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Verma S, Dangi RS, Rajak MK, Pal RK, Sundd M. The apo-acyl coenzyme A binding protein of Leishmania major forms a unique 'AXXA' motif mediated dimer. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:141016. [PMID: 38615987 DOI: 10.1016/j.bbapap.2024.141016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/22/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Acyl-Coenzyme A binding domain containing proteins (ACBDs) are ubiquitous in nearly all eukaryotes. They can exist as a free protein, or a domain of a large, multidomain, multifunctional protein. Besides modularity, ACBDs also display multiplicity. The same organism may have multiple ACBDs, differing in sequence and organization. By virtue of this diversity, ACBDs perform functions ranging from transport, synthesis, trafficking, signal transduction, transcription, and gene regulation. In plants and some microorganisms, these ACBDs are designated ACBPs (acyl-CoA binding proteins). The simplest ACBD/ACBP is a small, ∼10 kDa, soluble protein, comprising the acyl-CoA binding (ACB) domain. Most of these small ACBDs exist as monomers, while a few show a tendency to oligomerize. In sync with those studies, we report the crystal structure of two ACBDs from Leishmania major, named ACBP103, and ACBP96 based on the number of residues present. Interestingly, ACBP103 crystallized as a monomer and a dimer under different crystallization conditions. Careful examination of the dimer disclosed an exposed 'AXXA' motif in the helix I of the two ACBP103 monomers, aligned in a head-to-tail arrangement in the dimer. Glutaraldehyde cross-linking studies confirm that apo-ACBP103 can self-associate in solution. Isothermal titration calorimetry studies further show that ACBP103 can bind ligands ranging from C8 - to C20-CoA, and the data could be best fit to a 'two sets of sites'/sequential binding site model. Taken together, our studies show that Leishmania major ACBP103 can self-associate in the apo-form through a unique dimerization motif, an interaction that may play an important role in its function.
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Affiliation(s)
- Shalini Verma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Rohit Singh Dangi
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Manoj Kumar Rajak
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Ravi Kant Pal
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
| | - Monica Sundd
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India.
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Dani R, Pawloski W, Chaurasiya DK, Srilatha NS, Agarwal S, Fushman D, Naganathan AN. Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in Paralogous Plasmodium Acyl-CoA Binding Proteins. Biochemistry 2023; 62:2982-2996. [PMID: 37788430 PMCID: PMC10774088 DOI: 10.1021/acs.biochem.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Paralogous proteins confer enhanced fitness to organisms via complex sequence-conformation codes that shape functional divergence, specialization, or promiscuity. Here, we dissect the underlying mechanism of promiscuous binding versus partial subfunctionalization in paralogues by studying structurally identical acyl-CoA binding proteins (ACBPs) from Plasmodium falciparum that serve as promising drug targets due to their high expression during the protozoan proliferative phase. Combining spectroscopic measurements, solution NMR, SPR, and simulations on two of the paralogues, A16 and A749, we show that minor sequence differences shape nearly every local and global conformational feature. A749 displays a broader and heterogeneous native ensemble, weaker thermodynamic coupling and cooperativity, enhanced fluctuations, and a larger binding pocket volume compared to A16. Site-specific tryptophan probes signal a graded reduction in the sampling of substates in the holo form, which is particularly apparent in A749. The paralogues exhibit a spectrum of binding affinities to different acyl-CoAs with A749, the more promiscuous and hence the likely ancestor, binding 1000-fold stronger to lauroyl-CoA under physiological conditions. We thus demonstrate how minor sequence changes modulate the extent of long-range interactions and dynamics, effectively contributing to the molecular evolution of contrasting functional repertoires in paralogues.
