VOLUME THREE HUNDRED AND TWENTY ONE INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY International Review of Cell and Molecular Biology Series Editors GEOFFREY H BOURNE JAMES F DANIELLI KWANG W JEON MARTIN FRIEDLANDER JONATHAN JARVIK 1949—1988 1949—1984 1967— 1984—1992 1993—1995 Editorial Advisory Board PETER L BEECH ROBERT A BLOODGOOD BARRY D BRUCE DAVID M BRYANT KEITH BURRIDGE HIROO FUKUDA MAY GRIFFITH KEITH LATHAM WALLACE F MARSHALL BRUCE D MCKEE MICHAEL MELKONIAN KEITH E MOSTOV ANDREAS OKSCHE MADDY PARSONS TERUO SHIMMEN ALEXEY TOMILIN GARY M WESSEL VOLUME THREE HUNDRED AND TWENTY ONE INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY Edited by KWANG W JEON Department of Biochemistry University of Tennessee Knoxville, Tennessee AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, USA 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA 125 London Wall, London EC2Y 5AS, UK The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK Copyright © 2016 Elsevier Inc All rights reserved No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein) Notices Knowledge and best practice in this field are constantly changing As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein ISBN: 978-0-12-804707-1 ISSN: 1937-6448 For information on all Academic Press publications visit our website at http://store.elsevier.com/ CONTRIBUTORS Sara Aspengren Department of Biology and Environmental Sciences, University of Gothenburg, Goăteborg, Sweden Lidia Bakota Department of Neurobiology, University of Osnabruăck, Osnabruăck, Germany Roland Brandt Department of Neurobiology, University of Osnabruăck, Osnabruăck, Germany Elizabeth Calzada Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Karen L Cheney School of Biological Sciences, University of Queensland, Brisbane, Australia Steven M Claypool Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Yusuke Ito Plant Molecular Breeding Laboratory, Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan Jian-Ping Jin Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA Henriikka Kentala Minerva Foundation Institute for Medical Research, Biomedicum 2U, Helsinki, Finland Makoto Matsuoka Plant Molecular Breeding Laboratory, Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan Younes Medkour Department of Biology, Concordia University, Montreal, Quebec, Canada Yoichi Morinaka Plant Molecular Breeding Laboratory, Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan Vesa M Olkkonen Minerva Foundation Institute for Medical Research, Biomedicum 2U, Helsinki, Finland ix x Contributors Ouma Onguka Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA Reynante Ordonio Plant Molecular Breeding Laboratory, Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan Lore`ne Penazzi Department of Neurobiology, University of Osnabruăck, Osnabruăck, Germany Takashi Sazuka Plant Molecular Breeding Laboratory, Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan Helen Nilsson Skoăld Sven Loven Centre for Marine SciencesKristineberg, University of Gothenburg, Fiskebaăckskil, Sweden Veronika Svistkova Department of Biology, Concordia University, Montreal, Quebec, Canada Vladimir I Titorenko Department of Biology, Concordia University, Montreal, Quebec, Canada Margareta Wallin Department of Biology and Environmental Sciences, University of Gothenburg, Goăteborg, Sweden Marion Weber-Boyvat Minerva Foundation Institute for Medical Research, Biomedicum 2U, Helsinki, Finland CHAPTER ONE Evolution, Regulation, and Function of N-terminal Variable Region of Troponin T: Modulation of Muscle Contractility and Beyond Jian-Ping Jin* Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA *E-mail: jjin@med.wayne.edu Contents Introduction Molecular Structure of Troponin T Evolution of Troponin T Isoform Genes Alternative Splicing Developmental Regulations Posttranslational Modifications 6.1 Phosphorylation 6.2 Restrictive Proteolysis Conclusion and Perspectives Acknowledgments References 10 15 19 19 20 22 22 22 Abstract Troponin T (TnT) is the tropomyosin-binding and thin filament-anchoring subunit of the troponin complex in skeletal and cardiac muscles At the center of the sarcomeric thin filament regulatory system of striated muscles, TnT plays an essential role in transducing Ca2+ signals in the regulation of contraction Having emerged predating the history of vertebrates, TnT has gone through more than 500 million years of evolution that resulted in three muscle-type-specific isoforms and numerous alternative RNA splicing variants The N-terminal region of TnT is a hypervariable structure responsible for the differences among the TnT isoforms and splice forms This focused review summarizes our current knowledge of the molecular evolution of the Nterminal variable region and its role in the structure and function of TnT In addition International Review of Cell and Molecular Biology, Volume 321 ISSN 1937-6448 http://dx.doi.org/10.1016/bs.ircmb.2015.09.002 © 2016 Elsevier Inc All rights reserved Jian-Ping Jin to the physiologic and pathophysiologic significances in modifying the contractility of skeletal and cardiac muscles during development and in adaptation to stress and disease conditions, the hyperplasticity of the N-terminal region of TnT demonstrates an informative example for the evolution of protein three-dimensional structure and provides insights into the molecular evolution and functional potential of proteins INTRODUCTION The contractile machinery of striated muscles (represented by skeletal and cardiac muscles of vertebrates) is the myofibrils that consist of tandem repeats of sarcomeres A sarcomere is composed of overlapping myosin thick filaments and actin thin filaments Contraction is powered by actin-activated myosin ATPase-catalyzed ATP hydrolysis during actomyosin cross-bridge cycling This process is regulated by the thin filament-associated