ABB  Vol.10 No.4 , April 2019
Total RNA Degradation in Vitro and in Vitro by Glutamate Dehydrogenase-Synthesized RNA Enzyme: Biotechnological Applications
Glutamate dehydrogenase regulates crop development, growth, and biomass yield through its synthesis of non-genetic code-based RNA. Understanding the mechanism of GDH-synthesized RNA enzyme would enhance the agriculture innovation capacity of the more than a billion urban gardeners, smallholder, and limited resources indigenous farmers. Different metabolic variants were prepared by treating peanut growing on healthy soil with stoichiometric mixes of mineral salt solutions. Peanut GDH charge isomers were purified to homogeneity by electrophoresis, and made to synthesize RNA enzyme. Peanut total RNA was 5’-end labeled with [γ-32P]ATP and made to react as substrate in vitro with GDH-synthesized RNA from another metabolic variant of peanut. Agarose, and polyacrylamide gel electrophoresis of the reaction products showed that tRNA, rRNA, and most of the mRNAs were degraded to mononucleotides, but total RNAs that were not mixed with GDH-synthesized RNAs were not degraded. When the non-homologous sequence sections of the GDH-synthesized RNA were clipped out, the homologous sections failed to produce Northern bands with peanut total RNA. Therefore, the non-homologous sequence sections served to identify, position, and align the GDH-synthesized RNA to its target total RNA site independent of genetic code; the degradation of total RNA being via non-canonical base alignments in the enzyme-substrate complex, followed by electromagnetic destruction of the total RNA, the less stable of the two kinds of RNA. This is the science-based corner stone that buttresses the crop production efforts of limited resources farmers because GDH-synthesized RNAs quickly degrade superfluous total RNA of the crop in response to the soil mineral nutrient deficiencies thereby minimizing wastage of metabolic energy in the synthesis of unnecessary protein enzymes while optimizing biomass metabolism, crop growth, and maximum crop yields. In vitro hydrolysis of total RNA by GDH-synthesized RNA is the game changing, prototype, R&D methods for cleansing sick total RNA from cells, tissues, and whole organisms.
Cite this paper
Osuji, G. , Madu, W. and Johnson, P. (2019) Total RNA Degradation in Vitro and in Vitro by Glutamate Dehydrogenase-Synthesized RNA Enzyme: Biotechnological Applications. Advances in Bioscience and Biotechnology, 10, 59-85. doi: 10.4236/abb.2019.104005.
[1]   Osuji, G.O., Madu, W.C., Braithwaite, C., Beyene, A., Roberts, P.S., Bulgin, A. and Wright, V. (2003) Nucleotide-Dependent Isomerization of Glutamate Dehydrogenase in Relation to Total RNA Contents of Peanut. Biologia Plantarum, 47, 195-202.

[2]   Osuji, G.O. and Madu, W.C. (1997) Regulation of Sweetpotato Growth and Differentiation by Glutamate Dehydrogenase. Canadian Journal of Botany, 75, 1070-1078.

[3]   Osuji, G.O. and Madu, W.C. (1995) Ammonium Ion-Dependent Isomerization of Glutamate Dehydrogenase in Relation to Glutamate Synthesis in Maize. Phytochemistry, 39, 595-503.

[4]   Osuji, G.O. and Braithwaite, C. (1999) Signaling by Glutamate Dehydrogenase in Response to Pesticide Treatment and Nitrogen Fertilization of Peanut (Arachis hypogaea L.). Journal of Agricultural and Food Chemistry, 47, 3332-3344.

[5]   Osuji, G.O., Duffus, E., Johnson, P., Woldesenbet, S., Weerasooriya, A., et al. (2015) Enhancement of the Essential Amino Acid Composition of Food Crop Proteins through Biotechnology. American Journal of Plant Sciences, 6, 3091-3108.

[6]   Osuji, G.O. and Madu, W.C. (1996) Ammonium Ion Salvage by Glutamate Dehydrogenase during Defence Response in Maize. Phytochemistry, 42, 1491-1498.

[7]   Osuji, G.O. and Johnson, P.M. (2018) Structural Properties of the RNA Synthesized by Glutamate Dehydrogenase for the Degradation of Total RNA. Advances in Enzyme Research, 6, 29-52.

[8]   Watkins, A.M., Geniesse, C., Kladwang, W., Zakrevsky, P., Jaeger, L. and Das, R. (2018) Blind Prediction of Noncanonical RNA Structure at Atomic Accuracy. Science Advances, 4, eaar5316.

[9]   Halder, S. and Bhattacharyya, D. (2013) RNA Structure and Dynamics: A Base Pairing Perspective. Progress in Biophysics and Molecular Biology, 113, 264-283.

