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Liu Y, Mao L, Huang H, Li W, Man J, Zhang W, Wang L, Li L, Sun Y, Zhai T, Guo X, Du L, Huang J, Li H, Wan Y, Wei X. Clinical diagnosis of genetic disorders at both single-nucleotide and chromosomal levels based on BGISEQ-500 platform. Hum Genome Var 2023; 10:15. [PMID: 37217505 PMCID: PMC10203365 DOI: 10.1038/s41439-023-00238-9] [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: 04/26/2022] [Revised: 02/05/2023] [Accepted: 02/19/2023] [Indexed: 05/24/2023] Open
Abstract
Most variations in the human genome refer to single-nucleotide variation (SNV), small fragment insertions and deletions, and genomic copy number variation (CNV). Many human diseases including genetic disorders are associated with variations in the genome. These disorders are often difficult to be diagnosed because of their complex clinical conditions, therefore, an effective detection method is needed to facilitate clinical diagnosis and prevent birth defects. With the development of high-throughput sequencing technology, the method of targeted sequence capture chip has been extensively used owing to its high throughput, high accuracy, fast speed, and low cost. In this study, we designed a chip that potentially captured the coding region of 3043 genes associated with 4013 monogenic diseases, with an addition of 148 chromosomal abnormalities that can be identified by targeting specific regions. To assess the efficiency, a strategy of combining the BGISEQ500 sequencing platform with the designed chip was utilized to screen variants in 63 patients. Eventually, 67 disease-associated variants were found, 31 of which were novel. The results of the evaluation test also show that this combined strategy complies with the requirements of clinical testing and has proper clinical application value.
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Affiliation(s)
- Yanqiu Liu
- Department of Genetics, Jiangxi Maternal and Child Health Hospital, 330006, Nanchang, China
| | - Liangwei Mao
- BGI-Anhui Clinical Laboratory, BGI-Shenzhen, 236000, Fuyang, China
- The State Key Laboratory of Biocatalysis and Enzyme Engineering, College of Life Sciences, Hubei University, 430062, Wuhan, China
| | - Hui Huang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Wei Li
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Jianfen Man
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Wenqian Zhang
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Lina Wang
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Long Li
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Yan Sun
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Teng Zhai
- BGI Genomics, BGI-Shenzhen, 518083, Shenzhen, China
| | - Xueqin Guo
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Lique Du
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Jin Huang
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China
| | - Hao Li
- BGI-Anhui Clinical Laboratory, BGI-Shenzhen, 236000, Fuyang, China
| | - Yang Wan
- Department of Obstetrics and Gynecology, Fuyang People's Hospital, 236000, Fuyang, China.
| | - Xiaoming Wei
- BGI-Wuhan Clinical Laboratory, BGI-Shenzhen, 430074, Wuhan, China.
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2
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Sato Y, Terawaki S, Oikawa D, Shimizu K, Okina Y, Ito H, Tokunaga F. Involvement of heterologous ubiquitination including linear ubiquitination in Alzheimer's disease and amyotrophic lateral sclerosis. Front Mol Biosci 2023; 10:1089213. [PMID: 36726375 PMCID: PMC9884707 DOI: 10.3389/fmolb.2023.1089213] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
In neurodegenerative diseases such as Alzheimer's disease (AD) and amyotrophic lateral sclerosis (ALS), the progressive accumulation of ubiquitin-positive cytoplasmic inclusions leads to proteinopathy and neurodegeneration. Along with the seven types of Lys-linked ubiquitin chains, the linear ubiquitin chain assembly complex (LUBAC)-mediated Met1-linked linear ubiquitin chain, which activates the canonical NF-κB pathway, is also involved in cytoplasmic inclusions of tau in AD and TAR DNA-binding protein 43 in ALS. Post-translational modifications, including heterologous ubiquitination, affect proteasomal and autophagic degradation, inflammatory responses, and neurodegeneration. Single nucleotide polymorphisms (SNPs) in SHARPIN and RBCK1 (which encodes HOIL-1L), components of LUBAC, were recently identified as genetic risk factors of AD. A structural biological simulation suggested that most of the SHARPIN SNPs that cause an amino acid replacement affect the structure and function of SHARPIN. Thus, the aberrant LUBAC activity is related to AD. Protein ubiquitination and ubiquitin-binding proteins, such as ubiquilin 2 and NEMO, facilitate liquid-liquid phase separation (LLPS), and linear ubiquitination seems to promote efficient LLPS. Therefore, the development of therapeutic approaches that target ubiquitination, such as proteolysis-targeting chimeras (PROTACs) and inhibitors of ubiquitin ligases, including LUBAC, is expected to be an additional effective strategy to treat neurodegenerative diseases.
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Affiliation(s)
- Yusuke Sato
- Center for Research on Green Sustainable Chemistry, Graduate School of Engineering, Tottori University, Tottori, Japan,Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Seigo Terawaki
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan,Department of Molecular and Genetic Medicine, Kawasaki Medical School, Kurashiki, Japan
| | - Daisuke Oikawa
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Kouhei Shimizu
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yoshinori Okina
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Hidefumi Ito
- Department of Neurology, Wakayama Medical University, Wakayama, Japan
| | - Fuminori Tokunaga
- Department of Medical Biochemistry, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan,*Correspondence: Fuminori Tokunaga,
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Evidence for the Involvement of Pleckstrin Homology Domain-Containing Proteins in the Transport of Enterocin DD14 (EntDD14); a Leaderless Two-Peptide Bacteriocin. Int J Mol Sci 2021; 22:ijms222312877. [PMID: 34884682 PMCID: PMC8657885 DOI: 10.3390/ijms222312877] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 01/07/2023] Open
Abstract
Bacteriocins synthesis is initiated from an inactive precursor, which is composed of an N-terminal leader peptide attached to a C-terminal pro-peptide. However, leaderless bacteriocins (LLB) do not possess this N-terminal leader peptide nor undergo post-translational modifications. These atypical bacteriocins are observed to be immediately active after their translation in the cytoplasm. However, although considered to be simple, the biosynthetic pathway of LLB remains to be fully understood. Enterocin DD14 (EntDD14) is a two-peptide LLB produced by Enterococcus faecalis 14, which is a strain isolated from meconium. In silico analysis of DNA encoding EntDD14 located a cluster of 10 genes ddABCDEFGHIJ, where ddE and ddF encode the peculiar DdE and DdF proteins, carrying pleckstrin homology (PH) domains. These modules are quite common in Eucarya proteins and are known to be involved in intracellular signaling or cytoskeleton organization. To elucidate their role within the EntDD14 genetic determinants, we constructed deletion mutants of the ddE and ddF genes. As a result, the mutants were unable to export EntDD14 outside of the cytoplasm even though there was a clear expression of structural genes ddAB encoding EntDD14, and genes ddHIJ encoding an ABC transporter. Importantly, in these mutant strains (ΔddE and ΔddF), EntDD14 was detected by mass spectrometry in the intracellular soluble fraction exerting, upon its accumulation, a toxic effect on the producing strain as revealed by cell-counting and confocal microscopy analysis. Taken together, these results clearly indicate that PH domain-containing proteins, such as DdE and DdF, are involved in the transport of the leaderless two-peptide EntDD14.
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The GTPase Arf1 Is a Determinant of Yeast Vps13 Localization to the Golgi Apparatus. Int J Mol Sci 2021; 22:ijms222212274. [PMID: 34830155 PMCID: PMC8619211 DOI: 10.3390/ijms222212274] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022] Open
Abstract
VPS13 proteins are evolutionarily conserved. Mutations in the four human genes (VPS13A-D) encoding VPS13A-D proteins are linked to developmental or neurodegenerative diseases. The relationship between the specific localization of individual VPS13 proteins, their molecular functions, and the pathology of these diseases is unknown. Here we used a yeast model to establish the determinants of Vps13's interaction with the membranes of Golgi apparatus. We analyzed the different phenotypes of the arf1-3 arf2Δ vps13∆ strain, with reduced activity of the Arf1 GTPase, the master regulator of Golgi function and entirely devoid of Vps13. Our analysis led us to propose that Vps13 and Arf1 proteins cooperate at the Golgi apparatus. We showed that Vps13 binds to the Arf1 GTPase through its C-terminal Pleckstrin homology (PH)-like domain. This domain also interacts with phosphoinositol 4,5-bisphosphate as it was bound to liposomes enriched with this lipid. The homologous domain of VPS13A exhibited the same behavior. Furthermore, a fusion of the PH-like domain of Vps13 to green fluorescent protein was localized to Golgi structures in an Arf1-dependent manner. These results suggest that the PH-like domains and Arf1 are determinants of the localization of VPS13 proteins to the Golgi apparatus in yeast and humans.
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Puthenpura V, DeNunzio NJ, Zeng X, Giantsoudi D, Aboian M, Ebb D, Kahle KT, Yock TI, Marks AM. Radiation Necrosis with Proton Therapy in a Patient with Aarskog-Scott Syndrome and Medulloblastoma. Int J Part Ther 2021; 8:58-65. [PMID: 35127977 PMCID: PMC8768897 DOI: 10.14338/ijpt-21-00013.1] [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: 04/05/2021] [Accepted: 06/18/2021] [Indexed: 11/21/2022] Open
Abstract
PURPOSE Medulloblastoma is known to be associated with multiple cancer-predisposition syndromes. In this article, we explore a possible association among a patient's Aarskog-Scott syndrome, development of medulloblastoma, and subsequent brainstem radiation necrosis. CASE PRESENTATION A 5-year-old male with Aarskog-Scott syndrome initially presented to his pediatrician with morning emesis, gait instability, and truncal weakness. He was ultimately found to have a posterior fossa tumor with pathology consistent with group 3 medulloblastoma. After receiving a gross total resection and standard proton beam radiation therapy with concurrent vincristine, he was noted to develop brainstem radiation necrosis, for which he underwent therapy with high-dose dexamethasone, bevacizumab, and hyperbaric oxygen therapy with radiographic improvement and clinical stabilization. CONCLUSION Based on several possible pathologic correlates in the FDG1 pathway, there exists a potential association between this patient's Aarskog-Scott syndrome and medulloblastoma, which needs to be investigated further. In patients with underlying, rare genetic syndromes, further caution should be taken when evaluating chemotherapy and radiation dosimetry planning.