regulatory proteins troponin under the control of cytosolic Ca2+ (Gordon et al., 2000) Residing at ∼37-nm intervals along the thin filament in the form of F-actin-tropomyosin double helices (Galinska-Rakoczy et al., 2008; Lehman et al., 2009; Ohtsuki et al., 1967), the troponin complex consists of three protein subunits: the Ca2+-binding subunit troponin C (TnC1), actomyosin ATPase-inhibiting subunit troponin I (TnI), and tropomyosinbinding subunit troponin T (TnT) (Greaser and Gergely, 1971) To convert the cellular signal of cytosolic Ca2+ transient originated from sarcolemmal electrical activity to myofilament movements during each excitation– contraction–relaxation cycle, troponin functions through cooperative interactions among the three subunits and with tropomyosin (Gordon et al., 2000; Tobacman, 1996) Whereas TnC is a relative of the calmodulin gene family (Collins, 1991) and functions as the Ca2+ receptor of the thin filament regulatory system in striated muscle, TnI and TnT are striated-muscle-specific proteins encoded by closely linked genes and have coevolved into three pairs of fiber-type-specific isoforms (Chong and Jin, 2009; Jin et al., 2008) In addition to anchoring the troponin complex to the thin filament, TnT directly interacts with multiple proteins in the thin filament regulatory system to play an organizer role in the troponin complex (Perry, 1998) Through isoform gene regulation, alternative RNA splicing, and posttranslational modifications, structural and functional variations of TnT provide a mechanism to modulate striated muscle contraction and relaxation To understand the structure–function relationship of TnT, this review outlines the evolution of muscle type-specific TnT isoform genes, the Modulation of Muscle Contractility and Beyond multiple alternative splice forms, the developmental regulation of isoform expression and alternative splicing, and the posttranslational modifications during physiologic and pathophysiologic adaptations, with a focus on the Nterminal segment that is an evolutionarily diverged regulatory structure (Chong and Jin, 2009; Jin et al., 2008; Wei and Jin, 2011) For background information, comprehensive summaries of striated muscle thin filament regulation and the functions of TnC, TnI, and tropomyosin can be found in several previously published reviews (Collins, 1991; Gordon et al., 2000; Jin et al., 2008; Perry, 1998, 1999, 2001; Solaro and Rarick, 1998; Tobacman, 1996; Wei and Jin, 2011; Sheng and Jin, 2014) MOLECULAR STRUCTURE OF TROPONIN T TnT is a 30–35-kDa protein The sizes of vertebrate TnT with sequence information available range from 223 to 305 amino acids This large size variation is almost entirely due to the variable length of the Nterminal region, from nearly absent in certain fish fast skeletal muscle TnT to more than 70 amino acids long in avian and mammalian cardiac TnT (Jin et al., 2008; Wei and Jin, 2011) The hypervariable nature of the N-terminal domain of TnT is further demonstrated by the presence of 4–9 repeating sequence motifs in the breast muscle fast TnTof avian orders Galliformes and Craciformes (Jin and Smillie, 1994) These five amino acid repeats form a cluster of high-affinity transition metal binding sites that are only found in the adult breast muscle of these birds (Jin and Samanez, 2001; Ogut et al., 1999) While the N-terminal region of TnT is hypervariable in length and amino acid sequences, the amino acid sequences of the middle and Cterminal regions of TnT are highly conserved among the three muscletype-specific isoforms and across vertebrate species (Jin et al., 2008; Wei and Jin, 2011) Electron microscopic studies showed that the TnT molecule has an extended conformation (Cabral-Lilly et al., 1997; Wendt et al., 1997) The functional domains of TnT have been extensively studied using protein fragments generated from limited chymotryptic and CNBr digestions Protein-binding studies found that the ∼100 amino acids C-terminal chymotryptic fragment T2 interacts with TnI and TnC and binds to the middle region of tropomyosin (Heeley et al., 1987; Schaertl et al., 1995) The chymotryptic fragment T1 that contains both the N-terminal variable region and the middle conserved region of TnT binds the head–tail Jian-Ping Jin junction of tropomyosins in the actin thin filament (Heeley et al., 1987) The tropomyosin-binding activity of the T1 fragment resides in the 81 amino acids CNBr fragment CB2 of rabbit fast skeletal muscle TnT, which represents the middle conserved region of TnT The N-terminal segment of TnT (e.g., the CNBr fragment CB3 in rabbit fast skeletal muscle TnT) is the hypervariable region and does not bind any known thin filament proteins in the sarcomere (Perry, 1998) Consistent with the protein-binding data, X-ray crystallography determined the partial structure of cardiac and skeletal muscle troponin complex showing that the associations of TnTwith TnI and TnC are through the Cterminal T2 region (Takeda et al., 2003; Vinogradova et al., 2005) However, the crystallography data only determined the structure for a portion of the TnT–T2 region in the troponin complex The entire T1 region and the very C-terminal 13 amino acids of TnT were missing from the resolved highresolution structures (Takeda et al., 2003; Vinogradova et al., 2005) The 13 amino acid C-terminal end segment encoded by the last exon of the TnT gene is highly conserved among isoforms and across species (Jin et al., 2008; Wei and Jin, 2011) Deletion of the C-terminal 57 amino acids of fast TnT (Jha et al., 1996) or slow TnT (Jin and Chong, 2010) had no significant effect on the binding affinity of TnT for tropomyosin However, point mutations in this segment have been found to cause familial hypertrophic cardiomyopathy (Sheng and Jin, 2014); thus, its role in the structure and function of TnT remains to be investigated