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Iwaï H, Beyer HM, Johansson JEM, Li M, Wlodawer A. The three-dimensional structure of the Vint domain from Tetrahymena thermophila suggests a ligand-regulated cleavage mechanism by the HINT fold. FEBS Lett 2024; 598:864-874. [PMID: 38351630 DOI: 10.1002/1873-3468.14817] [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: 11/12/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 04/23/2024]
Abstract
Vint proteins have been identified in unicellular metazoans as a novel hedgehog-related gene family, merging the von Willebrand factor type A domain and the Hedgehog/INTein (HINT) domains. We present the first three-dimensional structure of the Vint domain from Tetrahymena thermophila corresponding to the auto-processing domain of hedgehog proteins, shedding light on the unique features, including an adduct recognition region (ARR). Our results suggest a potential binding between the ARR and sulfated glycosaminoglycans like heparin sulfate. Moreover, we uncover a possible regulatory role of the ARR in the auto-processing by Vint domains, expanding our understanding of the HINT domain evolution and their use in biotechnological applications. Vint domains might have played a crucial role in the transition from unicellular to multicellular organisms.
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Affiliation(s)
- Hideo Iwaï
- Institute of Biotechnology, University of Helsinki, Finland
| | - Hannes M Beyer
- Institute of Biotechnology, University of Helsinki, Finland
| | | | - Mi Li
- Center for Structural Biology, National Cancer Institute, Frederick, MD, USA
- Basic Science Program, Frederick National Laboratory for Cancer Research, MD, USA
| | - Alexander Wlodawer
- Center for Structural Biology, National Cancer Institute, Frederick, MD, USA
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2
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Ciulla DA, Xu Z, Pezzullo JL, Dranchak P, Wang C, Giner JL, Inglese J, Callahan BP. Paracatalytic induction: Subverting specificity in hedgehog protein autoprocessing with small molecules. Methods Enzymol 2023; 685:1-41. [PMID: 37245899 PMCID: PMC10294009 DOI: 10.1016/bs.mie.2023.03.001] [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] [Indexed: 05/30/2023]
Abstract
Paracatalytic inducers are antagonists that shift the specificity of biological catalysts, resulting in non-native transformations. In this Chapter we describe methods to discover paracatalytic inducers of Hedgehog (Hh) protein autoprocessing. Native autoprocessing uses cholesterol as a substrate nucleophile to assist in cleaving an internal peptide bond within a precursor form of Hh. This unusual reaction is brought about by HhC, an enzymatic domain that resides within the C-terminal region of Hh precursor proteins. Recently, we reported paracatalytic inducers as a novel class of Hh autoprocessing antagonists. These small molecules bind HhC and tilt the substrate specificity away from cholesterol in favor of solvent water. The resulting cholesterol-independent autoproteolysis of the Hh precursor generates a non-native Hh side product with substantially reduced biological signaling activity. Protocols are provided for in vitro FRET-based and in-cell bioluminescence assays to discover and characterize paracatalytic inducers of Drosophila and human hedgehog protein autoprocessing, respectively.
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Affiliation(s)
- Daniel A Ciulla
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States.
| | - Zihan Xu
- Chemistry Department, Binghamton University, Binghamton, NY, United States
| | - John L Pezzullo
- State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Patricia Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - José-Luis Giner
- State University of New York, College of Environmental Science and Forestry, Syracuse, NY, United States
| | - James Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, United States; National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Brian P Callahan
- Chemistry Department, Binghamton University, Binghamton, NY, United States
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3
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Kandel N, Wang C. Hedgehog Autoprocessing: From Structural Mechanisms to Drug Discovery. Front Mol Biosci 2022; 9:900560. [PMID: 35669560 PMCID: PMC9163320 DOI: 10.3389/fmolb.2022.900560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 04/21/2022] [Indexed: 11/13/2022] Open
Abstract
Hedgehog (Hh) signaling plays pivotal roles in embryonic development. In adults, Hh signaling is mostly turned off but its abnormal activation is involved in many types of cancer. Hh signaling is initiated by the Hh ligand, generated from the Hh precursor by a specialized autocatalytic process called Hh autoprocessing. The Hh precursor consists of an N-terminal signaling domain (HhN) and a C-terminal autoprocessing domain (HhC). During Hh autoprocessing, the precursor is cleaved between N- and C-terminal domain followed by the covalent ligation of cholesterol to the last residue of HhN, which subsequently leads to the generation of Hh ligand for Hh signaling. Hh autoprocessing is at the origin of canonical Hh signaling and precedes all downstream signaling events. Mutations in the catalytic residues in HhC can lead to congenital defects such as holoprosencephaly (HPE). The aim of this review is to provide an in-depth summary of the progresses and challenges towards an atomic level understanding of the structural mechanisms of Hh autoprocessing. We also discuss drug discovery efforts to inhibit Hh autoprocessing as a new direction in cancer therapy.
