1
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Morffy N, Van den Broeck L, Miller C, Emenecker RJ, Bryant JA, Lee TM, Sageman-Furnas K, Wilkinson EG, Pathak S, Kotha SR, Lam A, Mahatma S, Pande V, Waoo A, Wright RC, Holehouse AS, Staller MV, Sozzani R, Strader LC. Identification of plant transcriptional activation domains. Nature 2024; 632:166-173. [PMID: 39020176 DOI: 10.1038/s41586-024-07707-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 06/12/2024] [Indexed: 07/19/2024]
Abstract
Gene expression in Arabidopsis is regulated by more than 1,900 transcription factors (TFs), which have been identified genome-wide by the presence of well-conserved DNA-binding domains. Activator TFs contain activation domains (ADs) that recruit coactivator complexes; however, for nearly all Arabidopsis TFs, we lack knowledge about the presence, location and transcriptional strength of their ADs1. To address this gap, here we use a yeast library approach to experimentally identify Arabidopsis ADs on a proteome-wide scale, and find that more than half of the Arabidopsis TFs contain an AD. We annotate 1,553 ADs, the vast majority of which are, to our knowledge, previously unknown. Using the dataset generated, we develop a neural network to accurately predict ADs and to identify sequence features that are necessary to recruit coactivator complexes. We uncover six distinct combinations of sequence features that result in activation activity, providing a framework to interrogate the subfunctionalization of ADs. Furthermore, we identify ADs in the ancient AUXIN RESPONSE FACTOR family of TFs, revealing that AD positioning is conserved in distinct clades. Our findings provide a deep resource for understanding transcriptional activation, a framework for examining function in intrinsically disordered regions and a predictive model of ADs.
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Affiliation(s)
| | - Lisa Van den Broeck
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Caelan Miller
- Department of Biology, Duke University, Durham, NC, USA
| | - Ryan J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - John A Bryant
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Tyler M Lee
- Department of Biology, Duke University, Durham, NC, USA
| | | | | | - Sunita Pathak
- Department of Biology, Duke University, Durham, NC, USA
| | - Sanjana R Kotha
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Angelica Lam
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Saloni Mahatma
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Vikram Pande
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - Aman Waoo
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
| | - R Clay Wright
- Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St. Louis, St. Louis, MO, USA
| | - Max V Staller
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, USA
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2
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Liang Z, Hu S, Dong Y, Miao L, Zhu W, Feng B, Fu J, Luo M, Wang L, Dong Z. Molecular characterization and function of hif1a and fih1 in response to acute thermal stress in American shad (Alosa sapidissima). FISH PHYSIOLOGY AND BIOCHEMISTRY 2024; 50:1563-1581. [PMID: 38789648 DOI: 10.1007/s10695-024-01356-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 05/03/2024] [Indexed: 05/26/2024]
Abstract
In order to evaluate the function of hypoxia-inducible factor-1 alpha (hif1α) and factor inhibiting hif1α (fih1) in response to thermal stress, we first conducted a functional analysis of A. sapidissima hif1α and fih1, and determined hif1α and fih1 expressions in different tissues in response to thermal stress based on identified housekeeping genes (HKGs). The results showed that hif1α and fih1 were mainly located in the nucleus and cytoplasm. The full length cDNA sequence of hif1α and fih1 was 4073 bp and 2759 bp, respectively. The cDNA sequence of hif1α includes 15 exons encoding 750 amino acid residues, and the full length cDNA sequence of fih1 contains 9 exons encoding 354 amino acid residues. During the acute thermal stress transferring from 16 ± 0.5 °C (control) to 20 ± 0.5 °C, 25 ± 0.5 °C, and 30 ± 0.5 °C for 15 min, it was found that the expression trends of hif1α and fih1 showed an inhibitory regulation in the heart, while they consistently expressed in brain, intestine, muscle, gill, kidney and liver. In conclusion, this is the first study to identify the tissue-specific HKGs in A. sapidissima and found that ef1α and β-actin are the most suitable HKGs. Hif1α and Fih1 are mainly the nuclear and cytoplasmic proteins, respectively, having high levels in the heart and brain. Alosa sapidissima countered a temperature increase from 16 to 25 ℃ by regulating the expressions of hif1α and fih1, but their physiological regulatory functions were unable to cope with acute thermal stress when the temperature difference was 14 ℃ (from 16 to 30 ℃).
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Affiliation(s)
- Zhengyuan Liang
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Wuxi Raysun Fishery Science and Technology Company, Xingyuan North Road No. 401, P.O. Box D20-501, Wuxi Jiangsu, 214000, China
| | - Songqin Hu
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
| | - Yalun Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Linghong Miao
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Wenbin Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Bingbing Feng
- Fisheries Technology Extension Center of Jiangsu Province, Hanzhongmen Street No. 300, Nanjing Jiangsu, 210036, China
| | - Jianjun Fu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Mingkun Luo
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Lanmei Wang
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China
| | - Zaije Dong
- Wuxi Fisheries College, Nanjing Agricultural University, No.9 East Shanshui Road, Wuxi Jiangsu, 214081, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs; Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi Jiangsu, 214081, China.
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3
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Petrovicz VL, Pasztuhov I, Martinek TA, Hegedüs Z. Site-directed allostery perturbation to probe the negative regulation of hypoxia inducible factor-1α. RSC Chem Biol 2024; 5:711-720. [PMID: 39092442 PMCID: PMC11289882 DOI: 10.1039/d4cb00066h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/27/2024] [Indexed: 08/04/2024] Open
Abstract
The interaction between the intrinsically disordered transcription factor HIF-1α and the coactivator proteins p300/CBP is essential in the fast response to low oxygenation. The negative feedback regulator, CITED2, switches off the hypoxic response through a very efficient irreversible mechanism. The negative cooperativity with HIF-1α relies on the formation of a ternary intermediate that leads to allosteric structural changes in p300/CBP, in which the cooperative folding/binding of the CITED2 sequence motifs plays a key role. Understanding the contribution of a binding motif to the structural changes in relation to competition efficiency provides invaluable insights into the molecular mechanism. Our strategy is to site-directedly perturb the p300-CITED2 complex's structure without significantly affecting binding thermodynamics. In this way, the contribution of a sequence motif to the negative cooperativity with HIF-1α would mainly depend on the induced structural changes, and to a lesser extent on binding affinity. Using biophysical assays and NMR measurements, we show here that the interplay between the N-terminal tail and the rest of the binding motifs of CITED2 is crucial for the unidirectional displacement of HIF-1α. We introduce an advantageous approach for evaluating the roles of the different sequence parts with the help of motif-by-motif backbone perturbations.
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Affiliation(s)
- Vencel L Petrovicz
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
| | - István Pasztuhov
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
| | - Tamás A Martinek
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
- HUN-REN SZTE Biomimetic Systems Research Group 8 Dóm tér Szeged 6720 Hungary
| | - Zsófia Hegedüs
- University of Szeged, Department of Medical Chemistry 8 Dóm tér Szeged 6720 Hungary
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4
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McIvor JAP, Larsen DS, Mercadante D. Charge Relaying within a Phospho-Motif Rescue Binding Competency of a Disordered Transcription Factor. J Chem Inf Model 2024. [PMID: 39074869 DOI: 10.1021/acs.jcim.4c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Structural disorder in proteins is central to cellular signaling, where conformational plasticity equips molecules to promiscuously interact with different partners. By engaging with multiple binding partners via the rearrangement of its three helices, the nuclear coactivator binding domain (NCBD) of the CBP/p300 transcription factor is a paradigmatic example of promiscuity. Recently, molecular simulations and experiments revealed that, through the establishment of long-range electrostatic interactions, intended as salt-bridges formed between the post-translationally inserted phosphate and positively charged residues in helix H3 of NCBD, phosphorylation triggers NCBD compaction, lowering its affinity for binding partners. By means of extensive molecular simulations, we here investigated the effect of short-range electrostatics on the conformational ensemble of NCBD, by monitoring the interactions between a phosphorylated serine and conserved positively charged residues within the NCBD phospho-motif. We found that empowering proximal electrostatic interactions, as opposed to long-range electrostatics, can reshape the NCBD ensemble rescuing the binding competency of phosphorylated NCBD. Given the conservation of positive charges in phospho-motifs, proximal electrostatic interactions might dampen the effects of phosphorylation and act as a relay to regulate phosphorylated intrinsically disordered proteins, ultimately tuning the binding affinity for different cellular partners.
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Affiliation(s)
- Jordan A P McIvor
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Danaé S Larsen
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
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5
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Munshi R. How Transcription Factor Clusters Shape the Transcriptional Landscape. Biomolecules 2024; 14:875. [PMID: 39062589 PMCID: PMC11274464 DOI: 10.3390/biom14070875] [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: 06/01/2024] [Revised: 07/14/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter-TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.
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Affiliation(s)
- Rahul Munshi
- Joseph Henry Laboratories of Physics and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
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6
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Haghshenas S, Bout HJ, Schijns JM, Levy MA, Kerkhof J, Bhai P, McConkey H, Jenkins ZA, Williams EM, Halliday BJ, Huisman SA, Lauffer P, de Waard V, Witteveen L, Banka S, Brady AF, Galazzi E, van Gils J, Hurst ACE, Kaiser FJ, Lacombe D, Martinez-Monseny AF, Fergelot P, Monteiro FP, Parenti I, Persani L, Santos-Simarro F, Simpson BN, Alders M, Robertson SP, Sadikovic B, Menke LA. Menke-Hennekam syndrome; delineation of domain-specific subtypes with distinct clinical and DNA methylation profiles. HGG ADVANCES 2024; 5:100287. [PMID: 38553851 PMCID: PMC11040166 DOI: 10.1016/j.xhgg.2024.100287] [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: 10/20/2023] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/18/2024] Open
Abstract
CREB-binding protein (CBP, encoded by CREBBP) and its paralog E1A-associated protein (p300, encoded by EP300) are involved in histone acetylation and transcriptional regulation. Variants that produce a null allele or disrupt the catalytic domain of either protein cause Rubinstein-Taybi syndrome (RSTS), while pathogenic missense and in-frame indel variants in parts of exons 30 and 31 cause phenotypes recently described as Menke-Hennekam syndrome (MKHK). To distinguish MKHK subtypes and define their characteristics, molecular and extended clinical data on 82 individuals (54 unpublished) with variants affecting CBP (n = 71) or p300 (n = 11) (NP_004371.2 residues 1,705-1,875 and NP_001420.2 residues 1,668-1,833, respectively) were summarized. Additionally, genome-wide DNA methylation profiles were assessed in DNA extracted from whole peripheral blood from 54 individuals. Most variants clustered closely around the zinc-binding residues of two zinc-finger domains (ZZ and TAZ2) and within the first α helix of the fourth intrinsically disordered linker (ID4) of CBP/p300. Domain-specific methylation profiles were discerned for the ZZ domain in CBP/p300 (found in nine out of 10 tested individuals) and TAZ2 domain in CBP (in 14 out of 20), while a domain-specific diagnostic episignature was refined for the ID4 domain in CBP/p300 (in 21 out of 21). Phenotypes including intellectual disability of varying degree and distinct physical features were defined for each of the regions. These findings demonstrate existence of at least three MKHK subtypes, which are domain specific (MKHK-ZZ, MKHK-TAZ2, and MKHK-ID4) rather than gene specific (CREBBP/EP300). DNA methylation episignatures enable stratification of molecular pathophysiologic entities within a gene or across a family of paralogous genes.