The high-resolution structural data showed that the main TnT–TnI interface in the troponin complex is a coiled-coil structure (i.e., the I-T arm) formed by the segments of L224–V274 in cardiac TnT and F90–R136 in cardiac TnI in human cardiac troponin complex (Takeda et al., 2003) or E199–Q245 in fast TnTand G55–L102 in fast TnI in chicken fast skeletal muscle troponin (Vinogradova et al., 2005) The amino acid sequences of TnT and TnI in this coiled-coil interface are both highly conserved among isoforms and across vertebrate species (Jin et al., 2008; Wei and Jin, 2011) Whereas gross mapping of the tropomyosin-binding sites of TnT using the chymotrypsin and CNBr fragments had served in guiding the studies of TnT function and thin filament regulation of muscle contraction for over three decades (Perry, 1998), the precise localizations of the two tropomyosinbinding sites of TnT were not determined until recently using genetically engineered TnT fragments (Jin and Chong, 2010) Analysis of serial deletions of TnT protein and mapping using site-specific monoclonal antibody epitope probes showed that the T1 region tropomyosin-binding site of TnT Index bacterial cell communities, proliferation of, 280 F42G9.6, transcriptional regulation of, 282 Caffeic acid O-methyltransferase (COMT), 237 Ca2+ influx, 124 Ca2+ ions, 108, 121 Calcium signaling, 44 Caloric restriction (CR), 260 CaMKII accumulation/localization, 128 Camouflage, 194 cAMP-responsive element-binding (CREB) protein, 190 Candida albicans, 69 Candidate gene approach, 239 Candidiasis, 69 Candystripe sorghum, 222 Canine diaphragm muscle, hypoxia in, 20 Canine-dilated cardiomyopathy, 14 Carboxy-terminal region, 301 Carboxy-terminal transmembrane segment, 301 Cardiac muscles, 19 pathophysiologic remodeling, 19 striated muscle development, 19 Cardiac TnT cDNAs, 17 Cardiolipin (CL), 32 Casein kinase (CK2), 111 Cavefish, 193 cDNA cloning, 11 CDP-choline pathway, 47 CDP-diacylglycerol, 41 CDP-ethanolamine pathway, 33, 37, 38, 39, 51, 64, 66 Cell division, 51 Cell-to-cell communications, 272 Cellular cholesterol efflux, 313 Cellulosic biomass, 221 Central nervous system (CNS), 101 Centrosomes, 103, 105 Ceramide transporter (CERT), 299 Cereal crops, 221 CERT See Ceramide transporter (CERT) C4 grass, 221 Chaperone signaling pathways, 272 neuronal, 272 343 transcellular, 272 Charcot–Marie–Tooth disease, 13 Cholesterol, 31, 302 Chromatophores, 175 transdifferentiation between, 178 Chromis viridis See Blue-green chromis Chrysiptera cyanea See Blue damselfish Cichlid, 197 Cinnamyl alcohol dehydrogenase (CAD), 238 4CL See Arabidopsis4-coumarate:CoAligase (4CL) gene Cleaner wrasse, 198, 200 CMS See Cytoplasmic male sterile (CMS) lines Coastrange sculpins, 178, 194 Coiled-coil forming segments, 301 Color change, functional aspects of, 193, 203Fish chromatophores camouflage, 194 coastrange sculpins, 194 coral trout, 194 flounders, 194 Nassau groupers, 194 peacock flounder, 194 plaice, 194 rock pool gobies, 194 seahorses, 194 color change, regulation of, 185 costs of pigments, 193 cavefish, 193 color plasticity, level of, 193 food consumption, increased, 193 immune system, 193 Sculpins, 193 life stages, 200 black goby, 201 cleaner wrasse, 200 damselfish, 200 disruptive coloration, 200 emperor angelfish, 200 ontogenetic shifts in body color, 200 pink females, coral, 202 spadefish, 200 wrasse, 200 mimicry, 197 adaptive evolution, 197 344 Color change, functional aspects of (cont.) blue-green chromis, 198 bluestriped fangblenny, 198 cleaner wrasse, 198 coral reef fish, 197 dusky dottyback, 198 great barrier reef, 198 natural selection, 197 orange anthias, 198 physiological color change, 199 yellow damselfish, 198 signaling, 196 Bluehead wrasse, 197 cichlid, 197 ephemeral color changes, 197 gobies, 196 greenling, 197 nuptial coloration, 197 Pecos pupfish, 196 sexually monochromatic species, 197 Southern pygmy perch, 196, 197 three-spine sticklebacks, 196 ComamonasDA1877, 283 Compartmentalization, 297 COMT See Ca¡eic acid O-methyltransferase (COMT) Coniferyl alcohol, 236 Constans (SbCO)/heading date1 (SbHd1), 242 Coral trout, 194 Coris gaimard See Wrasse Corn leaf blight, 246 Cottus aleuticus See Coastrange sculpin C4 plants, 221 CPS See ent-copalyl diphosphate synthase (CPS) CR See Caloric restriction (CR) CREB See cAMP-responsive elementbinding protein Cryptic blenny, 204 Ctenolabrusrupestris See Goldsinny wrasse Cuckoo wrasse, 185 Culm juice, 223 Cyanide-deficient mutants, 240 CYP79A1, 240 CYP71E1, 240 UGT85D1, 240 Cyanogenic glucosides, 240 Index Cyanophores, 172 CYP79A1, 240 Cyprinodon pecosensis See Pecos pupfish Cytochrome c oxidase, 53 Cytokinesis, 51 Cytoplasmic carboxypeptidases (CCP1-6), 98 Cytoplasmic male sterile (CMS) lines, 246 Cytoskeleton, 90 and molecular motors, 181 D DAF-16 See Dauer formation protein 16 (DAF-16) Damselfish, 200 Dark sleeper goby, 175 Dauer formation protein 16 (DAF-16) 282 Deacetylation, of tubulin, 98 DELLA protein, 235 Demyelination, 13 Dendrites, 116 Dendritic arborization, 116 regulation by neuronal activity, 119–121 Dendritic microtubules assembly and transport, 118–119 Dendritic spines, 122, 123 morphologic diversity of, 122 structure and function, 122–124 Dendritogenesis, 116 Depolymerization, 96 Detyrosination/tyrosination cycle, 98 Dhurrin, 240 dhurrinase2 mutant, 240 Diacylglycerol (DAG), 37 1,2-Diacylglycerol ethanolamine phosphotransferase (ETP), 37 Diadema pseudochromis, 172 Dihydrosphingosine-1-lyase (Dpl1p), 37 Dilated cardiomyopathy, 12 Dinitrophenol, 45 Double Dwarf Yellow Milo (dw1dw2Dw3dw4), 244 Drebrin, 128 Drosophila melanogaster, 119 Dusky dottyback, 198 Dwarfing genes, 234 345 Index Dwarf Yellow Milo (dw1Dw2Dw3dw4) 244 Dyneins, 93, 100 Dyslipidemia, 326 E EAE See Experimental autoimmune encephalomyelitis Ebola glycoprotein mediated viral penetration, 321 Electrical syncytium, 