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Affiliation(s)
- Vidya Puthenpura
- Section of Pediatric Hematology and Oncology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Nicholas J. DeNunzio
- Department of Radiation Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Xue Zeng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Drosoula Giantsoudi
- Department of Radiation Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Mariam Aboian
- Section of Neuroradiology and Nuclear Medicine, Department of Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - David Ebb
- Department of Pediatric Hematology/Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Kristopher T. Kahle
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - Torunn I. Yock
- Department of Radiation Oncology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Asher M. Marks
- Section of Pediatric Hematology and Oncology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
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6
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Dziurdzik SK, Conibear E. The Vps13 Family of Lipid Transporters and Its Role at Membrane Contact Sites. Int J Mol Sci 2021; 22:ijms22062905. [PMID: 33809364 PMCID: PMC7999203 DOI: 10.3390/ijms22062905] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/08/2021] [Accepted: 03/09/2021] [Indexed: 12/27/2022] Open
Abstract
The conserved VPS13 proteins constitute a new family of lipid transporters at membrane contact sites. These large proteins are suspected to bridge membranes and form a direct channel for lipid transport between organelles. Mutations in the 4 human homologs (VPS13A–D) are associated with a number of neurological disorders, but little is known about their precise functions or the relevant contact sites affected in disease. In contrast, yeast has a single Vps13 protein which is recruited to multiple organelles and contact sites. The yeast model system has proved useful for studying the function of Vps13 at different organelles and identifying the localization determinants responsible for its membrane targeting. In this review we describe recent advances in our understanding of VPS13 proteins with a focus on yeast research.
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Affiliation(s)
- Samantha Katarzyna Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada;
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Correspondence:
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7
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Formosa T, Winston F. The role of FACT in managing chromatin: disruption, assembly, or repair? Nucleic Acids Res 2020; 48:11929-11941. [PMID: 33104782 PMCID: PMC7708052 DOI: 10.1093/nar/gkaa912] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription) has long been considered to be a transcription elongation factor whose ability to destabilize nucleosomes promotes RNAPII progression on chromatin templates. However, this is just one function of this histone chaperone, as FACT also functions in DNA replication. While broadly conserved among eukaryotes and essential for viability in many organisms, dependence on FACT varies widely, with some differentiated cells proliferating normally in its absence. It is therefore unclear what the core functions of FACT are, whether they differ in different circumstances, and what makes FACT essential in some situations but not others. Here, we review recent advances and propose a unifying model for FACT activity. By analogy to DNA repair, we propose that the ability of FACT to both destabilize and assemble nucleosomes allows it to monitor and restore nucleosome integrity as part of a system of chromatin repair, in which disruptions in the packaging of DNA are sensed and returned to their normal state. The requirement for FACT then depends on the level of chromatin disruption occurring in the cell, and the cell's ability to tolerate packaging defects. The role of FACT in transcription would then be just one facet of a broader system for maintaining chromatin integrity.
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Affiliation(s)
- Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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8
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Roy NS, Jian X, Soubias O, Zhai P, Hall JR, Dagher JN, Coussens NP, Jenkins LM, Luo R, Akpan IO, Hall MD, Byrd RA, Yohe ME, Randazzo PA. Interaction of the N terminus of ADP-ribosylation factor with the PH domain of the GTPase-activating protein ASAP1 requires phosphatidylinositol 4,5-bisphosphate. J Biol Chem 2019; 294:17354-17370. [PMID: 31591270 DOI: 10.1074/jbc.ra119.009269] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/02/2019] [Indexed: 12/15/2022] Open
Abstract
Arf GAP with Src homology 3 domain, ankyrin repeat, and pleckstrin homology (PH) domain 1 (ASAP1) is a multidomain GTPase-activating protein (GAP) for ADP-ribosylation factor (ARF)-type GTPases. ASAP1 affects integrin adhesions, the actin cytoskeleton, and invasion and metastasis of cancer cells. ASAP1's cellular function depends on its highly-regulated and robust ARF GAP activity, requiring both the PH and the ARF GAP domains of ASAP1, and is modulated by phosphatidylinositol 4,5-bisphosphate (PIP2). The mechanistic basis of PIP2-stimulated GAP activity is incompletely understood. Here, we investigated whether PIP2 controls binding of the N-terminal extension of ARF1 to ASAP1's PH domain and thereby regulates its GAP activity. Using [Δ17]ARF1, lacking the N terminus, we found that PIP2 has little effect on ASAP1's activity. A soluble PIP2 analog, dioctanoyl-PIP2 (diC8PIP2), stimulated GAP activity on an N terminus-containing variant, [L8K]ARF1, but only marginally affected activity on [Δ17]ARF1. A peptide comprising residues 2-17 of ARF1 ([2-17]ARF1) inhibited GAP activity, and PIP2-dependently bound to a protein containing the PH domain and a 17-amino acid-long interdomain linker immediately N-terminal to the first β-strand of the PH domain. Point mutations in either the linker or the C-terminal α-helix of the PH domain decreased [2-17]ARF1 binding and GAP activity. Mutations that reduced ARF1 N-terminal binding to the PH domain also reduced the effect of ASAP1 on cellular actin remodeling. Mutations in the ARF N terminus that reduced binding also reduced GAP activity. We conclude that PIP2 regulates binding of ASAP1's PH domain to the ARF1 N terminus, which may partially regulate GAP activity.
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Affiliation(s)
- Neeladri Sekhar Roy
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Olivier Soubias
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702
| | - Peng Zhai
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Jessica R Hall
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Jessica N Dagher
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Ruibai Luo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Itoro O Akpan
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Matthew D Hall
- Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - R Andrew Byrd
- Structural Biophysics Laboratory, Center for Cancer Research, NCI, National Institutes of Health, Frederick, Maryland 21702
| | - Marielle E Yohe
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892 .,Pediatric Oncology Branch, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
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Tewary SK, Zheng YG, Ho MC. Protein arginine methyltransferases: insights into the enzyme structure and mechanism at the atomic level. Cell Mol Life Sci 2019; 76:2917-2932. [PMID: 31123777 PMCID: PMC6741777 DOI: 10.1007/s00018-019-03145-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/10/2019] [Indexed: 02/06/2023]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze the methyl transfer to the arginine residues of protein substrates and are classified into three major types based on the final form of the methylated arginine. Recent studies have shown a strong correlation between PRMT expression level and the prognosis of cancer patients. Currently, crystal structures of eight PRMT members have been determined. Kinetic and structural studies have shown that all PRMTs share similar, but unique catalytic and substrate recognition mechanism. In this review, we discuss the structural similarities and differences of different PRMT members, focusing on their overall structure, S-adenosyl-L-methionine-binding pocket, substrate arginine recognition and catalytic mechanisms. Since PRMTs are valuable targets for drug discovery, we also rationally classify the known PRMT inhibitors into five classes and discuss their mechanisms of action at the atomic level.
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Affiliation(s)
| | - Y George Zheng
- College of Pharmacy, University of Georgia, Athens, GA, 30602, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan.
- Institute of Biochemical Sciences, National Taiwan University, Taipei, 106, Taiwan.
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10
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Vallbracht M, Backovic M, Klupp BG, Rey FA, Mettenleiter TC. Common characteristics and unique features: A comparison of the fusion machinery of the alphaherpesviruses Pseudorabies virus and Herpes simplex virus. Adv Virus Res 2019; 104:225-281. [PMID: 31439150 DOI: 10.1016/bs.aivir.2019.05.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Membrane fusion is a fundamental biological process that allows different cellular compartments delimited by a lipid membrane to release or exchange their respective contents. Similarly, enveloped viruses such as alphaherpesviruses exploit membrane fusion to enter and infect their host cells. For infectious entry the prototypic human Herpes simplex viruses 1 and 2 (HSV-1 and -2, collectively termed HSVs) and the porcine Pseudorabies virus (PrV) utilize four different essential envelope glycoproteins (g): the bona fide fusion protein gB and the regulatory heterodimeric gH/gL complex that constitute the "core fusion machinery" conserved in all members of the Herpesviridae; and the subfamily specific receptor binding protein gD. These four components mediate attachment and fusion of the virion envelope with the host cell plasma membrane through a tightly regulated sequential activation process. Although PrV and the HSVs are closely related and employ the same set of glycoproteins for entry, they show remarkable differences in the requirements for fusion. Whereas the HSVs strictly require all four components for membrane fusion, PrV can mediate cell-cell fusion without gD. Moreover, in contrast to the HSVs, PrV provides a unique opportunity for reversion analyses of gL-negative mutants by serial cell culture passaging, due to a limited cell-cell spread capacity of gL-negative PrV not observed in the HSVs. This allows a more direct analysis of the function of gH/gL during membrane fusion. Unraveling the molecular mechanism of herpesvirus fusion has been a goal of fundamental research for years, and yet important mechanistic details remain to be uncovered. Nevertheless, the elucidation of the crystal structures of all key players involved in PrV and HSV membrane fusion, coupled with a wealth of functional data, has shed some light on this complex puzzle. In this review, we summarize and discuss the contemporary knowledge on the molecular mechanism of entry and membrane fusion utilized by the alphaherpesvirus PrV, and highlight similarities but also remarkable differences in the requirements for fusion between PrV and the HSVs.
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Affiliation(s)
- Melina Vallbracht
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany.
| | - Marija Backovic
- Institut Pasteur, Unité de Virologie Structurale, UMR3569 (CNRS), Paris, France
| | - Barbara G Klupp
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
| | - Felix A Rey
- Institut Pasteur, Unité de Virologie Structurale, UMR3569 (CNRS), Paris, France
| | - Thomas C Mettenleiter
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Greifswald - Insel Riems, Germany
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11
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Pemberton JG, Balla T. Polyphosphoinositide-Binding Domains: Insights from Peripheral Membrane and Lipid-Transfer Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1111:77-137. [PMID: 30483964 DOI: 10.1007/5584_2018_288] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Within eukaryotic cells, biochemical reactions need to be organized on the surface of membrane compartments that use distinct lipid constituents to dynamically modulate the functions of integral proteins or influence the selective recruitment of peripheral membrane effectors. As a result of these complex interactions, a variety of human pathologies can be traced back to improper communication between proteins and membrane surfaces; either due to mutations that directly alter protein structure or as a result of changes in membrane lipid composition. Among the known structural lipids found in cellular membranes, phosphatidylinositol (PtdIns) is unique in that it also serves as the membrane-anchored precursor of low-abundance regulatory lipids, the polyphosphoinositides (PPIn), which have restricted distributions within specific subcellular compartments. The ability of PPIn lipids to function as signaling platforms relies on both non-specific electrostatic interactions and the selective stereospecific recognition of PPIn headgroups by specialized protein folds. In this chapter, we will attempt to summarize the structural diversity of modular PPIn-interacting domains that facilitate the reversible recruitment and conformational regulation of peripheral membrane proteins. Outside of protein folds capable of capturing PPIn headgroups at the membrane interface, recent studies detailing the selective binding and bilayer extraction of PPIn species by unique functional domains within specific families of lipid-transfer proteins will also be highlighted. Overall, this overview will help to outline the fundamental physiochemical mechanisms that facilitate localized interactions between PPIn lipids and the wide-variety of PPIn-binding proteins that are essential for the coordinate regulation of cellular metabolism and membrane dynamics.
