Whole body proteome response to a dietary lysine imbalance in zebrafish Danio rerio

Abimorad, 2009, Dietary supplementation of lysine and/or methionine on performance, nitrogen retention and excretion in pacu Piaractus mesopotamicus reared in cages, Aquaculture, 295, 266, 10.1016/j.aquaculture.2009.07.001 Allen, 2001, Postnatal myosin heavy chain isoform expression in normal mice and mice null for IIb or IId myosin heavy chains, Dev. Biol., 229, 383, 10.1006/dbio.2000.9974 ARC, 1981 Bélanger, 2002, Digestive capacity and compensatory growth in Atlantic cod (Gadus morhua), Fish Physiol. Biochem., 26, 121, 10.1023/A:1025461108348 Bialik, 2006, The death-associated protein kinases: structure, function, and beyond, Annu. Rev. Biochem., 75, 189, 10.1146/annurev.biochem.75.103004.142615 Biga, 2006, Zebrafish and giant Danio as models for muscle growth: determinate vs. indeterminate growth as determined by morphometric analysis, Am. J. Physiol. Regul. Integr. Comp. Physiol., 291, R1327, 10.1152/ajpregu.00905.2005 Billingsley, 2006, CRYBA4, a novel human cataract gene, is also involved in microphthalmia, Am. J. Hum. Genet., 79, 702, 10.1086/507712 Blaser, 2006, Migration of zebrafish primordial germ cells: a role for myosin contraction and cytoplasmic flow, Dev. Cell, 11, 613, 10.1016/j.devcel.2006.09.023 Bligh, 1959, A rapid method of total lipid extraction and purification, Can. J. Biochem. Physiol., 37, 911, 10.1139/o59-099 Boisen, 2000, Ideal amino acid profiles as a basis for feed protein evaluation, Livest. Prod. Sci., 64, 239, 10.1016/S0301-6226(99)00146-3 Cahu, 2003, Nutritional components affecting skeletal development in fish larvae, Aquaculture, 227, 245, 10.1016/S0044-8486(03)00507-6 Carvalho, 2006, Rearing zebrafish (Danio rerio) larvae without live food: evaluation of a commercial, a practical and a purified starter diet on larval performance, Aquacult. Res., 37, 1107, 10.1111/j.1365-2109.2006.01534.x Chen, 2001, Molecular cloning, developmental expression, and hormonal regulation of zebrafish (Danio rerio) β crystallin B1, a member of the superfamily of β crystallin proteins, Biochem. Biophys. Res. Commun., 285, 105, 10.1006/bbrc.2001.5099 Clemmesen, 1994, The effect of food availability, age or size on the RNA/DNA ratio of individually measured herring larvae: laboratory calibration, Mar. Biol., 118, 377, 10.1007/BF00350294 Cohen, 1993, Synthesis of a fluorescent derivatizing reagent, 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate, and its application for the analysis of hydrolysate amino acids via high-performance liquid chromatography, Anal. Biochem., 211, 279, 10.1006/abio.1993.1270 Conceicão, 2003, Amino acid requirements of fish larvae and post-larvae: new tools and recent findings, Aquaculture, 227, 221, 10.1016/S0044-8486(03)00505-2 Couture, 1998, Biochemical correlates of growth and condition in juvenile Atlantic cod (Gadus morhua) from Newfoundland, Can. J. Fish. Aquat. Sci., 55, 1591, 10.1139/f98-045 Dahlman, 2005, Zebrafish alpha-crystallins: protein structure and chaperone-like activity compared to their mammalian orthologs, Mol. Vis., 11, 88 Datta, 1999, Differential temperature-dependent chaperone-like activity of alphaA- and alphaB-crystallin homoaggregates, J. Biol. Chem., 274, 34773, 10.1074/jbc.274.49.34773 Espe, 2007, Assessment of lysine requirement for maximal protein accretion in Atlantic salmon using plant protein diets, Aquaculture, 263, 168, 