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Original Research

Bioinformatic studies of vertebrate enolases: multifunctional genes and proteins

Pages 43-59 | Published online: 09 Feb 2011

References

  • Rider CC, Taylor CB. Enolase isoenzymes in rat tissues. Electrophoretic, chromatographic, immunological and kinetic properties. Biochim Biophys Acta. 1974;365(1):285–300.
  • Semenza GL, Jiang BH, Leung SW, et al. Hypoxia response elements in the aldolase A, enolase 1, and lactate dehydrogenase A gene promoters contain essential binding sites for hypoxia-inducible factor 1. J Biol Chem. 1996;271(51):32529–32537.
  • He P, Naka T, Serada S, et al. Proteomics-based identification of alpha-enolase as a tumor antigen in non-small lung cancer. Cancer Sci. 2007;98(8):1234–1240.
  • Wygrecka M, Marsh LM, Morty RE, et al. Enolase-1 promotes plasminogen-mediated recruitment of monocytes to the acutely inflamed lung. Blood. 2009;113(22):5588–5598.
  • Kim RY, Lietman T, Piatigorsky J, Wistow GJ. Structure and expression of the duck alpha-enolase/tau-crystallin-encoding gene. Gene. 1991;103(2):193–200.
  • Wang W, Wang L, Endoh A, Hummelke G, Hawks CL, Hornsby PJ. Identification of alpha-enolase as a nuclear DNA-binding protein in the zona fasciculata but not the zona reticularis of the human adrenal cortex. J Endocrinol. 2005;184(1):85–94.
  • Keller A, Peltzer J, Carpentier G, et al. Interactions of enolase isoforms with tubulin and microtubules during myogenesis. Biochim Biophys Acta. 2007;1770(6):919–926.
  • McAleese SM, Dunbar B, Fothergill JE, Hinks LJ, Day IN. Complete amino acid sequence of the neurone-specific gamma isozyme of enolase (NSE) from human brain and comparison with the non-neuronal alpha form (NNE). Eur J Biochem. 1988;178(2):413–417.
  • Oliva D, Barba G, Barbieri G, Giallongo A, Feo S. Cloning, expression and sequence homologies of cDNA for human gamma enolase. Gene. 1989;79(2):355–360.
  • Feo S, Oliva D, Barbieri G, Xu WM, Fried M, Giallongo A. The gene for the muscle-specific enolase is on the short arm of human chromosome 17. Genomics. 1990;6(1):192–194.
  • Lander ES, Linton LM, Birren B, et al; International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001;409(6822):860–921.
  • Deloukas P, Earthrowl ME, Grafham DV et al. The DNA sequence and comparative analysis of human chromosome 10. Nature. 2004;429(6990):375–381.
  • Dolnick BJ. Cloning and characterization of a naturally occurring antisense RNA to human thymidylate synthase mRNA. Nucleic Acids Res. 1993;21(8):1747–1752.
  • Liang P, Nair JR, Song L, McGuire JJ, Dolnick BJ. Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene. BMC Genomics. 2005;6:125.
  • Verma M, Dutta SK. DNA sequences encoding enolase are remark conserved from yeast to mammals. Life Sci. 1994;55(12):893–899.
  • Sakimura K, Kushiya E, Ohshima-Ichimura Y, Mitsui H, Takahashi Y Structure and expression of rat muscle-specific enolase gene. FEBS Lett. 1990;277(1–2):78–82.
  • Keller A, Berod A, Dussaillant M, Lamande N, Gros F, Lucas M. Coexpression of alpha and gamma enolase genes in neurons of adult rat brain. J Neurosci Res. 1994;38(5):493–504.
  • Schmechel DE, Brightman MW, Marangos PJ. Neurons switch from non-neuronal enolase to neuron-specific enolase during differentiation. Brain Res. 1980;190(1):195–214.
  • Tanaka M, Sugisaki K, Nakashima K. Purification, characterization, and distribution of enolase isozymes in chicken. J Biochem. 1985;98(6):1527–1534.
  • Tracy MR, Hedges SB. Evolutionary history of the enolase gene family. Gene. 2000;259(1–2):129–138.
  • Duquerroy S, Camus C, Janin J. X-ray structure and catalytic mechanism of lobster enolase. Biochemistry. 1995;34(39):12513–12523.
  • Lebioda L, Stec B, Brewer JM. The structure of yeast enolase at 2.25-A resolution. An 8-fold beta + alpha-barrel with a novel beta beta alpha alpha (beta alpha)6 topology. J Biol Chem. 1989;264(7):3685–3693.
  • Reed GH, Poyner RR, Larsen TM, Wedekind JE, Rayment I. Structural and mechanistic studies of enolase. Curr Opin Struct Biol. 1996;6(6):736–743.