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Affiliation(s)
- Joshua G Pemberton
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Tamas Balla
- Section on Molecular Signal Transduction, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
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12
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Rai S, Mohanty P, Bhatnagar S. Modeling, dynamics and phosphoinositide binding of the pleckstrin homology domain of two novel PLCs: η1 and η2. J Mol Graph Model 2018; 85:130-144. [PMID: 30193228 DOI: 10.1016/j.jmgm.2018.07.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 11/16/2022]
Abstract
PH domains mediate interactions involved in cell signaling, intracellular membrane transport regulation and cytoskeleton organization. Some PH domains bind phosphoinositides with different affinity and specificity. The two novel PLCη (1 and 2) possess an N-terminal PH domain (PHη1 and PHη2 respectively) that has been implicated in membrane association and induction of PLC activity. Understanding of the structure and dynamics is crucial for future modulation of lipid-protein interactions in PHη1, PHη2 and other PH domains. Therefore, the three-dimensional structure of PHη1 and PHη2 was modeled using ITASSER and phosphoinositides (IP3 and IP4) were docked in the inferred binding site using HADDOCK server. Molecular Dynamics simulations of unliganded and phosphoinositide bound PHη1 and PHη2 were performed using AMBER14 to study the mechanism of interaction, and conformational dynamics in response to phosphoinositide binding. The binding affinity was predicted using Kdeep server. The models of PHη1 and PHη2 had a conserved structural core consisting of seven β-strands and a C-terminal α-helix as seen in other PH domains. Sequence/structure analysis showed that phosphoinositide ligands bind PHη1 and PHη2 at the canonical binding site. Phosphoinositide binding induced movement of positively charged side chains towards the ligand, changes in the secondary structure especially at the β5-β6 loop and allosteric changes at the interface of β1-β2 and β5-β6 loops. Dynamics studies showed that the size of the binding site and differential affinity for IP3/IP4 binding is coordinated by the number, length, flexibility, secondary structure and allosteric interactions of the loops surrounding the phosphoinositide binding site.
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Affiliation(s)
- Sneha Rai
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India
| | - Pallavi Mohanty
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, 110078, India.
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13
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Ali I, Eu S, Koch D, Bleimling N, Goody RS, Müller MP. Structure of the tandem PX-PH domains of Bem3 from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2018; 74:315-321. [PMID: 29718000 PMCID: PMC5931145 DOI: 10.1107/s2053230x18005915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/16/2018] [Indexed: 11/11/2022] Open
Abstract
The structure of the tandem lipid-binding PX and pleckstrin-homology (PH) domains of the Cdc42 GTPase-activating protein Bem3 from Saccharomyces cerevisiae (strain S288c) has been determined to a resolution of 2.2 Å (Rwork = 21.1%, Rfree = 23.4%). It shows that the domains adopt a relative orientation that enables them to simultaneously bind to a membrane and suggests possible cooperativity in membrane binding.
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Affiliation(s)
- Imtiaz Ali
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Sungmin Eu
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Daniel Koch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Nathalie Bleimling
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Roger S. Goody
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Matthias P. Müller
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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14
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Fidler DR, Murphy SE, Courtis K, Antonoudiou P, El-Tohamy R, Ient J, Levine TP. Using HHsearch to tackle proteins of unknown function: A pilot study with PH domains. Traffic 2016; 17:1214-1226. [PMID: 27601190 PMCID: PMC5091641 DOI: 10.1111/tra.12432] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 08/30/2016] [Accepted: 08/30/2016] [Indexed: 01/08/2023]
Abstract
Advances in membrane cell biology are hampered by the relatively high proportion of proteins with no known function. Such proteins are largely or entirely devoid of structurally significant domain annotations. Structural bioinformaticians have developed profile‐profile tools such as HHsearch (online version called HHpred), which can detect remote homologies that are missed by tools used to annotate databases. Here we have applied HHsearch to study a single structural fold in a single model organism as proof of principle. In the entire clan of protein domains sharing the pleckstrin homology domain fold in yeast, systematic application of HHsearch accurately identified known PH‐like domains. It also predicted 16 new domains in 13 yeast proteins many of which are implicated in intracellular traffic. One of these was Vps13p, where we confirmed the functional importance of the predicted PH‐like domain. Even though such predictions require considerable work to be corroborated, they are useful first steps. HHsearch should be applied more widely, particularly across entire proteomes of model organisms, to significantly improve database annotations.
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Affiliation(s)
- David R Fidler
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Sarah E Murphy
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Katherine Courtis
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | | | - Rana El-Tohamy
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Jonathan Ient
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK
| | - Timothy P Levine
- Department of Cell Biology, UCL Institute of Ophthalmology, London, UK.
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15
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Tong J, Manik MK, Yang H, Im YJ. Structural insights into nonvesicular lipid transport by the oxysterol binding protein homologue family. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:928-939. [DOI: 10.1016/j.bbalip.2016.01.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/23/2015] [Accepted: 01/14/2016] [Indexed: 10/22/2022]
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16
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Aberrant protein phosphorylation in Alzheimer disease brain disturbs pro-survival and cell death pathways. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1871-82. [PMID: 27425034 DOI: 10.1016/j.bbadis.2016.07.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/22/2016] [Accepted: 07/13/2016] [Indexed: 12/31/2022]
Abstract
Protein phosphorylation of serine, threonine, and tyrosine residues is one of the most prevalent post-translational modifications fundamental in mediating diverse cellular functions in living cells. Aberrant protein phosphorylation is currently recognized as a critical step in the pathogenesis and progression of Alzheimer disease (AD). Changes in the pattern of protein phosphorylation of different brain regions are suggested to promote AD transition from a presymptomatic to a symptomatic state in response to accumulating amyloid β-peptide (Aβ). Several experimental approaches have been utilized to profile alteration of protein phosphorylation in the brain, including proteomics. Among central pathways regulated by kinases/phosphatases those involved in the activation/inhibition of both pro survival and cell death pathways play a central role in AD pathology. We discuss in detail how aberrant phosphorylation could contribute to dysregulate p53 activity and insulin-mediated signaling. Taken together these results highlight that targeted therapeutic intervention, which can restore phosphorylation homeostasis, either acting on kinases and phosphatases, conceivably may prove to be beneficial to prevent or slow the development and progression of AD.
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17
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Bruce AG, Horst JA, Rose TM. Conservation of the glycoprotein B homologs of the Kaposi׳s sarcoma-associated herpesvirus (KSHV/HHV8) and old world primate rhadinoviruses of chimpanzees and macaques. Virology 2016; 494:29-46. [PMID: 27070755 DOI: 10.1016/j.virol.2016.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023]
Abstract
The envelope-associated glycoprotein B (gB) is highly conserved within the Herpesviridae and plays a critical role in viral entry. We analyzed the evolutionary conservation of sequence and structural motifs within the Kaposi׳s sarcoma-associated herpesvirus (KSHV) gB and homologs of Old World primate rhadinoviruses belonging to the distinct RV1 and RV2 rhadinovirus lineages. In addition to gB homologs of rhadinoviruses infecting the pig-tailed and rhesus macaques, we cloned and sequenced gB homologs of RV1 and RV2 rhadinoviruses infecting chimpanzees. A structural model of the KSHV gB was determined, and functional motifs and sequence variants were mapped to the model structure. Conserved domains and motifs were identified, including an "RGD" motif that plays a critical role in KSHV binding and entry through the cellular integrin αVβ3. The RGD motif was only detected in RV1 rhadinoviruses suggesting an important difference in cell tropism between the two rhadinovirus lineages.
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Affiliation(s)
- A Gregory Bruce
- Center for Global Infectious Disease Research, Seattle Children׳s Research Institute, Seattle, WA, United States
| | - Jeremy A Horst
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, United States
| | - Timothy M Rose
- Center for Global Infectious Disease Research, Seattle Children׳s Research Institute, Seattle, WA, United States; Department of Pediatrics, University of Washington, Seattle, WA, United States.
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18
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Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily. MEMBRANES 2015; 5:646-63. [PMID: 26512702 PMCID: PMC4704004 DOI: 10.3390/membranes5040646] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/15/2015] [Accepted: 10/16/2015] [Indexed: 12/23/2022]
Abstract
The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH) and Tec homology (TH) domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA) program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.
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19
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Raimondi F, Felline A, Fanelli F. Catching Functional Modes and Structural Communication in Dbl Family Rho Guanine Nucleotide Exchange Factors. J Chem Inf Model 2015; 55:1878-93. [PMID: 26322553 DOI: 10.1021/acs.jcim.5b00122] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Computational approaches such as Principal Component Analysis (PCA) and Elastic Network Model-Normal Mode Analysis (ENM-NMA) are proving to be of great value in investigating relevant biological problems linked to slow motions with no demand in computer power. In this study, these approaches have been coupled to the graph theory-based Protein Structure Network (PSN) analysis to dissect functional dynamics and structural communication in the Dbl family of Rho Guanine Nucleotide Exchange Factors (RhoGEFs). They are multidomain proteins whose common structural feature is a DH-PH tandem domain deputed to the GEF activity that makes them play a central role in cell and cancer biology. While their common GEF action is accomplished by the DH domain, their regulatory mechanisms are highly variegate and depend on the PH and the additional domains as well as on interacting proteins. Major evolutionary-driven deformations as inferred from PCA concern the α6 helix of DH that dictates the orientation of the PH domain. Such deformations seem to depend on the mechanisms adopted by the GEF to prevent Rho binding, i.e. functional specialization linked to autoinhibition. In line with PCA, ENM-NMA indicates α6 and the linked PH domain as the portions of the tandem domain holding almost the totality of intrinsic and functional dynamics, with the α6/β1 junction acting as a hinge point for the collective motions of PH. In contrast, the DH domain holds a static scaffolding and hub behavior, with structural communication playing a central role in the regulatory actions by other domains/proteins. Possible allosteric communication pathways involving essentially DH were indeed found in those RhoGEFs acting as effectors of small or heterotrimeric RasGTPases. The employed methodology is suitable for deciphering structure/dynamics relationships in large sets of homologous or analogous proteins.