10.1016/j.aquaculture.2006.10.018 Fielding, 1972, A protein cofactor of lecithin: cholesterol acyltransferase, Biochem. Biophys. Res. Commun., 46, 1493, 10.1016/0006-291X(72)90776-0 Forster, 1998, Lysine requirement of juvenile Japanese flounder Paralichthys olivaceus and juvenile red sea bream Pagrus major, Aquaculture, 161, 131, 10.1016/S0044-8486(97)00263-9 Furuya, 2004, Use of ideal protein concept for precision formulation of amino acid levels in fish-meal-free diets for juvenile Nile tilapia (Oreochromis niloticus L.), Aquacult. Res., 35, 1110, 10.1111/j.1365-2109.2004.01133.x Goishi, 2006, AlphaA-crystallin expression prevents gamma-crystallin insolubility and cataract formation in the zebrafish cloche mutant lens, Development, 133, 2585, 10.1242/dev.02424 Gómez-Requeni, 2003, Effects of dietary amino acid profile on growth performance, key metabolic enzymes and somatotropic axis responsiveness of gilthead sea bream (Sparus aurata), Aquaculture, 220, 749, 10.1016/S0044-8486(02)00654-3 Gómez-Requeni, 2004, Protein growth performance, amino acid utilization and somatotropic axis responsiveness to fish meal replacement by plant protein sources in gilthead sea bream (Sparus aurata), Aquaculture, 232, 493, 10.1016/S0044-8486(03)00532-5 Gómez-Requeni, 2005, Regulation of the somatotropic axis by dietary factors in rainbow trout (Oncorhynchus mykiss), Br. J. Nutr., 94, 353, 10.1079/BJN20051521 Gómez-Requeni, 2010, A reference growth curve for nutritional experiments in zebrafish (Danio rerio) and changes in whole body proteome during development, Fish Physiol. Biochem., 36, 1199, 10.1007/s10695-010-9400-0 Goolish, 1999, Growth and survivorship of larval zebrafish Danio rerio on processed diets, North Am. J. Aquacult., 61, 189, 10.1577/1548-8454(1999)061<0189:GASOLZ>2.0.CO;2 Graw, 1997, The crystallins: genes, proteins and diseases, Biol. Chem., 378, 1331 Greiling, 2009, The zebrafish lens proteome during development and aging, Mol. Vis., 15, 2313 Görg, 1998, Two-dimensional electrophoresis of proteins in an immobilized pH 4–12 gradient, Electrophoresis, 19, 1516, 10.1002/elps.1150190850 Görg, 2000, The current state of two-dimensional electrophoresis with immobilized pH gradients, Electrophoresis, 21, 1037, 10.1002/(SICI)1522-2683(20000401)21:6<1037::AID-ELPS1037>3.0.CO;2-V Hansen, 2007, Dietary plant protein utilization in Atlantic cod, Gadus morhua L, Aquacult. Nutr., 13, 200, 10.1111/j.1365-2095.2007.00486.x Harrison, 2008, DAPK-1 binding to a linear peptide motif in MAP1B stimulates autophagy and membrane blebbing, J. Biol. Chem., 283, 9999, 10.1074/jbc.M706040200 Hensley, 2010, A convenient dry feed for raising zebrafish larvae, Zebrafish, 7, 219, 10.1089/zeb.2010.0652 Herman, 1993, Actin isoforms, Curr. Opin. Cell Biol., 5, 48, 10.1016/S0955-0674(05)80007-9 Hevrøy, 2007, Lysine intake affects gene expression of anabolic hormones in Atlantic salmon, Salmo salar, Gen. Comp. Endocrinol., 152, 39, 10.1016/j.ygcen.2007.02.015 Horwitz, 2003, Alpha-crystallin, Exp. Eye Res., 76, 145, 10.1016/S0014-4835(02)00278-6 Houle, 2007, DAP kinase mediates the phosphorylation of tropomyosin-1 downstream of the ERK pathway, which regulates the formation of stress fibers in response to oxidative stress, J. Cell Sci., 120, 3666, 10.1242/jcs.003251 Jury, 2008, Effects of calorie restriction on the zebrafish liver proteome, Comp. Biochem. Physiol., 3D, 275 Kamm, 2001, Dedicated myosin light chain kinases with diverse cellular