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Affiliation(s)
- Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London ON N6A 5W9, Canada
| | - Hidde J Bout
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, 1105 Amsterdam, AZ, the Netherlands
| | - Josephine M Schijns
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, 1105 Amsterdam, AZ, the Netherlands
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London ON N6A 5W9, Canada
| | - Pratibha Bhai
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London ON N6A 5W9, Canada
| | - Zandra A Jenkins
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Ella M Williams
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Benjamin J Halliday
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Sylvia A Huisman
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, 1105 Amsterdam, AZ, the Netherlands; Zodiak, Prinsenstichting, Purmerend, JE 1444, the Netherlands
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam 1105 AZ, the Netherlands
| | - Vivian de Waard
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam Cardiovascular Sciences, Amsterdam, AZ 1105, the Netherlands
| | - Laura Witteveen
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, 1105 Amsterdam, AZ, the Netherlands
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9WL, UK; Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Angela F Brady
- North West Thames Regional Genetics Service, Northwick Park Hospital, Harrow HA1 3UJ, UK
| | - Elena Galazzi
- Department of Endocrine & Metabolic Diseases, San Luca Hospital, IRCCS Istituto Auxologico Italiano, 20100 Milan, Italy
| | - Julien van Gils
- Centre Hospitalier Universitaire Bordeaux, 33404 Bordeaux, France
| | - Anna C E Hurst
- Department of Genetics, University of Alabama, Birmingham, AL 35294-0024, USA
| | - Frank J Kaiser
- Institute of Human Genetics, University of Duisburg-Essen, 45122 Essen, Germany; Center for Rare Diseases, University Hospital Essen, 45122 Essen, Germany
| | - Didier Lacombe
- Centre Hospitalier Universitaire Bordeaux, 33404 Bordeaux, France
| | - Antonio F Martinez-Monseny
- Genètica Clínica, Servei de Medicina Genètica i Molecular, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | | | | | - Ilaria Parenti
- Institute of Human Genetics, University of Duisburg-Essen, 45122 Essen, Germany
| | - Luca Persani
- Department of Endocrine & Metabolic Diseases, San Luca Hospital, IRCCS Istituto Auxologico Italiano, 20100 Milan, Italy; Department of Medical Biotechnology and Translational Medicine, University of Milan, 20100 Milan, Italy
| | - Fernando Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, 28029 Madrid, Spain; Unit of Molecular Diagnostics and Clinical Genetics, Hospital Universitari Son Espases, Health Research Institute of the Balearic Islands (IdISBa), 07120 Palma, Spain
| | - Brittany N Simpson
- Department of Pediatrics, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, OH 45206, USA
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, Amsterdam 1105 AZ, the Netherlands
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada.
| | - Leonie A Menke
- Department of Pediatrics, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam Reproduction and Development Research Institute, 1105 Amsterdam, AZ, the Netherlands.
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7
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Kato H, Salgado M, Mendez D, Gonzalez N, Rawson J, Ligot D, Balandran B, Orr C, Quijano JC, Omori K, Qi M, Al-Abdullah IH, Mullen Y, Ku HT, Kandeel F, Komatsu H. Biological hypoxia in pre-transplant human pancreatic islets induces transplant failure in diabetic mice. Sci Rep 2024; 14:12402. [PMID: 38811610 PMCID: PMC11137081 DOI: 10.1038/s41598-024-61604-3] [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: 02/05/2024] [Accepted: 05/07/2024] [Indexed: 05/31/2024] Open
Abstract
Evaluating the quality of isolated human islets before transplantation is crucial for predicting the success in treating Type 1 diabetes. The current gold standard involves time-intensive in vivo transplantation into diabetic immunodeficient mice. Given the susceptibility of isolated islets to hypoxia, we hypothesized that hypoxia present in islets before transplantation could indicate compromised islet quality, potentially leading to unfavorable outcomes. To test this hypothesis, we analyzed expression of 39 hypoxia-related genes in human islets from 85 deceased donors. We correlated gene expression profiles with transplantation outcomes in 327 diabetic mice, each receiving 1200 islet equivalents grafted into the kidney capsule. Transplantation outcome was post-transplant glycemic control based on area under the curve of blood glucose over 4 weeks. In linear regression analysis, DDIT4 (R = 0.4971, P < 0.0001), SLC2A8 (R = 0.3531, P = 0.0009) and HK1 (R = 0.3444, P = 0.0012) had the highest correlation with transplantation outcome. A multiple regression model of 11 genes increased the correlation (R = 0.6117, P < 0.0001). We conclude that assessing pre-transplant hypoxia in human islets via gene expression analysis is a rapid, viable alternative to conventional in vivo assessments. This approach also underscores the importance of mitigating pre-transplant hypoxia in isolated islets to improve the success rate of islet transplantation.
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Affiliation(s)
- Hiroyuki Kato
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
- Department of Surgery, University of California, San Francisco, 513 Parnassus Ave., San Francisco, CA, 94143, USA
| | - Mayra Salgado
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Daniel Mendez
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Nelson Gonzalez
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Jeffrey Rawson
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Doreen Ligot
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Bennie Balandran
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Chris Orr
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Janine C Quijano
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Keiko Omori
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Meirigeng Qi
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Ismail H Al-Abdullah
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Yoko Mullen
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Hsun Teresa Ku
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Fouad Kandeel
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA
| | - Hirotake Komatsu
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes AND Metabolism Research Institute of City of Hope, 1500 E. Duarte Rd., Duarte, CA, 91010, USA.
- Department of Surgery, University of California, San Francisco, 513 Parnassus Ave., San Francisco, CA, 94143, USA.
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8
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Dai Q, Yuan Z, Sun Q, Ao Z, He B, Jiang Y. Discovery of novel nucleoside derivatives as selective lysine acetyltransferase p300 inhibitors for cancer therapy. Bioorg Med Chem Lett 2024; 104:129742. [PMID: 38604299 DOI: 10.1016/j.bmcl.2024.129742] [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: 11/28/2023] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
P300 and CBP are two closely related histone acetyltransferases that are important transcriptional coactivators of many cellular processes. Inhibition of the transcriptional regulator p300/CBP is a promising therapeutic approach in oncology. However, there are no reported single selective p300 or CBP inhibitors to date. In this study, we designed and optimized a series of lysine acetyltransferase p300 selective inhibitors bearing a nucleoside scaffold. Most compounds showed excellent inhibitory activity against p300 with IC50 ranging from 0.18 to 9.90 μM, except for J16, J29, J40, and J48. None of the compounds showed inhibitory activity against CBP (inhibition rate < 50 % at 10 µM). Then the cytotoxicity of the compounds against a series of cancer cells were evaluated. Compounds J31 and J32 showed excellent proliferation inhibitory activity on cancer cells T47D and H520 with desirable selectivity profile of p300 over CBP. These compounds could be promising lead compounds for the development of novel epigenetic inhibitors as antitumor agents.
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Affiliation(s)
- Qiuzi Dai
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China
| | - Zigao Yuan
- Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, China
| | - Qinsheng Sun
- Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, China
| | - Zhuolin Ao
- Division of Biosciences, Department of Biochemistry, University College London, London WC1E6AA, UK
| | - Binsheng He
- The Hunan Provincial University Key Laboratory of the Fundamental and Clinical Research on Functional Nucleic Acid, Hunan Key Laboratory of the Research and Development of Novel Pharmaceutical Preparations, Changsha Medical University, Changsha 410219, China.
| | - Yuyang Jiang
- Shenzhen Kivita Innovative Drug Discovery Institute, Shenzhen 518055, China; State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
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9
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Ciesla J, Huang KL, Wagner EJ, Munger J. A UL26-PIAS1 complex antagonizes anti-viral gene expression during Human Cytomegalovirus infection. PLoS Pathog 2024; 20:e1012058. [PMID: 38768227 PMCID: PMC11142722 DOI: 10.1371/journal.ppat.1012058] [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: 02/18/2024] [Revised: 05/31/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
Viral disruption of innate immune signaling is a critical determinant of productive infection. The Human Cytomegalovirus (HCMV) UL26 protein prevents anti-viral gene expression during infection, yet the mechanisms involved are unclear. We used TurboID-driven proximity proteomics to identify putative UL26 interacting proteins during infection to address this issue. We find that UL26 forms a complex with several immuno-regulatory proteins, including several STAT family members and various PIAS proteins, a family of E3 SUMO ligases. Our results indicate that UL26 prevents STAT phosphorylation during infection and antagonizes transcriptional activation induced by either interferon α (IFNA) or tumor necrosis factor α (TNFα). Additionally, we find that the inactivation of PIAS1 sensitizes cells to inflammatory stimulation, resulting in an anti-viral transcriptional environment similar to ΔUL26 infection. Further, PIAS1 is important for HCMV cell-to-cell spread, which depends on the presence of UL26, suggesting that the UL26-PIAS1 interaction is vital for modulating intrinsic anti-viral defense.
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Affiliation(s)
- Jessica Ciesla
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Kai-Lieh Huang
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Eric J. Wagner
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Joshua Munger
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
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10
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Tomasello B, Bellia F, Naletova I, Magrì A, Tabbì G, Attanasio F, Tomasello MF, Cairns WRL, Fortino M, Pietropaolo A, Greco V, La Mendola D, Sciuto S, Arena G, Rizzarelli E. BDNF- and VEGF-Responsive Stimulus to an NGF Mimic Cyclic Peptide with Copper Ionophore Capability and Ctr1/CCS-Driven Signaling. ACS Chem Neurosci 2024; 15:1755-1769. [PMID: 38602894 DOI: 10.1021/acschemneuro.3c00716] [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: 04/13/2024] Open
Abstract
Neurotrophins are a family of growth factors that play a key role in the development and regulation of the functioning of the central nervous system. Their use as drugs is made difficult by their poor stability, cellular permeability, and side effects. Continuing our effort to use peptides that mimic the neurotrophic growth factor (NGF), the family model protein, and specifically the N-terminus of the protein, here we report on the spectroscopic characterization and resistance to hydrolysis of the 14-membered cyclic peptide reproducing the N-terminus sequence (SSSHPIFHRGEFSV (c-NGF(1-14)). Far-UV CD spectra and a computational study show that this peptide has a rigid conformation and left-handed chirality typical of polyproline II that favors its interaction with the D5 domain of the NGF receptor TrkA. c-NGF(1-14) is able to bind Cu2+ with good affinity; the resulting complexes have been characterized by potentiometric and spectroscopic measurements. Experiments on PC12 cells show that c-NGF(1-14) acts as an ionophore, influencing the degree and the localization of both the membrane transporter (Ctr1) and the copper intracellular transporter (CCS). c-NGF(1-14) induces PC12 differentiation, mimics the protein in TrkA phosphorylation, and activates the kinase cascade, inducing Erk1/2 phosphorylation. c-NGF(1-14) biological activities are enhanced when the peptide interacts with Cu2+ even with the submicromolar quantities present in the culture media as demonstrated by ICP-OES measurements. Finally, c-NGF(1-14) and Cu2+ concur to activate the cAMP response element-binding protein CREB that, in turn, induces the brain-derived neurotrophic factor (BDNF) and the vascular endothelial growth factor (VEGF) release.
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Affiliation(s)
- Barbara Tomasello
- Department of Drug and Health Sciences, University of Catania, V.le Andrea Doria 6, Catania 95125, Italy
| | - Francesco Bellia
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
| | - Irina Naletova
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
| | - Antonio Magrì
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
| | - Giovanni Tabbì
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
| | | | | | - Warren R L Cairns
- Istituto di Scienze Polari (ISP), c/o Campus Scientifico, Università Ca' Foscari Venezia Via Torino, Venezia Mestre 155-30170, Italy
| | - Mariagrazia Fortino
- Dipartimento di Scienze della Salute, Università di Catanzaro, Viale Europa, Catanzaro 88100, Italy
| | - Adriana Pietropaolo
- Dipartimento di Scienze della Salute, Università di Catanzaro, Viale Europa, Catanzaro 88100, Italy
| | - Valentina Greco
- Department of Chemical Sciences, University of Catania, A. Doria 6, Catania 95125, Italy
| | - Diego La Mendola
- Department of Pharmaceutical Sciences, University of Pisa, Bonanno Pisano 12, Pisa 56126, Italy
| | - Sebastiano Sciuto
- Department of Chemical Sciences, University of Catania, A. Doria 6, Catania 95125, Italy
| | - Giuseppe Arena
- Department of Chemical Sciences, University of Catania, A. Doria 6, Catania 95125, Italy
| | - Enrico Rizzarelli
- Institute of Crystallography, CNR, P. Gaifami 18, Catania 95126, Italy
- Department of Chemical Sciences, University of Catania, A. Doria 6, Catania 95125, Italy
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11
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Kim S, Park J, Choi Y, Jeon H, Lim N. Investigating the Relevance of Cyclic Adenosine Monophosphate Response Element-Binding Protein to the Wound Healing Process: An In Vivo Study Using Photobiomodulation Treatment. Int J Mol Sci 2024; 25:4838. [PMID: 38732058 PMCID: PMC11084265 DOI: 10.3390/ijms25094838] [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: 02/24/2024] [Revised: 04/05/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Monitoring inflammatory cytokines is crucial for assessing healing process and photobiomodulation (PBM) enhances wound healing. Meanwhile, cAMP response element-binding protein (CREB) is a regulator of cellular metabolism and proliferation. This study explored potential links between inflammatory cytokines and the activity of CREB in PBM-treated wounds. A total of 48 seven-week-old male SD rats were divided into four groups (wound location, skin or oral; treatment method, natural healing or PBM treatment). Wounds with a 6 mm diameter round shape were treated five times with an 808 nm laser every other day (total 60 J). The wound area was measured with a caliper and calculated using the elliptical formula. Histological analysis assessed the epidermal regeneration and collagen expression of skin and oral tissue with H&E and Masson's trichrome staining. Pro-inflammatory (TNF-α) and anti-inflammatory (TGF-β) cytokines were quantified by RT-PCR. The ratio of phosphorylated CREB (p-CREB) to unphosphorylated CREB was identified through Western blot. PBM treatment significantly reduced the size of the wounds on day 3 and day 7, particularly in the skin wound group (p < 0.05 on day 3, p < 0.001 on day 7). The density of collagen expression was significantly higher in the PBM treatment group (in skin wound, p < 0.05 on day 3, p < 0.001 on day 7, and p < 0.05 on day 14; in oral wound, p < 0.01 on day 7). The TGF-β/TNF-α ratio and the p-CREB/CREB ratio showed a parallel trend during wound healing. Our findings suggested that the CREB has potential as a meaningful marker to track the wound healing process.
