Salmonid genomes have a remarkably expanded akirin family, coexpressed with genes from conserved pathways governing skeletal muscle growth and catabolism

Physiological Genomics

Volumn 42, Issue 1, 2010, Pages 134-148

  Macqueen, Daniel J ^a   Kristjánsson, Bjarni K ^b   Johnston, Ian A ^a  

^a UNIVERSITY OF ST ANDREWS   (United Kingdom)

^b HÓLAR UNIVERSITY COLLEGE   (Iceland)

Author keywords

Hierarchical clustering; Phosphorylation; Phylogenetic analysis; Salmonidae family

Indexed keywords

AKIRIN; NUCLEAR PROTEIN; PROTEIN 14 3 3; SOMATOMEDIN C RECEPTOR; TRANSCRIPTION FACTOR RELA; UBIQUITIN CONJUGATING ENZYME E2; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; CATABOLISM; CONTROLLED STUDY; GENE EXPRESSION; GENOME; MOLECULAR CLONING; MOLECULAR EVOLUTION; MUSCLE GROWTH; MUSCLE METABOLISM; MUSCLE TWITCH; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; NUCLEOTIDE SEQUENCE; NUTRITIONAL STATUS; PARALOGY; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; REAL TIME POLYMERASE CHAIN REACTION; REGULATORY MECHANISM; SALMONID; SKELETAL MUSCLE; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CLUSTER ANALYSIS; FISH PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; MUSCLE, SKELETAL; PHYLOGENY; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SALMON; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; SIGNAL TRANSDUCTION; TROUT;

INVERTEBRATA; METAZOA; PISCES; SALMONIDAE; SALVELINUS ALPINUS; SALVELINUS FONTINALIS; TELEOSTEI; TETRAPODA; VERTEBRATA;

EID: 77953193327     PISSN: 10948341     EISSN: 15312267     Source Type: Journal    
DOI: 10.1152/physiolgenomics.00045.2010     Document Type: Article

References (51)

1. Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-2105, 2005.
2. Aguilera C, Fernández-Majada V, Inglés-Esteve J, Rodilla V, Bigas A, Espinosa L. Efficient nuclear export of p65-IkappaBalpha complexes requires 14-3-3 proteins. J Cell Sci 119: 3695-3704, 2006.
3. Allendorf FW, Thorgaard GH. Tetraploidy and the evolution of salmonid fishes. In: Evolutionary Genetics of Fishes, edited by Turner BJ. New York: Plenum, 1984.
4. Andersen CL, Ledet-Jensen J, Ørntoft T. Normalization of real-time quantitative RT-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64: 5245-5250, 2004.
5. Bailey GS, Poulter RT, Stockwell PA. Gene duplication in tetraploid fish: model for gene silencing at unlinked duplicated loci. Proc Natl Acad Sci USA 75: 5575-5579, 1978.
6. Bakkar N, Wang J, Ladner KJ, Wang H, Dahlman JM, Carathers M, Acharyya S, Rudnicki MA, Hollenbach AD, Guttridge DC. IKK/NFkappaB regulates skeletal myogenesis via a signalling switch to inhibit differentiation and promote mitochondrial biogenesis. J Cell Biol 180: 787-802, 2008.
7. Blom N, Gammeltoft S, Brunak S. Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites. J Mol Biol 294: 1351-1362, 1999.
8. Bower NI, Li X, Taylor R, Johnston IA. Switching to fast growth: the insulin-like growth factor (IGF) system in skeletal muscle of Atlantic salmon. J Exp Biol 211: 3859-3870, 2008.
9. Bower NI, Taylor RG, Johnston IA. Phasing of muscle gene expression with fasting-induced recovery growth in Atlantic salmon. Front Zool 6: 18, 2009.
10. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622, 2009.
11. Cai D, Frantz JD, Tawa NE Jr, Melendez PA, Oh BC, Lidov HG, Hasselgren PO, Frontera WR, Lee J, Glass DJ, Shoelson SE. IKKbeta/ NF-kappaB activation causes severe muscle wasting in mice. Cell 119: 285-298, 2004.
12. Caraux G, Pinloche S. PermutMatrix: a graphical environment to arrange gene expression profiles in optimal linear order. Bioinformatics 21: 1280-1281, 2005.
13. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17: 540-552, 2000. (Pubitemid 30210700)
14. Chauvigné F, Gabillard JC, Weil C, Rescan PY. Effect of refeeding on IGFI, IGFII, IGF receptors, FGF2, FGF6, and myostatin mRNA expression in rainbow trout myotomal muscle. Gen Comp Endocrinol 132: 209-215, 2003.
15. Chi H, Barry SP, Roth RJ, Wu JJ, Jones EA, Bennett AM, Flavell RA. Dynamic regulation of pro- and anti-inflammatory cytokines by MAPK phosphatase 1 (MKP-1) in innate immune responses. Proc Natl Acad Sci USA 103: 2274-2279, 2006.
16. Cohen S, Brault JJ, Gygi SP, Glass DJ, Valenzuela DM, Gartner C, Latres E, Goldberg AL. During muscle atrophy, thick, but not thin, filament components are degraded by MuRF1-dependent ubiquitylation. J Cell Biol 185: 1083-1095, 2009.
17. de la Fuente J, Almazán C, Blas-Machado U, Naranjo V, Mangold AJ, Blouin EF, Gortazar C, Kocan KM. The tick protective antigen, 4D8, is a conserved protein involved in modulation of tick blood ingestion and reproduction. Vaccine 24: 4082-4095, 2006.
18. de la Fuente J, Maritz-Olivier C, Naranjo V, Ayoubi P, Nijhof AM, Almazán C, Canales M, Pérez de la Lastra JM, Galindo RC, Blouin EF, Gortazar C, Jongejan F, Kocan KM. Evidence of the role of tick subolesin in gene expression. BMC Genomics 9: 372, 2008.
19. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7: 214, 2007.
20. Fraser HB, Hirsh AE, Wall DP, Eisen MB. Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci USA 101: 9033-9038, 2004.
21. Ge H, Liu Z, Church GM, Vidal M. Coevolution of gene expression among interacting proteins. Nat Genet 29: 482-486.
22. Giot L, Bader JS, Brouwer C, Chaudhuri A, Kuang B, Li Y, Hao YL, Ooi CE, Godwin B, Vitols E, Vijayadamodar G, Pochart P, Machineni H, Welsh M, Kong Y, Zerhusen B, Malcolm R, Varrone Z, Collis A, Minto M, Burgess S, McDaniel L, Stimpson E, Spriggs F, Williams J, Neurath K, Ioime N, Agee M, Voss E, Furtak K, Renzulli R, Aanensen N, Carrolla S, Bickelhaupt E, Lazovatsky Y, DaSilva A, Zhong J, Stanyon CA, Finley RL Jr, White KP, Braverman M, Jarvie T, Gold S, Leach M, Knight J, Shimkets RA, McKenna MP, Chant J, Rothberg JM. A protein interaction map of Drosophila melanogaster. Science 302: 1727-1736, 2003.
23. Glass DJ. Skeletal muscle hypertrophy and atrophy signaling pathways. Int J Biochem Cell Biol 37: 1974-1984, 2005.
24. Gonzalez K, Baylies M. Bhringi: a novel Twist co-regulator. A Dros Res Conf 46: 320B, 2005.
25. Goto A, Matsushita K, Gesellchen V, El Chamy L, Kuttenkeuler D, Takeuchi O, Hoffmann JA, Akira S, Boutros M, Reichhart JM. Akirins are highly conserved nuclear proteins required for NF-kappaB-dependent gene expression in Drosophila and mice. Nat Immunol 9: 97-104, 2008.
26. Grigoriev A. A relationship between gene expression and protein interactions on the proteome scale: analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res 29: 3513-3519, 2001. (Pubitemid 32898765)
