Selection Signatures in Worldwide Sheep Populations

The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populations, (ii) make use of linkage disequilibrium information and (iii) focus specifically on either recent or older selection signatures. We show that this allows pinpointing several new selection signatures in the sheep genome and distinguishing those related to modern breeding objectives and to earlier post-domestication constraints. The newly identified regions, together with the ones previously identified, reveal the extensive genome response to selection on morphology, color and adaptation to new environments

Genetic testing for TMEM154 mutations associated with lentivirus susceptibility in sheep

Stefan Hiendleder is a member of the International Sheep Genomics ConsortiumIn sheep, small ruminant lentiviruses cause an incurable, progressive, lymphoproliferative disease that affects millions of animals worldwide. Known as ovine progressive pneumonia virus (OPPV) in the U.S., and Visna/Maedi virus (VMV) elsewhere, these viruses reduce an animal’s health, productivity, and lifespan. Genetic variation in the ovine transmembrane protein 154 gene (TMEM154) has been previously associated with OPPV infection in U.S. sheep. Sheep with the ancestral TMEM154 haplotype encoding glutamate (E) at position 35, and either form of an N70I variant, were highly-susceptible compared to sheep homozygous for the K35 missense mutation. Our current overall aim was to characterize TMEM154 in sheep from around the world to develop an efficient genetic test for reduced susceptibility. The average frequency of TMEM154 E35 among 74 breeds was 0.51 and indicated that highly-susceptible alleles were present in most breeds around the world. Analysis of whole genome sequences from an international panel of 75 sheep revealed more than 1,300 previously unreported polymorphisms in a 62 kb region containing TMEM154 and confirmed that the most susceptible haplotypes were distributed worldwide. Novel missense mutations were discovered in the signal peptide (A13V) and the extracellular domains (E31Q, I74F, and I102T) of TMEM154. A matrix-assisted laser desorption/ionization–time-of flight mass spectrometry (MALDI-TOF MS) assay was developed to detect these and six previously reported missense and two deletion mutations in TMEM154. In blinded trials, the call rate for the eight most common coding polymorphisms was 99.4% for 499 sheep tested and 96.0% of the animals were assigned paired TMEM154 haplotypes (i.e., diplotypes). The widespread distribution of highly-susceptible TMEM154 alleles suggests that genetic testing and selection may improve the health and productivity of infected flocks.Michael P. Heaton, Theodore S. Kalbfleisch, Dustin T. Petrik, Barry Simpson, James W. Kijas, Michael L. Clawson, Carol G. Chitko-McKown, Gregory P. Harhay, Kreg A. Leymaster, the International Sheep Genomics Consortiu

The Role Of The Opaque2 Transcriptional Factor In The Regulation Of Protein Accumulation And Amino Acid Metabolism In Maize Seeds.

[No abstract available]66 Su 1Pt 2

Lysine degradation through the saccharopine pathway in mammals: involvement of both bifunctional and monofunctional lysine-degrading enzymes in mouse

Lysine-oxoglutarate reductase and saccharopine dehydrogenase are enzymic activities that catalyse the first two steps of lysine degradation through the saccharopine pathway in upper eukaryotes. This paper describes the isolation and characterization of a cDNA clone encoding a bifunctional enzyme bearing domains corresponding to these two enzymic activities. We partly purified those activities from mouse liver and showed for the first time that both a bifunctional lysine-oxoglutarate reductase/saccharopine dehydrogenase and a monofunctional saccharopine dehydrogenase are likely to be present in this organ. Northern analyses indicate the existence of two mRNA species in liver and kidney. The longest molecule, 3.4 kb in size, corresponds to the isolated cDNA and encodes the bifunctional enzyme. The 2.4 kb short transcript probably codes for the monofunctional dehydrogenase. Sequence analyses show that the bifunctional enzyme is likely to be a mitochondrial protein. Furthermore, enzymic and expression analyses suggest that lysine-oxoglutarate reductase/saccharopine dehydrogenase levels increase in livers of mice under starvation. Lysine-injected mice also show an increase in lysine-oxoglutarate reductase and saccharopine dehydrogenase levels.344255556

Structure And Regulation Of The Bifunctional Enzyme Lysine-oxoglutarate Reductase-saccharopine Dehydrogenase In Maize