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Affiliation(s)
- Rahul Dani
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Westley Pawloski
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Dhruv Kumar Chaurasiya
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Sonal Agarwal
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - David Fushman
- Center for Biomolecular Structure & Organization, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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Zhang J, Lin X, Chen Y, Li T, Lee AC, Chow EY, Cho WC, Chan T. LAFITE Reveals the Complexity of Transcript Isoforms in Subcellular Fractions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2203480. [PMID: 36461702 PMCID: PMC9875686 DOI: 10.1002/advs.202203480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Characterization of the subcellular distribution of RNA is essential for understanding the molecular basis of biological processes. Here, the subcellular nanopore direct RNA-sequencing (DRS) of four lung cancer cell lines (A549, H1975, H358, and HCC4006) is performed, coupled with a computational pipeline, Low-abundance Aware Full-length Isoform clusTEr (LAFITE), to comprehensively analyze the full-length cytoplasmic and nuclear transcriptome. Using additional DRS and orthogonal data sets, it is shown that LAFITE outperforms current methods for detecting full-length transcripts, particularly for low-abundance isoforms that are usually overlooked due to poor read coverage. Experimental validation of six novel isoforms exclusively identified by LAFITE further confirms the reliability of this pipeline. By applying LAFITE to subcellular DRS data, the complexity of the nuclear transcriptome is revealed in terms of isoform diversity, 3'-UTR usage, m6A modification patterns, and intron retention. Overall, LAFITE provides enhanced full-length isoform identification and enables a high-resolution view of the RNA landscape at the isoform level.
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Affiliation(s)
- Jizhou Zhang
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Xiao Lin
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Yuelong Chen
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Tsz‐Ho Li
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SARChina
| | - Alan Chun‐Kit Lee
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
| | | | | | - Ting‐Fung Chan
- School of Life SciencesThe Chinese University of Hong KongShatinHong Kong SARChina
- State Key Laboratory of AgrobiotechnologyThe Chinese University of Hong KongShatinHong Kong SARChina
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Hamdan MF, Lung SC, Guo ZH, Chye ML. Roles of acyl-CoA-binding proteins in plant reproduction. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2918-2936. [PMID: 35560189 DOI: 10.1093/jxb/erab499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/11/2021] [Indexed: 06/15/2023]
Abstract
Acyl-CoA-binding proteins (ACBPs) constitute a well-conserved family of proteins in eukaryotes that are important in stress responses and development. Past studies have shown that ACBPs are involved in maintaining, transporting and protecting acyl-CoA esters during lipid biosynthesis in plants, mammals, and yeast. ACBPs show differential expression and various binding affinities for acyl-CoA esters. Hence, ACBPs can play a crucial part in maintaining lipid homeostasis. This review summarizes the functions of ACBPs during the stages of reproduction in plants and other organisms. A comprehensive understanding on the roles of ACBPs during plant reproduction may lead to opportunities in crop improvement in agriculture.
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Affiliation(s)
- Mohd Fadhli Hamdan
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Shiu-Cheung Lung
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Ze-Hua Guo
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Mee-Len Chye
- School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
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5
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Masmoudi-Kouki O, Namsi A, Hamdi Y, Bahdoudi S, Ghouili I, Chuquet J, Leprince J, Lefranc B, Ghrairi T, Tonon MC, Lizard G, Vaudry D. Cytoprotective and Neurotrophic Effects of Octadecaneuropeptide (ODN) in in vitro and in vivo Models of Neurodegenerative Diseases. Front Endocrinol (Lausanne) 2020; 11:566026. [PMID: 33250858 PMCID: PMC7672186 DOI: 10.3389/fendo.2020.566026] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/28/2020] [Indexed: 11/13/2022] Open
Abstract
Octadecaneuropeptide (ODN) and its precursor diazepam-binding inhibitor (DBI) are peptides belonging to the family of endozepines. Endozepines are exclusively produced by astroglial cells in the central nervous system of mammals, and their release is regulated by stress signals and neuroactive compounds. There is now compelling evidence that the gliopeptide ODN protects cultured neurons and astrocytes from apoptotic cell death induced by various neurotoxic agents. In vivo, ODN causes a very strong neuroprotective action against neuronal degeneration in a mouse model of Parkinson's disease. The neuroprotective activity of ODN is based on its capacity to reduce inflammation, apoptosis, and oxidative stress. The protective effects of ODN are mediated through its metabotropic receptor. This receptor activates a transduction cascade of second messengers to stimulate protein kinase A (PKA), protein kinase C (PKC), and mitogen-activated protein kinase (MAPK)-extracellular signal-regulated kinase (ERK) signaling pathways, which in turn inhibits the expression of proapoptotic factor Bax and the mitochondrial apoptotic pathway. In N2a cells, ODN also promotes survival and stimulates neurite outgrowth. During the ODN-induced neuronal differentiation process, numerous mitochondria and peroxisomes are identified in the neurites and an increase in the amount of cholesterol and fatty acids is observed. The antiapoptotic and neurotrophic properties of ODN, including its antioxidant, antiapoptotic, and pro-differentiating effects, suggest that this gliopeptide and some of its selective and stable derivatives may have therapeutic value for the treatment of some neurodegenerative diseases.