functions, J. Biol. Chem., 276, 4527, 10.1074/jbc.R000028200 Kaushik, 1995, Partial or total replacement of fish meal by soybean protein on growth, protein utilization, potential estrogenic or antigenic effects, cholesterolemia and flesh quality in rainbow trout, Oncorhynchus mykiss, Aquaculture, 133, 257, 10.1016/0044-8486(94)00403-B Kolditz, 2008, Changes induced by dietary energy intake and divergent selection for muscle fat content in rainbow trout (Oncorhynchus mykiss), assessed by transcriptome and proteome analysis of the liver, BMC Genomics, 9, 506, 10.1186/1471-2164-9-506 Lenaerts, 2006, Starvation induces phase-specific changes in the proteome of mouse small intestine, J. Proteome Res., 5, 2113, 10.1021/pr060183+ Malatesta, 2008, A long-term study on female mice fed on a genetically modified soybean: effects on liver ageing, Histochem. Cell Biol., 130, 967, 10.1007/s00418-008-0476-x Mambrini, 1995, Indispensable amino acid requirements of fish: correspondence between quantitative data and amino acid profiles of tissue proteins, J. Appl. Ichthyol., 11, 240, 10.1111/j.1439-0426.1995.tb00024.x Martin, 2001, Proteome analysis of rainbow trout (Oncorhynchus mykiss) liver proteins during short term starvation, Fish Physiol. Biochem., 24, 259, 10.1023/A:1014015530045 Martin, 2003, Proteomic sensitivity to dietary manipulations in rainbow trout, Biochim. Biophys. Acta, 23, 17, 10.1016/S1570-9639(03)00231-0 Martínez, 2003, Condition, prolonged swimming performance and muscle metabolic capacities of cod Gadus morhua, J. Exp. Biol., 206, 503, 10.1242/jeb.00098 Masuda, 2009, Feeding restriction alters expression of some ATP related genes more sensitively than the RNA/DNA ratio in zebrafish, Danio rerio, Comp. Biochem. Physiol., 152B, 287, 10.1016/j.cbpb.2008.12.008 Meinelt, 2000, Correlation of diets high in n-6 polyunsaturated fatty acids with high growth rate in zebrafish (Danio rerio), Comp. Med., 50, 43 Mendelsohn, 2009, Proteomic analysis of anoxia tolerance in the developing zebrafish embryo, Comp. Biochem. Physiol., 4D, 21 Neuhoff, 1988, Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coomassie Brilliant Blue G-250 and R-250, Electrophoresis, 9, 255, 10.1002/elps.1150090603 Nilsson, 2008, Does size matter for hypoxia tolerance in fish?, Biol. Rev., 83, 173, 10.1111/j.1469-185X.2008.00038.x NRC (National Research Council), 1993 O'Farrell, 1975, High resolution two-dimensional electrophoresis of proteins, J. Biol. Chem., 10, 4007, 10.1016/S0021-9258(19)41496-8 Ostaszewska, 2010, The effect of plant protein-based diet supplemented with dipeptide or free amino acids on digestive tract morphology and PepT1 and PepT2 expressions in common carp (Cyprinus carpio L.), Comp. Biochem. Physiol., 157A, 158, 10.1016/j.cbpa.2010.06.162 Ostaszewska, 2010, The effect of peptide absorption on PepT1 gene expression and digestive system hormones in rainbow trout (Oncorhynchus mykiss), Comp. Biochem. Physiol., 155A, 107, 10.1016/j.cbpa.2009.10.017 Peres, 2005, The effect of dietary protein replacement by crystalline amino acid on growth and nitrogen utilization of turbot Scophthalmus maximus juveniles, Aquaculture, 250, 755, 10.1016/j.aquaculture.2005.04.046 Perkins, 1999, Probability-based protein identification by searching sequence databases using mass spectrometry data, Electrophoresis, 20, 3551, 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 Plump, 1996, Apolipoprotein A-I is required for cholesteryl