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Affiliation(s)
- Nabin Kandel
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Chunyu Wang
- Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
- *Correspondence: Chunyu Wang,
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Kaushal JB, Batra SK, Rachagani S. Hedgehog signaling and its molecular perspective with cholesterol: a comprehensive review. Cell Mol Life Sci 2022; 79:266. [PMID: 35486193 PMCID: PMC9990174 DOI: 10.1007/s00018-022-04233-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/18/2022] [Accepted: 03/07/2022] [Indexed: 02/08/2023]
Abstract
Hedgehog (Hh) signaling is evolutionarily conserved and plays an instructional role in embryonic morphogenesis, organogenesis in various animals, and the central nervous system organization. Multiple feedback mechanisms dynamically regulate this pathway in a spatiotemporal and context-dependent manner to confer differential patterns in cell fate determination. Hh signaling is complex due to canonical and non-canonical mechanisms coordinating cell-cell communication. In addition, studies have demonstrated a regulatory framework of Hh signaling and shown that cholesterol is vital for Hh ligand biogenesis, signal generation, and transduction from the cell surface to intracellular space. Studies have shown the importance of a specific cholesterol pool, termed accessible cholesterol, which serves as a second messenger, conveying signals between smoothened (Smo) and patched 1 (Ptch1) across the plasma and ciliary membranes. Remarkably, recent high-resolution structural and molecular studies shed new light on the interplay between Hh signaling and cholesterol in membrane biology. These studies elucidated novel mechanistic insight into the release and dispersal of cholesterol-anchored Hh and the basis of Hh recognition by Ptch1. Additionally, the putative model of Smo activation by cholesterol binding and/or modification and Ptch1 antagonization of Smo has been explicated. However, the coupling mechanism of Hh signaling and cholesterol offered a new regulatory principle in cell biology: how effector molecules of the Hh signal network react to and remodel cholesterol accessibility in the membrane and selectively activate Hh signaling proteins thereof. Recognizing the biological importance of cholesterol in Hh signaling activation and transduction opens the door for translational research to develop novel therapeutic strategies. This review looks in-depth at canonical and non-canonical Hh signaling and the distinct proposed model of cholesterol-mediated regulation of Hh signaling components, facilitating a more sophisticated understanding of the Hh signal network and cholesterol biology.
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Affiliation(s)
- Jyoti B Kaushal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Fred and Pamela Buffet Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
| | - Satyanarayana Rachagani
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
- Fred and Pamela Buffet Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, 68198, USA.
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5
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Xu S, Tang C. Cholesterol and Hedgehog Signaling: Mutual Regulation and Beyond. Front Cell Dev Biol 2022; 10:774291. [PMID: 35573688 PMCID: PMC9091300 DOI: 10.3389/fcell.2022.774291] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
The Hedgehog (HH) signaling is one of the key agents that govern the precisely regulated developmental processes of multicellular organisms in vertebrates and invertebrates. The HH pathway in the receiving cell includes Patched1, a twelve-pass transmembrane receptor, and Smoothened, a seven-transmembrane G-protein coupled receptor (GPCR), and the downstream GLI family of three transcriptional factors (GLI1-GLI3). Mutations of HH gene and the main components in HH signaling are also associated with numerous types of diseases. Before secretion, the HH protein undergoes post-translational cholesterol modification to gain full activity, and cholesterol is believed to be essential for proper HH signaling transduction. In addition, results from recent studies show the reciprocal effect that HH signaling functions in cholesterol metabolism as well as in cholesterol homeostasis, which provides feedback to HH pathway. Here, we hope to provide new insights into HH signaling function by discussing the role of cholesterol in HH protein maturation, secretion and HH signaling transduction, and the potential role of HH in regulation of cholesterol as well.
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Dalton GD, Oh SH, Tang L, Zhang S, Brown AL, Varadharajan V, Baleanu-Gogonea C, Gogonea V, Pathak P, Brown JM, Diehl AM. Hepatocyte activity of the cholesterol sensor smoothened regulates cholesterol and bile acid homeostasis in mice. iScience 2021; 24:103089. [PMID: 34568800 PMCID: PMC8449244 DOI: 10.1016/j.isci.2021.103089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/06/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023] Open
Abstract
Cellular cholesterol is regulated by at least two transcriptional mechanisms involving sterol-regulatory-element-binding proteins (SREBPs) and liver X receptors (LXRs). Although SREBP and LXR pathways are the predominant mechanisms that sense cholesterol in the endoplasmic reticulum and nucleus to alter sterol-regulated gene expression, evidence suggests cholesterol in plasma membrane can be sensed by proteins in the Hedgehog (Hh) pathway which regulate organ self-renewal and are a morphogenic driver during embryonic development. Cholesterol interacts with the G-protein-coupled receptor Smoothened (Smo), which impacts downstream Hh signaling. Although evidence suggests cholesterol influences Hh signaling, it is not known whether Smo-dependent sterol sensing impacts cholesterol homeostasis in vivo. We examined dietary-cholesterol-induced reorganization of whole-body sterol and bile acid (BA) homeostasis in adult mice with inducible hepatocyte-specific Smo deletion. These studies demonstrate Smo in hepatocytes plays a regulatory role in sensing and feedback regulation of cholesterol balance driven by excess dietary cholesterol.
