for 2-KLG production. Forty components of CSLP were analyzed, and key components were correlated to biomass, 2-KLG productivity, and consumption rate of L-sorbose. Glycine had the greatest effect, followed by serine, biotin, proline, nicotinic acid, and threonine. The combination of 0.28 g L(-1) serine, 0.36 g L(-1) glycine, 0.18 g L(-1) threonine, 0.28 g L(-1) proline, 0.19 g L(-1) nicotinic acid, and 0.62 mg L(-1)biotin in a chemically defined medium produced the highest maximum biomass concentration (4.2 × 10(9) cfu mL(-1)), 2-KLG concentration (58 g L(-1)), and yield (0.76 g g(-1)) after culturing for 28 h.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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23
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Fernandez-Mejia C, Lazo-de-la-Vega-Monroy ML. Biological Effects of Pharmacological Concentrations of Biotin. J Evid Based Complementary Altern Med 2011. [DOI: 10.1177/1533210110392947] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Understanding the molecular mechanisms of vitamins has opened new perspectives regarding the relationship between nutritional signals and biological functions, which, in turn, has led to the development of new therapeutic agents. Although little is known about water-soluble vitamins as genetic modulators, evidence about their effects on gene expression has grown. In the case of biotin, besides its role as a carboxylase prosthetic group, it also affects gene expression and has a wide repertoire of effects on biological functions. Only recently, the role of pharmacological concentrations of biotin on systemic functions has attracted attention, and it is now being reconsidered with the help of new technologies. This novel approach could lead to new perspectives in its use as a therapeutic agent. The present review is focused on the effects of pharmacological concentrations of biotin on several biological functions and on the biotin signaling pathways that participate in gene expression.
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24
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Singh D, Pannier AK, Zempleni J. Identification of holocarboxylase synthetase chromatin binding sites in human mammary cell lines using the DNA adenine methyltransferase identification technology. Anal Biochem 2011; 413:55-9. [PMID: 21303649 DOI: 10.1016/j.ab.2011.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 01/30/2011] [Accepted: 02/01/2011] [Indexed: 12/28/2022]
Abstract
Holocarboxylase synthetase (HCS) is a chromatin protein that is essential for mediating the covalent binding of biotin to histones. Biotinylation of histones plays crucial roles in the repression of genes and repeats in the human genome. We tested the feasibility of DNA adenine methyltransferase identification (DamID) technology to map HCS binding sites in human mammary cell lines. Full-length HCS was fused to DNA adenine methyltransferase (Dam) for subsequent transfection into breast cancer (MCF-7) and normal breast (MCF-10A) cells. HCS docking sites in chromatin were identified by using the unique adenine methylation sites established by Dam in the fusion construct; docking sites were unambiguously identified using methylation-sensitive digestion, cloning, and sequencing. In total, 15 novel HCS binding sites were identified in the two cell lines, and the following 4 of the 15 overlapped between MCF-7 and MCF-10A cells: inositol polyphosphate-5-phosphatase A, corticotropin hormone precursor, ribosome biogenesis regulatory protein, and leptin precursor. We conclude that DamID is a useful technology to map HCS binding sites in human chromatin and propose that the entire set of HCS binding sites could be mapped by combining DamID with microarray technology.
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Affiliation(s)
- Dipika Singh
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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25
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Abstract
Nutrients can reverse or change epigenetic phenomena such as DNA methylation and histone modifications, thereby modifying the expression of critical genes associated with physiologic and pathologic processes, including embryonic development, aging, and carcinogenesis. It appears that nutrients and bioactive food components can influence epigenetic phenomena either by directly inhibiting enzymes that catalyze DNA methylation or histone modifications, or by altering the availability of substrates necessary for those enzymatic reactions. In this regard, nutritional epigenetics has been viewed as an attractive tool to prevent pediatric developmental diseases and cancer as well as to delay aging-associated processes. In recent years, epigenetics has become an emerging issue in a broad range of diseases such as type 2 diabetes mellitus, obesity, inflammation, and neurocognitive disorders. Although the possibility of developing a treatment or discovering preventative measures of these diseases is exciting, current knowledge in nutritional epigenetics is limited, and further studies are needed to expand the available resources and better understand the use of nutrients or bioactive food components for maintaining our health and preventing diseases through modifiable epigenetic mechanisms.
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Affiliation(s)
- Sang-Woon Choi
- Vitamins and Carcinogenesis Laboratory, Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111,To whom correspondence should be addressed. E-mail:
| | - Simonetta Friso
- Department of Medicine, University of Verona School of Medicine, Verona 37134, Italy
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26
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Novel histone biotinylation marks are enriched in repeat regions and participate in repression of transcriptionally competent genes. J Nutr Biochem 2010; 22:328-33. [PMID: 20691578 DOI: 10.1016/j.jnutbio.2010.02.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 02/14/2010] [Accepted: 02/23/2010] [Indexed: 11/24/2022]
Abstract
Covalent histone modifications play crucial roles in chromatin structure and genome stability. We previously reported biotinylation of lysine (K) residues in histones H2A, H3 and H4 by holocarboxylase synthetase and demonstrated that K12-biotinylated histone H4 (H4K12bio) is enriched in repeat regions and participates in gene repression. The biological functions of biotinylation marks other than H4K12bio are poorly understood. Here, novel biotinylation site-specific antibodies against H3K9bio, H3K18bio and H4K8bio were used in chromatin immunoprecipitation studies to obtain first insights into possible biological functions of these marks. Chromatin immunoprecipitation assays were conducted in human primary fibroblasts and Jurkat lymphoblastoma cells, and revealed that H3K9bio, H3K18bio and H4K8bio are enriched in repeat regions such as pericentromeric alpha satellite repeats and long-terminal repeats while being depleted in transcriptionally active promoters in euchromatin. Transcriptional stimulation of the repressed interleukin-2 promoter triggered a rapid depletion of histone biotinylation marks at this locus in Jurkat cells, which was paralleled by an increase in interleukin-2 mRNA. Importantly, the enrichment of H3K9bio, H3K18bio and H4K8bio at genomic loci depended on the concentration of biotin in culture media at nutritionally relevant levels, suggesting a novel mechanism of gene regulation by biotin.