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Affiliation(s)
- Sungyeon Kim
- Department of Plastic and Reconstructive Surgery, Dankook University College of Medicine, Cheonan 31116, Chungnam, Republic of Korea; (S.K.); (H.J.)
| | - Jion Park
- Department of Medical Laser, Graduate School, Dankook University, Cheonan 31116, Chungnam, Republic of Korea;
| | - Younghoon Choi
- Institute of Medical Science, Dankook University Hospital, Cheonan 31116, Chungnam, Republic of Korea;
| | - Hongbae Jeon
- Department of Plastic and Reconstructive Surgery, Dankook University College of Medicine, Cheonan 31116, Chungnam, Republic of Korea; (S.K.); (H.J.)
- Dankook Physician Scientist Research Center (DPSRC), Dankook University Hospital, Cheonan 31116, Chungnam, Republic of Korea
| | - Namkyu Lim
- Department of Plastic and Reconstructive Surgery, Dankook University College of Medicine, Cheonan 31116, Chungnam, Republic of Korea; (S.K.); (H.J.)
- Dankook Physician Scientist Research Center (DPSRC), Dankook University Hospital, Cheonan 31116, Chungnam, Republic of Korea
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12
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Inge MM, Miller R, Hook H, Bray D, Keenan JL, Zhao R, Gilmore TD, Siggers T. Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.05.588333. [PMID: 38617258 PMCID: PMC11014505 DOI: 10.1101/2024.04.05.588333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Transcription factor (TF)-cofactor (COF) interactions define dynamic, cell-specific networks that govern gene expression; however, these networks are understudied due to a lack of methods for high-throughput profiling of DNA-bound TF-COF complexes. Here we describe the Cofactor Recruitment (CoRec) method for rapid profiling of cell-specific TF-COF complexes. We define a lysine acetyltransferase (KAT)-TF network in resting and stimulated T cells. We find promiscuous recruitment of KATs for many TFs and that 35% of KAT-TF interactions are condition specific. KAT-TF interactions identify NF-κB as a primary regulator of acutely induced H3K27ac. Finally, we find that heterotypic clustering of CBP/P300-recruiting TFs is a strong predictor of total promoter H3K27ac. Our data supports clustering of TF sites that broadly recruit KATs as a mechanism for widespread co-occurring histone acetylation marks. CoRec can be readily applied to different cell systems and provides a powerful approach to define TF-COF networks impacting chromatin state and gene regulation.
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Affiliation(s)
- MM Inge
- Department of Biology, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- These authors contributed equally
| | - R Miller
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
- These authors contributed equally
| | - H Hook
- Department of Biology, Boston University, Boston, MA, USA
| | - D Bray
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - JL Keenan
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - R Zhao
- Department of Biology, Boston University, Boston, MA, USA
| | - TD Gilmore
- Department of Biology, Boston University, Boston, MA, USA
| | - T Siggers
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
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13
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Qian P, Wang S, Zhang T, Wu J. Transcriptional Expression of Histone Acetyltransferases and Deacetylases During the Recovery of Acute Exercise in Mouse Hippocampus. J Mol Neurosci 2024; 74:34. [PMID: 38565829 DOI: 10.1007/s12031-024-02215-5] [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: 11/06/2023] [Accepted: 03/21/2024] [Indexed: 04/04/2024]
Abstract
Protein acetylation, which is dynamically maintained by histone acetyltransferases (HATs) and deacetylases (HDACs), might play essential roles in hippocampal exercise physiology. However, whether HATs/HDACs are imbalanced during the recovery phase following acute exercise has not been determined. Groups of exercised mice with different recovery periods after acute exercise (0 h, 0.5 h, 1 h, 4 h, 7 h, and 24 h) were constructed, and a group of sham-exercised mice was used as the control. The mRNA levels of HATs and HDACs were detected via real-time quantitative polymerase chain reaction. Lysine acetylation on the total proteins and some specific locations on histones were detected via western blotting, as were various acylation modifications on the total proteins. Except for four unaffected genes (Hdac4, Ncoa1, Ncoa2, and Sirt1), the mRNA expression trajectories of 21 other HATs or HDACs affected by exercise could be categorized into three clusters. The genes in Cluster 1 increased quickly following exercise, with a peak at 0.5 h and/or 1 h, and remained at high levels until 24 h. Cluster 2 genes presented a gradual increase with a delayed peak at 4 h or 7 h postexercise before returning to baseline. The expression of Cluster 3 genes decreased at 0.5 h and/or 1 h, with some returning to overexpression (Hdac1 and Sirt3). Although most HATs were upregulated and half of the affected HDACs were downregulated at 0.5 h postexercise, the global or residue-specific histone acetylation levels were unchanged. In contrast, the levels of several metabolism-related acylation products of total proteins, including acetylation, succinylation, 2-hydroxyisobutyryllysine, β-hydroxybutyryllysine, and lactylation, decreased and mainly occurred on nonhistones immediately after exercise. During the 24-h recovery phase after acute exercise, the transcriptional trajectory of HATs or the same class of HDACs in the hippocampus exhibited heterogeneity. Although acute exercise did not affect the selected sites on histone lysine residues, it possibly incurred changes in acetylation and other acylation on nonhistone proteins.
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Affiliation(s)
- Ping Qian
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
- Department of Internal Medicine, Affiliated Children Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | - Shan Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jianxin Wu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, 100020, China.
- Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
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14
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Zavrtanik U, Medved T, Purič S, Vranken W, Lah J, Hadži S. Leucine Motifs Stabilize Residual Helical Structure in Disordered Proteins. J Mol Biol 2024; 436:168444. [PMID: 38218366 DOI: 10.1016/j.jmb.2024.168444] [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: 12/03/2023] [Revised: 12/31/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
Many examples are known of regions of intrinsically disordered proteins that fold into α-helices upon binding to their targets. These helical binding motifs (HBMs) can be partially helical also in the unbound state, and this so-called residual structure can affect binding affinity and kinetics. To investigate the underlying mechanisms governing the formation of residual helical structure, we assembled a dataset of experimental helix contents of 65 peptides containing HBM that fold-upon-binding. The average residual helicity is 17% and increases to 60% upon target binding. The helix contents of residual and target-bound structures do not correlate, however the relative location of helix elements in both states shows a strong overlap. Compared to the general disordered regions, HBMs are enriched in amino acids with high helix preference and these residues are typically involved in target binding, explaining the overlap in helix positions. In particular, we find that leucine residues and leucine motifs in HBMs are the major contributors to helix stabilization and target-binding. For the two model peptides, we show that substitution of leucine motifs to other hydrophobic residues (valine or isoleucine) leads to reduction of residual helicity, supporting the role of leucine as helix stabilizer. From the three hydrophobic residues only leucine can efficiently stabilize residual helical structure. We suggest that the high occurrence of leucine motifs and a general preference for leucine at binding interfaces in HBMs can be explained by its unique ability to stabilize helical elements.
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Affiliation(s)
- Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tadej Medved
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Samo Purič
- Graduate Study Program, Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Wim Vranken
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, Triomflaan, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB Structural Biology Research Centre, Brussels 1050, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia.
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15
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Udupa A, Kotha SR, Staller MV. Commonly asked questions about transcriptional activation domains. Curr Opin Struct Biol 2024; 84:102732. [PMID: 38056064 PMCID: PMC11193542 DOI: 10.1016/j.sbi.2023.102732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 12/08/2023]
Abstract
Eukaryotic transcription factors activate gene expression with their DNA-binding domains and activation domains. DNA-binding domains bind the genome by recognizing structurally related DNA sequences; they are structured, conserved, and predictable from protein sequences. Activation domains recruit chromatin modifiers, coactivator complexes, or basal transcriptional machinery via structurally diverse protein-protein interactions. Activation domains and DNA-binding domains have been called independent, modular units, but there are many departures from modularity, including interactions between these regions and overlap in function. Compared to DNA-binding domains, activation domains are poorly understood because they are poorly conserved, intrinsically disordered, and difficult to predict from protein sequences. This review, organized around commonly asked questions, describes recent progress that the field has made in understanding the sequence features that control activation domains and predicting them from sequence.
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Affiliation(s)
- Aditya Udupa
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA
| | - Sanjana R Kotha
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA; Center for Computational Biology, University of California, Berkeley, 94720, USA
| | - Max V Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, 94720, USA; Center for Computational Biology, University of California, Berkeley, 94720, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 94158, USA.
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16
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Gou P, Zhang W. Protein lysine acetyltransferase CBP/p300: A promising target for small molecules in cancer treatment. Biomed Pharmacother 2024; 171:116130. [PMID: 38215693 DOI: 10.1016/j.biopha.2024.116130] [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: 10/26/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Abstract
CBP and p300 are homologous proteins exhibiting remarkable structural and functional similarity. Both proteins function as acetyltransferase and coactivator, underscoring their significant roles in cellular processes. The function of histone acetyltransferases is to facilitate the release of DNA from nucleosomes and act as transcriptional co-activators to promote gene transcription. Transcription factors recruit CBP/p300 by co-condensation and induce transcriptional bursting. Disruption of CBP or p300 functions is associated with different diseases, especially cancer, which can result from either loss of function or gain of function. CBP and p300 are multidomain proteins containing HAT (histone acetyltransferase) and BRD (bromodomain) domains, which perform acetyltransferase activity and maintenance of HAT signaling, respectively. Inhibitors targeting HAT and BRD have been explored for decades, and some BRD inhibitors have been evaluated in clinical trials for treating hematologic malignancies or advanced solid tumors. Here, we review the development and application of CBP/p300 inhibitors. Several inhibitors have been evaluated in vivo, exhibiting notable potency but limited selectivity. Exploring these inhibitors emphasizes the promise of targeting CBP and p300 with small molecules in cancer therapy.
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Affiliation(s)
- Panhong Gou
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wenchao Zhang
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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17
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Shimoda LA. KAT's in the Cradle: p300/CBP and Regulation of HIF-1 and Blood Pressure during Intermittent Hypoxia. Am J Respir Cell Mol Biol 2024; 70:87-88. [PMID: 38109691 PMCID: PMC10848693 DOI: 10.1165/rcmb.2023-0435ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 12/20/2023] Open
Affiliation(s)
- Larissa A Shimoda
- Division of Pulmonary and Critical Care Medicine Johns Hopkins School of Medicine Baltimore, Maryland
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18
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Corda PO, Bollen M, Ribeiro D, Fardilha M. Emerging roles of the Protein Phosphatase 1 (PP1) in the context of viral infections. Cell Commun Signal 2024; 22:65. [PMID: 38267954 PMCID: PMC10807198 DOI: 10.1186/s12964-023-01468-8] [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: 10/16/2023] [Accepted: 12/30/2023] [Indexed: 01/26/2024] Open
Abstract
Protein Phosphatase 1 (PP1) is a major serine/threonine phosphatase in eukaryotes, participating in several cellular processes and metabolic pathways. Due to their low substrate specificity, PP1's catalytic subunits do not exist as free entities but instead bind to Regulatory Interactors of Protein Phosphatase One (RIPPO), which regulate PP1's substrate specificity and subcellular localization. Most RIPPOs bind to PP1 through combinations of short linear motifs (4-12 residues), forming highly specific PP1 holoenzymes. These PP1-binding motifs may, hence, represent attractive targets for the development of specific drugs that interfere with a subset of PP1 holoenzymes. Several viruses exploit the host cell protein (de)phosphorylation machinery to ensure efficient virus particle formation and propagation. While the role of many host cell kinases in viral life cycles has been extensively studied, the targeting of phosphatases by viral proteins has been studied in less detail. Here, we compile and review what is known concerning the role of PP1 in the context of viral infections and discuss how it may constitute a putative host-based target for the development of novel antiviral strategies.
