Comparative analysis and distribution of omega-3 lcPUFA biosynthesis genes in marine molluscs

PLoS ONE

Volumn 10, Issue 8, 2015, Pages

  Surm, Joachim M ^a   Prentis, Peter J ^a   Pavasovic, Ana ^a  

^a QUEENSLAND UNIVERSITY OF TECHNOLOGY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL COENZYME A DESATURASE; LONG CHAIN FATTY ACID; OMEGA 3 FATTY ACID; VERY LONG CHAIN FATTY ACID; FISH PROTEIN;

ANADARA TRAPEZIA; APLYSIA CALIFORNICA; ARTICLE; BINDING AFFINITY; BIOSYNTHESIS; CHLAMYS FARRERI; CLADISTICS; COMPARATIVE STUDY; CRASSOSTREA GIGAS; ELOVL GENE; FAD GENE; GENE AMPLIFICATION; GENE DUPLICATION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; LOLIGO PEALEII; LOTTIA GIGANTEA; MOLECULAR EVOLUTION; MOLLUSC; NERITA ALBICILLA; NERITA MELANOTRAGUS; NONHUMAN; PHYLOGENY; PROTEIN LOCALIZATION; PROTEIN MOTIF; SEQUENCE ALIGNMENT; AMINO ACID SEQUENCE; ANIMAL; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MOLECULAR GENETICS; SEQUENCE HOMOLOGY; SHELLFISH;

AMINO ACID SEQUENCE; ANIMALS; FATTY ACIDS, OMEGA-3; FISH PROTEINS; MOLECULAR SEQUENCE DATA; MOLLUSCA; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID; SHELLFISH;

EID: 84943340011     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0136301     Document Type: Article

References (60)

