A Differentially Expressed Gene from a High Oil Producer Cultivar of Castor Bean (<i>Ricinus communis</i>) Is Involved in the Biosynthesis of Ricinoleic Acid — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
A Differentially Expressed Gene from a High Oil Producer Cultivar of Castor Bean (<i>Ricinus communis</i>) Is Involved in the Biosynthesis of Ricinoleic Acid
Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
,
Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
,
Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
,
Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
,
Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
1 Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
2 Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
3 Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
4 Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
5 Department of Biological Sciences and CIBIOP Research Group, School of Sciences, Universidad EAFIT, Medellín, Colombia
Ricinus communis or castor bean is a non-edible oilseed plant widely cultivated worldwide for the high content of castor oil in its seeds and the different uses the oil has in the industry. An increase in its oil content and production efficiency is difficult, making understanding the molecular mechanisms underlying the synthesis of oils in the seed necessary. Here, a combined analysis of protein-protein interaction networks was performed using public data on differential gene expression in castor bean seeds at different stages of development. From this analysis, four key enzymes were selected and analyzed in the polyunsaturated fatty acids pathways, whose gene expression was subsequently quantified during the development of the seeds in a Colombian cultivar that produces high amounts of oils and contrasted with a lower producing cultivar. The gene coding FAH12 was differentially expressed in the early stages of seed development in the high oil-producing cultivar and has differences in amino acids A242V and Q319H. The analysis presents this gene as one of those responsible for early ricinoleic acid synthesis, making it a candidate for use in crop genetic improvement programs to increase the oil content in castor bean.
Davis, C.C., Latvis, M., Nickrent, D.L., Wurdack, K.J. and Baum, D.A. (2007) Floral Gigantism in Rafflesiaceae. Science, 315, 1812. https://doi.org/10.1126/science.1135260
Wurdack, K.J., Hoffmann, P. and Chase, M.W. (2005) Molecular Phylogenetic Analysis of Uniovulate Euphorbiaceae (Euphorbiaceae Sensu Stricto) Using Plastid RbcL and TrnL-F DNA Sequences. American Journal of Botany, 92, 1397-1420. https://doi.org/10.3732/ajb.92.8.1397
Roetheli, J.C., Glaser, L.K. and Brigham, R.D. (1990) Castor: Assessing the Feasibility of US Production. Workshop Summary, Plainview, September 1990, 18-19.
Johnson Jr., W. (2007) Final Report on the Safety Assessment of Ricinus communis (Castor) Seed Oil, Hydrogenated Castor Oil, Glyceryl Ricinoleate, Glyceryl Ricinoleate Se, Ricinoleic Acid, Potassium Ricinoleate, Sodium Ricinoleate, Zinc Ricinoleate, Cetyl Ricinoleate, Ethyl Ric. International Journal of Toxicology, 26, 31-77. https://doi.org/10.1080/10915810701663150
Stephen, G. (2009) An Investigation into the Components of Triricinoleic Acid Production in the Developing Castor Bean Endoplasmic Reticulum an Investigation into the Components of Triricinoleic Acid Production in the Developing Castor Bean Endoplasmic Retic. Doctoral E-Theses, Durham University, Durham.
Lima Da Silva, N., Wolf Maciel, M.R., Batistella, C.B. and Filho, R.M. (2006) Optimization of Biodiesel Production from Castor Oil. Applied Biochemistry and Biotechnology, 130, 405-414. https://doi.org/10.1385/ABAB:130:1:405
Brigham, R.D. (1993) Castor: Return of an Old Crop. New Crops. Wiley, New York, 380-383.
Qiu, L., Yang, C., Tian, B., Yang, J.-B. and Liu, A. (2010) Exploiting EST Databases for the Development and Characterization of EST-SSR Markers in Castor Bean (Ricinus communis L.). BMC Plant Biology, 10, Article No. 278. https://doi.org/10.1186/1471-2229-10-278
Allard, R.W., PDeT, A., Ashri, A. and Barton, J.H. (1991) Managing Global Genetic Resources; the US National Plant Germplasm System: Elements of the National Plant Germplasm System. The National Academies Press, Washington DC.
Navas, A. (2011) Evaluación de Cultivares Foráneos y Generación de Variedades Colombianas de Higuerilla Para La Producción de Biodiesel y Otros Usos En La Industria. CI La Selva, Rionegro.
Bafor, M., Smith, M., Jonsson, L., Stobart, K. and Stymne, S. (1991) Ricinoleic Acid Biosynthesis and Triacylglycerol Assembly in Microsomal Preparations from Developing Castor-Bean (Ricinus communis) Endosperm. The Biochemical Journal, 280, 507-514. https://doi.org/10.1042/bj2800507
Galliard, T. and Stumpf, P.K. (1966) Fat Metabolism in Higher Plants XXX. Enzymatic Synthesis of Ricinoleic Acid by a Microsomal Preparation from Developing Ricinus communis Seeds. Journal of Biological Chemistry, 241, 5806-5812.