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Affiliation(s)
- Pedro O Corda
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Mathieu Bollen
- Department of Cellular and Molecular Medicine, Laboratory of Biosignaling & Therapeutics, Katholieke Universiteit Leuven, Louvain, Belgium
| | - Daniela Ribeiro
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
| | - Margarida Fardilha
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.
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19
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Mellios N, Papageorgiou G, Gorgievski V, Maxson G, Hernandez M, Otero M, Varangis M, Dell'Orco M, Perrone-Bizzozero N, Tzavara E. Regulation of neuronal circHomer1 biogenesis by PKA/CREB/ERK-mediated pathways and effects of glutamate and dopamine receptor blockade. RESEARCH SQUARE 2024:rs.3.rs-3547375. [PMID: 38260249 PMCID: PMC10802743 DOI: 10.21203/rs.3.rs-3547375/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
There are currently only very few efficacious drug treatments for SCZ and BD, none of which can significantly ameliorate cognitive symptoms. Thus, further research is needed in elucidating molecular pathways linked to cognitive function and antipsychotic treatment. Circular RNAs (circRNAs) are stable brain-enriched non-coding RNAs, derived from the covalent back-splicing of precursor mRNA molecules. CircHomer1 is a neuronal-enriched, activity-dependent circRNA, derived from the precursor of the long HOMER1B mRNA isoform, which is significantly downregulated in the prefrontal cortex of subjects with psychosis and is able to regulate cognitive function. Even though its relevance to psychiatric disorders and its role in brain function and synaptic plasticity have been well established, little is known about the molecular mechanisms that underlie circHomer1 biogenesis in response to neuronal activity and psychiatric drug treatment. Here we suggest that the RNA-binding protein (RBP) FUS positively regulates neuronal circHomer1 expression. Furthermore, we show that the MEK/ERK and PKA/CREB pathways positively regulate neuronal circHomer1 expression, as well as promote the transcription of Fus and Eif4a3, another RBP previously shown to activate circHomer1 biogenesis. We then demonstrate via both in vitro and in vivo studies that NMDA and mGluR5 receptors are upstream modulators of circHomer1 expression. Lastly, we report that in vivo D2R antagonism increases circHomer1 expression, whereas 5HT2AR blockade reduces circHomer1 levels in multiple brain regions. Taken together, this study allows us to gain novel insights into the molecular circuits that underlie the biogenesis of a psychiatric disease-associated circRNA.
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20
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Liu Y, Joy ST, Henley MJ, Croskey A, Yates JA, Merajver SD, Mapp AK. Inhibition of CREB Binding and Function with a Dual-Targeting Ligand. Biochemistry 2024; 63:1-8. [PMID: 38086054 PMCID: PMC10836052 DOI: 10.1021/acs.biochem.3c00469] [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] [Indexed: 01/03/2024]
Abstract
CBP/p300 is a master transcriptional coactivator that regulates gene activation by interacting with multiple transcriptional activators. Dysregulation of protein-protein interactions (PPIs) between the CBP/p300 KIX domain and its activators is implicated in a number of cancers, including breast, leukemia, and colorectal cancer. However, KIX is typically considered "undruggable" because of its shallow binding surfaces lacking both significant topology and promiscuous binding profiles. We previously reported a dual-targeting peptide (MybLL-tide) that inhibits the KIX-Myb interaction with excellent specificity and potency. Here, we demonstrate a branched, second-generation analogue, CREBLL-tide, that inhibits the KIX-CREB PPI with higher potency and selectivity. Additionally, the best of these CREBLL-tide analogues shows excellent and selective antiproliferation activity in breast cancer cells. These results indicate that CREBLL-tide is an effective tool for assessing the role of KIX-activator interactions in breast cancer and expanding the dual-targeting strategy for inhibiting KIX and other coactivators that contain multiple binding surfaces.
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Affiliation(s)
- Yejun Liu
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Stephen T Joy
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Madeleine J Henley
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ayza Croskey
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joel A Yates
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Sofia D Merajver
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, Michigan 48109, United States
| | - Anna K Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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21
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DelRosso N, Bintu L. Using High-Throughput Measurements to Identify Principles of Transcriptional and Epigenetic Regulators. Methods Mol Biol 2024; 2842:79-101. [PMID: 39012591 DOI: 10.1007/978-1-0716-4051-7_4] [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: 07/17/2024]
Abstract
To achieve exquisite control over the epigenome, we need a better predictive understanding of how transcription factors, chromatin regulators, and their individual domain's function, both as modular parts and as full proteins. Transcriptional effector domains are one class of protein domains that regulate transcription and chromatin. These effector domains either repress or activate gene expression by interacting with chromatin-modifying enzymes, transcriptional cofactors, and/or general transcriptional machinery. Here, we discuss important design considerations for high-throughput investigations of effector domains, recent advances in discovering new domains in human cells and testing how domain function depends on amino acid sequence. For every effector domain, we would like to know the following: What role does the cell type, signaling state, and targeted context have on activation, silencing, and epigenetic memory? Large-scale measurements of transcriptional activities can help systematically answer these questions and identify general rules for how all these parameters affect effector domain activities. Last, we discuss what steps need to be taken to turn a newly discovered effector domain into a robust, precise epigenome editor. With more carefully considered high-throughput investigations, soon we will have better predictive control over the epigenome.
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22
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Patalano SD, Fuxman Bass P, Fuxman Bass JI. Transcription factors in the development and treatment of immune disorders. Transcription 2023:1-23. [PMID: 38100543 DOI: 10.1080/21541264.2023.2294623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
Immune function is highly controlled at the transcriptional level by the binding of transcription factors (TFs) to promoter and enhancer elements. Several TF families play major roles in immune gene expression, including NF-κB, STAT, IRF, AP-1, NRs, and NFAT, which trigger anti-pathogen responses, promote cell differentiation, and maintain immune system homeostasis. Aberrant expression, activation, or sequence of isoforms and variants of these TFs can result in autoimmune and inflammatory diseases as well as hematological and solid tumor cancers. For this reason, TFs have become attractive drug targets, even though most were previously deemed "undruggable" due to their lack of small molecule binding pockets and the presence of intrinsically disordered regions. However, several aspects of TF structure and function can be targeted for therapeutic intervention, such as ligand-binding domains, protein-protein interactions between TFs and with cofactors, TF-DNA binding, TF stability, upstream signaling pathways, and TF expression. In this review, we provide an overview of each of the important TF families, how they function in immunity, and some related diseases they are involved in. Additionally, we discuss the ways of targeting TFs with drugs along with recent research developments in these areas and their clinical applications, followed by the advantages and disadvantages of targeting TFs for the treatment of immune disorders.
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Affiliation(s)
- Samantha D Patalano
- Biology Department, Boston University, Boston, MA, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Paula Fuxman Bass
- Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Juan I Fuxman Bass
- Biology Department, Boston University, Boston, MA, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
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23
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Lackner A, Cabral JE, Qiu Y, Zhou H, Leonidas L, Pham MA, Macapagal A, Lin S, Armanus E, McNulty R. Small molecule inhibitor binds to NLRP3 and prevents inflammasome activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571573. [PMID: 38168343 PMCID: PMC10760093 DOI: 10.1101/2023.12.13.571573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Despite recent advances in the mechanism of oxidized DNA activating NLRP3, the molecular mechanism and consequence of oxidized DNA associating with NLRP3 remains unknown. Cytosolic NLRP3 binds oxidized DNA which has been released from the mitochondria, which subsequently triggers inflammasome activation. Human glycosylase (hOGG1) repairs oxidized DNA damage which inhibits inflammasome activation. The fold of NLRP3 pyrin domain contains amino acids and a protein fold similar to hOGG1. Amino acids that enable hOGG1 to bind and cleave oxidized DNA are conserved in NLRP3. We found NLRP3 could bind and cleave oxidized guanine within mitochondrial DNA. The binding of oxidized DNA to NLRP3 was prevented by small molecule drugs which also inhibit hOGG1. These same drugs also inhibited inflammasome activation. Elucidating this mechanism will enable design of drug memetics that treat inflammasome pathologies, illustrated herein by NLRP3 pyrin domain inhibitors which suppressed interleukin-1β (IL-1β) production in macrophages. One-Sentence Summary NLRP3 cleaves oxidized DNA and small molecule drug binding inhibits inflammasome activation.
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24
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Nicosia L, Spencer GJ, Brooks N, Amaral FMR, Basma NJ, Chadwick JA, Revell B, Wingelhofer B, Maiques-Diaz A, Sinclair O, Camera F, Ciceri F, Wiseman DH, Pegg N, West W, Knurowski T, Frese K, Clegg K, Campbell VL, Cavet J, Copland M, Searle E, Somervaille TCP. Therapeutic targeting of EP300/CBP by bromodomain inhibition in hematologic malignancies. Cancer Cell 2023; 41:2136-2153.e13. [PMID: 37995682 DOI: 10.1016/j.ccell.2023.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/07/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]
Abstract
CCS1477 (inobrodib) is a potent, selective EP300/CBP bromodomain inhibitor which induces cell-cycle arrest and differentiation in hematologic malignancy model systems. In myeloid leukemia cells, it promotes rapid eviction of EP300/CBP from an enhancer subset marked by strong MYB occupancy and high H3K27 acetylation, with downregulation of the subordinate oncogenic network and redistribution to sites close to differentiation genes. In myeloma cells, CCS1477 induces eviction of EP300/CBP from FGFR3, the target of the common (4; 14) translocation, with redistribution away from IRF4-occupied sites to TCF3/E2A-occupied sites. In a subset of patients with relapsed or refractory disease, CCS1477 monotherapy induces differentiation responses in AML and objective responses in heavily pre-treated multiple myeloma. In vivo preclinical combination studies reveal synergistic responses to treatment with standard-of-care agents. Thus, CCS1477 exhibits encouraging preclinical and early-phase clinical activity by disrupting recruitment of EP300/CBP to enhancer networks occupied by critical transcription factors.
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Affiliation(s)
- Luciano Nicosia
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Gary J Spencer
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | | | - Fabio M R Amaral
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Naseer J Basma
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - John A Chadwick
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Bradley Revell
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Bettina Wingelhofer
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Alba Maiques-Diaz
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Oliver Sinclair
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Francesco Camera
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Filippo Ciceri
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK
| | - Daniel H Wiseman
- Epigenetics of Haematopoiesis Group, The University of Manchester, Manchester M20 4BX, UK
| | - Neil Pegg
- CellCentric Ltd., Cambridge CB10 1XL, UK
| | - Will West
- CellCentric Ltd., Cambridge CB10 1XL, UK
| | | | - Kris Frese
- CellCentric Ltd., Cambridge CB10 1XL, UK
| | | | | | - James Cavet
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Mhairi Copland
- Paul O'Gorman Leukaemia Research Centre, University of Glasgow, Glasgow G12 0YN, UK
| | - Emma Searle
- The Christie NHS Foundation Trust, Manchester M20 4BX, UK
| | - Tim C P Somervaille
- Leukaemia Biology Laboratory, Cancer Research UK Manchester Institute, The University of Manchester, Manchester M20 4BX, UK; The Christie NHS Foundation Trust, Manchester M20 4BX, UK.