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27
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Bao B, Pestinger V, Hassan YI, Borgstahl GEO, Kolar C, Zempleni J. Holocarboxylase synthetase is a chromatin protein and interacts directly with histone H3 to mediate biotinylation of K9 and K18. J Nutr Biochem 2010; 22:470-5. [PMID: 20688500 DOI: 10.1016/j.jnutbio.2010.04.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/29/2010] [Accepted: 04/05/2010] [Indexed: 11/17/2022]
Abstract
Holocarboxylase synthetase (HCS) mediates the binding of biotin to lysine (K) residues in histones H2A, H3 and H4; HCS knockdown disturbs gene regulation and decreases stress resistance and lifespan in eukaryotes. We tested the hypothesis that HCS interacts physically with histone H3 for subsequent biotinylation. Co-immunoprecipitation experiments were conducted and provided evidence that HCS co-localizes with histone H3 in human cells; physical interactions between HCS and H3 were confirmed using limited proteolysis assays. Yeast two-hybrid (Y2H) studies revealed that the N-terminal and C-terminal domains in HCS participate in H3 binding. Recombinant human HCS was produced and exhibited biological activity, as evidenced by biotinylation of its known substrate, recombinant p67. Recombinant histone H3.2 and synthetic H3-based peptides were also good targets for biotinylation by recombinant HCS (rHCS) in vitro, based on tracing histone-bound biotin with [(3)H]biotin, streptavidin and anti-biotin antibody. Biotinylation site-specific antibodies were generated and revealed that both K9 and K18 in H3 were biotinylated by HCS. Collectively, these studies provide conclusive evidence that HCS interacts directly with histone H3, causing biotinylation of K9 and K18. We speculate that the targeting of HCS to distinct regions in human chromatin is mediated by DNA sequence, biotin, RNA, epigenetic marks or chromatin proteins.
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Affiliation(s)
- Baolong Bao
- Department of Nutrition and Health Sciences, University of Nebraska at Lincoln, Lincoln, NE 68583, USA
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28
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The prevalence of epigenetic mechanisms in the regulation of cognitive functions and behaviour. Curr Opin Neurobiol 2010; 20:441-9. [DOI: 10.1016/j.conb.2010.04.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2010] [Revised: 04/13/2010] [Accepted: 04/13/2010] [Indexed: 11/17/2022]
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29
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Bailey LM, Wallace JC, Polyak SW. Holocarboxylase synthetase: correlation of protein localisation with biological function. Arch Biochem Biophys 2010; 496:45-52. [PMID: 20153287 DOI: 10.1016/j.abb.2010.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/26/2010] [Accepted: 01/27/2010] [Indexed: 10/19/2022]
Abstract
Holocarboxylase synthetase (HCS) governs the cellular fate of the essential micronutrient biotin (Vitamin H or B7). HCS is responsible for attaching biotin onto the biotin-dependent enzymes that reside in the cytoplasm and mitochondria. Evidence for an alternative role, viz the regulation of gene expression, has also been reported. Recent immunohistochemical studies reported HCS is primarily nuclear, inconsistent with the location of HCS activity. Improved understanding of biotin biology demands greater knowledge about HCS. Here, we investigated the localisation of HCS and its isoforms. Three variants were observed that differ at the N-terminus. All HCS isoforms were predominantly non-nuclear, consistent with the distribution of biotin protein ligase activity. Unlike the longer constructs, the Met(58) isoform was also detected in the nucleus--a novel observation suggesting shuttling activity between nucleus and cytoplasm. We resolved that the previous controversies in the literature are due to specificity and detection limitations that arise when using partially purified antibodies.
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Affiliation(s)
- L M Bailey
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
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30
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Evertts AG, Zee BM, Garcia BA. Modern approaches for investigating epigenetic signaling pathways. J Appl Physiol (1985) 2010; 109:927-33. [PMID: 20110548 DOI: 10.1152/japplphysiol.00007.2010] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Epigenetics is increasingly being recognized as a central component of physiological processes as diverse as obesity and circadian rhythms. Primarily acting through DNA methylation and histone posttranslational modifications, epigenetic pathways enable both short- and long-term transcriptional activation and silencing, independently of the underlying genetic sequence. To more quantitatively study the molecular basis of epigenetic regulation in physiological processes, the present review informs the latest techniques to identify and compare novel DNA methylation marks and combinatorial histone modifications across different experimental conditions, and to localize both DNA methylation and histone modifications over specific genomic regions.
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Affiliation(s)
- Adam G Evertts
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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