Morris, L.J. (1967) The Mechanism of Ricinoleic Acid Biosynthesis in Ricinuscommunis Seeds. Biochemical and Biophysical Research Communications, 29, 311-315. https://doi.org/10.1016/0006-291X(67)90454-8
van de Loo, F.J., Broun, P., Turner, S. and Somerville, C. (1995) An Oleate 12-Hydroxylase from Ricinus communis L. Is a Fatty Acyl Desaturase Homolog. Proceedings of the National Academy of Sciences of the United States of America, 92, 6743-6747. https://doi.org/10.1073/pnas.92.15.6743
Broun, P. and Somerville, C. (1997) Accumulation of Ricinoleic, Lesquerolic, and Densipolic Acids in Seeds of Transgenic Arabidopsis Plants That Express a Fatty Acyl Hydroxylase CDNA from Castor Bean. Plant Physiology, 113, 933-942. https://doi.org/10.1104/pp.113.3.933
Thelen, J.J. and Ohlrogge, J.B. (2002) Metabolic Engineering of Fatty Acid Biosynthesis in Plants. Metabolic Engineering, 4, 12-21. https://doi.org/10.1006/mben.2001.0204
Lu, C., Fulda, M., Wallis, J.G. and Browse, J. (2006) A High-Throughput Screen for Genes from Castor That Boost Hydroxy Fatty Acid Accumulation in Seed Oils of Transgenic Arabidopsis. Plant Journal, 45, 847-856. https://doi.org/10.1111/j.1365-313X.2005.02636.x
Kroon, J.T.M., Wei, W., Simon, W.J. and Slabas, A.R. (2006) Identification and Functional Expression of a Type 2 Acyl-CoA: Diacylglycerol Acyltransferase (DGAT2) in Developing Castor Bean Seeds Which Has High Homology to the Major Triglyceride Biosynthetic Enzyme of Fungi and Animals. Phytochemistry, 67, 2541-2549. https://doi.org/10.1016/j.phytochem.2006.09.020
Burgal, J., Shockey, J., Lu, C., Dyer, J., Larson, T., Graham, I. and Browse, J. (2008) Metabolic Engineering of Hydroxy Fatty Acid Production in Plants: RcDGAT2 Drives Dramatic Increases in Ricinoleate Levels in Seed Oil. Plant Biotechnology Journal, 6, 819-831. https://doi.org/10.1111/j.1467-7652.2008.00361.x
Chen, G.Q., Turner, C., He, X., Nguyen, T., McKeon, T.A. and Laudencia-Chingcuanco, D. (2007) Expression Profiles of Genes Involved in Fatty Acid and Triacylglycerol Synthesis in Castor Bean (Ricinus communis L.). Lipids, 42, 263-274. https://doi.org/10.1007/s11745-007-3022-z
Imadi, S.R., Kazi, A.G., Ahanger, M.A., Gucel, S. and Ahmad, P. (2015) Plant Transcriptomics and Responses to Environmental Stress: An Overview. Journal of Genetics, 94, 525-537. https://doi.org/10.1007/s12041-015-0545-6
Chan, A.P., Crabtree, J., Zhao, Q., Lorenzi, H., Orvis, J., Puiu, D., Melake-Berhan, A., Jones, K.M., Redman, J., Chen, G., Cahoon, E.B., Gedil, M., Stanke, M., Haas, B.J., Wortman, J.R., Fraser-Liggett, C.M., Ravel, J. and Rabinowicz, P.D. (2010) Draft Genome Sequence of the Oilseed Species Ricinus communis. Nature Biotechnology, 28, 951-956. https://doi.org/10.1038/nbt.1674
Rivarola, M., Foster, J.T., Chan, A.P., Williams, A.L., Rice, D.W., Liu, X., Melake-Berhan, A., Creasy, H.H., Puiu, D., Rosovitz, M.J., Khouri, H.M., Beckstrom-Sternberg, S.M., Allan, G.J., Keim, P., Ravel, J. and Rabinowicz, P.D. (2011) Castor Bean Organelle Genome Sequencing and Worldwide Genetic Diversity Analysis. PLoS ONE, 6, e21743. https://doi.org/10.1371/journal.pone.0021743
Brown, A.P., Kroon, J.T.M., Swarbreck, D., Febrer, M., Larson, T.R., Graham, I.A., Caccamo, M. and Slabas, A.R. (2012) Tissue-Specific Whole Transcriptome Sequencing in Castor, Directed at Understanding Triacylglycerol Lipid Biosynthetic Pathways. PLoS ONE, 7, e30100. https://doi.org/10.1371/journal.pone.0030100
Chandrasekaran, U., Xu, W. and Liu, A. (2014) Transcriptome Profiling Identifies ABA Mediated Regulatory Changes towards Storage Filling in Developing Seeds of Castor Bean (Ricinus communis L.). Cell & Bioscience, 4, 33. https://doi.org/10.1186/2045-3701-4-33
Bassel, G.W., Gaudinier, A., Brady, S.M., Hennig, L., Rhee, S.Y. and De Smet, I. (2012) Systems Analysis of Plant Functional, Transcriptional, Physical Interaction, and Metabolic Networks. The Plant Cell, 24, 3859-3875. https://doi.org/10.1105/tpc.112.100776