  • Kornblatt MJ, Zheng SX, Lamande N, Lazar M. Cloning, expression and mutagenesis of a subunit contact of rabbit muscle-specific (betabeta) enolase. Biochim Biophys Acta. 2002;1597(2):311–319.
  • Chai G, Brewer JM, Lovelace LL, Aoki T, Minor W, Lebioda L. Expression, purification and the 1.8 angstroms resolution crystal structure of human neuron specific enolase. J Mol Biol. 2004;341(4):1015–1021.
  • Wedekind JE, Poyner RR, Reed GH, Rayment I. Chelation of serine 39 to Mg2+ latches a gate at the active site of enolase: structure of the bis(Mg2+) complex of yeast enolase and the intermediate analog phosphonoacetohydroxamate at 2.1-A resolution. Biochemistry. 1994;33(31):9333–9342.
  • Poyner RR, Larsen TM, Wong SW, Reed GH. Functional and structural changes due to a serine to alanine mutation in the active-site flap of enolase. Arch Biochem Biophys. 2002;401(2):155–163.
  • Schreier B, Hocker B. Engineering the enolase magnesium II binding site: implications for its evolution. Biochemistry. 2010;49(35):7582–7589.
  • Giallongo A, Oliva D, Cali L, Barba G, Barbieri G, Feo S. Structure ofthe human gene for alpha-enolase. Eur J Biochem. 1990;190(3):567–573.
  • Peshavaria M, Day IN. Molecular structure of the human muscle- specific enolase gene (ENO3). Biochem J. 1991;275(Pt 2):427^33.
  • Thierry-Mieg D, Thierry-Mieg J. AceView: a comprehensive cDNA- supported gene and transcripts annotation. Genome Biol. 2006;7 Suppl 1: S12.1-S12.14.
  • Feo S, Arcuri D, Piddini E, Passantino R, Giallongo A. ENO1 gene product binds to the c-myc promoter and acts as a transcriptional repressor: relationship with Myc promoter-binding protein 1 (MBP-1). FEBS Lett. 2000;473(1):47–52.
  • Lopez-Alemany R, Suelves M, Diaz-Ramos A, Vidal B, Munoz- Canoves P. Alpha-enolase plasminogen receptor in myogenesis. Front Biosci. 2005;10:30–36.
  • Perconti G, Ferro A, Amato F, et al. The Kelch protein NS1 -BP interacts with alpha-enolase/MBP-1 and is involved in c-Myc gene transcriptional control. Biochim Biophys Acta. 2007;1773(12):1774–1785.
  • Altschul SF, Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215(3):403–410.
  • Gibbs RA, Rogers J, Katze MG, et al; Rhesus Macaque Genome Sequencing and Analysis Consortium. Evolutionary and biomedical insights from the rhesus macaque genome. Science. 2007;316(5822):222–234.
  • Bovine Genome Project. 2008. Available from: http://www.hgsc.bcm.tmc.edu/projects/bovine. Accessed January 6, 2011.
  • Horse Genome Project. 2008. Available from: http://www.uky.edu/Ag/Horsemap/. Accessed January 6, 2011.
  • Waterston RH, Lindblad-Toh K, Birney E, et al; Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420(6915):520–562.
  • Gibbs RA, Weinstock GM, Metzker ML, et al; Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature. 2004;428(6982):493–521.
  • Mikkelsen TS, Wakefield MJ, Aken B, et al. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007;447(7141):167–177.
  • International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004;432(7018):695–716.
  • Hellsten U, Harland RM, Gilchrist MJ, et al. The genome of the western clawed frog Xenopus tropicalis. Science. 2010;328(5978):633–636.
  • Sprague J, Bayraktaroglu L, Clements D, et al. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res. 2005;34(Database issue):D581-D585.
  • Kent WJ, Sugnet CW, Furey TS, et al. The human genome browser at UCSC. Genome Res. 2002;12(6):996–1006.
  • McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics. 2000;16(4):404–405.
  • Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997;18(15):2714–2723.
  • Kopp J, Schwede T. The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res. 2004;32(Database issue):D230-D234.
  • Kang HJ, Jung SK, Kim SJ, Chung SJ. Structure of human alpha-enolase (hENO1), a multifunctional glycolytic enzyme. Acta Crystallogr D Biol Crystallogr. 2008;64(Pt 6):651–657.
  • Qin J, Chai G, Brewer JM, Lovelace LL, Lebioda L. Fluoride inhibition of enolase: crystal structure and thermodynamics. Biochemistry. 2006;45(3):793–800.
  • Chandran V, Luisi BF. Recognition of enolase in the Escherichia coli RNA degradosome. J Mol Biol. 2006;358(1):8–15.