27. Gu X. A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol 23: 1937-1945, 2006.
28. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704, 2003.
29. Jackman RW, Kandarian SC. The molecular basis of skeletal muscle atrophy. Am J Physiol Cell Physiol 287: C834-C843, 2004.
30. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biémont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, Guigó R, Zody MC, Mesirov J, Lindblad- Toh K, Birren B, Nusbaum C, Kahn D, Robinson-Rechavi M, Laudet V, Schachter V, Quétier F, Saurin W, Scarpelli C, Wincker P, Lander ES, Weissenbach J, Roest Crollius H. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431: 946-957, 2004.
31. Katoh K, Toh H. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298, 2008.
32. Knudsen B, Miyamoto MM, Laipis PJ, Silverman DN. Using evolutionary rates to investigate protein functional divergence and conservation. A case study of the carbonic anhydrases. Genetics 164: 1261-1269, 2003. (Pubitemid 37102194)
33. Komiya Y, Kurabe N, Katagiri K, Ogawa M, Sugiyama A, Kawasaki Y, Tashiro F. A novel binding factor of 14-3-3beta functions as a transcriptional repressor and promotes anchorage-independent growth, tumorigenicity, and metastasis. J Biol Chem 283: 18753-18764, 2008.
34. Li Q, Verma IM. NF-kappaB regulation in the immune system. Nat Rev Immunol 2: 725-734, 2002.
35. Li YP, Lecker SH, Chen Y, Waddell ID, Goldberg AL, Reid MB. TNF-alpha increases ubiquitin-conjugating activity in skeletal muscle by up-regulating UbcH2/E220k. FASEB J 17: 1048-1057, 2003.
36. Liu TJ, Lai HC, Ting CT, Wang PH. Bidirectional regulation of upstream IGF-I/insulin receptor signaling and downstream FOXO1 in cardiomyocytes. J Endocrinol 192: 149-158, 2007.
37. Macqueen DJ, Johnston IA. An update on MyoD evolution in teleosts and a proposed consensus nomenclature to accommodate the tetraploidization of different vertebrate genomes. PLoS One 3: e1567, 2008.
38. Macqueen DJ, Johnston IA. Evolution of the multifaceted eukaryotic akirin gene family. BMC Evol Biol 9: 34, 2009.
39. Maeda I, Kohara Y, Yamamoto M, Sugimoto A. Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr Biol 11: 171-176, 2001.
40. Marshall A, Salerno MS, Thomas M, Davies T, Berry C, Dyer K, Bracegirdle J, Watson T, Dziadek M, Kambadur R, Bower R, Sharma M. Mighty is a novel promyogenic factor in skeletal myogenesis. Exp Cell Res 314: 1013-1029, 2008.
41. Montserrat N, Gabillard JC, Capilla E, Navarro MI, Gutiérrez J. Role of insulin, insulin-like growth factors, and muscle regulatory factors in the compensatory growth of the trout (Oncorhynchus mykiss). Gen Comp Endocrinol 150: 462-472, 2007.
42. Nakai K, Horton P. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem Sci 24: 34-36, 1999.
43. Putnam NH, Butts T, Ferrier DE, Furlong RF, Hellsten U, Kawashima T, Robinson-Rechavi M, Shoguchi E, Terry A, Yu JK, Benito-Gutiérrez EL, Dubchak I, Garcia-Fernàndez J, Gibson-Brown JJ, Grigoriev IV, Horton AC, de Jong PJ, Jurka J, Kapitonov VV, Kohara Y, Kuroki Y, Lindquist E, Lucas S, Osoegawa K, Pennacchio LA, Salamov AA, Satou Y, Sauka-Spengler T, Schmutz J, Shin-IT, Toyoda A, Bronner-Fraser M, Fujiyama A, Holland LZ, Holland PW, Satoh N, Rokhsar DS. The amphioxus genome and the evolution of the chordate karyotype. Nature 453: 1064-1071, 2008.
44. Rodgers BD, Weber GM, Kelley KM, Levine MA. Prolonged fasting and cortisol reduce myostatin mRNA levels in tilapia larvae; short-term fasting elevates. Am J Physiol Regul Integr Comp Physiol 284: R1277-R1286, 2003.
45. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574, 2003.
46. Ruijter JM, Ramakers C, Hoogaars WM, Karlen Y, Bakker O, van den Hoff MJ, Moorman AF. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 37: e45, 2009.
47. Salerno MS, Dyer K, Bracegirdle J, Platt L, Thomas M, Siriett V, Kambadur R, Sharma M. Akirin1 (Mighty), a novel promyogenic factor regulates muscle regeneration and cell chemotaxis. Exp Cell Res 315: 2012-2021, 2009.
48. Songyang Z, Blechner S, Hoagland N, Hoekstra MF, Piwnica-Worms H, Cantley LC. Use of an oriented peptide library to determine the optimal substrates of protein kinases. Curr Biol 4: 973-982, 1994. (Pubitemid 124001033)
49. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24: 1596-1599, 2007.
50. Thorgaard GH, Bailey GS, Williams D, Buhler DR, Kaattari SL, Ristow SS, Hansen JD, Winton JR, Bartholomew JL, Nagler JJ, Walsh PJ, Vijayan MM, Devlin RH, Hardy RW, Overturf KE, Young WP, Robison BD, Rexroad C, Palti Y. Status and opportunities for genomics research with rainbow trout. Comp Biochem Physiol B Biochem Mol Biol 133: 609-646, 2002.
51. Tzivion G, Shen YH, Zhu J. 14-3-3 proteins; bringing new definitions to scaffolding. Oncogene 20: 6331-6338, 2001.