13 Electron transport chain, 53 EMC proteins, 43 Emperor angelfish, 200 EMS See Ethyl methane sulfonate (EMS) Endocytic membrane trafficking, 325 Endogenous microtubule modulators, 96 Endomembrane system, 36 Endoplasmic reticulum (ER), 276 activating transcription of genes ire-1, 278 xbp-1, 278 apoptotic cell death, 277 associated protein degradation, 277 biogenesis and vesicular trafficking, 277 ER–mitochondria encounter structure (ERMES), 42 ER–mitochondria junctions, 44 ER–mitochondria tethers, 44 lipid metabolism, 277 pathways, 36 protein folding in, 277 specific marker, 33 Endoribonuclease, 277 ent-Copalyl diphosphate synthase (CPS), 227 ent-Kaurene oxidase (KO), 227 ent-Kaurenoic acid oxidase (KAO), 227 Epinephelus striatus See Nassau groupers ER See Endoplasmic reticulum (ER) ER-mitochondria encounter structure (ERMES) complex, 42 ERMES-like proteins, 44 Erythrophores, 172 Escherichia coli, 280 OP50 strain of, 280 Q-less mutants, 283 Ethanol, 259Bioethanol as lifespan-shortening transmissible longevity factor, 260 Ethanolamine, 37, 64 phosphorylation of, 37 Ethanolamine kinase, 37 Ethyl methane sulfonate (EMS), 222 Euchromatin, 222 Eukaryotic cells, 91 Exocytosis, 321 schematic model of, 323 Experimental autoimmune encephalomyelitis (EAE), 136 Eye coloration, 203 F F-actin networks, 125 stability, 127 F-actin-tropomyosin, actomyosin ATPase-inhibiting subunit troponin I (TnI), Ca2+-binding subunit troponin C (TnC), tropomyosin binding subunit troponin T (TnT), Fatty acids, peroxisomal oxidation, 260 Fatty aldehyde, 37 Filopodia, 113 Fish chromatophores, 172 carotenoids, 174 color change, functional aspects of, 193 costs of pigments, 193 color change, regulation of, 185 physiological color change, regulation of, 185 color of, 172 disruptive coloration, 172 distribution of, 175 erythrophores, 172 fish coloration, 172 anenomefish, 174 carotenoids, 174 cell death, 173 cell differentiation, 173 cell migration, 173 cell proliferation, 173 cyanophores, 172 346 Fish chromatophores (cont.) dark sleeper goby, 175 diadema pseudochromis, 172 erythrophores, 172 interference phenomena, 172 iridiophores, 172 guanine platelet crystals, 175 leucophores, 172 mandarin fish, 172 medaka, 172 melanin, 173 neural crest, 173 physiological color change, 178 pigment synthesis, 173 pluripotent embryonic cell, transient, 173 postembryonic stem cells, 173 zebrafish, 175 gene expression profiles, 171 genetic divergence, suppress, 172 iridiophores, 172 role in positioning of the different chromatophores, 177 leucophores, 172 melanin, 173 melanophores, 171 nondermal chromatophores, 202 color change, 203 eye coloration, 203 internal pigmentation, 202 ontogenetic color change, 172 phenotypic plasticity, 171 speciation, 172 types of, 173 Fish coloration See also172Fish chromatophores morphological color change, 176 climate change, 178 coastrange sculpin, 178 cryptic coloration patterns, intensity of, 178 facilitate adaptation to novel environments, 179 invading species, 178 iridophores, 177 Japanese killifish, 177 regulation of, 176 Index Flatfish, 194 color change in, 194 Floral activator genes, 242 Flounders, 194 Fluid-phase endocytosis, 324 Functional genomics, 222 G GA See Gibberellin (GA) GAAC See General amino acid control (GAAC) GAI See GA-insensitive (GAI) GA2ox5, 234 GA2-oxidase, 234 GA3oxidase, 227 GA20-oxidase, 227 Gasterosteus aculeatus See Three-spine sticklebacks GBS See Genotyping-bysequencing (GBS) GCY-8 See Guanylyl cyclase (GCY-8) GEF See Guanine nucleotide exchange factor (GEF) General amino acid control (GAAC), 315 Genomic database, 221 Genotyping-bysequencing (GBS), 248 gh2 gene, 238 Gibberella fujikuroi, 235 Gibberellin (GA), 227 biosynthetic enzyme, 227 GA-insensitive (GAI), 227 insensitivity to, 227 related anomalies, 235 slender rice1 (slr1) mutant, 235 related mutants, 227 signaling repressor, 227 for stem elongation, 227 Glucose, 259 fermentation, 259 metabolism, 53 Glucose-regulated protein 75 (GRP75), 44 Glucosylceramide transfer protein, 299 Glutamate, 99 receptors, 120 Glutamatergic neurotransmission, 121 Glutamylation, 109 Glycerophospholipids, 31, 32 Glycolytic pathway, 259 347 Index Glycosylphosphatidylinositol (GPI), 33 Glyoxylate cycle, 266 Gobies, 196 Gobiusculus £avescens See Gobies Gobius niger See Black goby Gobius paganellus See Rock pool gobies Gold hull and internode2 (gh2) mutant, 236 Goldsinny wrasse, 202 Golgi apparatus, 103, 277 GPI-anchored proteins, 48, 58 G Protein-coupled metabotropic glutamatergic (mGluR), 120 G Protein-coupled thermal receptor (GTR-1), 269 Grain maturity, 223 Greenling, 197 Green revolution, mutants of, 227 reduced height-1 (Rht-1), 227 semidwarf1 (sd1), 227 Growth cones, 101 GTR-1 See G protein-coupled thermal receptor (GTR-1) Guanine nucleotide exchange factor (GEF), 323 Guanosine triphosphate (GTP), 93, 310 323 hydrolysis, 96 Guanylyl cyclase (GCY-8), 269 Gutamate, 93 GWAS analysis, 244 H hdhl See Highly digestible high-lysine (hdhl) mutant Heat shock proteins (HSPs), 269 Heat shock response (HSR), 267 pathways, integration of, 269 Heat shock transcription factor protein (HSF-1), 269 HeLa cells, 324 Hepatocytes, 53 membranes, maintenance of PC:PE ratio in, 67 Hepatoma cells, 325 Herbicides, 239 imidazolinones, 239 pyrimidyloxybenzoates, 239 sulfonylureas, 239 triazolopyrimidines, 239 Hereditary spastic paraplegia (HSP), 138 Hetero-oligomeric protein complex, 45 Heterotubulin isotypes, 91 HIF-1 See Hypoxia inducible factor-1 (HIF-1) High-affinity sterol ligand, 312 Highlydigestiblehigh-lysine(hdhl) mutant, 239 High-resolution genotyping, 244 Hippocampus erectus See seahorses Histone deacetylase, 98, 244 Homeostasis, 44, 53 Hormones, 185, 190 H2S See Hydrogen sulfide (H2S) HSF-1 See Heat shock transcription factor protein (HSF-1) HSP See Hereditary spastic paraplegia HSPs See Heat shock proteins (HSPs) HSR See Heat shock response (HSR) Hydrogen cyanide, 240 Hydrogen peroxide, 266 Hydrogen sulfide (H2S), 263 fat-soluble, 263 as lifespan-extending gas, 263 water-soluble, 263 Hydrophobicity, 31 25-Hydroxycholesterol (25OHC), 302 p-Hydroxymandelonitrile, 240 Hypertension, 66 Hypertriglyceridemia, 66 Hypoxia inducible factor-1 (HIF-1), 278 I IFITM3 See Interferon-inducible transmembrane protein (IFITM3) Infectious disease, 67 candida virulence, 69 pathogenic prion generation, 67 Inositol-4-phosphate-binding cleft, 303 Inositol-requiring protein (IRE-1), 276 Inositol 1,4,5-trisphosphate receptor (IP3R), 44 In silico analyses, 301 Interferon-inducible transmembrane protein (IFITM3), 321 348 Internal pigmentation, 202 Intracellular cholesterol trafficking, 313 Intracellular lipid transport, 297 mechanisms, 298 Ca2+ regulation, 298 compartmentalization, 297 nonvesicular mechanisms, 298 signaling events, 298 In vitro sterol transfer activity, 314 IRE-1 See Inositol-requiring protein (IRE-1) Isoform gene regulation, Itraconazole (ITZ), 320 ITZ See Itraconazole (ITZ) K Kafirins, 239 α, 239 β, 239 γ, 239 KAO See ent-Kaurenoic acid oxidase (KAO) Katanin, 114 7KC See 7-Ketocholesterol (7KC) 7-Ketocholesterol (7KC), 302 Kinesins 1, 2, 13, 100 Knockdown-induced cholesterol, 309 KO See ent-Kaurene oxidase (KO) L Labroides dimididatus See Cleaner wrasse Labroides phthirophagu See Cleaner wrasse Labrus mixtus See Cuckoo wrasse Lactic acid, 262 Lactose permease, 49 LDs See Lipid droplets (LDs) Leucophores, 172 uric acid, 175 Lifespan-prolonging molecules, 263 Life stages, 200 Lignin biosynthesis, 222, 236, 237 Lipid-binding/transfer proteins (LTPs), 298 Lipid carrier(s), 42, 45 Lipid droplets (LDs), 297 membrane signaling, 311 membrane trafficking, 311 metabolic energy storage, 311 Index multifunctional organelles, 311 steroid hormone biosynthesis, 311 Lipids, 31, 297 bidirectional transfer model, 316 carrier function, 299 enzymatic editing of, 312 fluxes, 297 hydrophobic molecules, 299 interorganelle transport, 298 intracellular transport, 313 metabolism, 313 ORPs ligands, 302 sensors, 299 synthetic reactions, 297 cellular organelle, 310 trafficking, 44, 326 Liposomes, 49 Liver disease PE:PC ratio in, 68 Liver steatosis, 65, 67 balance of PE and PC in, 65–67 Longevity-defining molecules, 262, 265 dimorphic transition, 265 microcolony unification, 265 quorum-sensing system, 265 spatiotemporal dynamics, 265 yeast cells colony, 265 L-serine, 41 LTPs See Lipid-binding/transfer proteins (LTPs) Lysine, 98 Lyso-PE, 38 M Macroautophagy, 55 MAM-associated α-synuclein, 64 Mandarin fish, 172 MAPs See Microtubule-associated proteins (MAPs) Mass spectrometry, 38, 44 MCH See melatonin-concentrating hormone MCSs See Membrane contact sites (MCSs) MDR See Multidrug resistant (MDR) Medaka, 172 Melanin, 173 eumelanin, 173 Index melanocytes, 174 pheomelanin, 174 melanogenesis, 173 melanosomes, 173 receptors of, 185 synthesis of, 174 Melanophores, 171 mutual repulsion between, 177 Melatonin-concentrating hormone (MCH), 185 Membrane contact sites (MCSs) 298 Membrane fusion, 51 Membrane proteins, 49 Metabolic syndrome, 66 Methylation, 58 of PE to form PC, 47 Microfilaments, 90 Microtubule-associated proteins (MAPs), 90, 96 compartment-specific distribution, 96 MT-binding capacity, 121 neuronal MAPs, 126 role in regulating, 96 subcellular distribution, during neuronal development MAP2 and MAP1B, 103 Microtubule dynamics, 94 alterations during aging, 129 Alzheimer’s disease, development of, 131 intracellular mechanisms, 129 microtubules during axonal damage, 136 microtubule-targeted therapies, 138 neuron structure, changes in, 129 pathologic intersection of Ab and MAPs, 134 reactive oxygen species, 129 sporadic alzheimer’s disease, morphologic changes in, 130 during axonogenesis, 102 during branch formation, 111–114 in dendrites, 116 in mature axon and during neuronal plasticity, 105 neurodegeneration, 129 349 and regulations, schematic representation, 95 Microtubules (MTs), 90, 181 Seealso headings starting with Microtubules in axon initial segment, 109–111 binding proteins, 96 during dendritic spine formation, and plasticity, 125–128 during dendritogenesis, and in mature dendrites, 117–118 dependent motility, 325 distribution, confocal laser scanning micrograph, 104 dynamic instability, 96 GTP-cap model, 96 nucleation, 94 organization and posttranslational modifications, 92 polymerization, 92 properties, 98 reorganization, during distinct steps of axon collateral formation and maturation, 113 Microtubules, during axonal damage, 136 Amyotrophic lateral sclerosis (ALS), 138 Ca2+ influx, 137 copper/zinc superoxide dismutase (SOD1), 138 experimental autoimmune encephalomyelitis (EAE), 136 Hereditary spastic paraplegia (HSP), 138 huntingtin protein (HTT), 137 Huntington’s disease (HD), 136 multiple sclerosis (MS), 136 Na+/K+-ATPase pump, impairment of function, 136 polyglutamine (polyQ), 137 progressive neurodegenerative disorder, 138 relapsing–remitting phase (RRMS), 136 tubulin acetylation, level of, 137 tubulin deacetylation, 137 Microtubule-targeted therapies, 138 blood–brain barrier (BBB), 139 epothilones, 139 frontotemporal lobar degeneration, 139 glutamate excitotoxicity, 139 350 Microtubule-targeted therapies (cont.) neuronal plasticity, 138 nocodazole, 138 spinal cord injury, 139 taxol, 138 Midas cichlids, 192 Mimicry, 197 Miscanthus species, 221 Missense mutations, 222 Mitochondrion, 31, 33, 36, 123, 297 fusion/fission, 55 involvement of GTPases, 55 GTPase, 42 membranes, 38, 42 mitochondrial-associated membrane (MAM), 33 mitochondrial contact site and cristae organizing system (MICOS), 45 NBD signal, 58 oxidative phosphorylation, 266 PC:PE ratio, 53 phosphatidylethanolamine (PE) function in, 52 phosphatidylserine decarboxylase (Psd) pathway, 38 protein biogenesis and activity, 54 Mitofusin (MFN2), 44 Molecular motors, regulation