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25
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Zhang L, Zhu K, Xu J, Chen X, Sheng C, Zhang D, Yang Y, Sun L, Zhao H, Wang X, Tao B, Zhou L, Liu J. Acetyltransferases CBP/p300 Control Transcriptional Switch of β-Catenin and Stat1 Promoting Osteoblast Differentiation. J Bone Miner Res 2023; 38:1885-1899. [PMID: 37850815 DOI: 10.1002/jbmr.4925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/02/2023] [Accepted: 10/13/2023] [Indexed: 10/19/2023]
Abstract
CREB-binding protein (CBP) (CREBBP) and p300 (EP300) are multifunctional histone acetyltransferases (HATs) with extensive homology. Germline mutations of CBP or p300 cause skeletal abnormalities in humans and mice. However, the precise roles of CBP/p300 in bone homeostasis remain elusive. Here, we report that conditional knockout of CBP or p300 in osteoblasts results in reduced bone mass and strength due to suppressed bone formation. The HAT activity is further confirmed to be responsible for CBP/p300-mediated osteogenesis using A-485, a selective inhibitor of CBP/p300 HAT. Mechanistically, CBP/p300 HAT governs osteogenic gene expression in part through transcriptional activation of β-catenin and inhibition of Stat1. Furthermore, acetylation of histone H3K27 and the transcription factor Foxo1 are demonstrated to be involved in CBP/p300 HAT-regulated β-catenin and Stat1 transcription, respectively. Taken together, these data identify acetyltransferases CBP/p300 as critical regulators that promote osteoblast differentiation and reveal an epigenetic mechanism responsible for maintaining bone homeostasis. © 2023 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Linlin Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Kecheng Zhu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jingzun Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaojing Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunxiang Sheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Deng Zhang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuying Yang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lihao Sun
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyan Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bei Tao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Libin Zhou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianmin Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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26
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Maruyama S, Yamazaki M, Abé T, Cheng J, Saku T, Tanuma JI. Hypoxia-Induced Biosynthesis of the Extracellular Matrix Molecules, Perlecan and Fibronectin, Promotes the Growth of Pleomorphic Adenoma Cells In Vitro Models. Biomedicines 2023; 11:2981. [PMID: 38001981 PMCID: PMC10669301 DOI: 10.3390/biomedicines11112981] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Salivary pleomorphic adenoma is histopathologically characterized by its colorful stroma with myxoid, chondroid, and hyaline appearances, due to enhanced biosynthesis of extracellular matrix (ECM) molecules and poor vascularity. Thus, pleomorphic adenoma cells embedded in the stroma typically survive under hypoxic conditions. We determined the expression kinetics of ECM molecules, such as perlecan and fibronectin (FN), under hypoxia in SM-AP1 cells which are duct epithelial differentiated cells, and in SM-AP4 cells, which are myoepithelial differentiated cells, cloned from pleomorphic adenoma of the parotid gland. We investigated hypoxia-inducible factor-1α (HIF-1α)-inducing pathways through a variety of ECM molecules in association with their cellular proliferation and migration. We observed that hypoxic conditions with elevated HIF-1α protein levels induced increased expression of perlecan and FN in SM-AP cells than in controls. Moreover, perlecan and FN knockdown reduced the proliferation of SM-AP1 and SM-AP4 cells under hypoxia. Further, SM-AP1 cell migration was enhanced by both perlecan and FN knockdown, whereas SM-AP4 cell migration was increased by perlecan knockdown and inhibited by fibronectin knockdown. The results indicated that pleomorphic adenoma cells can survive under hypoxic conditions by promoting cell proliferation via enhanced synthesis of ECM molecules. Overall, ECM molecules may be a new anti-tumor target under hypoxic conditions.
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Affiliation(s)
- Satoshi Maruyama
- Oral Pathology Section, Department of Surgical Pathology, Niigata University Hospital, 1-754 Asahimachi-dori, Chuo-ku, Niigata 951-8520, Japan
| | - Manabu Yamazaki
- Division of Oral Pathology, Department of Tissue Regeneration and Reconstruction, Faculty of Dentistry & Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkoucho-dori, Chuo-ku, Niigata 951-8514, Japan (T.A.); (J.-i.T.)
| | - Tatsuya Abé
- Division of Oral Pathology, Department of Tissue Regeneration and Reconstruction, Faculty of Dentistry & Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkoucho-dori, Chuo-ku, Niigata 951-8514, Japan (T.A.); (J.-i.T.)
| | - Jun Cheng
- Division of Oral Pathology, Department of Tissue Regeneration and Reconstruction, Faculty of Dentistry & Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkoucho-dori, Chuo-ku, Niigata 951-8514, Japan (T.A.); (J.-i.T.)
| | - Takashi Saku
- PCL Fukuoka Pathology Cytology Center, 4-11-32 Yoshizuka, Hakata-ku, Fukuoka 812-0041, Japan
| | - Jun-ichi Tanuma
- Division of Oral Pathology, Department of Tissue Regeneration and Reconstruction, Faculty of Dentistry & Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkoucho-dori, Chuo-ku, Niigata 951-8514, Japan (T.A.); (J.-i.T.)
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27
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Khan K, Zafar S, Badshah Y, Ashraf NM, Rafiq M, Danish L, Shabbir M, Trembley JH, Afsar T, Almajwal A, Razak S. Cross talk of tumor protein D52 (TPD52) with KLF9, PKCε, and MicroRNA 223 in ovarian cancer. J Ovarian Res 2023; 16:202. [PMID: 37833790 PMCID: PMC10571360 DOI: 10.1186/s13048-023-01292-1] [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: 04/26/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Gynecologic cancers comprise malignancies in the female reproductive organs. Ovarian cancer ranks sixth in terms of incidence rates while seventh in terms of mortality rates. The stage at which ovarian cancer is diagnosed mainly determines the survival outcomes of patients. Various screening approaches are presently employed for diagnosing ovarian cancer; however, these techniques have low accuracy and are non-specific, resulting in high mortality rates of patients due to this disease. Hence, it is crucial to identify improved screening and diagnostic markers to overcome this cancer. This study aimed to find new biomarkers to facilitate the prognosis and diagnosis of ovarian cancer. METHODS Bioinformatics approaches were used to predict the tertiary structure and cellular localization along with phylogenetic analysis of TPD52. Its molecular interactions were determined through KEGG analysis, and real-time PCR-based expression analysis was performed to assess its co-expression with another oncogenic cellular pathway (miR-223, KLF9, and PKCε) proteins in ovarian cancer. RESULTS Bioinformatics analysis depicted the cytoplasmic localization of TPD52 and the high conservation of its coiled-coil domains. Further study revealed that TPD52 mRNA and miRNA-223 expression was elevated, while the expression of KLF 9 and PKCε was reduced in the blood of ovarian cancer patients. Furthermore, TPD52 and miR-223 expression were upregulated in the early stages of cancer and non-metastatic cancers. CONCLUSION TPD52, miR-223, PKCε, and KLF9, can be used as a blood based markers for disease prognosis, metastasis, and treatment response. The study outcomes hold great potential to be translated at the clinical level after further validation on larger cohorts.
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Affiliation(s)
- Khushbukhat Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan
| | - Sameen Zafar
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan
| | - Yasmin Badshah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Mehak Rafiq
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology, Islamabad, 44000, Pakistan
| | - Lubna Danish
- Agricultural Research Institute, Tarnab, Peshawar, Pakistan
| | - Maria Shabbir
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan.
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
| | - Janeen H Trembley
- Research Service, Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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28
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Kotha SR, Staller MV. Clusters of acidic and hydrophobic residues can predict acidic transcriptional activation domains from protein sequence. Genetics 2023; 225:iyad131. [PMID: 37462277 PMCID: PMC10550315 DOI: 10.1093/genetics/iyad131] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/03/2023] [Indexed: 10/06/2023] Open
Abstract
Transcription factors activate gene expression in development, homeostasis, and stress with DNA binding domains and activation domains. Although there exist excellent computational models for predicting DNA binding domains from protein sequence, models for predicting activation domains from protein sequence have lagged, particularly in metazoans. We recently developed a simple and accurate predictor of acidic activation domains on human transcription factors. Here, we show how the accuracy of this human predictor arises from the clustering of aromatic, leucine, and acidic residues, which together are necessary for acidic activation domain function. When we combine our predictor with the predictions of convolutional neural network (CNN) models trained in yeast, the intersection is more accurate than individual models, emphasizing that each approach carries orthogonal information. We synthesize these findings into a new set of activation domain predictions on human transcription factors.
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Affiliation(s)
- Sanjana R Kotha
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
| | - Max Valentín Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- Center for Computational Biology, University of California, Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub—San Francisco, San Francisco, CA 94158, USA
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29
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Brown AD, Vergunst KL, Branch M, Blair CM, Dupré DJ, Baillie GS, Langelaan DN. Structural basis of CBP/p300 recruitment by the microphthalmia-associated transcription factor. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119520. [PMID: 37353163 DOI: 10.1016/j.bbamcr.2023.119520] [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: 03/07/2023] [Revised: 05/19/2023] [Accepted: 06/08/2023] [Indexed: 06/25/2023]
Abstract
The microphthalmia-associated transcription factor (MITF) is a master regulator of the melanocyte cell lineage. Aberrant MITF activity can lead to multiple malignancies including skin cancer, where it modulates the progression and invasiveness of melanoma. MITF-regulated gene expression requires recruitment of the transcriptional co-regulator CBP/p300, but details of this process are not fully defined. In this study, we investigate the structural and functional interaction between the MITF N-terminal transactivation domain (MITFTAD) and CBP/p300. Using pulldown assays and nuclear magnetic resonance spectroscopy we determined that MITFTAD is intrinsically disordered and binds to the TAZ1 and TAZ2 domains of CBP/p300 with moderate affinity. The solution-state structure of the MITFTAD:TAZ2 complex reveals that MITF interacts with a hydrophobic surface of TAZ2, while remaining somewhat dynamic. Peptide array and mutagenesis experiments determined that an acidic motif is integral to the MITFTAD:TAZ2 interaction and is necessary for transcriptional activity of MITF. Peptides that bind to the same surface of TAZ2 as MITFTAD, such as the adenoviral protein E1A, are capable of displacing MITF from TAZ2 and inhibiting transactivation. These findings provide insight into co-activator recruitment by MITF that are fundamental to our understanding of MITF targeted gene regulation and melanoma biology.
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Affiliation(s)
- Alexandra D Brown
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Kathleen L Vergunst
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Makenzie Branch
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Connor M Blair
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - Denis J Dupré
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - George S Baillie
- School of Cardiovascular & Metabolic Health, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom of Great Britain and Northern Ireland
| | - David N Langelaan
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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30
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Can AT, Mitchell JS, Dutton M, Bennett M, Hermens DF, Lagopoulos J. Insights into the neurobiology of suicidality: explicating the role of glutamatergic systems through the lens of ketamine. Psychiatry Clin Neurosci 2023; 77:513-529. [PMID: 37329495 DOI: 10.1111/pcn.13572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/16/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]
Abstract
Suicidality is a prevalent mental health condition, and managing suicidal patients is one of the most challenging tasks for health care professionals due to the lack of rapid-acting, effective psychopharmacological treatment options. According to the literature, suicide has neurobiological underpinnings that are not fully understood, and current treatments for suicidal tendencies have considerable limitations. To treat suicidality and prevent suicide, new treatments are required; to achieve this, the neurobiological processes underlying suicidal behavior must be thoroughly investigated. Although multiple neurotransmitter systems, particularly serotonergic systems, have been studied in the past, less has been reported in relation to disruptions in glutamatergic neurotransmission, neuronal plasticity, and neurogenesis that result from stress-related abnormalities of the hypothalamic-pituitary-adrenal system. Informed by the literature, which reports robust antisuicidal and antidepressive properties of subanaesthetic doses of ketamine, this review aims to provide an examination of the neurobiology of suicidality (and relevant mood disorders) with implications of pertinent animal, clinical, and postmortem studies. We discuss dysfunctions in the glutamatergic system, which may play a role in the neuropathology of suicidality and the role of ketamine in restoring synaptic connectivity at the molecular levels.
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Affiliation(s)
- Adem Tevfik Can
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| | - Jules Shamus Mitchell
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| | - Megan Dutton
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| | - Maxwell Bennett
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
| | | | - Jim Lagopoulos
- Thompson Institute, University of the Sunshine Coast, Birtinya, Queensland, Australia
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31
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Yang T, Buholzer KJ, Sottini A, Cao X, deMello A, Nettels D, Schuler B. Rapid droplet-based mixing for single-molecule spectroscopy. Nat Methods 2023; 20:1479-1482. [PMID: 37749213 DOI: 10.1038/s41592-023-01995-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 08/02/2023] [Indexed: 09/27/2023]
Abstract
Probing non-equilibrium dynamics with single-molecule spectroscopy is important for dissecting biomolecular mechanisms. However, existing microfluidic rapid-mixing systems for this purpose are incompatible with surface-adhesive biomolecules, exhibit undesirable flow dispersion and are often demanding to fabricate. Here we introduce droplet-based microfluidic mixing for single-molecule spectroscopy to overcome these limitations in a wide range of applications. We demonstrate its robust functionality with binding kinetics of even very surface-adhesive proteins on the millisecond timescale.