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Affiliation(s)
- Francesco Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia , via Campi 103, 41125 Modena, Modena, Italy
| | - Angelo Felline
- Department of Life Sciences, University of Modena and Reggio Emilia , via Campi 103, 41125 Modena, Modena, Italy
| | - Francesca Fanelli
- Department of Life Sciences, University of Modena and Reggio Emilia , via Campi 103, 41125 Modena, Modena, Italy
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20
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PtdIns(4)P signalling and recognition systems. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 991:59-83. [PMID: 23775691 DOI: 10.1007/978-94-007-6331-9_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The Golgi apparatus is a sorting platform that exchanges extensively with the endoplasmic reticulum (ER), endosomes (Es) and plasma membrane (PM) compartments. The last compartment of the Golgi, the trans-Golgi Network (TGN) is a large complex of highly deformed membranes from which vesicles depart to their targeted organelles but also are harbored from retrograde pathways. The phosphoinositide (PI) composition of the TGN is marked by an important contingent of phosphatidylinositol-4-phosphate (PtdIns(4)P). Although this PI is present throughout the Golgi, its proportion grows along the successive cisternae and peaks at the TGN. The levels of this phospholipid are controlled by a set of kinases and phosphatases that regulate its concentrations in the Golgi and maintain a dynamic gradient that determines the cellular localization of several interacting proteins. Though not exclusive to the Golgi, the synthesis of PtdIns(4)P in other membranes is relatively marginal and has unclear consequences. The significance of PtdIns(4)P within the TGN has been demonstrated for numerous cellular events such as vesicle formation, lipid metabolism, and membrane trafficking.
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21
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Behr M, Serchi T, Cocco E, Guignard C, Sergeant K, Renaut J, Evers D. Description of the mechanisms underlying geosmin production in Penicillium expansum using proteomics. J Proteomics 2013; 96:13-28. [PMID: 24189443 DOI: 10.1016/j.jprot.2013.10.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 09/30/2013] [Accepted: 10/24/2013] [Indexed: 11/25/2022]
Abstract
UNLABELLED A 2D-DIGE proteomics experiment was performed to describe the mechanism underlying the production of geosmin, an earthy-smelling sesquiterpene which spoils wine, produced by Penicillium expansum. The strains were identified by sequencing of the ITS and beta-tubulin regions. This study was based on a selection of four strains showing different levels of geosmin production, assessed by GC-MS/MS. The proteomics study revealed the differential abundance of 107 spots between the different strains; these were picked and submitted to MALDI-TOF-TOF MS analysis for identification. They belonged to the functional categories of protein metabolism, redox homeostasis, metabolic processes (glycolysis, ATP production), cell cycle and cell signalling pathways. From these data, an implication of oxidative stress in geosmin production may be hypothesized. Moreover, the differential abundance of some glycolytic enzymes may explain the different patterns of geosmin biosynthesis. This study provides data for the characterisation of the mechanism and the regulation of the production of this off-flavour, which are so far not described in filamentous fungi. BIOLOGICAL SIGNIFICANCE Green mould on grapes, caused by P. expansum may be at the origin of off-flavours in wine. These are characterized by earthy-mouldy smells and are due to the presence of the compound geosmin. This work aims at describing how geosmin is produced by P. expansum. This knowledge is of use for the research community on grapes for understanding why these off-flavours occasionally occur in vintages.
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Affiliation(s)
- Marc Behr
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Tommaso Serchi
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Emmanuelle Cocco
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Cédric Guignard
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Kjell Sergeant
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Jenny Renaut
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
| | - Danièle Evers
- Centre de Recherche Public-Gabriel Lippmann, Département Environnement et Agro-biotechnologies, Belvaux, Luxembourg.
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22
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Hart R, Stanley P, Chakravarty P, Hogg N. The kindlin 3 pleckstrin homology domain has an essential role in lymphocyte function-associated antigen 1 (LFA-1) integrin-mediated B cell adhesion and migration. J Biol Chem 2013; 288:14852-62. [PMID: 23595985 DOI: 10.1074/jbc.m112.434621] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The protein kindlin 3 is mutated in the leukocyte adhesion deficiency III (LAD-III) disorder, leading to widespread infection due to the failure of leukocytes to migrate into infected tissue sites. To gain understanding of how kindlin 3 controls leukocyte function, we have focused on its pleckstrin homology (PH) domain and find that deletion of this domain eliminates the ability of kindlin 3 to participate in adhesion and migration of B cells mediated by the leukocyte integrin lymphocyte function-associated antigen 1 (LFA-1). PH domains are often involved in membrane localization of proteins through binding to phosphoinositides. We show that the kindlin 3 PH domain has binding affinity for phosphoinositide PI(3,4,5)P3 over PI(4,5)P2. It has a major role in membrane association of kindlin 3 that is enhanced by the binding of LFA-1 to intercellular adhesion molecule 1 (ICAM-1). A splice variant, kindlin 3-IPRR, has a four-residue insert in the PH domain at a critical site that influences phosphoinositide binding by enhancing binding to PI(4,5)P2 as well as by binding to PI(3,4,5)P3. However kindlin 3-IPRR is unable to restore the ability of LAD-III B cells to adhere to and migrate on LFA-1 ligand ICAM-1, potentially by altering the dynamics or PI specificity of binding to the membrane. Thus, the correct functioning of the kindlin 3 PH domain is central to the role that kindlin 3 performs in guiding lymphocyte adhesion and motility behavior, which in turn is required for a successful immune response.
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Affiliation(s)
- Rosie Hart
- Leukocyte Adhesion Laboratory, Cancer Research United Kingdom London Research Institute, London WC2A 3LY, United Kingdom
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23
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Boyken SE, Fulton DB, Andreotti AH. Rescue of the aggregation prone Itk Pleckstrin Homology domain by two mutations derived from the related kinases, Btk and Tec. Protein Sci 2012; 21:1288-97. [PMID: 22761113 DOI: 10.1002/pro.2114] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 06/19/2012] [Accepted: 06/20/2012] [Indexed: 12/18/2022]
Abstract
IL-2 inducible T-cell kinase (Itk) is a Tec family non-receptor tyrosine kinase involved in signaling downstream of the T-cell receptor. Itk contains an amino-terminal Pleckstrin Homology (PH) domain that binds phosphatidylinositol (3,4,5)-trisphosphate, recruiting Itk to the plasma membrane upon T-cell receptor activation. In addition to phosphoinositide binding, accumulating data suggest that the Itk PH domain likely mediates additional interactions outside of the phosphoinositide ligand binding pocket. The structural basis for additional PH domain functions remains elusive because of the poor recombinant expression and in vitro solution behavior of the Itk PH domain. Here, we determine that the lone α-helix in the Itk PH domain is responsible for the poor solution properties and that mutation of just two residues in the Itk α-helix to the corresponding amino acids in Btk or Tec dramatically improves the soluble recombinant expression and solution behavior of the Itk PH domain. We present this double mutant as a valuable tool to characterize the structure and function of the Itk PH domain. It is also interesting to note that the precise sites of mutation identified in this study appear as somatic mutations associated with cancerous tissue. Collectively, the findings suggest that the two helical residues in the Itk PH domain may serve an important and unique structural role in wild-type Itk that differentiates this tyrosine kinase from its related family members.
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Affiliation(s)
- Scott E Boyken
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
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24
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Lauks J, Klemmer P, Farzana F, Karupothula R, Zalm R, Cooke NE, Li KW, Smit AB, Toonen R, Verhage M. Synapse associated protein 102 (SAP102) binds the C-terminal part of the scaffolding protein neurobeachin. PLoS One 2012; 7:e39420. [PMID: 22745750 PMCID: PMC3380004 DOI: 10.1371/journal.pone.0039420] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/23/2012] [Indexed: 12/22/2022] Open
Abstract
Neurobeachin (Nbea) is a multidomain scaffold protein abundant in the brain, where it is highly expressed during development. Nbea-null mice have severe defects in neuromuscular synaptic transmission resulting in lethal paralysis of the newborns. Recently, it became clear that Nbea is important also for the functioning of central synapses, where it is suggested to play a role in trafficking membrane proteins to both, the pre- and post-synaptic sites. So far, only few binding partners of Nbea have been found and the precise mechanism of their trafficking remains unclear. Here, we used mass spectrometry to identify SAP102, a MAGUK protein implicated in trafficking of the ionotropic glutamate AMPA- and NMDA-type receptors during synaptogenesis, as a novel Nbea interacting protein in mouse brain. Experiments in heterologous cells confirmed this interaction and revealed that SAP102 binds to the C-terminal part of Nbea that contains the DUF, PH, BEACH and WD40 domains. Furthermore, we discovered that introducing a mutation in Nbea's PH domain, which disrupts its interaction with the BEACH domain, abolishes this binding, thereby creating an excellent starting point to further investigate Nbea-SAP102 function in the central nervous system.
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Affiliation(s)
- Juliane Lauks
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Patricia Klemmer
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Fatima Farzana
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Ramesh Karupothula
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Robbert Zalm
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nancy E. Cooke
- Department of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Ruud Toonen
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
| | - Matthijs Verhage
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam and VU Medical Center, Amsterdam, The Netherlands
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25
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Scheffzek K, Welti S. Pleckstrin homology (PH) like domains - versatile modules in protein-protein interaction platforms. FEBS Lett 2012; 586:2662-73. [PMID: 22728242 DOI: 10.1016/j.febslet.2012.06.006] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 06/07/2012] [Accepted: 06/08/2012] [Indexed: 12/21/2022]
Abstract
The initial reports on pleckstrin homology (PH) domains almost 20 years ago described them as sequence feature of proteins involved in signal transduction processes. Investigated at first along the phospholipid binding properties of a small subset of PH representatives, the PH fold turned out to appear as mediator of phosphotyrosine and polyproline peptide binding to other signaling proteins. While phospholipid binding now seems rather the exception among PH-like domains, protein-protein interactions established as more and more important feature of these modules. In this review we focus on the PH superfold as a versatile protein-protein interaction platform and its three-dimensional integration in an increasing number of available multidomain structures.