ester accumulation in steroidogenic cells and for normal adrenal steroid production, J. Clin. Invest., 97, 2660, 10.1172/JCI118716 Posner, 2008, A proteome map of the zebrafish (Danio rerio) lens reveals similarities between zebrafish and mammalian crystallin expression, Mol. Vis., 14, 806 Ribeiro, 1991, Effect of dietary fish oil and corn oil on lipid metabolism and apolipoprotein gene expression by rat liver, Eur. J. Biochem., 196, 499, 10.1111/j.1432-1033.1991.tb15842.x Rodehutscord, 2000, Availability and utilisation of free lysine in rainbow trout (Oncorhynchus mykiss): 1. Effect of dietary crude protein level, Aquaculture, 187, 163, 10.1016/S0044-8486(99)00388-9 Rønnestad, 1999, Fish larval nutrition: a review of recent advances in roles of amino acids, Aquaculture, 177, 201, 10.1016/S0044-8486(99)00082-4 Rønnestad, 2003, The supply of amino acids during early feeding stages of marine fish larvae: a review of recent findings, Aquaculture, 227, 147, 10.1016/S0044-8486(03)00500-3 Saavedra, 2008, Effect of lysine and tyrosine supplementation in the amino acid metabolism of Diplodus sargus larvae fed rotifers, Aquaculture, 284, 180, 10.1016/j.aquaculture.2008.07.021 Saavedra, 2008, Metabolism of tryptophan, methionine and arginine in Diplodus sargus larvae fed rotifers: effect of amino acid supplementation, Amino Acids, 35, 59, 10.1007/s00726-007-0632-y Siccardi, 2009, Growth and survival of zebrafish (Danio rerio) fed different commercial and laboratory diets, Zebrafish, 6, 275, 10.1089/zeb.2008.0553 Silva, 2009, Senegalese sole juveniles (Solea senegalensis Kaup, 1858) grow equally well on diets devoid of fish meal provided the dietary amino acids are balanced, Aquaculture, 296, 309, 10.1016/j.aquaculture.2009.08.031 Sissener, 2010, Zebrafish (Danio rerio) as a model for investigating the safety of GM feed ingredients (soya and maize); performance, stress response and uptake of dietary DNA sequences, Br. J. Nutr., 103, 3, 10.1017/S0007114509991401 Sissener, 2010, Proteomic profiling of liver from Atlantic salmon (Salmo salar) fed genetically modified soy compared to the near-isogenic non-GM line, Mar. Biotechnol., 12, 273, 10.1007/s10126-009-9214-1 Small, 2000, Quantitative dietary lysine requirement of juvenile striped bass Morone saxatilis, Aquacult. Nutr., 6, 207, 10.1046/j.1365-2095.2000.00140.x Smith, 2009, Proteomic changes in the crucian carp brain during exposure to anoxia, Proteomics, 9, 2217, 10.1002/pmic.200800662 Soyal, 1995, Thyroid hormone influences the maturation of apolipoprotein A-I messenger RNA in rat liver, J. Biol. Chem., 270, 3996, 10.1074/jbc.270.8.3996 Vihtelic, 2005, Expressed sequence tag analysis of zebrafish eye tissues for NEIBank, Mol. Vis., 11, 1083 Vilhelmsson, 2004, Dietary plant-protein substitution affects hepatic metabolism in rainbow trout (Oncorhynchus mykiss), Br. J. Nutr., 92, 71, 10.1079/BJN20041176 Webster, 2000, Differences in growth in blue catfish Ictalurus furcatus and channel catfish I. punctatus fed low-protein diets with and without supplemental methionine and/or lysine, J. World Aquacult. Soc., 31, 195, 10.1111/j.1749-7345.2000.tb00353.x Wilson, 1994, Amino acid requirements of finfish, 377 Wilson, 2002, Amino acid and proteins, 162 Zhang, 2006, Indispensable amino acid concentrations decrease in tissues of stomachless fish, common carp in response to free amino acid- or peptide-based diets, Amino Acids, 31, 165, 10.1007/s00726-006-0345-7