The lysine-oxoglutarate reductase (LOR) domain of the bifunctional enzyme lysine-oxoglutarate reductase-saccharopine dehydrogenase (LOR/SDH) from maize endosperm was shown to be activated by Ca 2+, high salt concentration, organic solvents and Mg 2+. The Ca 2+-dependent enhancement of LOR activity was inhibited by the calmodulin antagonists N-(6-aminohexyl)- 5-chloro-1-naphthalenesulfonamide (w7) and calmidazolium. Limited proteolysis was used to assess the structure/function relationship of the enzyme. Digestion with elastase separated the bifunctional 125-kDa polypeptide into two polypeptides of 65 kDa and 57 kDa, containing the functional domains of LOR and SDH, respectively. Proteolysis did not affect SDH activity, while LOR showed a time-dependent and protease-concentration-dependent inactivation followed by reactivation. Prolonged digestion or increasing amounts of elastase produced a complex pattern of limit polypeptides derived from additional cleavage sites within the 65-kDa (LOR) and 57-kDa (SDH) domains. The SDH-containing polypeptides inhibited the enzymatic activity of LOR- containing polypeptides. When separated from the SDH domain by limited proteolysis and ion-exchange chromatography, the LOR domain retained its Ca 2+ activation property, but was no longer activated by high salt concentrations. These results suggest that the LOR activity of the native enzyme is normally inhibited such that after modulation, the enzyme undergoes a conformational alteration to expose the catalytic domain for substrate binding.2533720729Markovitz, P.J., Chuang, D.T., The bifunctional aminoadipic semialdehyde synthase in lysine degradation (1987) J. Biol. Chem., 262, pp. 9353-9358Gonçalves-Butruille, M., Szajner, P., Torigoi, E., Leite, A., Arruda, P., Purification and characterization of the bifunctional enzyme lysine-oxoglutarate reductase/saccharopine dehydrogenase from maize (1996) Plant Physiol. (Rockv.), 110, pp. 765-771Jones, E.E., Broquist, H.P., Saccharopine, an intermediate of the aminoadipic acid pathway of lysine biosynthesis II: Studies in Saccharomyces cerevisiae (1965) J. Biol. Chem., 240, pp. 2531-2536Jones, E.E., Broquist, H.P., Saccharopine, an intermediate of the aminoadipic acid pathway of lysine biosynthesis III: Aminoadipic semialdehyde-glutamate reductase (1966) J. Biol. Chem., 241, pp. 3440-3444Saunders, P.P., Broquist, H.P., Saccharopine, an intermediate of the aminoadipic acid pathway of lysine biosynthesis IV: Saccharopine dehydrogenase (1966) J. Biol. Chem., 241, pp. 3435-3440Fjellstedt, T.A., Robinson, J.C., Purification and properties of L-lysine-α-ketoglutarate reductase from human placenta (1975) Arch. Biochem. Biophys., 168, pp. 536-548Arruda, P., Sodek, L., Silva, W.J., Lysine-ketoglutarate reductase activity in developing maize endosperm (1982) Plant Physiol. (Rockv.), 69, pp. 988-989Fjellstedt, T.A., Robinson, J.C., Properties of partially purified saccharopine dehydrogenase from human placenta (1975) Arch. Biochem. Biophys., 171, pp. 191-196Ramos, F., Dubois, E., Piérard, A., Control of enzyme synthesis in the lysine biosynthetic pathway of Saccharomyces cerevisiae: Evidence for a regulatory route of gene LYS 14 (1988) Eur. J. Biochem., 171, pp. 171-176Borell, C.W., Urrestarazu, L.A., Bhattacharjee, J.K., Two unlinked lysine genes (LYS9 and LYS14) are required for the synthesis of saccharopine reductase in Saccharomyces cerevisiae (1984) J. Bacteriol., 159, pp. 429-432Feller, A., Dubois, E., Ramos, F., Piérard, A., Repression of the genes for lysine biosynthesis in Saccharomyces cerevisiae is caused by limitation of LYS 14-dependent transcriptional activation (1994) Mol. Cell. Biol., 14, pp. 6411-6418Foster, A.R., Scislowski, P.W.D., Harris, C.I., Fuller, M.F., Metabolic response of liver lysine α-ketoglutarate reductase activity in rats fed lysine limiting or lysine excessive diets (1993) Nutr. Res., 13, pp. 1433-1443Karchi, H., Orit, S., Galili, G., Lysine synthesis and catabolism are coordenately regulated during tobacco seed development (1994) Proc. Natl Acad. Sci. USA, 91, pp. 2577-2581Scislowski, P.W.D., Foster, A.R., Fuller, M.F., Regulation of oxidative degradation of L-lysine in rat liver mitochondria (1994) Biochem. J., 99, pp. 887-891Karchi, H., Daphna, M., Yaacov, S., Galili, G., The lysine-dependent stimulation of lysine catabolism in tobacco seeds