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Affiliation(s)
- Tianjin Yang
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
| | - Karin J Buholzer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Xiaobao Cao
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Andrew deMello
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
- Department of Physics, University of Zurich, Zurich, Switzerland.
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32
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Park GT, Moon JK, Park S, Park SK, Baek J, Seo MS. Genome-wide analysis of KIX gene family for organ size regulation in soybean ( Glycine max L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1252016. [PMID: 37828927 PMCID: PMC10565003 DOI: 10.3389/fpls.2023.1252016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/11/2023] [Indexed: 10/14/2023]
Abstract
The KIX domain, conserved among various nuclear and co-activator factors, acts as a binding site that interacts with other transcriptional activators and co-activators, playing a crucial role in gene expression regulation. In plants, the KIX domain is involved in plant hormone signaling, stress response regulation, cell cycle control, and differentiation, indicating its potential relevance to crop productivity. This study aims to identify and characterize KIX domains within the soybean (Glycine max L.) genome to predict their potential role in improving crop productivity. The conservation and evolutionary history of the KIX domains were explored in 59 plant species, confirming the presence of the KIX domains in diverse plants. Specifically, 13 KIX domains were identified within the soybean genome and classified into four main groups, namely GmKIX8/9, GmMED15, GmHAC, and GmRECQL, through sequence alignment, structural analysis, and phylogenetic tree construction. Association analysis was performed between KIX domain haplotypes and soybean seed-related agronomic traits using re-sequencing data from a core collection of 422 accessions. The results revealed correlations between SNP variations observed in GmKIX8-3 and GmMED15-4 and soybean seed phenotypic traits. Additionally, transcriptome analysis confirmed significant expression of the KIX domains during the early stages of soybean seed development. This study provides the first characterization of the structural, expression, genomic haplotype, and molecular features of the KIX domain in soybean, offering a foundation for functional analysis of the KIX domain in soybean and other plants.
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Affiliation(s)
- Gyu Tae Park
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
| | - Jung-Kyung Moon
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
| | - Sewon Park
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
| | - Soo-Kwon Park
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
| | - JeongHo Baek
- Gene Engineering Division, National Institute of Agricultural Science, Rural Development Administration (RDA), Jeonju, Republic of Korea
| | - Mi-Suk Seo
- Crop Foundation Research Division, National Institute of Crop Sciences, Rural Development Administration (RDA), Wanju-gun, Republic of Korea
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33
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Brown AD, Lynch K, Langelaan DN. The C-terminal transactivation domain of MITF interacts promiscuously with co-activator CBP/p300. Sci Rep 2023; 13:16094. [PMID: 37752231 PMCID: PMC10522771 DOI: 10.1038/s41598-023-43207-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/21/2023] [Indexed: 09/28/2023] Open
Abstract
The microphthalmia-associated transcription factor (MITF) is one of four closely related members of the MiT/TFE family (TFEB, TFE3, TFEC) that regulate a wide range of cellular processes. MITF is a key regulator of melanocyte-associated genes, and essential to proper development of the melanocyte cell lineage. Abnormal MITF activity can contribute to the onset of several diseases including melanoma, where MITF is an amplified oncogene. To enhance transcription, MITF recruits the co-activator CREB-binding protein (CBP) and its homolog p300 to gene promoters, however the molecular determinants of their interaction are not yet fully understood. Here, we characterize the interactions between the C-terminal MITF transactivation domain and CBP/p300. Using NMR spectroscopy, protein pulldown assays, and isothermal titration calorimetry we determine the C-terminal region of MITF is intrinsically disordered and binds with high-affinity to both TAZ1 and TAZ2 of CBP/p300. Mutagenesis studies revealed two conserved motifs within MITF that are necessary for TAZ2 binding and critical for MITF-dependent transcription of a reporter gene. Finally, we observe the transactivation potential of the MITF C-terminal region is reliant on the N-terminal transactivation domain for function. Taken together, our study helps elucidate the molecular details of how MITF interacts with CBP/p300 through multiple redundant interactions that lend insight into MITF function in melanocytes and melanoma.
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Affiliation(s)
- Alexandra D Brown
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Kyle Lynch
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - David N Langelaan
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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Rubio K, Molina-Herrera A, Pérez-González A, Hernández-Galdámez HV, Piña-Vázquez C, Araujo-Ramos T, Singh I. EP300 as a Molecular Integrator of Fibrotic Transcriptional Programs. Int J Mol Sci 2023; 24:12302. [PMID: 37569677 PMCID: PMC10418647 DOI: 10.3390/ijms241512302] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/13/2023] Open
Abstract
Fibrosis is a condition characterized by the excessive accumulation of extracellular matrix proteins in tissues, leading to organ dysfunction and failure. Recent studies have identified EP300, a histone acetyltransferase, as a crucial regulator of the epigenetic changes that contribute to fibrosis. In fact, EP300-mediated acetylation of histones alters global chromatin structure and gene expression, promoting the development and progression of fibrosis. Here, we review the role of EP300-mediated epigenetic regulation in multi-organ fibrosis and its potential as a therapeutic target. We discuss the preclinical evidence that suggests that EP300 inhibition can attenuate fibrosis-related molecular processes, including extracellular matrix deposition, inflammation, and epithelial-to-mesenchymal transition. We also highlight the contributions of small molecule inhibitors and gene therapy approaches targeting EP300 as novel therapies against fibrosis.
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Affiliation(s)
- Karla Rubio
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus Valsequillo, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
- Laboratoire IMoPA, Université de Lorraine, CNRS, UMR 7365, F-54000 Nancy, France
| | - Alejandro Molina-Herrera
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus Valsequillo, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
| | - Andrea Pérez-González
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, Ecocampus Valsequillo, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72570, Mexico
| | - Hury Viridiana Hernández-Galdámez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07360, Mexico
| | - Carolina Piña-Vázquez
- Departamento de Biología Celular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México 07360, Mexico
| | - Tania Araujo-Ramos
- Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Indrabahadur Singh
- Emmy Noether Research Group Epigenetic Machineries and Cancer, Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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35
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Guo Z, Yu X, Zhao S, Zhong X, Huang D, Feng R, Li P, Fang Z, Hu Y, Zhang Z, Abdurahman M, Huang L, Zhao Y, Wang X, Ge J, Li H. SIRT6 deficiency in endothelial cells exacerbates oxidative stress by enhancing HIF1α accumulation and H3K9 acetylation at the Ero1α promoter. Clin Transl Med 2023; 13:e1377. [PMID: 37598403 PMCID: PMC10440057 DOI: 10.1002/ctm2.1377] [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: 01/09/2023] [Revised: 08/06/2023] [Accepted: 08/11/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND SIRT6, an important NAD+ -dependent protein, protects endothelial cells from inflammatory and oxidative stress injuries. However, the role of SIRT6 in cardiac microvascular endothelial cells (CMECs) under ischemia-reperfusion injury (IRI) remains unclear. METHODS The HUVECs model of oxygen-glucose deprivation/reperfusion (OGD/R) was established to simulate the endothelial IRI in vitro. Endoplasmic reticulum oxidase 1 alpha (Ero1α) mRNA and protein levels in SIRT6-overexpressing or SIRT6-knockdown cells were measured by qPCR and Western blotting. The levels of H2 O2 and mitochondrial reactive oxygen species (ROS) were detected to evaluate the status of oxidative stress. The effects of SIRT6 deficiency and Ero1α knockdown on cellular endoplasmic reticulum stress (ERS), inflammation, apoptosis and barrier function were detected by a series of molecular biological experiments and functional experiments in vitro. Chromatin immunoprecipitation, Western blotting, qPCR, and site-specific mutation experiments were used to examine the underlying molecular mechanisms. Furthermore, endothelial cell-specific Sirt6 knockout (ecSirt6-/- ) mice were subjected to cardiac ischemia-reperfusion surgery to investigate the effects of SIRT6 in CMECs in vivo. RESULTS The expression of Ero1α was significantly upregulated in SIRT6-knockdown endothelial cells, and high Ero1α expression correlated with the accumulation of H2 O2 and mitochondrial ROS. In addition, SIRT6 deficiency increased ERS, inflammation, apoptosis and endothelial permeability, and these effects could be significantly attenuated by Ero1α knockdown. The deacetylase catalytic activity of SIRT6 was important in regulating Ero1α expression and these biological processes. Mechanistically, SIRT6 inhibited the enrichment of HIF1α and p300 at the Ero1α promoter through deacetylating H3K9, thereby antagonizing HIF1α/p300-mediated Ero1α expression. Compared with SIRT6-wild-type (SIRT6-WT) cells, cells expressing the SIRT6-H133Y-mutant and SIRT6-R65A-mutant exhibited increased Ero1α expression. Furthermore, ecSirt6-/- mice subjected to ischemia-reperfusion surgery exhibited increased Ero1α expression and ERS in CMECs and worsened injuries to microvascular barrier function and cardiac function. CONCLUSIONS Our results revealed an epigenetic mechanism associated with SIRT6 and Ero1α expression and highlighted the therapeutic potential of targeting the SIRT6-HIF1α/p300-Ero1α axis.
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Affiliation(s)
- Zhenyang Guo
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Xueting Yu
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Shuang Zhao
- Department of Medical ExaminationShanghai Xuhui District Central HospitalShanghaiChina
| | - Xin Zhong
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Dong Huang
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Runyang Feng
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Peng Li
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Zheyan Fang
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Yiqing Hu
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Zhentao Zhang
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Mukaddas Abdurahman
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
| | - Lei Huang
- Department of MolecularCell and Cancer BiologyProgram in Molecular MedicineUniversity of Massachusetts Medical SchoolMAUSA
| | - Yun Zhao
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- State Key Laboratory of Cell BiologyCenter for Excellence in Molecular Cell ScienceChinese Academy of SciencesShanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang ProvinceSchool of Life ScienceHangzhou Institute for Advanced Study, University of Chinese Academy of SciencesHangzhouChina
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care MedicineZhongshan HospitalShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Junbo Ge
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
- Department of CardiologyZhongshan Hospital, Fudan UniversityShanghaiChina
- National Clinical Research Center for Interventional MedicineShanghaiChina
- Shanghai Clinical Research Center for Interventional MedicineShanghaiChina
- Key Laboratory of Viral Heart DiseasesNational Health CommissionShanghaiChina
- Key Laboratory of Viral Heart DiseasesChinese Academy of Medical SciencesShanghaiChina
| | - Hua Li
- Department of Cardiology, Zhongshan HospitalShanghai Institute of Cardiovascular Diseases, Fudan UniversityShanghaiChina
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Ryakiotakis E, Fousfouka D, Stamatakis A. Maternal neglect alters reward-anticipatory behavior, social status stability, and reward circuit activation in adult male rats. Front Neurosci 2023; 17:1201345. [PMID: 37521688 PMCID: PMC10375725 DOI: 10.3389/fnins.2023.1201345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/15/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Adverse early life experiences affect neuronal growth and maturation of reward circuits that modify behavior under reward predicting conditions. Previous studies demonstrate that rats undergoing denial of expected reward in the form of maternal contact (DER-animal model of maternal neglect) during early post-natal life developed anhedonia, aggressive play-fight behaviors and aberrant prefrontal cortex structure and neurochemistry. Although many studies revealed social deficiency following early-life stress most reports focus on individual animal tasks. Thus, attention needs to be given on the social effects during group tasks in animals afflicted by early life adversity. Methods To investigate the potential impact of the DER experience on the manifestation of behavioral responses induced by natural rewards, we evaluated: 1) naïve adult male sexual preference and performance, and 2) anticipatory behavior during a group 2-phase food anticipation learning task composed of a context-dependent and a cue-dependent learning period. Results DER rats efficiently spent time in the vicinity of and initiated sexual intercourse with receptive females suggesting an intact sexual reward motivation and consummation. Interestingly, during the context-dependent phase of food anticipation training DER rats displayed a modified exploratory activity and lower overall reward-context association. Moreover, during the cue-dependent phase DER rats displayed a mild deficit in context-reward association while increased cue-dependent locomotion. Additionally, DER rats displayed unstable food access priority following food presentation. These abnormal behaviours were accompanied by overactivation of the ventral prefrontal cortex and nucleus accumbens, as assessed by pCREB levels. Conclusions/discussion Collectively, these data show that the neonatal DER experience resulted in adulthood in altered activation of the reward circuitry, interfered with the normal formation of context-reward associations, and disrupted normal reward access hierarchy formation. These findings provide additional evidence to the deleterious effects of early life adversity on reward system, social hierarchy formation, and brain function.