1. Burri L, Hoem N, Banni S, Berge K. Marine Omega-3 Phospholipids: Metabolism and Biological Activities. Int. J Mol Sci.2012; 13:15401-15419. doi: 10.3390/ijms131115401 PMID: 23203133
2. Calder PC, Yaqoob P. Omega-3 polyunsaturated fatty acids and human health outcomes. BioFactors. 2009; 35:266-272. doi: 10.1002/biof.42 PMID: 19391122
3. Harris WS, Lavie CJ, Lee JH, O'Keefe JH Omega-3 fatty acids: cardiovascular benefits, sources and sustainability. Nat Rev Cardiol. 2009; 6:753 doi: 10.1038/nrcardio.2009.188 PMID: 19859067
4. Mozaffarian D, Wu JHY. Omega-3 fatty acids and cardiovascular disease: effects on risk factors, molecular pathways, and clinical events. J Am Coll Cardiol. 2011; 58:2047-2067 doi: 10.1016/j.jacc.2011.06.063 PMID: 22051327
5. Mozaffarian D, Wu JHY. (n-3) Fatty Acids and Cardiovascular Health: Are Effects of EPA and DHA Shared or Complementary? J Nutr. 2012; 142:614S-625S doi: 10.3945/jn.111.149633 PMID: 22279134
6. Swanson D, Block R, Mousa SA. Omega-3 Fatty Acids EPA and DHA: Health Benefits Throughout Life12. Adv. Nutr.2012; 3:1-7 doi: 10.3945/an.111.000893 PMID: 22332096
7. Calder PC. Very long chain omega-3 (n-3) fatty acids and human health. Eur J Lipid Sci Technol. 2014; 116:1280-1300. doi: 10.1002/ejlt.201400025
8. Patterson E, Wall R, Fitzgerald GF, Ross RP, Stanton C. Health Implications of High Dietary Omega-6 Polyunsaturated Fatty Acids. J Nutr Metab. 2012; 2012: e539426. doi: 10.1155/2012/539426
9. Simopoulos AP. Evolutionary aspects of diet: the omega-6/omega-3 ratio and the brain. Mol. Neurobiol. 2011; 44:203-215 doi: 10.1007/s12035-010-8162-0 PMID: 21279554
10. Monroig Ó, Tocher DR, Navarro JC. Biosynthesis of Polyunsaturated Fatty Acids in Marine Invertebrates: Recent Advances in Molecular Mechanisms. Mar Drugs. 2013; 11:3998-4018. doi: 10.3390/md11103998 PMID: 24152561
11. Vannice G, Rasmussen H. Position of the Academy of Nutrition and Dietetics: Dietary Fatty Acids for Healthy Adults. J Acad Nutr Diet. 2014; 114:136-153. doi: 10.1016/j.jand.2013.11.001 PMID: 24342605
12. Green CD, Ozguden-Akkoc CG, Wang Y, Jump DB, Olson LK. Role of fatty acid elongases in determination of de novo synthesized monounsaturated fatty acid species. J Lipid Res. 2010; 51:1871-1877. doi: 10.1194/jlr.M004747 PMID: 20228221
13. Morais S, Monroig Ó, Zheng X, Leaver MJ, Tocher DR. Highly Unsaturated Fatty Acid Synthesis in Atlantic Salmon: Characterization of ELOVL5- and ELOVL2-like Elongases. Mar Biotechnol. 2009; 11:627-639. doi: 10.1007/s10126-009-9179-0 PMID: 19184219
14. Zheng X, Ding Z, Xu Y, Monroig Ó, Morais S, Tocher DR. Physiological roles of fatty acyl desaturases and elongases in marine fish: Characterisation of cDNAs of fatty acyl Δ6 desaturase and elovl5 elongase of cobia (Rachycentron canadum). Aquaculture. 2009; 290:122-131. doi: 10.1016/j.aquaculture.2009.02.010
15. Hastings N, Agaba M, Tocher DR, Leaver MJ, Dick JR, Sargent JR, et al. A vertebrate fatty acid desaturase with Δ5 and Δ6 activities. Proc Natl Acad Sci U S A. 2001; 98:14304-14309. doi: 10.1073/pnas.251516598 PMID: 11724940
16. Monroig Ó, Navarro JC, Dick JR, Alemany F, Tocher DR. Identification of a Δ5-like Fatty Acyl Desaturase from the Cephalopod Octopus vulgaris (Cuvier 1797) Involved in the Biosynthesis of Essential Fatty Acids. Mar Biotechnol. 2011; 14:411-422. doi: 10.1007/s10126-011-9423-2 PMID: 22160425
17. Nakamura MT, Nara TY. Structure, Function, and Dietary Regulation of Δ6, Δ5, and Δ9 Desaturases. Annu Rev Nutr. 2004; 24:345-376. doi: 10.1146/annurev.nutr.24.121803.063211 PMID: 15189125
18. Zheng X, Seiliez I, Hastings N, Tocher DR, Panserat S, Dickson CA, et al. Characterization and comparison of fatty acyl Δ6 desaturasecDNAs from freshwater and marine teleost fish species. Comp Biochem Physiol B Biochem Mol Biol. 2004; 139:269-279. doi: 10.1016/j.cbpc.2004.08.003 PMID: 15465674
19. Monroig Ó, Webb K, Ibarra-Castro L, Holt GJ, Tocher DR. Biosynthesis of long-chain polyunsaturated fatty acids in marine fish: Characterization of an Elovl4-like elongase from cobia Rachycentron canadum and activation of the pathway during early life stages. Aquaculture. 2011; 312:145-153. doi: 10.1016/j.aquaculture.2010.12.024