[10]   Chandrasekhar, K. and Malath, R. (2003) Non-Watson Crick Base Pairs Might Stabilize RNA Structural Motifs in Ribozymes—A Comparative Study of Group-I Intron Structures. Journal of Bioscience, 28, 547-555.

[11]   Holbrook, S.R., Cheong, C., Tinoco, I. and Kim, S. (1991) Crystal Structure of an RNA Double Helix Incorporating a Track of Non-Watson-Crick Base Pairs. Nature, 353, 579-581.

[12]   Doc-Bregeon, A.C., Chevrier, B., Podjaryn, A., Johnson, J., De Bear, J.S., Gough, G.R., Gilham, P.T. and Moras, D. (1989) Crystallographic Structure of an RNA Helix: [U(UA)6A]2. Journal of Molecular Biology, 209, 459-474.

[13]   Gupta, S., Yadav, B. S., Raj, U., Freilich, S. and Varadwaj, P.K. (2017) Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrient Deficiency. Frontiers in Plant Sciences, 22, 1025.

[14]   Haimovich, G., Medina, D.A., Causse, S.Z., Garber, M., Milan-Zambrano, G., et al. (2013) Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis. Cell, 153, 1000-1011.

[15]   Houseley, J. and Tollervey, D. (2009) The Many Pathways of RNA Degradation. Cell, 136, 763-776.

[16]   Eulalio, A., Huntzinger, E. and Izaurralde, E. (2008) Getting to the Root of miRNA-Mediated Gene Silencing. Cell, 132, 9-14.

[17]   Tuschl, T., Zamore, P.D., Lehmann, R., Bartel, D.P. and Sharp, P.A. (1999) Targeted mRNA Degradation by Double-Stranded RNA in Vitro. Genes and Development, 13, 3191-3197.

[18]   Meister, G. and Tuschl, T. (2004) Mechanisms of Gene Silencing by Double-Stranded RNA. Nature, 431, 343-349.

[19]   Biggar, K.K. and Storey, K.B. (2011) The Emerging Roles of microRNAs in the Molecular Responses of Metabolic Rate Depression. Journal of Molecular Cell Biology, 3, 167-175.

[20]   Waterhouse, P.M., Wang, M.B. and Lough, T. (2001) Gene Silencing as an Adaptive Defence Against Viruses. Nature, 411, 834-842.

[21]   Osuji, G.O., Brown, T.K., South, S.M., Duncan, J.C., Johnson, D. and Hyllam, S. (2012) Molecular Adaptation of Peanut Metabolic Pathways to Wide Variations of Mineral Ion Composition and Concentration. American Journal of Plant Sciences, 3, 33-50.

[22]   Osuji, G.O., Reyes, J.C. and Mangaroo, A.S. (1998) Glutamate Dehydrogenase Isomerization: A Simple Method for Diagnosing Nitrogen, Phosphorus, and Potassium Sufficiency in Maize (Zea mays L.). Journal of Agricultural and Food Chemistry, 46, 2395-2401.

[23]   Osuji, G.O., Brown, T.K., South, S.M., Duncan, J.C. and Johnson, D. (2011) Doubling of Crop Yield through Permutation of Metabolic Pathways. Advances in Biosciences and Biotechnology, 2, 364-379.

[24]   Agren, G.I., Watterstedt, J.A.M. and Billberger, M.F.K. (2012) Nutrient Limitation on Terrestrial Plant Growth—Modeling the Interactions between Nitrogen and Phosphorus. New Phytologist, 194, 953-960.

[25]   Prinzenberg, A.E., Barbier, H., Salt, D.E., Stich, B. and Reymond, M. (2010) Relationships between Growth, Growth Response to Nutrient Supply, and Ion Content Using a Recombinant Inbred Line Population in Arabidopsis. Plant Physiology, 154, 1361-1371.

[26]   Wu, G., Zhang, C., Chu, L. and Shao, H. (2017) Responses of Higher Plants to Abiotic Stresses and Agricultural Sustainable Development. Journal of Plant Interactions, 2, 135-147.

[27]   Chapin, F.S. and Van Cleve, K. (1991) Approaches to Studying Nutrient Uptake, Use and Loss in Plants. In: Pearcy, R.W., Ehleringer, J.R., Mooney, H.A. and Rundel, P.W., Eds., Plant Physiological Ecology: Field Methods and Instrumentation, Chapman and Hall, New York, 185-207.

[28]   Osvalde, A. (2011) Optimization of Plant Mineral Nutrition Revisited: The Roles of Plant Requirements, Nutrient Interactions, and Soil Properties in Fertilization Management. Environmental and Experimental Biology, 9, 1-8.

[29]   Liu, Y., Beyer, A. and Aebersold, R. (2016) On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell, 165, 535-550.