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Affiliation(s)
- Olfa Masmoudi-Kouki
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation, LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Amira Namsi
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation, LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
- Team Bio-PeroxIL, Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism/University Bourgogne Franche-Comté (UBFC)/Inserm, Dijon, France
| | - Yosra Hamdi
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation, LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Seyma Bahdoudi
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation, LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
- Normandy University, Neuronal and Neuroendocrine Differentiation and Communication, Inserm U1239, Rouen, France
| | - Ikram Ghouili
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation, LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Julien Chuquet
- Normandy University, Neuronal and Neuroendocrine Differentiation and Communication, Inserm U1239, Rouen, France
| | - Jérôme Leprince
- Normandy University, Neuronal and Neuroendocrine Differentiation and Communication, Inserm U1239, Rouen, France
- Normandy University, Regional Platform for Cell Imaging of Normandy (PRIMACEN), Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Benjamin Lefranc
- Normandy University, Neuronal and Neuroendocrine Differentiation and Communication, Inserm U1239, Rouen, France
- Normandy University, Regional Platform for Cell Imaging of Normandy (PRIMACEN), Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Taoufik Ghrairi
- Laboratory of Neurophysiology Cellular Physiopathology and Biomolecule Valorisation, LR18ES03, Faculty of Sciences of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Marie-Christine Tonon
- Normandy University, Neuronal and Neuroendocrine Differentiation and Communication, Inserm U1239, Rouen, France
| | - Gérard Lizard
- Team Bio-PeroxIL, Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism/University Bourgogne Franche-Comté (UBFC)/Inserm, Dijon, France
| | - David Vaudry
- Normandy University, Neuronal and Neuroendocrine Differentiation and Communication, Inserm U1239, Rouen, France
- Normandy University, Regional Platform for Cell Imaging of Normandy (PRIMACEN), Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
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6
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Tonon MC, Vaudry H, Chuquet J, Guillebaud F, Fan J, Masmoudi-Kouki O, Vaudry D, Lanfray D, Morin F, Prevot V, Papadopoulos V, Troadec JD, Leprince J. Endozepines and their receptors: Structure, functions and pathophysiological significance. Pharmacol Ther 2020; 208:107386. [DOI: 10.1016/j.pharmthera.2019.06.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/20/2019] [Indexed: 02/06/2023]
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7
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Ghouili I, Bahdoudi S, Morin F, Amri F, Hamdi Y, Coly PM, Walet-Balieu ML, Leprince J, Zekri S, Vaudry H, Vaudry D, Castel H, Amri M, Tonon MC, Masmoudi-Kouki O. Endogenous Expression of ODN-Related Peptides in Astrocytes Contributes to Cell Protection Against Oxidative Stress: Astrocyte-Neuron Crosstalk Relevance for Neuronal Survival. Mol Neurobiol 2017; 55:4596-4611. [PMID: 28698967 DOI: 10.1007/s12035-017-0630-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/22/2017] [Indexed: 11/29/2022]
Abstract
Astroglial cells are important actors in the defense of brain against oxidative stress injuries. Glial cells synthesize and release the octadecaneuropeptide ODN, a diazepam-binding inhibitor (DBI)-related peptide, which acts through its metabotropic receptor to protect neurons and astrocytes from oxidative stress-induced apoptosis. The purpose of the present study is to examine the contribution of the endogenous ODN in the protection of astrocytes and neurons from moderate oxidative stress. The administration of H2O2 (50 μM, 6 h) induced a moderate oxidative stress in cultured astrocytes, i.e., an increase in reactive oxygen species, malondialdehyde, and carbonyl group levels, but it had no effect on astrocyte death. Mass spectrometry and QPCR analysis revealed that 50 μM H2O2 increased ODN release and DBI mRNA levels. The inhibition of ODN release or pharmacological blockage of the effects of ODN revealed that in these conditions, 50 μM H2O2 induced the death of astrocytes. The transfection of astrocytes with DBI siRNA increased the vulnerability of cells to moderate stress. Finally, the addition of 1 nM ODN to culture media reversed cell death observed in DBI-deficient astrocytes. The treatment of neurons with media from 50 μM H2O2-stressed astrocytes significantly reduced the neuronal death induced by H2O2; this effect is greatly attenuated by the administration of an ODN metabotropic receptor antagonist. Overall, these results indicate that astrocytes produce authentic ODN, notably in a moderate oxidative stress situation, and this glio- and neuro-protective agent may form part of the brain defense mechanisms against oxidative stress injury.
