- About this Journal ·
- Abstracting and Indexing ·
- Advance Access ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Articles in Press ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 856521, 12 pages
The Evolutionary Pattern and the Regulation of Stearoyl-CoA Desaturase Genes
1State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
2Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China
3Department of Life Science and Biotechnology, Kunming University, Kunming 650214, China
Received 23 January 2013; Accepted 14 September 2013
Academic Editor: William Piel
Copyright © 2013 Xiaoyun Wu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- F. S. Heinemann and J. Ozols, “Stearoyl-CoA desaturase, a short-lived protein of endoplasmic reticulum with multiple control mechanisms,” Prostaglandins Leukotrienes and Essential Fatty Acids, vol. 68, no. 2, pp. 123–133, 2003.
- P. Strittmatter, L. Spatz, and D. Corcoran, “Purification and properties of rat liver microsomal stearyl coenzyme A desaturase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 71, no. 11, pp. 4565–4569, 1974.
- J. Wang, L. Yu, R. E. Schmidt et al., “Characterization of HSCD5, a novel human stearoyl-CoA desaturase unique to primates,” Biochemical and Biophysical Research Communications, vol. 332, no. 3, pp. 735–742, 2005.
- C. M. Paton and J. M. Ntambi, “Biochemical and physiological function of stearoyl-CoA desaturase,” American Journal of Physiology—Endocrinology and Metabolism, vol. 297, no. 1, pp. E28–E37, 2009.
- M. T. Flowers and J. M. Ntambi, “Role of stearoyl-coenzyme A desaturase in regulating lipid metabolism,” Current Opinion in Lipidology, vol. 19, no. 3, pp. 248–256, 2008.
- L. F. C. Castro, J. M. Wilson, O. Gonçalves, S. Galante-Oliveira, E. Rocha, and I. Cunha, “The evolutionary history of the stearoyl-CoA desaturase gene family in vertebrates,” BMC Evolutionary Biology, vol. 11, no. 1, article 132, 2011.
- J. L. Watts and J. Browse, “A palmitoyl-CoA-specific Δ9 fatty acid desaturase from Caenorhabditis elegans,” Biochemical and Biophysical Research Communications, vol. 272, no. 1, pp. 263–269, 2000.
- T. J. Brock, J. Browse, and J. L. Watts, “Genetic regulation of unsaturated fatty acid composition in C. elegans,” PLoS Genetics, vol. 2, no. 7, article e108, 2006.
- T. J. Brock, J. Browse, and J. L. Watts, “Fatty acid desaturation and the regulation of adiposity in Caenorhabditis elegans,” Genetics, vol. 176, no. 2, pp. 865–875, 2007.
- J. E. Stukey, V. M. McDonough, and C. E. Martin, “Isolation and characterization of OLE1, a gene affecting fatty acid desaturation from Saccharomyces cerevisiae,” The Journal of Biological Chemistry, vol. 264, no. 28, pp. 16537–16544, 1989.
- A. J. Lengi and B. A. Corl, “Comparison of pig, sheep and chicken SCD5 homologs: evidence for an early gene duplication event,” Comparative Biochemistry and Physiology B, vol. 150, no. 4, pp. 440–446, 2008.
- H. Evans, T. De Tomaso, M. Quail et al., “Ancient and modern duplication events and the evolution of stearoyl-CoA desaturases in teleost fishes,” Physiological Genomics, vol. 35, no. 1, pp. 18–29, 2008.
- D. Mauvoisin and C. Mounier, “Hormonal and nutritional regulation of SCD1 gene expression,” Biochimie, vol. 93, no. 1, pp. 78–86, 2011.
- T. A. Hall, “Bioedit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/Nt,” Nucleic Acids Symposium Series, vol. 41, pp. 95–98, 1999.
- S. Guindon and O. Gascuel, “A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood,” Systematic Biology, vol. 52, no. 5, pp. 696–704, 2003.
- M. N. Price, P. S. Dehal, and A. P. Arkin, “FastTree 2—approximately maximum-likelihood trees for large alignments,” PLoS ONE, vol. 5, no. 3, Article ID e9490, 2010.
- J. Felsenstein, “Confidence limits on phylogenies: an approach using bootstrap,” Evolution, vol. 39, pp. 783–791, 1985.
- S. Guindon, F. Delsuc, J.-F. Dufayard, and O. Gascuel, “Estimating maximum likelihood phylogenies with PhyML,” Methods in Molecular Biology, vol. 537, pp. 113–137, 2009.
- S. Guindon, J.-F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel, “New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0,” Systematic Biology, vol. 59, no. 3, pp. 307–321, 2010.
- K. Tamura, J. Dudley, M. Nei, and S. Kumar, “MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1596–1599, 2007.
- X. Messeguer, R. Escudero, D. Farré, O. Núñez, J. Martínez, and M. M. Albà, “PROMO: detection of known transcription regulatory elements using species-tailored searches,” Bioinformatics, vol. 18, no. 2, pp. 333–334, 2002.