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Affiliation(s)
- Klaus Scheffzek
- Division Biological Chemistry, Biocenter, Innsbruck Medical University, Innrain 80/82, A-6020 Innsbruck, Austria.
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26
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Stieglitz B, Haire LF, Dikic I, Rittinger K. Structural analysis of SHARPIN, a subunit of a large multi-protein E3 ubiquitin ligase, reveals a novel dimerization function for the pleckstrin homology superfold. J Biol Chem 2012; 287:20823-9. [PMID: 22549881 PMCID: PMC3375506 DOI: 10.1074/jbc.m112.359547] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/17/2012] [Indexed: 11/06/2022] Open
Abstract
SHARPIN (SHANK-associated RH domain interacting protein) is part of a large multi-protein E3 ubiquitin ligase complex called LUBAC (linear ubiquitin chain assembly complex), which catalyzes the formation of linear ubiquitin chains and regulates immune and apoptopic signaling pathways. The C-terminal half of SHARPIN contains ubiquitin-like domain and Npl4-zinc finger domains that mediate the interaction with the LUBAC subunit HOIP and ubiquitin, respectively. In contrast, the N-terminal region does not show any homology with known protein interaction domains but has been suggested to be responsible for self-association of SHARPIN, presumably via a coiled-coil region. We have determined the crystal structure of the N-terminal portion of SHARPIN, which adopts the highly conserved pleckstrin homology superfold that is often used as a scaffold to create protein interaction modules. We show that in SHARPIN, this domain does not appear to be used as a ligand recognition domain because it lacks many of the surface properties that are present in other pleckstrin homology fold-based interaction modules. Instead, it acts as a dimerization module extending the functional applications of this superfold.
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Affiliation(s)
- Benjamin Stieglitz
- From the Division of Molecular Structure, Medical Research Council National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom and
| | - Lesley F. Haire
- From the Division of Molecular Structure, Medical Research Council National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom and
| | - Ivan Dikic
- the Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, Goethe University School of Medicine, D-60590 Frankfurt, Germany
| | - Katrin Rittinger
- From the Division of Molecular Structure, Medical Research Council National Institute for Medical Research, The Ridgeway, London NW7 1AA, United Kingdom and
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Abstract
NF1 (neurofibromatosis type I) is a common genetic disease that affects one in 3500 individuals. The disease is completely penetrant but shows variable phenotypic expression in patients. NF1 is a large gene, and its pre-mRNA undergoes alternative splicing. The NF1 protein, neurofibromin, is involved in diverse signalling cascades. One of the best characterized functions of NF1 is its function as a Ras-GAP (GTPase-activating protein). NF1 exon 23a is an alternative exon that lies within the GAP-related domain of neurofibromin. This exon is predominantly included in most tissues, and it is skipped in CNS (central nervous system) neurons. The isoform in which exon 23a is skipped has 10 times higher Ras-GAP activity than the isoform in which exon 23a is included. Exon 23a inclusion is tightly regulated by at least three different families of RNA-binding proteins: CELF {CUG-BP (cytosine-uridine-guanine-binding protein) and ETR-3 [ELAV (embryonic lethal abnormal vision)-type RNA-binding protein]-like factor}, Hu and TIA-1 (T-cell intracellular antigen 1)/TIAR (T-cell intracellular antigen 1-related protein). The CELF and Hu proteins promote exon 23a skipping, while the TIA-1/TIAR proteins promote its inclusion. The widespread clinical variability that is observed among NF1 patients cannot be explained by NF1 mutations alone and it is believed that modifier genes may have a role in the variability. We suggest that the regulation of alternative splicing may act as a modifier to contribute to the variable expression in NF1 patients.
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Zhang W, Zhao Y, Guo Y, Ye K. Plant actin-binding protein SCAB1 is dimeric actin cross-linker with atypical pleckstrin homology domain. J Biol Chem 2012; 287:11981-90. [PMID: 22356912 DOI: 10.1074/jbc.m111.338525] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SCAB1 is a novel plant-specific actin-binding protein that binds, bundles, and stabilizes actin filaments and regulates stomatal movement. Here, we dissected the structure and function of SCAB1 by structural and biochemical approaches. We show that SCAB1 is composed of an actin-binding domain, two coiled-coil (CC) domains, and a fused immunoglobulin and pleckstrin homology (Ig-PH) domain. We determined crystal structures for the CC1 and Ig-PH domains at 1.9 and 1.7 Å resolution, respectively. The CC1 domain adopts an antiparallel helical hairpin that further dimerizes into a four-helix bundle. The CC2 domain also mediates dimerization. At least one of the coiled coils is required for actin binding, indicating that SCAB1 is a bivalent actin cross-linker. The key residues required for actin binding were identified. The PH domain lacks a canonical basic phosphoinositide-binding pocket but can bind weakly to inositol phosphates via a basic surface patch, implying the involvement of inositol signaling in SCAB1 regulation. Our results provide novel insights into the functional organization of SCAB1.
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Affiliation(s)
- Wei Zhang
- College of Biological Sciences, China Agricultural University, Beijing 10019, China
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29
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Structural basis for recognition of H3K56-acetylated histone H3-H4 by the chaperone Rtt106. Nature 2012; 483:104-7. [PMID: 22307274 DOI: 10.1038/nature10861] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 01/16/2012] [Indexed: 01/10/2023]
Abstract
Dynamic variations in the structure of chromatin influence virtually all DNA-related processes in eukaryotes and are controlled in part by post-translational modifications of histones. One such modification, the acetylation of lysine 56 (H3K56ac) in the amino-terminal α-helix (αN) of histone H3, has been implicated in the regulation of nucleosome assembly during DNA replication and repair, and nucleosome disassembly during gene transcription. In Saccharomyces cerevisiae, the histone chaperone Rtt106 contributes to the deposition of newly synthesized H3K56ac-carrying H3-H4 complex on replicating DNA, but it is unclear how Rtt106 binds H3-H4 and specifically recognizes H3K56ac as there is no apparent acetylated lysine reader domain in Rtt106. Here, we show that two domains of Rtt106 are involved in a combinatorial recognition of H3-H4. An N-terminal domain homodimerizes and interacts with H3-H4 independently of acetylation while a double pleckstrin-homology (PH) domain binds the K56-containing region of H3. Affinity is markedly enhanced upon acetylation of K56, an effect that is probably due to increased conformational entropy of the αN helix of H3. Our data support a mode of interaction where the N-terminal homodimeric domain of Rtt106 intercalates between the two H3-H4 components of the (H3-H4)(2) tetramer while two double PH domains in the Rtt106 dimer interact with each of the two H3K56ac sites in (H3-H4)(2). We show that the Rtt106-(H3-H4)(2) interaction is important for gene silencing and the DNA damage response.
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Wang X, Schröder HC, Wiens M, Schloßmacher U, Müller WEG. Biosilica: Molecular Biology, Biochemistry and Function in Demosponges as well as its Applied Aspects for Tissue Engineering. ADVANCES IN MARINE BIOLOGY 2012; 62:231-271. [PMID: 22664124 DOI: 10.1016/b978-0-12-394283-8.00005-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Biomineralization, biosilicification in particular (i.e. the formation of biogenic silica, SiO(2)), has become an exciting source of inspiration for the development of novel bionic approaches following 'nature as model'. Siliceous sponges are unique among silica-forming organisms in their ability to catalyze silica formation using a specific enzyme termed silicatein. In this study, we review the present state of knowledge on silicatein-mediated 'biosilica' formation in marine demosponges, the involvement of further molecules in silica metabolism and their potential applications in nano-biotechnology and bio-medicine. While most forms of multicellular life have developed a calcium-based skeleton, a few specialized organisms complement their body plan with silica. Only sponges (phylum Porifera) are able to polymerize silica enzymatically mediated in order to generate massive siliceous skeletal elements (spicules) during a unique reaction, at ambient temperature and pressure. During this biomineralization process (i.e. biosilicification), hydrated, amorphous silica is deposited within highly specialized sponge cells, ultimately resulting in structures that range in size from micrometres to metres. This peculiar phenomenon has been comprehensively studied in recent years, and in several approaches, the molecular background was explored to create tools that might be employed for novel bioinspired biotechnological and biomedical applications. Thus, it was discovered that spiculogenesis is mediated by the enzyme silicatein and starts intracellularly. The resulting silica nanoparticles fuse and subsequently form concentric lamellar layers around a central protein filament, consisting of silicatein and the scaffold protein silintaphin-1. Once the growing spicule is extruded into the extracellular space, it obtains final size and shape. Again, this process is mediated by silicatein and silintaphin-1/silintaphin-1, in combination with other molecules such as galectin and collagen. The molecular toolbox generated so far allows the fabrication of novel micro- and nano-structured composites, contributing to the economical and sustainable synthesis of biomaterials with unique characteristics. In this context, first bioinspired approaches implement recombinant silicatein and silintaphin-1 for applications in the field of biomedicine (biosilica-mediated regeneration of tooth and bone defects) with promising results.
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Affiliation(s)
- Xiaohong Wang
- National Research Center for Geoanalysis, Chinese Academy of Geological Sciences, Beijing 100037, China; ERC Advanced Investigator Grant Research Group, Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University Mainz, Duesbergweg 6, 55128 Mainz, Germany
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31
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Nagano M, Hoshino D, Koshiba S, Shuo T, Koshikawa N, Tomizawa T, Hayashi F, Tochio N, Harada T, Akizawa T, Watanabe S, Handa N, Shirouzu M, Kigawa T, Yokoyama S, Seiki M. ZF21 protein, a regulator of the disassembly of focal adhesions and cancer metastasis, contains a novel noncanonical pleckstrin homology domain. J Biol Chem 2011; 286:31598-609. [PMID: 21768110 PMCID: PMC3173091 DOI: 10.1074/jbc.m110.199430] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 07/09/2011] [Indexed: 12/20/2022] Open
Abstract
Directional migration of adherent cells on an extracellular matrix requires repeated formation and disassembly of focal adhesions (FAs). Directional migration of adherent cells We have identified ZF21 as a regulator of disassembly of FAs and cell migration, and increased expression of the gene has been linked to metastatic colon cancer. ZF21 is a member of a protein family characterized by the presence of the FYVE domain, which is conserved among Fab1p, YOPB, Vps27p, and EEA1 proteins, and has been shown to mediate the binding of such proteins to phosphoinositides in the lipid layers of cell membranes. ZF21 binds multiple factors that promote disassembly of FAs such as FAK, β-tubulin, m-calpain, and SHP-2. ZF21 does not contain any other known protein motifs other than the FYVE domain, but a region of the protein C-terminal to the FYVE domain is sufficient to mediate binding to β-tubulin. In this study, we demonstrate that the C-terminal region is important for the ability of ZF21 to induce disassembly of FAs and cell migration, and to promote an early step of experimental metastasis to the lung in mice. In light of the importance of the C-terminal region, we analyzed its ternary structure using NMR spectroscopy. We demonstrate that this region exhibits a structure similar to that of a canonical pleckstrin homology domain, but that it lacks a positively charged interface to bind phosphatidylinositol phosphate. Thus, ZF21 contains a novel noncanonical PH-like domain that is a possible target to develop a therapeutic strategy to treat metastatic cancer.