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Affiliation(s)
- Ikram Ghouili
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Research Unit UR/11ES09, Laboratory of Functional Neurophysiology and Pathology, 2092, Tunis, Tunisia
| | - Seyma Bahdoudi
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Research Unit UR/11ES09, Laboratory of Functional Neurophysiology and Pathology, 2092, Tunis, Tunisia.,Inserm U1239, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen Normandie, 76128, Mont-Saint-Aignan, France
| | - Fabrice Morin
- Inserm U1239, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen Normandie, 76128, Mont-Saint-Aignan, France
| | - Fatma Amri
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Research Unit UR/11ES09, Laboratory of Functional Neurophysiology and Pathology, 2092, Tunis, Tunisia
| | - Yosra Hamdi
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Research Unit UR/11ES09, Laboratory of Functional Neurophysiology and Pathology, 2092, Tunis, Tunisia
| | - Pierre Michael Coly
- Inserm U1239, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen Normandie, 76128, Mont-Saint-Aignan, France
| | - Marie-Laure Walet-Balieu
- Regional Proteomic Platform (Pissaro), IRIB, University of Rouen Normandie, Mont-Saint-Aignan, France
| | - Jérôme Leprince
- Inserm U1239, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen Normandie, 76128, Mont-Saint-Aignan, France.,Regional Platform for Cell Imaging of Normandie (PRIMACEN), IRIB, University of Rouen Normandie, Mont-Saint-Aignan, France.,International Associated Laboratory Samuel de Champlain, University of Rouen Normandie, Mont-Saint-Aignan, France
| | - Sami Zekri
- Electron Microscopy Laboratory, Faculty of Medicine of Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Hubert Vaudry
- Regional Platform for Cell Imaging of Normandie (PRIMACEN), IRIB, University of Rouen Normandie, Mont-Saint-Aignan, France.,International Associated Laboratory Samuel de Champlain, University of Rouen Normandie, Mont-Saint-Aignan, France
| | - David Vaudry
- Inserm U1239, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen Normandie, 76128, Mont-Saint-Aignan, France.,Regional Proteomic Platform (Pissaro), IRIB, University of Rouen Normandie, Mont-Saint-Aignan, France.,Regional Platform for Cell Imaging of Normandie (PRIMACEN), IRIB, University of Rouen Normandie, Mont-Saint-Aignan, France.,International Associated Laboratory Samuel de Champlain, University of Rouen Normandie, Mont-Saint-Aignan, France
| | - Hélène Castel
- Inserm U1239, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen Normandie, 76128, Mont-Saint-Aignan, France
| | - Mohamed Amri
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Research Unit UR/11ES09, Laboratory of Functional Neurophysiology and Pathology, 2092, Tunis, Tunisia
| | - Marie-Christine Tonon
- Inserm U1239, Laboratory of Neuronal and Neuroendocrine Communication and Differentiation, Institute for Research and Innovation in Biomedicine (IRIB), University of Rouen Normandie, 76128, Mont-Saint-Aignan, France.
| | - Olfa Masmoudi-Kouki
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Research Unit UR/11ES09, Laboratory of Functional Neurophysiology and Pathology, 2092, Tunis, Tunisia.