- D. Farré, R. Roset, M. Huerta et al., “Identification of patterns in biological sequences at the ALGGEN server: PROMO and MALGEN,” Nucleic Acids Research, vol. 31, no. 13, pp. 3651–3653, 2003.
- M. Robinson-Rechavi and D. Huchon, “RRTree: relative-rate tests between groups of sequences on a phylogenetic tree,” Bioinformatics, vol. 16, no. 3, pp. 296–297, 2000.
- Z. Yang and R. Nielsen, “Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models,” Molecular Biology and Evolution, vol. 17, no. 1, pp. 32–43, 2000.
- Z. Yang, “PAML 4: phylogenetic analysis by maximum likelihood,” Molecular Biology and Evolution, vol. 24, no. 8, pp. 1586–1591, 2007.
- Z. Yang, “Inference of selection from multiple species alignments,” Current Opinion in Genetics and Development, vol. 12, no. 6, pp. 688–694, 2002.
- J. Zhang, R. Nielsen, and Z. Yang, “Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level,” Molecular Biology and Evolution, vol. 22, no. 12, pp. 2472–2479, 2005.
- H. B. Sanchez, L. Yieh, and T. F. Osborne, “Cooperation by sterol regulatory element-binding protein and Sp1 in sterol regulation of low density lipoprotein receptor gene,” The Journal of Biological Chemistry, vol. 270, no. 3, pp. 1161–1169, 1995.
- S. M. Jackson, J. Ericsson, R. Mantovani, and P. A. Edwards, “Synergistic activation of transcription by nuclear factor Y and sterol regulatory element binding protein,” Journal of Lipid Research, vol. 39, no. 4, pp. 767–776, 1998.
- K. A. Dooley, S. Millinder, and T. F. Osborne, “Sterol regulation of 3-hydroxy-3-methylglutaryl-coenzyme A synthase gene through a direct interaction between sterol regulatory element binding protein and the trimeric CCAAT-binding factor/nuclear factor Y,” The Journal of Biological Chemistry, vol. 273, no. 3, pp. 1349–1356, 1998.
- B. D. Reed, A. E. Charos, A. M. Szekely, S. M. Weissman, and M. Snyder, “Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes,” PLoS Genetics, vol. 4, no. 7, Article ID e1000133, 2008.
- J. A. Foekens, A. M. Sieuwerts, M. Smid et al., “Four miRNAs associated with aggressiveness of lymph node-negative, estrogen receptor-positive human breast cancer,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 35, pp. 13021–13026, 2008.
- M. V. Iorio, M. Ferracin, C.-G. Liu et al., “MicroRNA gene expression deregulation in human breast cancer,” Cancer Research, vol. 65, no. 16, pp. 7065–7070, 2005.
- N. Kondo, T. Toyama, H. Sugiura, Y. Fujii, and H. Yamashita, “MiR-206 expression is down-regulated in estrogen receptor α-positive human breast cancer,” Cancer Research, vol. 68, no. 13, pp. 5004–5008, 2008.
- A. Lujambio, S. Ropero, E. Ballestar et al., “Genetic unmasking of an epigenetically silenced microRNA in human cancer cells,” Cancer Research, vol. 67, no. 4, pp. 1424–1429, 2007.
- X.-H. Huang, Q. Wang, J.-S. Chen et al., “Bead-based microarray analysis of microRNA expression in hepatocellular carcinoma: MiR-338 is downregulated,” Hepatology Research, vol. 39, no. 8, pp. 786–794, 2009.
- L. Gramantieri, M. Ferracin, F. Fornari et al., “Cyclin G1 is a target of miR-122a, a MicroRNA frequently down-regulated in human hepatocellular carcinoma,” Cancer Research, vol. 67, no. 13, pp. 6092–6099, 2007.
- Y. Zhao, H.-L. Jia, H.-J. Zhou et al., “Identification of metastasis-related microRNAs of hepatocellular carcinoma in hepatocellular carcinoma cell lines by quantitative real time PCR,” Chinese Journal of Hepatology, vol. 17, no. 7, pp. 526–530, 2009.
- S. Volinia, G. A. Calin, C. G. Liu, et al., “A microRNA expression signature of human solid tumors defines cancer gene targets,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 7, pp. 2257–2261, 2006.
- J. L. Eun, Y. Gusev, J. Jiang et al., “Expression profiling identifies microRNA signature in pancreatic cancer,” International Journal of Cancer, vol. 120, no. 5, pp. 1046–1054, 2007.
- L. Zheng, G.-C. Lv, J. Sheng, and Y.-D. Yang, “Effect of miRNA-10b in regulating cellular steatosis level by targeting PPAR-α expression, a novel mechanism for the pathogenesis of NAFLD,” Journal of Gastroenterology and Hepatology, vol. 25, no. 1, pp. 156–163, 2010.
- A. Alisi, L. Da Sacco, G. Bruscalupi et al., “Mirnome analysis reveals novel molecular determinants in the pathogenesis of diet-induced nonalcoholic fatty liver disease,” Laboratory Investigation, vol. 91, no. 2, pp. 283–293, 2011.