[30]   Guimaraes-Dias, F., Neves-Borges, A.C., Viana, A.A.B., Mesquita, R.O., Romano, E., Grossi-de-Sa, M., Nepomuceno, A.L. and Alves-Ferreira, M. (2012) Expression Analyses in Response to Drought Stress in Soybeans: Shedding Light on the Regulation of Metabolic Pathway Genes. Genetics and Molecular Biology, 35, 222-232.

[31]   UN World Population in Prospects: The 2006 Revision.

[32]   Food and Agriculture Organization (2014) The State of Food and Agriculture 2014 in Brief.

[33]   The World Bank (2013) Urban Population.

[34]   Flygare, S., Griffin, T., Larsson, P. and Mosbach, K. (1983) Affinity Precipitation of Dehydrogenases. Analytical Biochemistry, 133, 409-416.

[35]   McCarthy, A.D., Walker, J.M. and Tipton, K.F. (1980) Purification of Glutamate Dehydrogenase from ox Brain and Liver. Evidence That Commercially Available Preparations of the Enzyme from ox Liver Have Suffered Proteolytic Cleavage. Biochemical Journal, 191, 605-611.

[36]   Godinot, C., Julliard, J. H. and Gautheron, D.C. (1974) A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose. Analytical Biochemistry, 61, 264-270.

[37]   Osuji, G.O., Konan, J. and M’Mbijjewe, G. (2004) RNA Synthetic Activity of Glutamate Dehydrogenase. Applied Biochemistry Biotechnology, 119, 209-228.

[38]   Osuji, G.O., Brown, T.K. and South, S.M. (2010) Optimized Fat and Cellulosic Biomass Accumulation in Peanut through Biotechnology. International Journal of Biotechnology and Biochemistry, 6, 455-476.

[39]   Osuji, G.O, Brown, T.K., South, S.M., Johnson, D. and Hyllam, S. (2012) Molecular Modeling of Metabolism for Allergen-Free Low Linoleic Acid Peanuts. Applied Biochemistry and Biotechnology, 168, 805-823.

[40]   Osuji, G.O., Cuero, R.G. and Washington, A.C. (1991) Effects of α-Ketoglutarate on the Activities of the Glutamate Synthase, Glutamate Dehydrogenase, and Aspartate Transaminase of Sweet potato, Yam Tuber, and Cream Pea. Journal of Agricultural and Food Chemistry, 39, 1590-1596.

[41]   Osuji, G.O., Braithwaite, C., Fordjour, K., Madu, W.C., Beyene, A., Roberts, P.S. and Wright, V. (2003) Purification of Glutamate Dehydrogenase Isoenzymes and Characterization of Their Substrate Specificities. Preparative Biochemistry and Biotechnology, 33, 13-28.

[42]   Grierson, D., Slater, J. and Tucker, G.A. (1985) The Appearance of Polygalacturonase mRNA in Tomatoes: One of a Series of Changes in Gene Expression during Development and ripening. Planta, 163, 263-271.

[43]   Sambrook, J. and Russel, D.W. (2001) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

[44]   Osuji, G.O., Brown, T.K. and South, S.M. (2009) Nucleotide-Dependent Reprogramming of mRNAs Encoding Acetyl Coenzyme a Carboxylase and Lipoxygenase in Relation to the Fat Contents of Peanut. Journal of Botany, 2009, Article ID: 278324.

[45]   Grabczyk, E., Mancuso, M. and Sammarco, M.C. (2007) A Persistent RNA·DNA Hybrid Formed by Transcription of the Friedreich Ataxia Triplet in Live Bacteria, and by RNAP in Vitro. Nucleic Acids Research, 35, 5351-5359.

[46]   Gunnarsson, G.H., Gudmundsson, B., Thormar, H.G., Alfredsson, A. and Jonsson, J.J. (2006) Two-Dimensional Stradededness-Dependent Electrophoresis: A Method to Characterize Single-Stranded DNA, Double-Stranded DNA, and RNA-DNA Hybrids in Complex Samples. Analytical Biochemistry, 350, 120-127.

[47]   Osuji, G.O. and Brown, T. (2007) Environment-Wide Reprogramming of mRNAs Encoding Phosphate Translocator and Glucosyltransferase in Relation to Cellulosic Biomass Accumulation in Peanut. The ICFAI Journal of Biotechnology, 1, 35-47.

[48]   Osuji, G.O. and Brown, T. (2007) Role of the RNAs Synthesized by Glutamate Dehydrogenase in the Coordinate Regulation of Metabolic Processes. The ICFAI Journal of Biotechnology, 1, 37-48.

[49]   Osuji, G.O., Johnson, P., Duffus, E., Woldesenbet, S. and Kirven, J.M. (2017) Horticultural Production of Ultra High Resveratrol Peanut. Agricultural Science, 8, 1173-1194.