20. Monroig Ó, Rotllant J, Cerdá-Reverter JM, Dick JR, Figueras A, Tocher DR. Expression and role of Elovl4 elongases in biosynthesis of very long-chain fatty acids during zebrafish Danio rerio early embryonic development. BBA Molecular and Cell Biology of Lipids. 2010; 1801(10):1145-1154. http://doi.org/10.1016/j.bbalip.2010.06.005 doi: 10.1016/j.bbalip.2010.06.005 PMID: 20601113
21. Pereira SL, Leonard AE, Mukerji P. Recent advances in the study of fatty acid desaturases from animals and lower eukaryotes. Prostag Leukotr Essnt Fatty Acids. 2003; 68:97-106. doi: 10.1016/S0952-3278(02)00259-4
22. Giri A, Ohshima T. Chapter 5-Bioactive Marine Peptides: Nutraceutical Value and Novel Approaches. In: Kim S-K, editor. Advances in Food and Nutrition Research. Academic Press; 2012.pp.73-105. Available:http://www.sciencedirect.com/science/article/pii/B9780124160033000056 doi: 10.1016/B978-0-12-416003-3.00005-6 PMID: 22361181
23. Monroig Ó, Guinot D, Hontoria F, Tocher DR, Navarro JC. Biosynthesis of essential fatty acids in Octopus vulgaris (Cuvier, 1797): Molecular cloning, functional characterisation and tissue distribution of a fatty acyl elongase. Aquaculture. 2012; 360-361:45-53. doi: 10.1016/j.aquaculture.2012.07.016
24. Reis DB, Acosta NG, Almansa E, Navarro JC, Tocher DR, Monroig Ó, et al. In vivo metabolism of unsaturated fatty acids in Octopus vulgaris hatchlings determined by incubation with 14C-labelled fatty acids added directly to seawater as protein complexes. Aquaculture, 2014; 431:28-33. doi.org/10.1016/j
25. Li M, Mai K, He G, Ai Q, Zhang W, Xu W, et al. Characterization of two Δ5 fatty acyl desaturases in abalone (Haliotis discus hannai Ino). Aquaculture. 2013; 416-417:48-56. doi: 10.1016/j.aquaculture.2013.08.030
26. Liu H, Guo Z, Zheng H, Wang S, Wang Y, Liu W, et al. Functional characterization of a Δ5-likefatty acyl desaturase and its expression during early embryogenesis in the noble scallop Chlamys nobilis Reeve. Mol Biol Rep. 2014; 41:7437-7445. doi: 10.1007/s11033-014-3633-4 PMID: 25081650
27. Liu H, Zheng H, Wang S, Wang Y, Li S, Liu W, et al. Cloning and functional characterization of a polyunsaturated fatty acid elongase in a marine bivalve noble scallop Chlamys nobilis Reeve. Aquaculture. 2013; 416-417:146-151. doi: 10.1016/j.aquaculture.2013.09.015
28. Ekblom R, Stapley J, Ball AD, Birkhead T, Burke T, Slate J. Genetic mapping of the major histocompatibility complex in the zebra finch (Taeniopygia guttata). Immunogenetics. 2011; 63:523-530. doi: 10.1007/s00251-011-0525-9 PMID: 21494955
29. Prentis PJ, Pavasovic A. The Anadara trapezia transcriptome: A resource for molluscan physiological genomics. Mar Genomics. 2014; 18, Part B: 113-115. doi: 10.1016/j.margen.2014.08.004
30. Przeslawski R. Temporal patterns of gastropod egg mass deposition on southeastern Australian shores. Mar Freshwater Res. 2008; 59:457-466. doi.org/10.1071/MF07229
31. Saito H, Aono H. Characteristics of lipid and fatty acid of marine gastropod Turbo cornutus: High levels of arachidonic and n-3 docosapentaenoic acid. Food Chem. 2014; 145:135-144. doi: 10.1016/j.foodchem.2013.08.011 PMID: 24128459
32. Abbas Alkarkhi FM, Ismail N, Easa AM. Assessment of arsenic and heavy metal contents in cockles (Anadara granosa) using multivariate statistical techniques. J Hazard Mater. 2008; 150:783-789. doi: 10.1016/j.jhazmat.2007.05.035 PMID: 17590506
33. Nell JA, O'Connor WA, Heasman MP, Goard LJ. Hatchery production of the venerid clam Katelysia rhytiphora (Lamy) and the Sydney cockle Anadara trapezia (Deshayes). Aquaculture. 1994; 119:149-156. doi: 10.1016/0044-8486(94)90171-6
34. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotech. 2011; 29:644-652. doi: 10.1038/nbt.1883
35. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics. 2012; 28:3150-3152. doi: 10.1093/bioinformatics/bts565 PMID: 23060610
36. Götz S, Arnold R, Sebastián-León P, Martín-Rodríguez S, Tischler P, Jehl M-A, et al. B2G-FAR, a species-centered GO annotation repository. Bioinformatics. 2011; 27:919-924. doi: 10.1093/bioinformatics/btr059 PMID: 21335611
37. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014; 42:D222-D230. doi: 10.1093/nar/gkt1223 PMID: 24288371
38. Cai Y, Luqing P, Fengxiao H, Qian Ji, Tong L. Deep Sequencing-Based Transcriptome Profiling Analysis of Chlamys farreri Exposed to Benzo[a]pyrene. Gene. 2014; 551(2):261-70. doi: 10.1016/j.gene.2014.09.003 PMID: 25194896