- N. Klöting, S. Berthold, P. Kovacs et al., “MicroRNA expression in human omental and subcutaneous adipose tissue,” PLoS ONE, vol. 4, no. 3, Article ID e4699, 2009.
- M. Kato, S. Putta, M. Wang et al., “TGF-β activates Akt kinase through a microRNA-dependent amplifying circuit targeting PTEN,” Nature Cell Biology, vol. 11, no. 7, pp. 881–889, 2009.
- K. Abu-Elneel, T. Liu, F. S. Gazzaniga et al., “Heterogeneous dysregulation of microRNAs across the autism spectrum,” Neurogenetics, vol. 9, no. 3, pp. 153–161, 2008.
- B. Malzkorn, M. Wolter, F. Liesenberg et al., “Identification and functional characterization of microRNAs involved in the malignant progression of gliomas,” Brain Pathology, vol. 20, no. 3, pp. 539–550, 2010.
- D. O. Perkins, C. D. Jeffries, L. F. Jarskog et al., “MicroRNA expression in the prefrontal cortex of individuals with schizophrenia and schizoaffective disorder,” Genome Biology, vol. 8, no. 2, article R27, 2007.
- M. Bloomston, W. L. Frankel, F. Petrocca et al., “MicroRNA expression patterns to differentiate pancreatic adenocarcinoma from normal pancreas and chronic pancreatitis,” The Journal of the American Medical Association, vol. 297, no. 17, pp. 1901–1908, 2007.
- J.-K. Park, E. J. Lee, C. Esau, and T. D. Schmittgen, “Antisense inhibition of microRNA-21 or -221 arrests cell cycle, induces apoptosis, and sensitizes the effects of gemcitabine in pancreatic adenocarcinoma,” Pancreas, vol. 38, no. 7, pp. e190–e199, 2009.
- T. Greither, L. F. Grochola, A. Udelnow, C. Lautenschläger, P. Würl, and H. Taubert, “Elevated expression of microRNAs 155, 203, 210 and 222 in pancreatic tumors is associated with poorer survival,” International Journal of Cancer, vol. 126, no. 1, pp. 73–80, 2010.
- J. Z. Zhang, “Evolution by gene duplication: an update,” Trends in Ecology and Evolution, vol. 18, no. 6, pp. 292–298, 2003.
- M. A. Nowak, M. C. Boerlijst, J. Cooke, and J. M. Smith, “Evolution of genetic redundancy,” Nature, vol. 388, no. 6638, pp. 167–171, 1997.
- A. Wagner, “Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 12, pp. 6579–6584, 2000.
- Z. Gu, D. Nicolae, H. H.-S. Lu, and W.-H. Li, “Rapid divergence in expression between duplicate genes inferred from microarray data,” Trends in Genetics, vol. 18, no. 12, pp. 609–613, 2002.
- A. Force, M. Lynch, F. B. Pickett, A. Amores, Y.-L. Yan, and J. Postlethwait, “Preservation of duplicate genes by complementary, degenerative mutations,” Genetics, vol. 151, no. 4, pp. 1531–1545, 1999.
- D. I. Sinner, G. J. Kim, G. C. Henderson, and R. A. Igal, “StearoylCoA desaturase-5: a novel regulator of neuronal cell proliferation and differentiation,” PLoS One, vol. 7, no. 6, Article ID e39787, 2012.
- A. J. Lengi and B. A. Corl, “Identification and characterization of a novel bovine stearoyl-CoA desaturase isoform with homology to human SCD5,” Lipids, vol. 42, no. 6, pp. 499–508, 2007.
- S. Rome, V. Lecomte, E. Meugnier et al., “Microarray analyses of SREBP-1a and SREBP-1c target genes identify new regulatory pathways in muscle,” Physiological Genomics, vol. 34, no. 3, pp. 327–337, 2008.
- A. J. Lengi and B. A. Corl, “Regulation of the bovine SCD5 promoter by EGR2 and SREBP1,” Biochemical and Biophysical Research Communications, vol. 421, no. 2, pp. 375–379, 2012.
- X. Gu, Z. Su, and Y. Huang, “Simultaneous expansions of micrornas and protein-coding genes by gene/genome duplications in early vertebrates,” Journal of Experimental Zoology B, vol. 312, no. 3, pp. 164–170, 2009.
- E. Berezikov, “Evolution of microRNA diversity and regulation in animals,” Nature Reviews Genetics, vol. 12, no. 12, pp. 846–860, 2011.
- C. Cheng, N. Bhardwaj, and M. Gerstein, “The relationship between the evolution of microRNA targets and the length of their UTRs,” BMC Genomics, vol. 10, article 431, 2009.
- H. Mziaut, G. Korza, and J. Ozols, “The N terminus of microsomal Δ9 stearoyl-CoA desaturase contains the sequence determinant for its rapid degradation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 97, no. 16, pp. 8883–8888, 2000.
- L. Zhang, L. Ge, T. Tran, K. Stenn, and S. M. Prouty, “Isolation and characterization of the human stearoyl-CoA desaturase gene promoter: requirement of a conserved CCAAT cis-element,” Biochemical Journal, vol. 357, part 1, pp. 183–193, 2001.