Cagliari, A., Margis-Pinheiro, M., Loss, G., Mastroberti, A.A., de Araujo Mariath, J.E. and Margis, R. (2010) Identification and Expression Analysis of Castor Bean (Ricinus communis) Genes Encoding Enzymes from the Triacylglycerol Biosynthesis Pathway. Plant Science, 179, 499-509. https://doi.org/10.1016/j.plantsci.2010.07.015
Pertea, M., Kim, D., Pertea, G.M., Leek, J.T. and Salzberg, S.L. (2016) Transcript-Level Expression Analysis of RNA-Seq Experiments with HISAT, String Tie and Ballgown. Nature Protocols, 11, 1650-1667. https://doi.org/10.1038/nprot.2016.095
Childs, K.L., Hamilton, J.P., Zhu, W., Ly, E., Cheung, F., Wu, H., Rabinowicz, P.D., Town, C.D., Buell, C.R. and Chan, A.P. (2007) The TIGR Plant Transcript Assemblies Database. Nucleic Acids Research, 35, D846-D851. https://doi.org/10.1093/nar/gkl785
Trapnell, C., Hendrickson, D.G., Sauvageau, M., Goff, L., Rinn, J.L. and Pachter, L. (2013) Differential Analysis of Gene Regulation at Transcript Resolution with RNA-Seq. Nature Biotechnology, 31, 46-53. https://doi.org/10.1038/nbt.2450
Fischer, S., Brunk, B.P., Chen, F., Gao, X., Harb, O.S., Iodice, J.B., Shanmugam, D., Roos, D.S. and Stoeckert, C.J. (2011) Using OrthoMCL to Assign Proteins to OrthoMCL-DB Groups or to Cluster Proteomes into New Ortholog Groups. Current Protocols in Bioinformatics, 1-23. https://doi.org/10.1002/0471250953.bi0612s35
Bustin, S., Benes, V., Garson, J., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M.W., Shipley, G.L., Vandesompele, J. and Wittwer, C.T. (2009) The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clinical Chemistry, 55, 611-622. https://doi.org/10.1373/clinchem.2008.112797
Rozen, S. and Skaletsky, H. (2000) Primer3 on the www for General Users and for Biologist Programmers. In: Misener, S. and Krawetz, S.A., Eds., Bioinformatics Methods and Protocols, Humana Press, Totowa, 365-386. https://doi.org/10.1385/1-59259-192-2:365
Talavera, G. and Castresana, J. (2007) Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments. Systematic Biology, 56, 564-577. https://doi.org/10.1080/10635150701472164
Geneious. Bioinformatics Software for Sequence Data Analysis. https://www.geneious.com
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., Mcgettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007) Clustal W and Clustal X Version 2.0. Bioinformatics, 23, 2947-2948. https://doi.org/10.1093/bioinformatics/btm404
Wernersson, R. (2006) Virtual Ribosome—A Comprehensive DNA Translation Tool with Support for Integration of Sequence Feature Annotation. Nucleic Acids Research, 34, W385-W388. https://doi.org/10.1093/nar/gkl252
Katoh, K. and Standley, D.M. (2013) MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Molecular Biology and Evolution, 30, 772-780. https://doi.org/10.1093/molbev/mst010
Wernersson, R. and Pedersen, A.G. (2003) RevTrans: Multiple Alignment of Coding DNA from Aligned Amino Acid Sequences. Nucleic Acids Research, 31, 3537-3539. https://doi.org/10.1093/nar/gkg609
Finn, R.D., Coggill, P., Eberhardt, R.Y., Eddy, S.R., Mistry, J., Mitchell, A.L., Potter, S.C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G.A., Tate, J. and Bateman, A. (2016) The Pfam Protein Families Database: Towards a More Sustainable Future. Nucleic Acids Research, 44, D279-D285. https://doi.org/10.1093/nar/gkv1344
Lanfear, R., Frandsen, P.B., Wright, A.M., Senfeld, T. and Calcott, B. (2016) PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses. Molecular Biology and Evolution, 34, 772-773. https://doi.org/10.1093/molbev/msw260
Lin, J.T., Woodruff, C.L., Lagouche, O.J., McKeon, T.A., Stafford, A.E., Goodrich-Tanrikulu, M., Singleton, J.A. and Haney, C.A. (1998) Biosynthesis of Triacylglycerols Containing Ricinoleate in Castor Microsomes Using 1-Acyl-2-Oleoyl-Sn-Glycero-3-Phosphocholine as the Substrate of Oleoyl-12-Hydroxylase. Lipids, 33, 59-69. https://doi.org/10.1007/s11745-998-0180-3
Venegas-Calerón, M., Sánchez, R., Salas, J.J., Garcés, R. and Martínez-Force, E. (2016) Molecular and Biochemical Characterization of the OLE-1 High-Oleic Castor Seed (Ricinus communis L.) Mutant. Planta, 244, 245-258. https://doi.org/10.1007/s00425-016-2508-4