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8
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Neess D, Bek S, Engelsby H, Gallego SF, Færgeman NJ. Long-chain acyl-CoA esters in metabolism and signaling: Role of acyl-CoA binding proteins. Prog Lipid Res 2015; 59:1-25. [PMID: 25898985 DOI: 10.1016/j.plipres.2015.04.001] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/11/2015] [Accepted: 04/09/2015] [Indexed: 02/03/2023]
Abstract
Long-chain fatty acyl-CoA esters are key intermediates in numerous lipid metabolic pathways, and recognized as important cellular signaling molecules. The intracellular flux and regulatory properties of acyl-CoA esters have been proposed to be coordinated by acyl-CoA-binding domain containing proteins (ACBDs). The ACBDs, which comprise a highly conserved multigene family of intracellular lipid-binding proteins, are found in all eukaryotes and ubiquitously expressed in all metazoan tissues, with distinct expression patterns for individual ACBDs. The ACBDs are involved in numerous intracellular processes including fatty acid-, glycerolipid- and glycerophospholipid biosynthesis, β-oxidation, cellular differentiation and proliferation as well as in the regulation of numerous enzyme activities. Little is known about the specific roles of the ACBDs in the regulation of these processes, however, recent studies have gained further insights into their in vivo functions and provided further evidence for ACBD-specific functions in cellular signaling and lipid metabolic pathways. This review summarizes the structural and functional properties of the various ACBDs, with special emphasis on the function of ACBD1, commonly known as ACBP.
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Affiliation(s)
- Ditte Neess
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Signe Bek
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Hanne Engelsby
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Sandra F Gallego
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Nils J Færgeman
- Villum Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark.
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Abstract
Since their introduction in the 1960s, benzodiazepines (BZs) remain one of the most commonly prescribed medications, acting as potent sedatives, hypnotics, anxiolytics, anticonvulsants, and muscle relaxants. The primary neural action of BZs and related compounds is augmentation of inhibitory transmission, which occurs through allosteric modulation of the gamma-aminobutyric acid (GABA)-induced current at the gamma-aminobutyric acid receptor (GABAAR). The discovery of the BZ-binding site on GABAARs encouraged many to speculate that the brain produces its own endogenous ligands to this site (Costa & Guidotti, 1985). The romanticized quest for endozepines, endogenous ligands to the BZ-binding site, has uncovered a variety of ligands that might fulfill this role, including oleamides (Cravatt et al., 1995), nonpeptidic endozepines (Rothstein et al., 1992), and the protein diazepam-binding inhibitor (DBI) (Costa & Guidotti, 1985). Of these ligands, DBI, and affiliated peptide fragments, is the most extensively studied endozepine. The quest for the "brain's Valium" over the decades has been elusive as mainly negative allosteric modulatory effects have been observed (Alfonso, Le Magueresse, Zuccotti, Khodosevich, & Monyer, 2012; Costa & Guidotti, 1985), but recent evidence is accumulating that DBI displays regionally discrete endogenous positive modulation of GABA transmission through activation of the BZ receptor (Christian et al., 2013). Herein, we review the literature on this topic, focusing on identification of the endogenous molecule and its region-specific expression and function.
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10
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Wong MS, Wright WE, Shay JW. Alternative splicing regulation of telomerase: a new paradigm? Trends Genet 2014; 30:430-8. [PMID: 25172021 DOI: 10.1016/j.tig.2014.07.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 01/01/2023]
Abstract
Alternative splicing affects approximately 95% of eukaryotic genes, greatly expanding the coding capacity of complex genomes. Although our understanding of alternative splicing has increased rapidly, current knowledge of splicing regulation has largely been derived from studies of highly expressed mRNAs. Telomerase is a key example of a protein that is alternatively spliced, but it is expressed at very low levels and although it is known that misregulation of telomerase splicing is a hallmark of nearly all cancers, the details of this process are unclear. Here we review work showing that hTERT expression is in part regulated by atypical alternative splicing, perhaps due to its exceptionally low expression level. We propose that these differential regulatory mechanisms may be widely applicable to other genes and may provide new opportunities for the development of cancer therapeutics.