of, 188 Monolignol biosynthesis, 238 Morphological color change, regulation of, 176, 190 differentiation and apoptosis, regulation of balance between, 192 Midas cichlids, 192 hormones, 190 cAMP-responsive element-binding (CREB), 190 melanogenesis, 190 melanophore apoptosis, 190 Mitf, Expression of, 190 PKA signaling pathway, 190 Rho family proteins, 190 somatolactin-producing cells, 190 neuronal regulation, 191 apoptosis, 191 cAMP-PKA signaling, 191 Motile iridophores, 184 Index Motor neurons, 111 Motor proteins, 100 MTs See Microtubules (MTs) Multidrug resistant (MDR), 243 Multifunctional protein, 44 Multiprotein complex, 42 Mutagenesis, 222 saturation, 222 Mutant library, 222 gamma-ray-induced, 223 of T-DNA, 222 Myeloblastosis (MYB)-transcription factor family, 222 Myofibrils, Myosin, N NAD+ See Nicotinamide adenine dinucleotide (NAD+) NADPH-cytochrome-c reductase, 33 Nannoperca australis See Southern pygmy perch Nassau groupers, 194 body patterns of, 194 spawning activities of, 194 Nematode longevity, 267 aging-associated proteotoxic stress, 267 cellular proteostasis, 267 heat shock response (HSR), 267 by host–gut microbiota interactions 279 cell-nonautonomous mechanisms, 280 tissue regulation communication, 267 Nematode molting, 283 Neurofilaments, 90 Neurons, 91, 104 depolarization, 121 development, 101 differentiation, 102 polarity, 97, 102, 109 regulation, 187, 191 structure, changes in, 129 brain weight, reduction in, 129 dendritic alterations, 129 dendritic arborization, 129 351 Index UPRER network in, 276 ATF-6, ER-resident transmembrane proteins, 276 IRE-1, 276 IRE-1/XBP-1s branch of, 278 neuronal activation of, 279 selective stimulation of, 279 PERK, 276 Neurotransmitters, 278 Next generation sequencing (NGS) techniques, 222 NGS See Next generation sequencing (NGS) NHR-69 See Nuclear hormone receptor family protein 69 (NHR-69) Nicotinamide adenine dinucleotide (NAD+), 263 Nicotinamide riboside, 263 Nicotinic acid, 263 Niemann–Pick C1 (NPC1), 311 Nitric oxide (NO), 282 NMDAR activation, 127 N-Methyl-D-aspartate (NMDAR), 120 Nonalcoholic fatty liver disease (NAFLD), 65 Nonalcoholic steatohepatitis (NASH), 66 Nondermal chromatophores, 202 color change, 203 eye coloration, 203 cryptic blenny, 204 eye coloration and color change, 205 lower vertebrates, irises of, 203 noradrenaline, 204 predator attacks, prevents, 203 prolactin, 204 internal pigmentation, 202 goldsinny wrasse, 202 UV protection, 202 NPC1 See Niemann-Pick C1 (NPC1) Nuclear genes, 278 Nuclear hormone receptor family protein 69 (NHR-69), 269 Null mutation, 119 O Odontobutis obscura See dark sleeper goby 25OHC See 25-hydroxycholesterol (25OHC) Oncoprotein 18a, 97 Open-reading frames (ORFs), 246 Orange anthias, 198 ORFs See Open-reading frames (ORFs) ORP See OSBP-related proteins (ORP) ORP2–VAP complexes, 312 Oryzias latipes See medaka OSBP See Oxysterol-binding protein (OSBP) OSBP homolog (OSH) genes, 299 OSBPL2 gene, 313 OSBP-related proteins (ORP), 299 in β-lipoprotein secretion, 325 in dyslipidemia, 325 and endocytosis, 324 involvement in vesicle transport, 321 lipid ligands of, 302 as lipid transporters or sensors, 313 by mammalian ORPs, 316 in regulatory components, 317 by S cerevisiae Osh proteins, 313 for viral replication, 320 structural features of, 299 subcellular targeting of, 303 dual membrane targeting principle, 303 endoplasmic reticulum and endosomes/vacuole, 310 and golgi complex, 307 and lipid droplets, 311 and plasma membrane, 305 OsCAD2 gene, 238 OSH See OSBP homolog (OSH) genes Osh4p in exocytosis, function of, 321 Oxaloacetate, 266 Oxidative phosphorylation, 45, 46, 53 Oxylebius pictus See greenling Oxysterol, 312 Oxysterol-binding protein (OSBP), 299 P PA See Phosphatidic acid (PA) Paired-helical filaments (PHF), 132 Palmitoylation, 98 Paradise whiptail, 184 Paralichthys lethostigma See flounders Parkinson’s disease (PD), 62–65 352 Passive diffusion, 42, 44 Pathologic intersection of Ab and MAPs, 134 cell death, neuronal, 134 neurodegenerative triad, 134 spastin, 136 Src family tyrosine kinase, 135 tau–Fyn interaction, 135 PC See Phosphatidylcholine (PC) PCD See Programmed cell death (PCD) p-Coumaryl alcohol, 236 PCYT2 gene, 37 PE See Phosphatidylethanolamine (PE) Peacock flounder, 194 Pecos pupfish, 196 PE methyltransferase (Pem1p), 33, 47 PEMT ablation, 53 PE N-methyl transferase (PEMT), 47 Pentapodus paradiseus See paradise whiptail P450 enzyme, 240 Perennial plant, 221 PERK See Protein kinase RNA-like ER kinase (PERK) Peroxisomes, 297 PG See Phosphatidylglycerol (PG) PH See Pleckstrin homology (PH) Phenotypic plasticity, 171 Phenylalanine, 50 PHF See Paired-helical filaments Phosphatidic acid (PA), 32 Phosphatidylcholine (PC), 32 Phosphatidylethanolamine, 32 Phosphatidylethanolamine (PE), 29 biosynthesis, 33 cellular/molecular functions, 49 as determinant of protein topology, 49–50 and diseases, 59 importance in topological orientation, 50 inducing topological inversion of TM domains LacY, 49 lipidation of Atg8p, 58 methylation to form PC, 47 in mitochondrial function, 52 pivotal role in fusion of Golgi membranes, 51 Index as precursor for other lipids and substrate for posttranslational modifications, 47 produced by Psd1p, fate of, 46 Phosphatidylglycerol (PG), 32 Phosphatidylinositol (PI), 32 Phosphatidylinositol-4, 5-bisphosphate (PIP2), 314 Phosphatidyl-N-monomethylethanolamine (PMME), 47 Phosphatidylserine (PS), 32, 302 synthase, 33 transport, 42 into mitochondria, 42–44 within mitochondria, 45–46 Phosphatidylserine decarboxylase (Psd1p), 34, 38–40, 42, 55 fate of PE produced by, 46 Phosphatidylserine decarboxylase (Psd) pathway, 34 Phosphatidylserine synthase-1 (PSS1), 41 Phosphoethanolamine, 37 for GPI anchor formation, 48 Phosphoethanolamine cytidylyltransferase, 37 Phosphofurin acid cluster sorting-protein (PACS-2), 44 Phospho-glycoproteins (P-GPs), 243 Phospholipase