  • Larkin MA, Blackshields G, Brown NP, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–2948.
  • Giallongo A, Feo S, Moore R, Croce CM, Showe LC. Molecular cloning and nucleotide sequence of a full-length cDNA for human alpha enolase. Proc Natl Acad Sci U S A. 1986;83(18):6741–6745.
  • Cali L, Feo S, Oliva D, Giallongo A. Nucleotide sequence of a cDNA encoding the human muscle-specific enolase (MSE). Nucleic Acids Res. 1990;18(7):1893.
  • Vollmar M, Krysztofinska E, Chaikuad A, et al. Crystal structure of human beta enolase ENOB. Protein Data Bank Entry 2XSX. 2010; unpublished.
  • Kim SC, Sprung R, Chen Y, et al. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol Cell. 2006;23(4):607–618.
  • Zhou W, Capello M, Fredolini C, et al. Mass spectrometry analysis of the post-translational modifications of alpha-enolase from pancreatic ductal adenocarcinoma cells. JProteomeRes. 2010;9(6):2929–2936.
  • Ballif BA, Carey GR, Sunyaev SR, Gygi SP. Large-scale identification and evolution indexing of tyrosine phosphorylation sites from murine brain. J Proteome Res. 2008;7(1):311–318.
  • Lamande N, Mazo AM, Lucas M, et al. Murine muscle-specific enolase: cDNA cloning, sequence, and developmental expression. Proc Natl Acad Sci USA. 1989;86(12):4445^449.
  • Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci US A. 2006;103(5):1412–1417.
  • Safran M, Kaelin WG Jr. HIF hydroxylation and the mammalian oxygen- sensing pathway. J Clin Invest. 2003;111(6):779–783.
  • Sousa LP, Brasil BS, Silva Bde M, et al. Characterization of alpha- enolase as an interferon-alpha 2 alpha 1 regulated gene. Front Biosci. 2005;10:2534–2547.
  • Taylor JM, Davies JD, Peterson CA. Regulation of the myoblast-specific expression of the human beta-enolase gene. J Biol Chem. 1995;270(6):2535–2540.
  • Feo S, Antona V, Barbieri G, Passantino R, Cali L, Giallongo A. Transcription of the human beta enolase gene (ENO-3) is regulated by an intronic muscle-specific enhancer that binds myocyte-specific enhancer factor 2 proteins and ubiquitous G-rich-box binding factors. Mol Cell Biol. 1995;15(11):5991–6002.
  • Su AI, Wiltshire T, Batalov S, et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A. 2004;101(16):6062–6067.
  • Keller A, Ott MO, Lamande N, et al. Activation of the gene encoding the glycolytic enzyme beta-enolase during early myogenesis precedes an increased expression during fetal muscle development. Mech Dev. 1992;38(1):41–54.
  • Gerhard DS, Wagner L, Feingold EA, et al; MGC Project Team. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004;14(10B):2121–2127.
  • Merkulova T, Lucas M, Jabet C, et al. Biochemical characterization of the mouse muscle-specific enolase: developmental changes in electrophoretic variants and selective binding to other proteins. Biochem J. 1997;323(Pt 3):791–800.
  • Keller A, Demeurie J, Merkulova T, et al. Fibre-type distribution and subcellular localisation of alpha and beta enolase in mouse striated muscle. Biol Cell. 2000;92(7):527–535.
  • Comi GP, Fortunato F, Lucchiari S, et al. Beta-enolase deficiency, a new metabolic myopathy of distal glycolysis. Ann Neurol. 2001;50(2):202–207.
  • Mitchell BF, Pedersen LB, Feely M, Rosenbaum JL, Mitchell DR. ATP production in Chlamydomonas reinhardtii flagella by glycolytic enzymes. Mol Biol Cell. 2005;16(10):4509^518.
  • Morita T, Kawamoto H, Mizota T, Inada T, Aiba H. Enolase in the RNA degradosome plays a crucial role in the rapid decay of glucose transporter mRNA in the response to phosphosugar stress in Escherichia coli. Mol Microbiol. 2004;54(4):1063–1075.
  • Donoghue PC, Benton MJ. Rocks and clocks: calibrating the tree of life using fossils and molecules. Trends Ecol Evol. 2007;22(8):424–431.
  • Zhao S, Choy BS, Kornblatt MJ. Effects of the G376E and G157D mutations on the stability of yeast enolase - a model for human muscle enolase deficiency. FEBS J. 2008;275(1):97–106.
  • Hyo JK, Jung S-K, Kim SJ, Chung SJ (2008) Structure of human alpha-enolase (hENO1), a multifunctional glycolytic enzyme. Acta CrystallD. 64:651–657.