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Affiliation(s)
- Makoto Nagano
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
- the Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotogecho, Hirakata Osaka, 573-0101
| | - Daisuke Hoshino
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Seizo Koshiba
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takuya Shuo
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Naohiko Koshikawa
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
| | - Tadashi Tomizawa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Fumiaki Hayashi
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Naoya Tochio
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takushi Harada
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Toshifumi Akizawa
- the Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotogecho, Hirakata Osaka, 573-0101
| | - Satoru Watanabe
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Noriko Handa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Mikako Shirouzu
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
| | - Takanori Kigawa
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, 4259 Nagatsuda-cho, Midori-ku, Yokohama 226-8502, and
| | - Shigeyuki Yokoyama
- the RIKEN Systems and Structural Biology Center, Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045
- the Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motoharu Seiki
- From the Division of Cancer Cell Research, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, 108-8639
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32
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Baumann MK, Swann MJ, Textor M, Reimhult E. Pleckstrin Homology-Phospholipase C-δ1 Interaction with Phosphatidylinositol 4,5-Bisphosphate Containing Supported Lipid Bilayers Monitored in Situ with Dual Polarization Interferometry. Anal Chem 2011; 83:6267-74. [DOI: 10.1021/ac2009178] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Martina K. Baumann
- Department of Materials, Laboratory for Surface Science and Technology (LSST), ETH Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland
| | - Marcus J. Swann
- Farfield Group, Farfield House, Southmere Court, Electra Way, Crewe Business Park, Crewe CW1 6GU, United Kingdom
| | - Marcus Textor
- Department of Materials, Laboratory for Surface Science and Technology (LSST), ETH Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland
| | - Erik Reimhult
- Department of Materials, Laboratory for Surface Science and Technology (LSST), ETH Zurich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland
- Department of Nanobiotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 11, A-1190 Vienna, Austria
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Fritz RD, Radziwill G. CNK1 and other scaffolds for Akt/FoxO signaling. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1813:1971-7. [PMID: 21320536 DOI: 10.1016/j.bbamcr.2011.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 02/01/2011] [Accepted: 02/05/2011] [Indexed: 11/28/2022]
Abstract
FoxO transcription factors mediate anti-proliferative and pro-apoptotic signals and act as tumor suppressors in cancer. Posttranslational modifications including phosphorylation and acetylation regulate FoxO activity by a cytoplasmic-nuclear shuttle mechanism. Scaffold proteins coordinating signaling pathways in time and space play a critical role in this process. CNK1 acts as a scaffold protein in several signaling pathways controlling the function of FoxO proteins. An understanding of CNK1 and other scaffolds in the FoxO signaling network will provide insights how to release the tumor suppressor function of FoxO as a possibility to block oncogenic pathways. This article is part of a Special Issue entitled: P13K-AKT-FoxO axis in cancer and aging.
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Affiliation(s)
- Rafael D Fritz
- Department of Biomedicine, Institute of Biochemistry and Genetics, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland.
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Impact of valency of a glycoprotein B-specific monoclonal antibody on neutralization of herpes simplex virus. J Virol 2010; 85:1793-803. [PMID: 21123390 DOI: 10.1128/jvi.01924-10] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Herpes simplex virus (HSV) glycoprotein B (gB) is an integral part of the multicomponent fusion system required for virus entry and cell-cell fusion. Here we investigated the mechanism of viral neutralization by the monoclonal antibody (MAb) 2c, which specifically recognizes the gB of HSV type 1 (HSV-1) and HSV-2. Binding of MAb 2c to a type-common discontinuous epitope of gB resulted in highly efficient neutralization of HSV at the postbinding/prefusion stage and completely abrogated the viral cell-to-cell spread in vitro. Mapping of the antigenic site recognized by MAb 2c to the recently solved crystal structure of the HSV-1 gB ectodomain revealed that its discontinuous epitope is only partially accessible within the observed multidomain trimer conformation of gB, likely representing its postfusion conformation. To investigate how MAb 2c may interact with gB during membrane fusion, we characterized the properties of monovalent (Fab and scFv) and bivalent [IgG and F(ab')(2)] derivatives of MAb 2c. Our data show that the neutralization capacity of MAb 2c is dependent on cross-linkage of gB trimers. As a result, only bivalent derivatives of MAb 2c exhibited high neutralizing activity in vitro. Notably, bivalent MAb 2c not only was capable of preventing mucocutaneous disease in severely immunodeficient NOD/SCID mice upon vaginal HSV-1 challenge but also protected animals even with neuronal HSV infection. We also report for the first time that an anti-gB specific monoclonal antibody prevents HSV-1-induced encephalitis entirely independently from complement activation, antibody-dependent cellular cytotoxicity, and cellular immunity. This indicates the potential for further development of MAb 2c as an anti-HSV drug.
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Two mutations in the KINDLIN3 gene of a new leukocyte adhesion deficiency III patient reveal distinct effects on leukocyte function in vitro. Blood 2010; 115:4834-42. [PMID: 20357244 DOI: 10.1182/blood-2009-08-238709] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In the disorder leukocyte adhesion deficiency III (LAD-III), integrins on platelets and leukocytes are expressed but fail to function and this leads to severe bleeding and infections at an early age. Mutation in the KINDLIN3 (FERMT3) gene is the cause of LAD-III in patients from the Middle East, Malta, and Turkey. We describe 2 novel homozygous mutations in the KINDLIN3 gene of a new African-American patient that destabilize KINDLIN3 mRNA leading to loss of kindlin-3 protein. Transfection of wild-type (WT) KINDLIN3 cDNA restored integrin-related adhesion and migration in the LAD-III patient's T and B lymphocytes. We analyzed the individual mutations separately in vitro to learn more about the function of the kindlin-3 protein. The first G>A mutation gives rise to a Gly308Arg change at the end of FERM (protein 4.1, ezrin, radixin, moesin) subdomain 2, and the second mutation is a base deletion causing early termination within the pleckstrin homology (PH) domain. This second mutation prevented membrane association of kindlin-3 and did not restore either adhesion or migration, whereas the FERM subdomain 2 mutation affected only migration. Thus, these LAD-III patient mutations have highlighted functionally important regions of kindlin-3 that alter leukocyte integrin-dependent function in 2 distinct ways.
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36
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Bacterial pleckstrin homology domains: a prokaryotic origin for the PH domain. J Mol Biol 2009; 396:31-46. [PMID: 19913036 PMCID: PMC2817789 DOI: 10.1016/j.jmb.2009.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 11/03/2009] [Accepted: 11/04/2009] [Indexed: 11/23/2022]
Abstract
Pleckstrin homology (PH) domains have been identified only in eukaryotic proteins to date. We have determined crystal structures for three members of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the existence of PH-like domains in bacteria (PHb). The first two structures contain a single PHb domain that forms a dome-shaped, oligomeric ring with C(5) symmetry. The third structure has an additional helical hairpin attached at the C-terminus and forms a similar but much larger ring with C(12) symmetry. Thus, both molecular assemblies exhibit rare, higher-order, cyclic symmetry but preserve a similar arrangement of their PHb domains, which gives rise to a conserved hydrophilic surface at the intersection of the beta-strands of adjacent protomers that likely mediates protein-protein interactions. As a result of these structures, additional families of PHb domains were identified, suggesting that PH domains are much more widespread than originally anticipated. Thus, rather than being a eukaryotic innovation, the PH domain superfamily appears to have existed before prokaryotes and eukaryotes diverged.
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Soranzo N, Spector TD, Mangino M, Kühnel B, Rendon A, Teumer A, Willenborg C, Wright B, Chen L, Li M, Salo P, Voight BF, Burns P, Laskowski RA, Xue Y, Menzel S, Altshuler D, Bradley JR, Bumpstead S, Burnett MS, Devaney J, Döring A, Elosua R, Epstein SE, Erber W, Falchi M, Garner SF, Ghori MJR, Goodall AH, Gwilliam R, Hakonarson HH, Hall AS, Hammond N, Hengstenberg C, Illig T, König IR, Knouff CW, McPherson R, Melander O, Mooser V, Nauck M, Nieminen MS, O'Donnell CJ, Peltonen L, Potter SC, Prokisch H, Rader DJ, Rice CM, Roberts R, Salomaa V, Sambrook J, Schreiber S, Schunkert H, Schwartz SM, Serbanovic-Canic J, Sinisalo J, Siscovick DS, Stark K, Surakka I, Stephens J, Thompson JR, Völker U, Völzke H, Watkins NA, Wells GA, Wichmann HE, Van Heel DA, Tyler-Smith C, Thein SL, Kathiresan S, Perola M, Reilly MP, Stewart AFR, Erdmann J, Samani NJ, Meisinger C, Greinacher A, Deloukas P, Ouwehand WH, Gieger C. A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium. Nat Genet 2009; 41:1182-90. [PMID: 19820697 PMCID: PMC3108459 DOI: 10.1038/ng.467] [Citation(s) in RCA: 419] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 07/07/2009] [Indexed: 12/18/2022]
Abstract
The number and volume of cells in the blood affect a wide range of disorders including cancer and cardiovascular, metabolic, infectious and immune conditions. We consider here the genetic variation in eight clinically relevant hematological parameters, including hemoglobin levels, red and white blood cell counts and platelet counts and volume. We describe common variants within 22 genetic loci reproducibly associated with these hematological parameters in 13,943 samples from six European population-based studies, including 6 associated with red blood cell parameters, 15 associated with platelet parameters and 1 associated with total white blood cell count. We further identified a long-range haplotype at 12q24 associated with coronary artery disease and myocardial infarction in 9,479 cases and 10,527 controls. We show that this haplotype demonstrates extensive disease pleiotropy, as it contains known risk loci for type 1 diabetes, hypertension and celiac disease and has been spread by a selective sweep specific to European and geographically nearby populations.