requires calcium and protein phosphorilation (1995) Plant Cell, 7, pp. 1963-1970Brochetto-Braga, M.R., Leite, A., Arruda, P., Partial purification and characterization of lysine-oxoglutarate reductase activity in normal and opaque-2 maize endosperms (1992) Plant Physiol. (Rockv.), 98, pp. 1139-1147Lohmer, S., Maddaloni, M., Motto, M., Di Fonzo, N., Hartings, H., Salamini, F., Thompson, R.D., The maize regulatory locus Opaque 2 encodes a DNA-binding protein which activates the transcription of the b-32 gene (1991) EMBO J., 10, pp. 617-624Schmidt, R.J., Ketudat, M., Aukerman, M.J., Hoschek, G., Opaque2 is a transcriptional activator that recognizes a specific target site in 22 kDa zein genes (1992) Plant Cell, 4, pp. 689-700Cord Neto, G., Yunes, J.A., Vettore, A.L., Da Silva, M.J., Arruda, P., Leite, A., The involvement of Opaque-2 on β-prolamin gene regulation in maize and Coix suggests a more general role for this transcriptional activator (1995) Plant Mol. Biol., 27, pp. 1015-1029Mauri, I., Maddaloni, M., Lohmer, S., Motto, M., Salamini, F., Thompson, R.D., Martegani, E., Functional expression of the transcriptional activator Opaque-2 of Zea mays in transformed yeast (1993) Mol. Gen. Genet., 241, pp. 319-326Hinnebush, A.G., Mechanisms of regulation in the general control of amino acid biosynthesis in Saccharomyces cerevisiae (1988) Microbiol. Rev., 52, pp. 248-273Laemmli, U.K., Cleavage of structural proteins during the assembly of the head of bacteriophage T4 (1970) Nature, 277, pp. 680-685Timmons, T.M., Dunbar, B.S., Protein blotting and immunodetection (1990) Methods Enzymol., 182, pp. 679-688Gallagher, S., Immunoblot detection (1996) Current Protocols in Protein Science, pp. 10101-101012. , Coligan, J. E., Dunn, B. M., Ploegh, H. L., Speicher, D. W. & Wingfield, P. T. eds John Wiley & Sons, New YorkBradford, M.M., A rapid and sensitive method for quantification of microgram quantities of protein utilizing the principle of protein-dye binding (1976) Anal. Biochem., 72, pp. 248-254Tang, G., Miron, D., Zhu-Shimoni, J.X., Galili, G., Regulation of lysine catabolism through lysine-oxoglutarate reductase and saccharopine dehydrogenase in Arabidopsis (1997) Plant Cell, 9, pp. 1305-1316Shearwin, K., Nanhua, C., Masters, C., Interactions between glycolytic enzymes and cytoskeletal structure. The influence of ionic strength and molecular crowding (1990) Biochem. Internat., 21, pp. 53-60Roberts, D.M., Harmon, A.C., Calcium-modulated proteins: Targets of intracellular calcium signals in higher plants (1992) Annu. Rev. Plant Physiol. Plant Mol. Biol., 43, pp. 375-414Wu, D., Ahmed, S.N., Lian, W., Hersh, L.B., Activation of rat choline acetyltransferase by limited proteolysis (1995) J. Biol. Chem., 270, pp. 19395-19401Kaufmann, M., Schwarz, T., Jaenicke, R., Schnackerz, K.D., Neyer, H.E., Bartholmes, P., Limited proteolysis of the beta 2-dimer of tryptophan synthase yields an enzymatically active derivative that binds alpha-subunits (1991) Biochemistry, 30, pp. 4173-4179Hilton, S., McCubbin, W.D., Kay, C.M., Buckley, T., Purification and spectral study of a microbial fatty acyltransferase: Activation by limited proteolysis (1990) Biochemistry, 29, pp. 9072-9078Snedden, W.A., Arazi, T., Fromm, H., Shelp, B.J., Calcium/calmodulin activation of soybean glutamate decarboxylase (1995) Plant Physiol. (Rockv.), 108, pp. 543-549Carafoli, E., Calcium pump of the plasma membrane (1991) Physiol. Rev., 71, pp. 129-153Arazi, T., Baum, G., Snedden, W.A., Shelp, B.J., Fromm, H., Molecular and biochemical analysis of calmodulin interactions with the calmodulin-binding domain of plant glutamate decarboxylase (1995) Plant Physiol. (Rockv.), 108, pp. 551-561Baum, G., Chen, Y., Arazi, T., Takatsuji, H., Fromm, H., A plant glutamate-decarboxylase containing a calmodulin binding domain - Cloning, sequence, and functional-analysis (1993) J. Biol. Chem., 268, pp. 19610-19617Baum, G., Lev-Yadun, S., Fridmann, Y., Arazi, T., Katsnelson, H., Zik, M., Fromm, H., Calmodulin binding to glutamate decarboxylase is required for regulation of glutamate and GABA metabolism and normal development in plants (1996) EMBO J., 15, pp. 2988-2996Miron, D., Ben-Yaacov, S., Karchi, H., Galili, G., In vitro dephosphorylation inhibits the activity of soybean lysine-oxoglutarate reductase in a lysine-regulated manner (1997) Plant J., 12, pp. 1453-145