39. Du Xuedi, Li Li, Zhang Shoudu, Meng Fei, and Zhang Guofan. "SNP Identification by Transcriptome Sequencing and Candidate Gene-Based Association Analysis for Heat Tolerance in the Bay Scallop Argopecten irradians." PLoS ONE 9, no. 8 (August 14, 2014):e104960. doi: 10.1371/journal.pone.0104960
40. Riesgo A, Andrade SCS, Sharma PP, Novo M, Pérez-Porro AR, Vahtera V, et al. Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa. Frontiers in Zoology. 2012; 9:33. doi: 10.1186/1742-9994-9-33 PMID: 23190771
41. ORF Finder-(http://www.ncbi.nlm.nih.gov/gorf/gorf.html)
42. Letunic I, Copley RR, Pils B, Pinkert S, Schultz J, Bork P. SMART 5: domains in the context of genomes and networks. Nucleic Acids Res. 2006; 34:D257-D260. doi: 10.1093/nar/gkj079 PMID: 16381859
43. Leonard AE, Pereira SL, Sprecher H, Huang Y-S. Elongation of long-chain fatty acids. Prog Lipid Res. 2004; 43:36-54. doi: 10.1016/S0163-7827(03)00040-7 PMID: 14636670
44. Krogh A, Larsson B, von Heijne G, Sonnhammer EL. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001; 305:567-580. doi: 10.1006/jmbi.2000.4315 PMID: 11152613
45. Ensembl Metazoa database (http://metazoa.ensembl.org/index.html).
46. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S, et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28:1647-1649. doi: 10.1093/bioinformatics/bts199 PMID: 22543367
47. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci U S A. 1992; 89:10915-10919. PMID: 1438297
48. Hall, T. (2005). BioEdit v. 7.0.5: Biological sequence alignment editor for Windows. Ibis Therapeutics a Division of Isis Pharmaceuticals. Retrieved from http://www.mbio.ncsu.edu/BioEdit/bioedit.html
49. Notredame C, Higgins DG, Heringa J. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000; 302:205-217. doi: 10.1006/jmbi.2000.4042 PMID: 10964570
50. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol. 2013; 30:2725-2729. doi: 10.1093/molbev/mst197 PMID: 24132122
51. Prentis PJ, Woolfit M, Thomas-Hall SR, Daniel Ortiz-Barrientos, Pavasovic A, Lowe AJ, et al. Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant. Ann Bot. 2010; mcq201. doi: 10.1093/aob/mcq201
52. Liu H, Zhang H, Zheng H, Wang S, Guo Z, Zhang G. PUFA Biosynthesis Pathway in Marine Scallop Chlamys nobilis Reeve. J Agricult Food Chem. 2014; 62(51):12384-12391. doi.org/10.1021/jf504648f
53. Stoger I, Sigwart JD, Kano Y, Knebelsberger T, Marshall BA, et al. The Continuing Debate on Deep Molluscan Phylogeny: Evidence for Serialia (Mollusca, Monoplacophora. BioMed Research International. 2013; 2013:e407072. doi: 10.1155/2013/407072
54. Castro LFC, Monroig Ó, Leaver MJ, Wilson J, Cunha I, Tocher DR. Functional desaturase Fads1 (Δ5) and Fads2 (Δ6) orthologues evolved before the origin of jawed vertebrates. PLoS ONE. 2012; 7: e31950. doi: 10.1371/journal.pone.0031950 PMID: 22384110
55. Monroig Ó, Zheng X, Morais S, Leaver MJ, Taggart JB, Tocher DR. Multiple genes for functional 6 fatty acyl desaturases (Fad) in Atlantic salmon (Salmo salar L.): gene and cDNA characterization, functional expression, tissue distribution and nutritional regulation. Biochim Biophys Acta. 2010; 1801:1072-1081. doi: 10.1016/j.bbalip.2010.04.007 PMID: 20403458
56. Saito H, Marty Y. High levels of icosapentaenoic acid in the lipids of oyster Crassostrea gigas ranging over both Japan and France. J Oleo Sci. 2010; 59:281-292. PMID: 20484833
57. Waldock MJ, Holland DL. Fatty acid metabolism in young oysters, Crassostrea gigas: Polyunsaturated fatty acids. Lipids. 1984; 19:332-336. doi: 10.1007/BF02534783
58. Monroig Ó, Wang S, Zhang L, You C, Tocher DR, Li Y. Elongation of long-chain fatty acids in rabbitfish Siganus canaliculatus: Cloning, functional characterisation and tissue distribution of Elovl5-and Elovl4- like elongases. Aquaculture. 2012; 350-353:63-70. doi: 10.1016/j.aquaculture.2012.04.017
59. Carmona-Antoñanzas G, Tocher DR, Taggart JB, Leaver MJ. An evolutionary perspective on Elovl5 fatty acid elongase: comparison of Northern pike and duplicated paralogs from Atlantic salmon. BMC Evolutionary Biology. 2013; 13:85. doi: 10.1186/1471-2148-13-85 PMID: 23597093
60. Helm RR, Siebert S, Tulin S, Smith J, Dunn CW. Characterization of differential transcript abundance through time during Nematostella vectensis development. BMC Genomics. 2013; 14:266. doi: 10.1186/1471-2164-14-266 PMID: 23601508