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Affiliation(s)
- Mandy S Wong
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Woodring E Wright
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390-9039, USA
| | - Jerry W Shay
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390-9039, USA; Center for Excellence in Genomics Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.
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11
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Farkas MH, Grant GR, White JA, Sousa ME, Consugar MB, Pierce EA. Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. BMC Genomics 2013; 14:486. [PMID: 23865674 PMCID: PMC3924432 DOI: 10.1186/1471-2164-14-486] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 07/15/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel, that are expressed in a given tissue has become vital for understanding the mechanisms underlying the pathology of disease. RESULTS We sequenced RNA prepared from three normal human retinas and characterized the retinal transcriptome at an unprecedented level due to the increased depth of sampling provided by the RNA-seq approach. We used a non-redundant reference transcriptome from all of the empirically-determined human reference tracks to identify annotated and novel sequences expressed in the retina. We detected 79,915 novel alternative splicing events, including 29,887 novel exons, 21,757 3' and 5' alternate splice sites, and 28,271 exon skipping events. We also identified 116 potential novel genes. These data represent a significant addition to the annotated human transcriptome. For example, the novel exons detected increase the number of identified exons by 3%. Using a high-throughput RNA capture approach to validate 14,696 of these novel transcriptome features we found that 99% of the putative novel events can be reproducibly detected. Further, 15-36% of the novel splicing events maintain an open reading frame, suggesting they produce novel protein products. CONCLUSIONS To our knowledge, this is the first application of RNA capture to perform large-scale validation of novel transcriptome features. In total, these analyses provide extensive detail about a previously uncharacterized level of transcript diversity in the human retina.
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Affiliation(s)
- Michael H Farkas
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Gregory R Grant
- Penn Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph A White
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Maria E Sousa
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Mark B Consugar
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
- Berman-Gund Laboratory for the Study of Retinal Degenerations, Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
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Mills JD, Nalpathamkalam T, Jacobs HI, Janitz C, Merico D, Hu P, Janitz M. RNA-Seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism. Neurosci Lett 2013; 536:90-5. [DOI: 10.1016/j.neulet.2012.12.042] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 12/25/2012] [Indexed: 11/26/2022]
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Hardwick JP, Eckman K, Lee YK, Abdelmegeed MA, Esterle A, Chilian WM, Chiang JY, Song BJ. Eicosanoids in metabolic syndrome. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2013; 66:157-266. [PMID: 23433458 DOI: 10.1016/b978-0-12-404717-4.00005-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chronic persistent inflammation plays a significant role in disease pathology of cancer, cardiovascular disease, and metabolic syndrome (MetS). MetS is a constellation of diseases that include obesity, diabetes, hypertension, dyslipidemia, hypertriglyceridemia, and hypercholesterolemia. Nonalcoholic fatty liver disease (NAFLD) is associated with many of the MetS diseases. These metabolic derangements trigger a persistent inflammatory cascade, which includes production of lipid autacoids (eicosanoids) that recruit immune cells to the site of injury and subsequent expression of cytokines and chemokines that amplify the inflammatory response. In acute inflammation, the transcellular synthesis of antiinflammatory eicosanoids resolve inflammation, while persistent activation of the autacoid-cytokine-chemokine cascade in metabolic disease leads to chronic inflammation and accompanying tissue pathology. Many drugs targeting the eicosanoid pathways have been shown to be effective in the treatment of MetS, suggesting a common linkage between inflammation, MetS and drug metabolism. The cross-talk between inflammation and MetS seems apparent because of the growing evidence linking immune cell activation and metabolic disorders such as insulin resistance, dyslipidemia, and hypertriglyceridemia. Thus modulation of lipid metabolism through either dietary adjustment or selective drugs may become a new paradigm in the treatment of metabolic disorders. This review focuses on the mechanisms linking eicosanoid metabolism to persistent inflammation and altered lipid and carbohydrate metabolism in MetS.
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Affiliation(s)
- James P Hardwick
- Biochemistry and Molecular Pathology, Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, Ohio, USA.
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