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Affiliation(s)
- George D. Dalton
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Seh-Hoon Oh
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Linda Tang
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Stephanie Zhang
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Amanda L. Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | | | - Valentin Gogonea
- Department of Chemistry, Cleveland State University, Cleveland, OH 44115, USA
| | - Preeti Pathak
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - J. Mark Brown
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Anna Mae Diehl
- Division of Gastroenterology, Department of Medicine, Duke University, Durham, NC 27710, USA
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Gu Y, Liu X, Liao L, Gao Y, Shi Y, Ni J, He G. Relationship between lipid metabolism and Hedgehog signaling pathway. J Steroid Biochem Mol Biol 2021; 209:105825. [PMID: 33529733 DOI: 10.1016/j.jsbmb.2021.105825] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 10/28/2020] [Accepted: 01/13/2021] [Indexed: 02/08/2023]
Abstract
The Hedgehog (Hh) signaling pathway is highly conserved signaling pathway in cells. Steroids was found to play a vital role in Hh signaling pathway and aberrant Hh signaling was found to lead a series of disease correlate with abnormal lipid metabolism. This paper aimed to elucidate the relationship between lipid metabolism and Hedgehog signaling pathway.
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Affiliation(s)
- Yuan Gu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Hunan 410011, PR China
| | - Xiaochen Liu
- University of Toledo Medical Center 3000 Arlington Ave. Toledo, OH 43614, USA
| | - Lele Liao
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Hunan 410011, PR China
| | - Yongquan Gao
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Hunan 410011, PR China
| | - Yu Shi
- West China School of Stomatology, Sichuan University, Chengdu 610041, PR China; State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, PR China
| | - Jiangdong Ni
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Hunan 410011, PR China
| | - Guangxu He
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Hunan 410011, PR China.
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Mafi A, Purohit R, Vielmas E, Lauinger AR, Lam B, Cheng YS, Zhang T, Huang Y, Kim SK, Goddard WA, Ondrus AE. Hedgehog proteins create a dynamic cholesterol interface. PLoS One 2021; 16:e0246814. [PMID: 33630857 PMCID: PMC7906309 DOI: 10.1371/journal.pone.0246814] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/26/2021] [Indexed: 12/27/2022] Open
Abstract
During formation of the Hedgehog (Hh) signaling proteins, cooperative activities of the Hedgehog INTein (Hint) fold and Sterol Recognition Region (SRR) couple autoproteolysis to cholesterol ligation. The cholesteroylated Hh morphogens play essential roles in embryogenesis, tissue regeneration, and tumorigenesis. Despite the centrality of cholesterol in Hh function, the full structure of the Hint-SRR ("Hog") domain that attaches cholesterol to the last residue of the active Hh morphogen remains enigmatic. In this work, we combine molecular dynamics simulations, photoaffinity crosslinking, and mutagenesis assays to model cholesterolysis intermediates in the human Sonic Hedgehog (hSHH) protein. Our results provide evidence for a hydrophobic Hint-SRR interface that forms a dynamic, non-covalent cholesterol-Hog complex. Using these models, we suggest a unified mechanism by which Hh proteins can recruit, sequester, and orient cholesterol, and offer a molecular basis for the effects of disease-causing hSHH mutations.
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Affiliation(s)
- Amirhossein Mafi
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Rahul Purohit
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Erika Vielmas
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Alexa R. Lauinger
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Brandon Lam
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Yu-Shiuan Cheng
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Tianyi Zhang
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Yiran Huang
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Soo-Kyung Kim
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - William A. Goddard
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (AEO); (WAG)
| | - Alison E. Ondrus
- Department of Chemistry, Division of Chemistry & Chemical Engineering, California Institute of Technology, Pasadena, California, United States of America
- * E-mail: (AEO); (WAG)
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9
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Dual roles of the sterol recognition region in Hedgehog protein modification. Commun Biol 2020; 3:250. [PMID: 32440000 PMCID: PMC7242414 DOI: 10.1038/s42003-020-0977-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 04/28/2020] [Indexed: 11/08/2022] Open
Abstract
Nature provides a number of mechanisms to encode dynamic information in biomolecules. In metazoans, there exist rare chemical modifications that occur in entirely unique regimes. One such example occurs in the Hedgehog (Hh) morphogens, proteins singular across all domains of life for the nature of their covalent ligation to cholesterol. The isoform- and context-specific efficiency of this ligation profoundly impacts the activity of Hh morphogens and represents an unexplored facet of Hh ligand-dependent cancers. To elucidate the chemical mechanism of this modification, we have defined roles of the uncharacterized sterol recognition region (SRR) in Hh proteins. We use a combination of sequence conservation, directed mutagenesis, and biochemical assays to specify residues of the SRR participate in cellular and biochemical aspects of Hh cholesterolysis. Our investigations offer a functional portrait of this region, providing opportunities to identify parallel reactivity in nature and a template to design tools in chemical biology.
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