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Affiliation(s)
- Ermis Ryakiotakis
- Laboratory of Biology-Biochemistry, Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitra Fousfouka
- Laboratory of Biology-Biochemistry, Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
- MSc Program in Molecular Biomedicine, Medical School of National and Kapodistrian University of Athens, Athens, Greece
| | - Antonios Stamatakis
- Laboratory of Biology-Biochemistry, Faculty of Nursing, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
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Gioukaki C, Georgiou A, Gkaralea LE, Kroupis C, Lazaris AC, Alamanis C, Thomopoulou GE. Unravelling the Role of P300 and TMPRSS2 in Prostate Cancer: A Literature Review. Int J Mol Sci 2023; 24:11299. [PMID: 37511059 PMCID: PMC10379122 DOI: 10.3390/ijms241411299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/26/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Prostate cancer is one of the most common malignant diseases in men, and it contributes significantly to the increased mortality rate in men worldwide. This study aimed to review the roles of p300 and TMPRSS2 (transmembrane protease, serine 2) in the AR (androgen receptor) pathway as they are closely related to the development and progression of prostate cancer. This paper represents a library-based study conducted by selecting the most suitable, up-to-date scientific published articles from online journals. We focused on articles that use similar techniques, particularly those that use prostate cancer cell lines and immunohistochemical staining to study the molecular impact of p300 and TMPRSS2 in prostate cancer specimens. The TMPRSS2:ERG fusion is considered relevant to prostate cancer, but its association with the development and progression as well as its clinical significance have not been fully elucidated. On the other hand, high p300 levels in prostate cancer biopsies predict larger tumor volumes, extraprostatic extension of disease, and seminal vesicle involvement at prostatectomy, and may be associated with prostate cancer progression after surgery. The inhibition of p300 has been shown to reduce the proliferation of prostate cancer cells with TMPRSS2:ETS (E26 transformation-specific) fusions, and combining p300 inhibitors with other targeted therapies may increase their efficacy. Overall, the interplay between the p300 and TMPRSS2 pathways is an active area of research.
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Affiliation(s)
- Charitomeni Gioukaki
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Alexandros Georgiou
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | | | - Christos Kroupis
- Department of Clinical Biochemistry, Attikon University Hospital, National and Kapodistrian University of Athens, 12461 Athens, Greece
| | - Andreas C Lazaris
- First Department of Pathology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Christos Alamanis
- 1st Urology Department, Laiko Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Georgia Eleni Thomopoulou
- Cytopathology Department, Attikon University Hospital, National and Kapodistrian University of Athens, 12461 Athens, Greece
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Wang Q, Zhou M, Zhang H, Hou Z, Liu D. Hypoxia Treatment of Adipose Mesenchymal Stem Cells Promotes the Growth of Dermal Papilla Cells via HIF-1α and ERK1/2 Signaling Pathways. Int J Mol Sci 2023; 24:11198. [PMID: 37446376 DOI: 10.3390/ijms241311198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/25/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Dermal papilla cells (DPCs) cultured in vitro induce hair follicle formation. Using a hypoxic microenvironment to culture adipose mesenchymal stem cells (ADSCs) can promote hair follicle growth. However, the exact molecular mechanisms underlying this process remain unclear. In this study, ADSCs and DPCs from Arbas Cashmere goats were used. A hypoxic microenvironment promoted the proliferation of ADSCs and increased the pluripotency of ADSCs. The growth factors vascular endothelial growth factor (VEGF), basic fibroblast growth factor (bFGF), and platelet-derived growth factor (PDGF) were upregulated in ADSCs in the hypoxia-conditioned medium (Hypo-cm). Hypo-cm also enhanced the ability of DPCs to induce hair follicle formation. Inhibitors of the ERK1/2 signaling pathway caused the expressions of growth factors that increased in hypoxic microenvironments to decrease; moreover, hypoxia-inducible factor-1α (HIF-1α) increased the expression levels of VEGF, bFGF, and PDGF and inhibited the expression of bone morphogenic protein 7 (BMP7). In conclusion, these findings improve the theoretical basis for the development of gene therapy drugs for the treatment of alopecia areata and hair thinning.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Mei Zhou
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Hongyan Zhang
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Zhuang Hou
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
| | - Dongjun Liu
- State Key Laboratory of Reproductive Regulation & Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China
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Larsen K, Callesen H. Developmental expression of CREB1 and NFATC2 in pig embryos. Mol Biol Rep 2023:10.1007/s11033-023-08501-6. [PMID: 37171550 DOI: 10.1007/s11033-023-08501-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND The CREB1 gene encodes the cAMP response element binding protein 1 (CREB1), a leucine zipper transcription factor that regulates cellular gene expression in response to elevated levels of intracellular cAMP. When activated by phosphorylation, CREB1 binds to the cAMP response element (CRE) of the promoters of its target genes. CREB1 is an essential component in many physiological processes, and its function is correlated to neurodevelopment, plasticity and cell survival, and learning and memory. The NFATC2 gene codes for the nuclear factor of activated T-cells 2 protein. The NFATC2 protein is a DNA-binding protein that functions as an inducer of gene transcription during immune response. METHODS AND RESULTS The aim of the present study was to examine the developmental expression of porcine CREB1 and NFACT2 transcripts. The expression of CREB1 and NFACT2 mRNA was examined by quantitative real-time RT-PCR. For the CREB1 transcript, we found significant reduction in transcript levels in the brain stem and basal ganglia during porcine embryo development, determined from day 60 to day 115 of gestation. In contrast, a significant increase in CREB1 mRNA was detected in the lungs during embryo development. No significant changes in the NFATC2 transcript were detected in porcine brain tissue during embryo development. CONCLUSIONS Differential CREB1 mRNA expression was found in pig brain tissues during embryo development.
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Affiliation(s)
- Knud Larsen
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus C, DK-8000, Denmark.
| | - Henrik Callesen
- Henrik Callesen, Department of Animal and Veterinary Sciences, Blichers Allé 20, Tjele, DK-8830, Denmark
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40
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Cermakova K, Hodges HC. Interaction modules that impart specificity to disordered protein. Trends Biochem Sci 2023; 48:477-490. [PMID: 36754681 PMCID: PMC10106370 DOI: 10.1016/j.tibs.2023.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 02/09/2023]
Abstract
Intrinsically disordered regions (IDRs) are especially enriched among proteins that regulate chromatin and transcription. As a result, mechanisms that influence specificity of IDR-driven interactions have emerged as exciting unresolved issues for understanding gene regulation. We review the molecular elements frequently found within IDRs that confer regulatory specificity. In particular, we summarize the differing roles of disordered low-complexity regions (LCRs) and short linear motifs (SLiMs) towards selective nuclear regulation. Examination of IDR-driven interactions highlights SLiMs as organizers of selectivity, with widespread roles in gene regulation and integration of cellular signals. Analysis of recurrent interactions between SLiMs and folded domains suggests diverse avenues for SLiMs to influence phase-separated condensates and highlights opportunities to manipulate these interactions for control of biological activity.
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Affiliation(s)
- Katerina Cermakova
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - H Courtney Hodges
- Department of Molecular and Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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41
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Sato N, Suetaka S, Hayashi Y, Arai M. Rational peptide design for inhibition of the KIX-MLL interaction. Sci Rep 2023; 13:6330. [PMID: 37072438 PMCID: PMC10113271 DOI: 10.1038/s41598-023-32848-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/03/2023] [Indexed: 05/03/2023] Open
Abstract
The kinase-inducible domain interacting (KIX) domain is an integral part of the general transcriptional coactivator CREB-binding protein, and has been associated with leukemia, cancer, and various viral diseases. Hence, the KIX domain has attracted considerable attention in drug discovery and development. Here, we rationally designed a KIX inhibitor using a peptide fragment corresponding to the transactivation domain (TAD) of the transcriptional activator, mixed-lineage leukemia protein (MLL). We performed theoretical saturation mutagenesis using the Rosetta software to search for mutants expected to bind KIX more tightly than the wild-type MLL TAD. Mutant peptides with higher helical propensities were selected for experimental characterization. We found that the T2857W mutant of the MLL TAD peptide had the highest binding affinity for KIX compared to the other 12 peptides designed in this study. Moreover, the peptide had a high inhibitory effect on the KIX-MLL interaction with a half-maximal inhibitory concentration close to the dissociation constant for this interaction. To our knowledge, this peptide has the highest affinity for KIX among all previously reported inhibitors that target the MLL site of KIX. Thus, our approach may be useful for rationally developing helical peptides that inhibit protein-protein interactions implicated in the progression of various diseases.
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Affiliation(s)
- Nao Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Shunji Suetaka
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
- Environmental Science Center, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-0033, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
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42
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DelRosso N, Tycko J, Suzuki P, Andrews C, Aradhana, Mukund A, Liongson I, Ludwig C, Spees K, Fordyce P, Bassik MC, Bintu L. Large-scale mapping and mutagenesis of human transcriptional effector domains. Nature 2023; 616:365-372. [PMID: 37020022 PMCID: PMC10484233 DOI: 10.1038/s41586-023-05906-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Human gene expression is regulated by more than 2,000 transcription factors and chromatin regulators1,2. Effector domains within these proteins can activate or repress transcription. However, for many of these regulators we do not know what type of effector domains they contain, their location in the protein, their activation and repression strengths, and the sequences that are necessary for their functions. Here, we systematically measure the effector activity of more than 100,000 protein fragments tiling across most chromatin regulators and transcription factors in human cells (2,047 proteins). By testing the effect they have when recruited at reporter genes, we annotate 374 activation domains and 715 repression domains, roughly 80% of which are new and have not been previously annotated3-5. Rational mutagenesis and deletion scans across all the effector domains reveal aromatic and/or leucine residues interspersed with acidic, proline, serine and/or glutamine residues are necessary for activation domain activity. Furthermore, most repression domain sequences contain sites for small ubiquitin-like modifier (SUMO)ylation, short interaction motifs for recruiting corepressors or are structured binding domains for recruiting other repressive proteins. We discover bifunctional domains that can both activate and repress, some of which dynamically split a cell population into high- and low-expression subpopulations. Our systematic annotation and characterization of effector domains provide a rich resource for understanding the function of human transcription factors and chromatin regulators, engineering compact tools for controlling gene expression and refining predictive models of effector domain function.
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Affiliation(s)
| | - Josh Tycko
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Peter Suzuki
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Cecelia Andrews
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Aradhana
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Adi Mukund
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Ivan Liongson
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Connor Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Polly Fordyce
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- ChEM-H Institute, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
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43
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Brown AD, Cranstone C, Dupré DJ, Langelaan DN. β-Catenin interacts with the TAZ1 and TAZ2 domains of CBP/p300 to activate gene transcription. Int J Biol Macromol 2023; 238:124155. [PMID: 36963539 DOI: 10.1016/j.ijbiomac.2023.124155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 03/26/2023]
Abstract
The transcriptional co-regulator β-catenin is a critical member of the canonical Wnt signaling pathway, which plays an important role in regulating cell fate. Deregulation of the Wnt/β-catenin pathway is characteristic in the development of major types of cancer, where accumulation of β-catenin promotes cancer cell proliferation and renewal. β-catenin gene expression is facilitated through recruitment of co-activators such as histone acetyltransferases CBP/p300; however, the mechanism of their interaction is not fully understood. Here we investigate the interaction between the C-terminal transactivation domain of β-catenin and CBP/p300. Using a combination of pulldown assays, isothermal titration calorimetry, and nuclear resonance spectroscopy we determine the disordered C-terminal region of β-catenin binds promiscuously to the TAZ1 and TAZ2 domains of CBP/p300. We then map the interaction site of the C-terminal β-catenin transactivation domain onto TAZ1 and TAZ2 using chemical-shift perturbation studies. Luciferase-based gene reporter assays indicate Asp750-Leu781 is critical to β-catenin gene activation, and mutagenesis revealed that acidic and hydrophobic residues within this region are necessary to maintain TAZ1 binding. These results outline a mechanism of Wnt/β-catenin gene regulation that underlies cell development and provides a framework to develop methods to block β-catenin dependent signaling.