C, 68 Phospholipid methyltransferase (Pem2p), 47 Phospholipids, 30–33, 36, 38, 44, 68 biosynthetic enzymes, 33 Phosphoproteins, 115 Phosphorylation, 19, 97, 109, 126 of MAP2, 121 tau, 115 PHYB See Phytochrome B (PHYB) Physiological color change, 171, 178 crystals, shifts in angles of, 178 cytoskeleton and molecular motors 181 ATP hydrolysis, 181 dynactin, 181 dynein, 181 immunoelectron microscopy, 183 intracellular motor transport, 181 kinesin-II, 181 Index kinesin motors, 181 melanophilin, 183 microtubules (MTs), 181 MT-organizing center, 181 multimeric protein complex, 181 myosin-V, 183 polyglutamylated tubulin, antibody against, 181 posttranslational modifications, evolutionary conserved, 181 taxol, 181 motile iridophores, 184 blue damselfish, 184 calmodulin, 184 colchicine, administration of, 184 cytochalasine B, administration of, 184 epinephrine, 184 opsins, 184 paradise whiptail, 184 Siamese fighting fish, 184 pigment mass translocations, 180 hormonal stimuli, dose of the, 180 intracellular cAMP, levels of, 180 melanocyte stimulating hormone (MSH), 180 pigment organelles, mass translocations of, 178 social signaling, 180 Physiological color change, regulation 185 hormones, 185 adrenocorticotropic hormone, 186 barfin flounder, 185 circadian hormone, 185 Cuckoo wrasse, 185 G-protein coupled receptor, 185 intracellular Ca2+, 185 intracellular cAMP, 185 melatonin-concentrating hormone (MCH), 185 physiological color change in the flatfish, Pleuronectes platessa, 187 pineal gland, 185 prolactin, 186 protein kinase C (PKC), 185 molecular motors, regulation of, 188 353 neuronal regulation, 187 α2-adrenoreceptor, 187 β2-adrenoreceptor, 188 Ca2+–calmodulin system, 187 diacylglycerol triphosphate pathway, 187 light-scattering organelles, 187 noradrenaline, release of, 187 protein kinase A, inactivation of, 187 signal transduction pathways, 188 calcineurin, 188 cAMP/PKA, 188 dephosphorylation, 188 latrunculin, 188 phosphatases, 188 phosphorylation, 188 Phytochrome B (PHYB), 242 PI See Phosphatidylinositol (PI) Pigment mass translocations, 180 PI4KB See PI 4-kinase III β (PI4KB) PI 4-kinase III β (PI4KB), 320 PIP2 See Phosphatidylinositol-4,5bisphosphate (PIP2) PISD gene, 53 PI synthase, 33 PKC See protein kinase C (PKC) PKD See Protein kinase D (PKD) Plagiotremusrhinorhynchos See Bluestriped fangblenny Plaice, 194 Plasma membrane (PM), 31, 38, 51, 115, 297 PC:PE ratio, 67 Plasticity, 90 Platax pinnatus See Spadefish Pleckstrin homology (PH), 301 Plectropomusleopardus See Coral trout Pleuronectes platessa See plaice PM See Plasma membrane (PM) Poaceae, 221 Polarity, 102 Polyamines, 109 Polyglutamylation, 98, 99 of tubulin, 99, 100 Polyglycylation, 98 Polymer transport model, 105 Polymorphisms, 326 354 Polyribosomes, 116 Polyunsaturated fatty acids, 33 Pomacanthus imperator See Emperor angelfish Pomacentrus amboinensis See yellow damselfish Pomacentrus molucensis See Yellow damselfish Pomacentrus partitus See Damselfish Postsynaptic densities (PSDs), 118 Posttranslational modifications, 2, 40, 92, 97 PE as precursor for lipids and substrate for, 47 proteins, 19 Premnas biaculeatus See anenomefish Prions, 67 propagation, 68 Programmed cell death (PCD), 260 Protein biogenesis, 54 Protein conformations, 68 Protein kinase A (PKA), 117 Protein kinase C (PKC), 19, 185 phosphorylation sites, 19 Ser201, 19 Thr197, 19 Thr206, 19 Thr286, 19 Protein kinase D (PKD), 308 Protein kinase RNA-like ER kinase (PERK), 276 self phosphorylation, 277 translation initiation factor eIF2α, inactivation of, 277 Protein–protein interactions, 301 Proteostasis stress signals, 269 PS See Phosphatidylserine (PS) Pseudanthias huchti See Orange anthias Pseudanthias squamipinnis See Orange anthias Pseudanthias tuka See Orange anthias Pseudochromis diadema See diadema pseudochromis Pseudochromis fuscus See Dusky dottyback Pseudomonas sp., 280 Pseudopleuronectes americanus See flounders Pseudoresponse regulatorprotein37 (PRR37), 242 Index Purkinje cells, 98 Pyruvoyl groups, 40 Q QTLs See Quantitative trait loci (QTLs) Quantitative trait loci (QTLs), 221 R Rab-family GTPases, 321 Ypt32p, 323 Rab7-interacting lysosomal protein (RILP), 310 Reactive oxygen species (ROS), 261 Recombinant inbred line (RIL), 241 Reducing sugars, 223 fructose, 223 glucose, 223 Relapsing–remitting phase (RRMS), 136 Reptiles, 175 light-reflecting platelets, 175 Restorer of fertility (Rf) genes, 246 Restrictive proteolysis, 20 Reverse genetics screening approach, 222 Rf genes See Restorer of fertility (Rf) genes Rho-family GTPases, 321 Ribosomes, 116 RIL See Recombinant inbred line (RIL) RILP See Rab7-interacting lysosomal protein (RILP) RNAi inhibition, 53 RNAi silencing, of PISD, 38 RNA splicing, 2, 10 of exon 4, 13 Rock pool gobies, 194 ROS See Reactive oxygen species (ROS) RRMS See Relapsing-remitting phase S Saccharification, 236 Saccharinae, 221 Saccharomyces cerevisiae, 299 high-resolution structure, 299 Sarcomeres, SbCAD2 gene, 238 Sb04g005210, 238 Sb06g015420, 244 Index Sb08g007610, 240 S bicolo, 222 Sbprr37-1 allele, 242 SCG10 protein, 112 SCVs See Small clear vesicles (SCVs) SD1 gene, 227 Seahorses, 194 Secreted ER stress signals (SERSS) 278 Secretory pathway, 321 Semi-arid environments, 221 Serine protease, 40 Serinolysis, 40 SERSS See Secreted ER stress signals (SERSS) Shotgun sequencing technique, 221 Siamese fighting fish, 184 Signal transduction pathways, 188 Sinapyl alcohol, 236 Single nucleotide polymorphisms (SNPs), 241 SIRT2 enzyme, 98 SLR1 , 235 SM See Sphingomyelin (SM) Small clear vesicles (SCVs), 278 Smooth endoplasmic reticulum (SER), 116 SNPs See Single nucleotide polymorphisms (SNPs) SOD1 See Superoxide dismutase Sorghum, 221 adaptability in semi-arid/arid environments, 221 brown midribs in, 236 culm bending in, 227 dwarfism in, 227, 233 EMS-treated population of, 239 GA-deficient mutants of, 227 gene isolation, 