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Affiliation(s)
- Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK.
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ARAP3 binding to phosphatidylinositol-(3,4,5)-trisphosphate depends on N-terminal tandem PH domains and adjacent sequences. Cell Signal 2009; 22:257-64. [PMID: 19786092 DOI: 10.1016/j.cellsig.2009.09.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 09/14/2009] [Indexed: 11/21/2022]
Abstract
Pleckstrin homology (PH) domains are modules characterised by a conserved three-dimensional protein fold. Several PH domains bind phosphoinositides with high affinity and specificity whilst most others do not. ARAP3 is a dual GTPase activating protein for Arf6 and RhoA which was identified in a screen for phosphatidylinositol-(3,4,5)-trisphophate (PtdIns(3,4,5)P(3)) binding proteins. It is a regulator of cell shape and adhesion, and is itself regulated by PtdIns(3,4,5)P(3,) which acts to recruit ARAP3 to the plasma membrane and to catalytically activate it. We show here that ARAP3 binds to PtdIns(3,4,5)P(3) in an unusual, PH domain-dependent manner. None of the five PH domains are sufficient to bind PtdIns(3,4,5)P(3) in isolation. Instead, the minimal PtdIns(3,4,5)P(3) binding fragment comprises ARAP3's N-terminal tandem PH domains, and an N-terminal linker region. For substantial binding, the N-terminal sterile alpha motif (SAM) domain is also required. Site-directed mutagenesis of either of the two N-terminal PH domains within the fragment greatly reduces binding to PtdIns(3,4,5)P(3), however, in the context of the full-length protein, point mutations in the second PH domain have a lesser effect on binding, whilst deletion of any one of the five PH domains abolishes PtdIns(3,4,5)P(3) binding. We propose a mechanism by which basic residues from the N-terminal tandem PH domains, and from elsewhere in the protein synergise to mediate strong, specific PtdIns(3,4,5)P(3) binding.
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Su Z, Cox A, Shen Y, Stylianou IM, Paigen B. Farp2 and Stk25 are candidate genes for the HDL cholesterol locus on mouse chromosome 1. Arterioscler Thromb Vasc Biol 2009; 29:107-13. [PMID: 18988887 PMCID: PMC2782635 DOI: 10.1161/atvbaha.108.178384] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To identify the gene responsible for the quantitative trait locus (QTL) Hdlq14, a high-density lipoprotein cholesterol (HDL) QTL previously identified in a C57BL/6Jx129S1/SvImJ cross. METHODS AND RESULTS Hdlq14 was first confirmed as an independent QTL by detecting it in an intercross between NZB/B1NJ and NZW/LacJ, 2 strains that had identical genotypes at nearby QTL genes on chromosome 1. Using the bioinformatics tools of combined cross data and haplotype analysis, we narrowed this QTL from a 45-Mb 225-gene region to 2 genes, Farp2 and Stk25. Sequencing and expression studies showed that Farp2 had an amino acid polymorphism in an important plekstrin domain and that Stk25 had a significant expression difference between the parental strains. These 2 genes are immediately adjacent to each other and share the same haplotype over 45 inbred strains. The haplotype was associated with a significant difference in HDL levels among these strains. CONCLUSIONS We confirmed Hdlq14 as a separate independent QTL for HDL and narrowed the region to 2 genes, Farp2 and Stk25, with considerable evidence for both. Additional studies are needed to choose between these 2 genes or to show that both are important in determining HDL levels.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Animals
- Atherosclerosis/genetics
- Cholesterol, HDL/genetics
- Chromosome Mapping
- Chromosomes, Mammalian/genetics
- Crosses, Genetic
- Diet, Atherogenic
- Disease Models, Animal
- Female
- Genotype
- Guanine Nucleotide Exchange Factors/genetics
- Intracellular Signaling Peptides and Proteins/genetics
- Lipoproteins, HDL/genetics
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred Strains
- Phenotype
- Polymorphism, Genetic
- Protein Serine-Threonine Kinases/genetics
- Quantitative Trait Loci
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Affiliation(s)
- Zhiguang Su
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | - Allison Cox
- The Jackson Laboratory, Bar Harbor, Maine 04609
| | - Yuan Shen
- The Jackson Laboratory, Bar Harbor, Maine 04609
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40
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Peterson FC, Volkman BF. Diversity of polyproline recognition by EVH1 domains. Front Biosci (Landmark Ed) 2009; 14:833-46. [PMID: 19273103 DOI: 10.2741/3281] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enabled/VASP Homology-1 (EVH1) domains function primarily as interaction modules that link signaling proteins by binding to proline-rich sequences. EVH1 domains are ~115 residues in length and adopt the pleckstrin homology (PH) fold. Four different protein families contain EVH1 domains: Ena/VASP, Homer, WASP and SPRED. Except for the SPRED domains, for which no binding partners are known, EVH1 domains use a conserved hydrophobic cleft to bind a four-residue motif containing 2-4 prolines. Conserved aromatic residues, including an invariant tryptophan, create a wedge-shaped groove on the EVH1 surface that matches the triangular profile of a polyproline type II helix. Hydrophobic residues adjacent to the polyproline motif dock into complementary sites on the EVH1 domain to enhance ligand binding specificity. Pseudosymmetry in the polyproline type II helix allows peptide ligands to bind in either of two N-to-C terminal orientations, depending on interactions between sequences flanking the prolines and the EVH1 domain. EVH1 domains also recognize non-proline motifs, as illustrated by the structure of an EVH1:LIM3 complex and the extended EVH1 ligands of the verprolin family.
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Affiliation(s)
- Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA
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41
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Abstract
This overview provides an illustrated, comprehensive survey of some commonly observed protein‐fold families and structural motifs, chosen for their functional significance. It opens with descriptions and definitions of the various elements of protein structure and associated terminology. Following is an introduction into web‐based structural bioinformatics that includes surveys of interactive web servers for protein fold or domain annotation, protein‐structure databases, protein‐structure‐classification databases, structural alignments of proteins, and molecular graphics programs available for personal computers. The rest of the overview describes selected families of protein folds in terms of their secondary, tertiary, and quaternary structural arrangements, including ribbon‐diagram examples, tables of representative structures with references, and brief explanations pointing out their respective biological and functional significance.
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Affiliation(s)
- Peter D Sun
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, USA
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42
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Human biliverdin reductase is an ERK activator; hBVR is an ERK nuclear transporter and is required for MAPK signaling. Proc Natl Acad Sci U S A 2008; 105:6870-5. [PMID: 18463290 DOI: 10.1073/pnas.0800750105] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activation of the MEK/ERK/Elk-signaling cascade is a mechanism for relaying mitogenic and stress stimuli for gene activation. MEK1 is the proximate kinase for activation of ERK1/2, and nuclear targeting of ERK1/2 is obligatory for Elk1 transcriptional activity. Human biliverdin reductase (hBVR) is a recently described Ser/Thr/Tyr kinase in the MAPK insulin/insulin-like growth factor 1 (IGF1)-signaling cascade. Using 293A cells and in vitro experiments, we detail the formation of a ternary complex of MEK/ERK/hBVR, activation of MEK1 and ERK1/2 kinase activities by hBVR, and phosphorylation of hBVR by ERK1/2. hBVR is nearly as effective as IGF1 in activating ERK; intact hBVR ATP-binding domain is necessary for Elk1 activation, whereas protein-protein interaction is the basis for hBVR activation of MEK1 and ERK. The two MAPK docking consensus sequences present in hBVR, F(162)GFP and K(275)KRILHCLGL (C- and D-box, respectively), are ERK interactive sites; interaction at each site is critical for ERK/Elk1 activation. Transfection with mutant hBVR-P(165) or peptides corresponding to the C- or D-box blocked activation of ERK by IGF1. Transfection with D-box mutant hBVR prevented the activation of ERK by wild-type protein and dramatically decreased Elk1 transcriptional activity. hBVR is a nuclear transporter of ERK; experiments with hBVR nuclear export signal (NES) and nuclear localization signal (NLS) mutants demonstrated its critical role in the nuclear localization of IGF-stimulated ERK for Elk1 activation. These findings, together with observations that si-hBVR blocked activation of ERK and Elk1 by IGF1 and prevented formation of ternary complex between MEK/ERK/hBVR, define the critical role of hBVR in ERK signaling and nuclear functions of the kinase.
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43
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Wang L, Deng W, Shi T, Ma D. URP2SF, a FERM and PH domain containing protein, regulates NF-kappaB and apoptosis. Biochem Biophys Res Commun 2008; 368:899-906. [PMID: 18280249 DOI: 10.1016/j.bbrc.2008.02.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Accepted: 02/02/2008] [Indexed: 12/25/2022]
Abstract
The transcription factor NF-kappaB plays an important role in inflammation and cell survival. Here, we report the functional characterization of URP2SF (UNC-112 related protein 2 short form), which is a novel protein containing FERM and PH domains. The protein is conserved in evolution across different species. Northern blot and RT-PCR analysis revealed that the expression of URP2SF appeared to be primarily confined to immune system. URP2SF protein localized to the whole cell. Over-expression of URP2SF strongly repressed NF-kappaB activity in the absence or presence of NF-kappaB stimulus. Importantly, URP2SF over-expression also induced cell apoptosis. Furthermore, suppression of URP2SF expression by small interference RNA significantly activated the NF-kappaB reporter gene activities, as well as attenuated TNF-alpha induced apoptosis. Therefore, our data show for the first time that URP2SF may act as a transcriptional repressor in NF-kappaB signaling pathway and regulate cell apoptotic pathway.