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Affiliation(s)
- Alexandra D Brown
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Connor Cranstone
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Denis J Dupré
- Department of Pharmacology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - David N Langelaan
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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Leopold Wager CM, Bonifacio JR, Simper J, Naoun AA, Arnett E, Schlesinger LS. Activation of transcription factor CREB in human macrophages by Mycobacterium tuberculosis promotes bacterial survival, reduces NF-kB nuclear transit and limits phagolysosome fusion by reduced necroptotic signaling. PLoS Pathog 2023; 19:e1011297. [PMID: 37000865 PMCID: PMC10096260 DOI: 10.1371/journal.ppat.1011297] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 04/12/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023] Open
Abstract
Macrophages are a first line of defense against pathogens. However, certain invading microbes modify macrophage responses to promote their own survival and growth. Mycobacterium tuberculosis (M.tb) is a human-adapted intracellular pathogen that exploits macrophages as an intracellular niche. It was previously reported that M.tb rapidly activates cAMP Response Element Binding Protein (CREB), a transcription factor that regulates diverse cellular responses in macrophages. However, the mechanism(s) underlying CREB activation and its downstream roles in human macrophage responses to M.tb are largely unknown. Herein we determined that M.tb-induced CREB activation is dependent on signaling through MAPK p38 in human monocyte-derived macrophages (MDMs). Using a CREB-specific inhibitor, we determined that M.tb-induced CREB activation leads to expression of immediate early genes including COX2, MCL-1, CCL8 and c-FOS, as well as inhibition of NF-kB p65 nuclear localization. These early CREB-mediated signaling events predicted that CREB inhibition would lead to enhanced macrophage control of M.tb growth, which we observed over days in culture. CREB inhibition also led to phosphorylation of RIPK3 and MLKL, hallmarks of necroptosis. However, this was unaccompanied by cell death at the time points tested. Instead, bacterial control corresponded with increased colocalization of M.tb with the late endosome/lysosome marker LAMP-1. Increased phagolysosomal fusion detected during CREB inhibition was dependent on RIPK3-induced pMLKL, indicating that M.tb-induced CREB signaling limits phagolysosomal fusion through inhibition of the necroptotic signaling pathway. Altogether, our data show that M.tb induces CREB activation in human macrophages early post-infection to create an environment conducive to bacterial growth. Targeting certain aspects of the CREB-induced signaling pathway may represent an innovative approach for development of host-directed therapeutics to combat TB.
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Affiliation(s)
- Chrissy M. Leopold Wager
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Jordan R. Bonifacio
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Jan Simper
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- Medical Scientist Training Program, Department of Microbiology, Immunology and Molecular Genetics, UT Health Science Center San Antonio, San Antonio, Texas, United States of America
| | - Adrian A. Naoun
- Department of Biology, The University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Eusondia Arnett
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Larry S. Schlesinger
- Host Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
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Effects of the Acetyltransferase p300 on Tumour Regulation from the Novel Perspective of Posttranslational Protein Modification. Biomolecules 2023; 13:biom13030417. [PMID: 36979352 PMCID: PMC10046601 DOI: 10.3390/biom13030417] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
p300 acts as a transcription coactivator and an acetyltransferase that plays an important role in tumourigenesis and progression. In previous studies, it has been confirmed that p300 is an important regulator in regulating the evolution of malignant tumours and it also has extensive functions. From the perspective of non-posttranslational modification, it has been proven that p300 can participate in regulating many pathophysiological processes, such as activating oncogene transcription, promoting tumour cell growth, inducing apoptosis, regulating immune function and affecting embryo development. In recent years, p300 has been found to act as an acetyltransferase that catalyses a variety of protein modification types, such as acetylation, propanylation, butyylation, 2-hydroxyisobutyration, and lactylation. Under the catalysis of this acetyltransferase, it plays its crucial tumourigenic driving role in many malignant tumours. Therefore, the function of p300 acetyltransferase has gradually become a research hotspot. From a posttranslational modification perspective, p300 is involved in the activation of multiple transcription factors and additional processes that promote malignant biological behaviours, such as tumour cell proliferation, migration, and invasion, as well as tumour cell apoptosis, drug resistance, and metabolism. Inhibitors of p300 have been developed and are expected to become novel anticancer drugs for several malignancies. We review the characteristics of the p300 protein and its functional role in tumour from the posttranslational modification perspective, as well as the current status of p300-related inhibitor research, with a view to gaining a comprehensive understanding of p300.
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46
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Bai Z, Li G, Kong X. Case report: a Chinese girl like atypical Rubinstein-Taybi syndrome caused by a novel heterozygous mutation of the EP300 gene. BMC Med Genomics 2023; 16:24. [PMID: 36797748 PMCID: PMC9933371 DOI: 10.1186/s12920-022-01424-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/19/2022] [Indexed: 02/18/2023] Open
Abstract
BACKGROUND Rubinstein-Taybi syndrome (RSTS) is an extremely rare autosomal dominant inheritable disorder caused by CREBBP and EP300 mutations, while atypical RSTS harbouring variant from the same genes but not obvious resembling RSTS. There are only a few cases of Menke-Hennekam syndrome (MKHK) with variant of exon 30 or 31 of CREBBP or EP300 gene have been reported that not resembling RSTS recent years. Atypical RSTS cannot be accurately classified as MKHK, nor is it easy to identify the obvious classic characteristics of RSTS. The clinical manifestations and genetic variation of atypical RSTS are not fully understood. CASE PRESENTATION We present a Chinese core family with a girl had recurrent respiratory tract infection and developmental delay. The patient with language and motor mild development retardation, she has slight abnormal facial features, mild hirsutism and post-axial hexadactylia of left foot. Her cisterna magna is enlarged to connect with the fourth ventricle, and the ventricular system is enlarged. She has a malacia beside the posterior horn of the left lateral ventricle. The patient has primary low immunoglobulin G and A, but her level of immunoglobulin M content in blood is normal. The patient harbors a novel heterozygous frameshift variant of c.2499dupG in exon 14 of EP300 gene, that it is proved to de novo origin. The mutation is judged to be a pathogenic mutation, and it has high-grade pathogenic evidence. CONCLUSION The clinical and genetic evaluation of this case corroborates that clinical features caused by c.2499dupG in exon 14 of EP300 are less marked than RSTS2 patient although it is difficult to establish an accurate genotype-phenotype correlation. Our additional case also helps to deepen the clinical and genetic spectrum in this disorder. The case provides a novel mutation of EP300 and enriches the phenotypes related with the gene. We have contributed new variation and disease information for guardians and doctors to broaden the knowledge about EP300-RSTS genotype and phenotype, this may contribute to ameliorate the health management of patients and improve the genetic counseling to the families.
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Affiliation(s)
- Zhouxian Bai
- grid.412633.10000 0004 1799 0733The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Gaopan Li
- grid.412633.10000 0004 1799 0733The Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 Henan China
| | - Xiangdong Kong
- The Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China.
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47
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Advances in the Histone Acetylation Modification in the Oral Squamous Cell Carcinoma. JOURNAL OF ONCOLOGY 2023. [DOI: 10.1155/2023/4616682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Oral squamous cell carcinoma (OSCC) is one of the common malignant tumors in the head and neck, characterized by high malignancy, rapid growth and metastasis, high invasive ability, and high mortality. In recent years, surgery combined with chemotherapy or radiotherapy remains the preferred clinical treatment for OSCC, despite considerable advances in diagnostic and therapeutic techniques. Hence, new targeted therapy is urgently needed. Histone modification affects the function of massive cells through histone acetyltransferase and histone deacetylase. Accompanied by the progress of some diseases, especially tumors, these proteins often show abnormal functions, and by reversing these abnormalities with drugs or gene therapy, the cancer phenotype can even be restored to normal. As a result, they are potential drug targets. This article reviewed the role of the histone dynamic process of acetylation modifications and their associated active modifying enzymes in the pathogenesis and progress of OSCC. Moreover, we explored the value of histone acetylation modification as a potential therapeutic target and the new progress of related drugs in clinical treatment.
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48
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Diabetes and Its Cardiovascular Complications: Potential Role of the Acetyltransferase p300. Cells 2023; 12:cells12030431. [PMID: 36766773 PMCID: PMC9914144 DOI: 10.3390/cells12030431] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Diabetes has been shown to accelerate vascular senescence, which is associated with chronic inflammation and oxidative stress, both implicated in the development of endothelial dysfunction. This condition represents the initial alteration linking diabetes to related cardiovascular (CV) complications. Recently, it has been hypothesised that the acetyltransferase, p300, may contribute to establishing an early vascular senescent phenotype, playing a relevant role in diabetes-associated inflammation and oxidative stress, which drive endothelial dysfunction. Specifically, p300 can modulate vascular inflammation through epigenetic mechanisms and transcription factors acetylation. Indeed, it regulates the inflammatory pathway by interacting with nuclear factor kappa-light-chain-enhancer of activated B cells p65 subunit (NF-κB p65) or by inducing its acetylation, suggesting a crucial role of p300 as a bridge between NF-κB p65 and the transcriptional machinery. Additionally, p300-mediated epigenetic modifications could be upstream of the activation of inflammatory cytokines, and they may induce oxidative stress by affecting the production of reactive oxygen species (ROS). Because several in vitro and in vivo studies shed light on the potential use of acetyltransferase inhibitors, a better understanding of the mechanisms underlying the role of p300 in diabetic vascular dysfunction could help in finding new strategies for the clinical management of CV diseases related to diabetes.
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49
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Evolutionary fine-tuning of residual helix structure in disordered proteins manifests in complex structure and lifetime. Commun Biol 2023; 6:63. [PMID: 36653471 PMCID: PMC9849366 DOI: 10.1038/s42003-023-04445-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Transcription depends on complex networks, where folded hub proteins interact with intrinsically disordered transcription factors undergoing coupled folding and binding. For this, local residual structure, a prototypical feature of intrinsic disorder, is key. Here, we dissect the unexplored functional potential of residual structure by comparing structure, kinetics, and thermodynamics within the model system constituted of the DREB2A transcription factor interacting with the αα-hub RCD1-RST. To maintain biological relevance, we developed an orthogonal evolutionary approach for the design of variants with varying amounts of structure. Biophysical analysis revealed a correlation between the amount of residual helical structure and binding affinity, manifested in altered complex lifetime due to changed dissociation rate constants. It also showed a correlation between helical structure in free and bound DREB2A variants. Overall, this study demonstrated how evolution can balance and fine-tune residual structure to regulate complexes in coupled folding and binding, potentially affecting transcription factor competition.
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50
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Buholzer KJ, McIvor J, Zosel F, Teppich C, Nettels D, Mercadante D, Schuler B. Multilayered allosteric modulation of coupled folding and binding by phosphorylation, peptidyl-prolyl cis/trans isomerization, and diversity of interaction partners. J Chem Phys 2022; 157:235102. [PMID: 36550025 DOI: 10.1063/5.0128273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) play key roles in cellular regulation, including signal transduction, transcription, and cell-cycle control. Accordingly, IDPs can commonly interact with numerous different target proteins, and their interaction networks are expected to be highly regulated. However, many of the underlying regulatory mechanisms have remained unclear. Here, we examine the representative case of the nuclear coactivator binding domain (NCBD) of the large multidomain protein CBP, a hub in transcriptional regulation, and the interaction with several of its binding partners. Single-molecule Förster resonance energy transfer measurements show that phosphorylation of NCBD reduces its binding affinity, with effects that vary depending on the binding partner and the site and number of modifications. The complexity of the interaction is further increased by the dependence of the affinities on peptidyl-prolyl cis/trans isomerization in NCBD. Overall, our results reveal the potential for allosteric regulation on at least three levels: the different affinities of NCBD for its different binding partners, the differential modulation of these affinities by phosphorylation, and the effect of peptidyl-prolyl cis/trans isomerization on binding.
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Affiliation(s)
- Karin J Buholzer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Jordan McIvor
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Franziska Zosel
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Christian Teppich
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Davide Mercadante
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
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