227 genes present in, 228 genomics, 221 database of, 221 sequence, 221 as green fuel alternative, 221 mutant libraries of, 222 mutant use in gene functional analysis, 227 cyanide-deficient mutants, 240 355 herbicide-resistant mutant, 239 low kafirin mutants, 239 low lignin mutants, 236 plant height-related mutants, 227 brassinosteroid (BR), 236 gibberellin (GA), 227 provitamin A content, increase in, 248 quantitative trait loci, 221 research and breeding, transgenic approach for, 247 semidwarfism of, 243 slender mutants, 235 trait loci, identification of, 241 biomass yield and sugar content, 245 heading date, 242 hybrid systems, fertility restoration in, 246 plant height, 243 wild-type (WT) plants, 227 Sorghum bicolor L Moench See Sorghum Sorting and assembly machinery (SAM) complex, 54 Southern pygmy perch, 196 Spadefish, 200 Spastin, 114 Spermidine, 109 Spermine, 109 Sphingolipids, 31 Sphingomyelin (SM), 308 Sphingosine-1-phosphate, 37 Spine Seealso Microtubules (MTs) geometry, 123 organization and stimulation-dependent changes in, 124 shape, 124 Spodoptera frugiperda See Armyworm Src kinase regulator p140Cap, 127 SREBP See Sterol-regulatory elementbinding protein (SREBP) Stathmin, 97, 134 expression of, 134 Steatohepatitis, 65 balance of PE and PC in, 65–67 Stereocilia, 313 Sterol-regulatory element-binding protein (SREBP), 309 356 Sterols, 31 STOP protein, 107, 108 Striated muscles, contractile machinery of, Sugarcane, 221 Superoxide dismutase (SOD1), 138 Sweet sorghum, 223, 224 morphologic mutants, 226 Synchiropus splendidus See mandarin fish α-Synuclein, 64 T Targeting-induced local lesions in genomes (TILLING), 222 Tau protein, 94, 97, 99, 132 Fyn protein, 135 hyperphosphorylation of, 132 phosphorylation of, 132 role of, 134 subcellular distribution, during neuronal development, 103 tau–PSD-95 interaction, 126 tcd1 See totally cyanide de¢cient (tcd1) TG See Triglycerides (TG) TGN See trans-Golgi network (TGN) Thalassoma bifasciatum See Bluehead wrasse Three-spine sticklebacks, 196 TILLING See Targeting-induced local lesions in genomes (TILLING) TnI (R111C), 14 TnT gene, 11, 15 in adult dog hearts, 20 N-terminal variable region modification of, 11, 15, 16 point mutation in, 12 posttranslational modifications of, 21 restrictive proteolysis of cardiac, 21 Ser2, constitutive phosphorylation of, 12 in transgenic mouse cardiac muscle, 12 Toad cardiac muscle, 10 TOM complex, 54 Totally cyanide deficient (tcd1), 240 Trafficking mechanisms, 33 Transcellular stress factors, 271 Transfection, 107 Transgenic mouse, 12 calpain activation in, 21 Index ischemia–reperfusion-like treatment of, 21 trans-Golgi network (TGN), 309 Translocase, 54 Transmissible lifespan-shortening molecules, 259 acetic acid, 259 ethanol, 259 Tricarboxylic acid cycle, 53 Triglycerides (TG), 68, 312 Triglyceride synthesis, 67 Tripterygion delaisi See Cryptic blenny Tropomyosin binding subunit troponin T (TnT), 2, 19 alternative splicing, 10 in Craciformes, developmental regulations, 15 fast skeletal muscle (TNNT3), fluorescence spectrometry, use of, in Galliformes, α-helix interactions, isoform genes, isoform genes, evolution of, isoform genes of, isoforms in cardiac muscle (TNNT2), molecular structure of, posttranslational modifications, 2, 19 phosphorylation, 19 restrictive proteolysis, 20 serial deletions, analysis in, slow skeletal muscle (TNNT1), structural and functional domains of, 5, structure–function relationship of, TnT in rat heart, 19 TnT mRNA, alternative splicing of, 12 TnT splicing variants, 14 Troponin complex, in human cardiac, TnT–TnI interface in, x-ray crystallography of, Tubulin acetylation, 98 deacetylation of, 98 detyrosination, 98 heterogeneity, 91 interacting proteins, 96 modification, 98 357 Index posttranslational modifications (PTMs) of, 93, 96 proteins, 92 transport of, 107 α-tubulin, 92, 93 monomers, 93 β-tubulin isotypes, overexpression of, 91 monomers, 93 γ-tubulins, 104 tubulin tyrosine ligase (TTL), 98 tubulin tyrosine ligase like (TTLL) proteins, 99 tyrosination, 98 tyrosine carboxypeptidase, 98 Tyrosination, 98 Tyrosine phosphorylation, 188 Tyr-tubulins, 98, 117 U UGT85B1, 240 Unsaturated sn-2 fatty acyl chain, 303 Ups family of proteins (Ups1-3p), 45 Ups1p/Mdm35p complex, 45 V VAMP-associated proteins (VAPs) 301 VAPs See VAMP-associated proteins (VAPs) v-CLAMP expression, 44 VDAC channel, 44 Ventricular muscle, desynchronized activation of, 14 Verasper moseri See Barfin flounder Vesicle budding, 323 Vesicular transport, 42 Vimentin filament organization, 326 bundle-like structures, 326 ORP4 modified, 326 vimentin network, 326 Volatile ammonia, 265 Voltage-dependent anion channels (VDAC), 44 Voltage-dependent ion channels, 120 Voltage-gated channels, 109 W Whole-transcriptome sorghum microarray, 248 Wrasse, 200 X Xanthophores, 172 carotenoids, 174 extending pseudopodia, 177 pterinosomes, 174 X-box binding protein (XBP-1), 277 XBP-1 See X-box binding protein (XBP-1) Y Yeast, 259Saccharomyces cerevisiae altering longevity, 259 chronological aging of, 262 lifespan, 262 modulating aging, 259 osh proteins, 302 transmissible longevity factors, 259 Yellow damselfish, 198 Z Zebrafish, 175 dark stripes of, 175 stripe formation, 177 UV protection, 180 ... evolution of the Nterminal variable region and its role in the structure and function of TnT In addition International Review of Cell and Molecular Biology, Volume 321 ISSN 1937-6448 http://dx.doi.org/10.1016/bs.ircmb.2015.09.002... that include serving as a precursor for phosphatidylcholine and a substrate International Review of Cell and Molecular Biology, Volume 321 ISSN 1937-6448 http://dx.doi.org/10.1016/bs.ircmb.2015.10.001... MELKONIAN KEITH E MOSTOV ANDREAS OKSCHE MADDY PARSONS TERUO SHIMMEN ALEXEY TOMILIN GARY M WESSEL VOLUME THREE HUNDRED AND TWENTY ONE INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY Edited