Structure and regulation of the bifunctional enzyme-lysine-oxoglutarate reductase-saccharopine dehydrogenase in maize

The lysine-oxoglutarate reductase (LOR) domain of the bifunctional enzyme lysine-oxoglutarate reductase-saccharopine dehydrogenase (LOR/SDH) from maize endosperm was shown to be activated by Ca2+, high salt concentration, organic solvents and Mg2+. The Ca2+-dependent enhancement of LOR activity was inhibited by the calmodulin antagonists N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W7) and calmidazolium. Limited proteolysis was used to assess the structure/function relationship of the enzyme. Digestion with elastase separated the bifunctional 125-kDa polypeptide into two polypeptides of 65 kDa and 57 kDa, containing the functional domains of LOR and SDH, respectively. Proteolysis did not affect SDH activity, while LOR showed a time-dependent and protease-concentration-dependent inactivation Followed by reactivation. Prolonged digestion or increasing amounts of elastase produced a complex pattern of limit polypeptides derived from additional cleavage sites within the 65-kDa (LOR) and 57-kDa (SDH) domains. The SDH-containing polypeptides inhibited the enzymatic activity of LOR-containing polypeptides. When separated from the SDH domain by limited proteolysis and ion-exchange chromatography, the LOR domain retained its Ca2+ activation property, but was no longer activated by high salt concentrations. These results suggest that the LOR activity of the native enzyme is normally inhibited such that after modulation, the enzyme undergoes a conformational alteration to expose the catalytic domain for substrate binding.253372072

The Involvement Of Opaque 2 On Beta-prolamin Gene Regulation In Maize And Coix Suggests A More General Role For This Transcriptional Activator.

The maize opaque 2 (o2) mutation is known to have numerous pleiotropic effects. Some polypeptides have their expression depressed while others are enhanced. The best characterized effects of the o2 mutation are those exerted on endosperm genes encoding the storage protein class of the 22 kDa alpha-zeins and the ribosome inactivating protein b-32. The Opaque 2 (O2) locus encodes a basic domain-leucine zipper DNA-binding factor, O2, which transcriptionally regulates these genes. In the maize-related grass Coix lacryma-jobi, an O2-homologous protein regulates the 25 kDa alpha-coixin family. We show in this paper that O2 transcriptionally regulates the structurally and developmentally different class of the beta-prolamins. A new O2-binding box was identified in beta-prolamin genes from maize and Coix that, together with the boxes previously identified in other endosperm expressed genes, forms a curious collection of O2 cis elements. This may have regulatory implications on the role of O2 in the mechanism that controls coordinated gene expression in the developing endosperm. Considering that the O2 locus controls at least three distinct classes of genes in maize endosperm, we propose that the O2 protein may play a more general role in maize endosperm development than previously conceived.271015-2