[50]   Das, S., Marwal, A., Choudhary, D.K., Gupta, V.K. and Gaur, R.K. (2011) Mechanism of RNA Interference (RNAi): Current Concepts. International Proceedings of Chemical, Biological and Environmental Engineering, 9, 240-245.

[51]   Davidson, J.N. (2012) The Biochemistry of Nucleic Acids. 7th Edition, Academic Press, London.

[52]   Meyer, P. and Saedler, H. (1996) Homology-Dependent Gene Silencing in Plants. Annual Review of Plant Physiology and Plant Molecular Biology, 47, 23-48.

[53]   Sanchez-Calderon, L., Lopez-Bucio, J., Chacon-Lopez, A., Gutierrez-Ortega, A., Hernandez-Abreu, E. and Herrera-Estrella, L. (2006) Characterization of a low phosphorus insensitive Mutants Reveal a Crosstalk between Low Phosphorus-Induced Determinate Root Development and the Activation of Genes Involved in the Adaptation of Arabidopsis to Phosphorus Deficiency. Plant Physiology, 140, 879-889.

[54]   Pang, J., Tibbett, M., Denton, M.D., Lambers, H., Siddique, K.H.M., Bolland, M.D.A., Revell, C.K. and Ryan, M.H. (2010) Variation in Seedling Growth of 11 Perennial Legume Sin Response to Phosphorus Supply. Plant and Soil, 238, 133-143.

[55]   Hermans, C., Hammond, J.P., White, P.J. and Verbruggen, N. (2006) How Do Plants Respond to Nutrient Shortage by Biomass Allocation? Trends in Plant Science, 11, 610-617.

[56]   Hirai, M.Y., Yano, M., Goodenowe, D.B., Kanaya, S., Kimura, T., Awazuhara, M., Fujiwara, T. and Saito, K. (2004) Integration of Transcriptomics and Metabolomics for Understanding of Global Responses to Nutritional Stresses in Aribidopsis thaliana. Proceedings of the National Academy of Sciences of the United States of America, 101, 10205-10210.

[57]   De Groot, C.C., Van Den Boogaard, R., Marcells, L.F.M., Harbinson, J. and Lambers, H. (2003) Contrasting Effects of N and P Deprivation on the Regulation of Photosynthesis in Tomato Plants in Relation to Feedback Limitation. Journal of Experimental Botany, 54, 1957-1967.

[58]   Andreev, D.E., Dmitriev, S.E., Loughran, G., Terenin, I.M., Baranov, P.V. and Shatsky, I.N. (2018) Translational Control of mRNAs Encoding Translational Initiation Factore. Gene, 651, 174-182.

[59]   Hershey, J.W., Sonenberg, N. and Mathews, M.B. (2019) Principles of Translational Control: An Overview. Cold Spring Harbor Perspectives in Biology, 4, a011528.

[60]   Southeast Farm Press (2018) Peanut Production 101: Rotation Key to Bigger Yields.

[61]   USDA (2018) Oilseeds: World Markets and Trends. Foreign Agricultural Service Office of Global Analysis, 39.

[62]   Lee, W., Shin, S., Cho, S.S. and Park, J. (1999) Purification and Characterization of Glutamate Dehydrogenase as Another Isoprotein Binding to the Membrane of Rough Endoplasmic Reticulum. Journal of Cellular Biochemistry, 76, 244-253.<244::AID-JCB8>3.0.CO;2-K

[63]   Brodelius, P.E. and Kaplan, N.O. (1979) Studies on Bovine Liver Glutamate Dehydrogenase by Analytical Affinity Chromatography and Immobilized AMP Analogs. Archives Biochemistry and Biophysics, 194, 449-456.

[64]   Osuji, G.O., Mangaroo, A.S. and Roberts, P.S. (2001) In Vitro Isomerization of Glutamate Dehydrogenase in Relation to Phytosequestration of Lead. SAAS Bulletin: Biochemistry and Biotechnology, 14, 60-72.

[65]   Cooke, P.D.A. (2001) The Sensitivity of Glutamate Dehydrogenase to the Presence of the Herbicide Gramoxone (Paraquat) in Caprine Diets. MS Degree Thesis, Animal Science Department, Prairie View A&M University, Prairie View, Texas, USA.

[66]   King, N.I. (2000) The Change of Caprine Glutamate Dehydrogenase in Response to Atrazine Adulterated Diet. MS Degree Thesis, Animal Science Department, Prairie View A&M University, Prairie View, TX, USA.

[67]   Muhs, M., Yamamoto, H., Ismer, J., Takaku, H., Nashimoto, M., et al. (2011) Structural Basis for the Binding of IRES RNAs to the Head of the Ribosomal 40S Subunit. Nucleic Acids Research, 39, 5264-5275.