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Affiliation(s)
- Lan Wang
- Chinese National Human Genome Center, No. 3-707 North YongChang Road BDA, Beijing 100176, PR China
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44
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Leone M, Yu EC, Liddington RC, Pasquale EB, Pellecchia M. The PTB domain of tensin: NMR solution structure and phosphoinositides binding studies. Biopolymers 2008; 89:86-92. [DOI: 10.1002/bip.20862] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Anders N, Nielsen M, Keicher J, Stierhof YD, Furutani M, Tasaka M, Skriver K, Jürgens G. Membrane association of the Arabidopsis ARF exchange factor GNOM involves interaction of conserved domains. THE PLANT CELL 2008; 20:142-51. [PMID: 18203920 PMCID: PMC2254928 DOI: 10.1105/tpc.107.056515] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 12/19/2007] [Accepted: 12/30/2007] [Indexed: 05/22/2023]
Abstract
The GNOM protein plays a fundamental role in Arabidopsis thaliana development by regulating endosome-to-plasma membrane trafficking required for polar localization of the auxin efflux carrier PIN1. GNOM is a family member of large ARF guanine nucleotide exchange factors (ARF-GEFs), which regulate vesicle formation by activating ARF GTPases on specific membranes in animals, plants, and fungi. However, apart from the catalytic exchange activity of the SEC7 domain, the functional significance of other conserved domains is virtually unknown. Here, we show that a distinct N-terminal domain of GNOM mediates dimerization and in addition interacts heterotypically with two other conserved domains in vivo. In contrast with N-terminal dimerization, the heterotypic interaction is essential for GNOM function, as mutations abolishing this interaction inactivate the GNOM protein and compromise its membrane association. Our results suggest a general model of large ARF-GEF function in which regulated changes in protein conformation control membrane association of the exchange factor and, thus, activation of ARFs.
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Affiliation(s)
- Nadine Anders
- Center of Molecular Biology of Plants, University of Tübingen, 72076 Tübingen, Germany
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46
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Li J, Mao X, Dong LQ, Liu F, Tong L. Crystal structures of the BAR-PH and PTB domains of human APPL1. Structure 2007; 15:525-33. [PMID: 17502098 DOI: 10.1016/j.str.2007.03.011] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 03/21/2007] [Accepted: 03/23/2007] [Indexed: 10/23/2022]
Abstract
APPL1 interacts with adiponectin receptors and other important signaling molecules. It contains a BAR and a PH domain near its N terminus, and the two domains may function as a unit (BAR-PH domain). We report here the crystal structures of the BAR-PH and PTB domains of human APPL1. The structures reveal novel features for BAR domain dimerization and for the interactions between the BAR and PH domains. The BAR domain dimer of APPL1 contains two four-helical bundles, whereas other BAR domain dimers have only three helices in each bundle. The PH domain is located at the opposite ends of the BAR domain dimer. Yeast two-hybrid assays confirm the interactions between the BAR and PH domains. Lipid binding assays show that the BAR, PH, and PTB domains can bind phospholipids. The ability of APPL1 to interact with multiple signaling molecules and phospholipids supports an important role for this adaptor in cell signaling.
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Affiliation(s)
- Jiang Li
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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47
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Troffer-Charlier N, Cura V, Hassenboehler P, Moras D, Cavarelli J. Functional insights from structures of coactivator-associated arginine methyltransferase 1 domains. EMBO J 2007; 26:4391-401. [PMID: 17882262 PMCID: PMC2034665 DOI: 10.1038/sj.emboj.7601855] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 08/21/2007] [Indexed: 11/08/2022] Open
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1), a protein arginine methyltransferase recruited by several transcription factors, methylates a large variety of proteins and plays a critical role in gene expression. We report, in this paper, four crystal structures of isolated modules of CARM1. The 1.7 A crystal structure of the N-terminal domain of CARM1 reveals an unexpected PH domain, a scaffold frequently found to regulate protein-protein interactions in a large variety of biological processes. Three crystal structures of the CARM1 catalytic module, two free and one cofactor-bound forms (refined at 2.55 A, 2.4 A and 2.2 A, respectively) reveal large structural modifications including disorder to order transition, helix to strand transition and active site modifications. The N-terminal and the C-terminal end of CARM1 catalytic module contain molecular switches that may inspire how CARM1 regulates its biological activities by protein-protein interactions.
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Affiliation(s)
- Nathalie Troffer-Charlier
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
| | - Vincent Cura
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
| | - Pierre Hassenboehler
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
| | - Dino Moras
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
| | - Jean Cavarelli
- Département de Biologie et Génomique Structurales, IGBMC (Institut de Génétique et de Biologie Moléculaire et Cellulaire) (UMR 7104 CNRS, U596 INSERM, ULP), Illkirch, France
- Laboratoire de Biologie et Génomique Structurales, IGBMC (CNRS/INSERM/ULP), 1 rue Laurent Fries, BP 10142, Ilkirch 67404, France. Tel.: +33 388 65 5793; Fax: +33 388 65 3276; E-mail:
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48
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Ritter B, Denisov AY, Philie J, Allaire PD, Legendre-Guillemin V, Zylbergold P, Gehring K, McPherson PS. The NECAP PHear domain increases clathrin accessory protein binding potential. EMBO J 2007; 26:4066-77. [PMID: 17762867 PMCID: PMC2230672 DOI: 10.1038/sj.emboj.7601836] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Accepted: 07/30/2007] [Indexed: 11/08/2022] Open
Abstract
AP-2 is a key regulator of the endocytic protein machinery driving clathrin-coated vesicle (CCV) formation. One critical function, mediated primarily by the AP-2 alpha-ear, is the recruitment of accessory proteins. NECAPs are alpha-ear-binding proteins that enrich on CCVs. Here, we have solved the structure of the conserved N-terminal region of NECAP 1, revealing a unique module in the pleckstrin homology (PH) domain superfamily, which we named the PHear domain. The PHear domain binds accessory proteins bearing FxDxF motifs, which were previously thought to bind exclusively to the AP-2 alpha-ear. Structural analysis of the PHear domain reveals the molecular surface for FxDxF motif binding, which was confirmed by site-directed mutagenesis. The reciprocal analysis of the FxDxF motif in amphiphysin I identified distinct binding requirements for binding to the alpha-ear and PHear domain. We show that NECAP knockdown compromises transferrin uptake and establish a functional role for NECAPs in clathrin-mediated endocytosis. Our data uncover a striking convergence of two evolutionarily and structurally distinct modules to recognize a common peptide motif and promote efficient endocytosis.
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Affiliation(s)
- Brigitte Ritter
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Alexei Yu Denisov
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jacynthe Philie
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Patrick D Allaire
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Valerie Legendre-Guillemin
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Peter Zylbergold
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Kalle Gehring
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, Canada H3G 1Y6. Tel.: +514 398 7287; Fax: +514 847 0220; E-mail:
| | - Peter S McPherson
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, 3801 University Street, Montreal, Canada H3A 2B4. Tel.: +514 398 7355; Fax: +514 398 8106; E-mail:
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49
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Lerner-Marmarosh N, Miralem T, Gibbs PEM, Maines MD. Regulation of TNF-alpha-activated PKC-zeta signaling by the human biliverdin reductase: identification of activating and inhibitory domains of the reductase. FASEB J 2007; 21:3949-62. [PMID: 17639074 DOI: 10.1096/fj.07-8544com] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Human biliverdin reductase (hBVR) is a dual function enzyme: a catalyst for bilirubin formation and a S/T/Y kinase that shares activators with protein kinase C (PKC) -zeta, including cytokines, insulin, and reactive oxygen species (ROS). Presently, we show that hBVR increases PKC-zeta autophosphorylation, stimulation by TNF-alpha, as well as cytokine stimulation of NF-kappaB DNA binding and promoter activity. S149 in hBVR S/T kinase domain and S230 in YLS230F in hBVR's docking site for the SH2 domain of signaling proteins are phosphorylation targets of PKC-zeta. Two hBVR-based peptides, KRNRYLS230F (#1) and KKRILHC281 (#2), but not their S-->A or C-->A derivatives, respectively, blocked PKC-zeta stimulation by TNF-alpha and its membrane translocation. The C-terminal-based peptide KYCCSRK296 (#3), enhanced PKC-zeta stimulation by TNF-alpha; for this, Lys296 was essential. In metabolically 32P-labeled HEK293 cells transfected with hBVR or PKC-zeta, TNF-alpha increased hBVR phosphorylation. TNF-alpha did not stimulate PKC-zeta in cells infected with small interfering RNA for hBVR or transfected with hBVR with a point mutation in the nucleotide-binding loop (G17), S149, or S230; this was similar to the response of "kinase-dead" PKC-zeta(K281R). We suggest peptide #1 blocks PKC-zeta-docking site interaction, peptide #2 disrupts function of the PKC-zeta C1 domain, and peptide #3 alters ATP presentation to the kinase. The findings are of potential significance for development of modulators of PKC-zeta activity and cellular response to cytokines.
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Affiliation(s)
- Nicole Lerner-Marmarosh
- University of Rochester School of Medicine and Dentistry, Department of Biochemistry and Biophysics, 601 Elmwood Avenue, Rochester, NY 14642, USA
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50
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Maystadt I, Rezsöhazy R, Barkats M, Duque S, Vannuffel P, Remacle S, Lambert B, Najimi M, Sokal E, Munnich A, Viollet L, Verellen-Dumoulin C. The nuclear factor kappaB-activator gene PLEKHG5 is mutated in a form of autosomal recessive lower motor neuron disease with childhood onset. Am J Hum Genet 2007; 81:67-76. [PMID: 17564964 PMCID: PMC1950913 DOI: 10.1086/518900] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 04/05/2007] [Indexed: 12/11/2022] Open
Abstract
Lower motor neuron diseases (LMNDs) include a large spectrum of clinically and genetically heterogeneous disorders. Studying a large inbred African family, we recently described a novel autosomal recessive LMND variant characterized by childhood onset, generalized muscle involvement, and severe outcome, and we mapped the disease gene to a 3.9-cM interval on chromosome 1p36. We identified a homozygous missense mutation (c.1940 T-->C [p.647 Phe-->Ser]) of the Pleckstrin homology domain-containing, family G member 5 gene, PLEKHG5. In transiently transfected HEK293 and MCF10A cell lines, we found that wild-type PLEKHG5 activated the nuclear factor kappa B (NF kappa B) signaling pathway and that both the stability and the intracellular location of mutant PLEKHG5 protein were altered, severely impairing the NF kappa B transduction pathway. Moreover, aggregates were observed in transiently transfected NSC34 murine motor neurons overexpressing the mutant PLEKHG5 protein. Both loss of PLEKHG5 function and aggregate formation may contribute to neurotoxicity in this novel form of LMND.
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Affiliation(s)
- Isabelle Maystadt
- Centre de Génétique Humaine et Unité de Génétique Médicale, Université Catholique de Louvain, Brussels, Belgium.
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