Synchronized turbo apoptosis induced by cold-shock

In our research on the role of apoptosis in the pathogenesis of the autoimmune disease systemic lupus erythematosus (SLE), we aim to evaluate the effects of early and late apoptotic cells and blebs on antigen presenting cells. This requires the in vitro generation of sufficiently large and homogeneous populations of early and late apoptotic cells. Here, we present a quick method encountered by serendipity that results in highly reproducible synchronized homogeneous apoptotic cell populations. In brief, granulocytic 32Dcl3 cells are incubated on ice for 2 h and subsequently rewarmed at 37°C. After 30–90 min at 37°C more than 80–90% of the cells become early apoptotic (Annexin V positive/propidium iodide negative). After 24 h of rewarming at 37°C 98% of the cells were late apoptotic (secondary necrotic; Annexin V positive/propidium iodide positive). Cells already formed apoptotic blebs at their cell surface after approximately 20 min at 37°C. Inter-nucleosomal chromatin cleavage and caspase activation were other characteristics of this cold-shock-induced process of apoptosis. Consequently, apoptosis could be inhibited by a caspase inhibitor. Finally, SLE-derived anti-chromatin autoantibodies showed a high affinity for apoptotic blebs generated by cold-shock. Overall, cold-shock induced apoptosis is achieved without the addition of toxic compounds or antibodies, and quickly leads to synchronized homogeneous apoptotic cell populations, which can be applied for various research questions addressing apoptosis

Parainfluenza virus 5 genomes are located in viral cytoplasmic bodies whilst the virus dismantles the interferon-induced antiviral state of cells

Although the replication cycle of parainfluenza virus type 5 (PIV5) is initially severely impaired in cells in an interferon (IFN)-induced antiviral state, the virus still targets STAT1 for degradation. As a consequence, the cells can no longer respond to IFN and after 24−48 h, they go out of the antiviral state and normal virus replication is established. Following infection of cells in an IFN-induced antiviral state, viral nucleocapsid proteins are initially localized within small cytoplasmic bodies, and appearance of these cytoplasmic bodies correlates with the loss of STAT1 from infected cells. In situ hybridization, using probes specific for the NP and L genes, demonstrated the presence of virus genomes within these cytoplasmic bodies. These viral cytoplasmic bodies do not co-localize with cellular markers for stress granules, cytoplasmic P-bodies or autophagosomes. Furthermore, they are not large insoluble aggregates of viral proteins and/or nucleocapsids, as they can simply and easily be dispersed by ‘cold-shocking’ live cells, a process that disrupts the cytoskeleton. Given that during in vivo infections, PIV5 will inevitably infect cells in an IFN-induced antiviral state, we suggest that these cytoplasmic bodies are areas in which PIV5 genomes reside whilst the virus dismantles the antiviral state of the cells. Consequently, viral cytoplasmic bodies may play an important part in the strategy that PIV5 uses to circumvent the IFN system

Evaluation of the Influenza A Replicon for Transient Expression of Recombinant Proteins in Mammalian Cells

Recombinant protein expression in mammalian cells has become a very important technique over the last twenty years. It is mainly used for production of complex proteins for biopharmaceutical applications. Transient recombinant protein expression is a possible strategy to produce high quality material for preclinical trials within days. Viral replicon based expression systems have been established over the years and are ideal for transient protein expression. In this study we describe the evaluation of an influenza A replicon for the expression of recombinant proteins. We investigated transfection and expression levels in HEK-293 cells with EGFP and firefly luciferase as reporter proteins. Furthermore, we studied the influence of different influenza non-coding regions and temperature optima for protein expression as well. Additionally, we exploited the viral replication machinery for the expression of an antiviral protein, the human monoclonal anti-HIV-gp41 antibody 3D6. Finally we could demonstrate that the expression of a single secreted protein, an antibody light chain, by the influenza replicon, resulted in fivefold higher expression levels compared to the usually used CMV promoter based expression. We emphasize that the influenza A replicon system is feasible for high level expression of complex proteins in mammalian cells

Serine phosphorylation regulates paxillin turnover during cell migration

BACKGROUND: Paxillin acts as an adaptor protein that localizes to focal adhesion. This protein is regulated during cell migration by phosphorylation on tyrosine, serine and threonine residues. Most of these phosphorylations have been implicated in the regulation of different steps of cell migration. The two major phosphorylation sites of paxillin in response to adhesion to an extracellular matrix are serines 188 and 190. However, the function of this phosphorylation event remains unknown. The purpose of this work was to determine the role of paxillin phosphorylation on residues S188 and S190 in the regulation of cell migration. RESULTS: We used NBT-II epithelial cells that can be induced to migrate when plated on collagen. To examine the role of paxillin serines 188/190 in cell migration, we constructed an EGFP-tagged paxillin mutant in which S188/S190 were mutated into unphosphorylatable alanine residues. We provide evidence that paxillin is regulated by proteasomal degradation following polyubiquitylation of the protein. During active cell migration on collagen, paxillin is protected from proteasome-dependent degradation. We demonstrate that phosphorylation of serines 188/190 is necessary for the protective effect of collagen. In an effort to understand the physiological relevance of paxillin protection from degradation, we show that cells expressing the paxillin S188/190A interfering mutant spread less, have reduced protrusive activity but migrate more actively. CONCLUSION: Our data demonstrate for the first time that serine-regulated degradation of paxillin plays a key role in the modulation of membrane dynamics and consequently, in the control of cell motility

Regulation of translation initiation under biotic and abiotic stresses

[EN] Plants have developed versatile strategies to deal with the great variety of challenging conditions they are exposed to. Among them, the regulation of translation is a common target to finely modulate gene expression both under biotic and abiotic stress situations. Upon environmental challenges, translation is regulated to reduce the consumption of energy and to selectively synthesize proteins involved in the proper establishment of the tolerance response. In the case of viral infections, the situation is more complex, as viruses have evolved unconventional mechanisms to regulate translation in order to ensure the production of the viral encoded proteins using the plant machinery. Although the final purpose is different, in some cases, both plants and viruses share common mechanisms to modulate translation. In others, the mechanisms leading to the control of translation are viral- or stress-specific. In this paper, we review the different mechanisms involved in the regulation of translation initiation under virus infection and under environmental stress in plants. In addition, we describe the main features within the viral RNAs and the cellular mRNAs that promote their selective translation in plants undergoing biotic and abiotic stress situations.This work was supported by the ERC Starting Grant 260468 to M. Mar Castellano.Echevarria-Zomeno, S.; Yanguez, E.; Fernandez-Bautista, N.; Castro-Sanz, AB.; Ferrando Monleón, AR.; Castellano, MM. (2013). Regulation of translation initiation under biotic and abiotic stresses. International Journal of Molecular Sciences. 14(3):4670-4683. https://doi.org/10.3390/ijms14034670S46704683143Dever, T. E., & Green, R. (2012). The Elongation, Termination, and Recycling Phases of Translation in Eukaryotes. Cold Spring Harbor Perspectives in Biology, 4(7), a013706-a013706. doi:10.1101/cshperspect.a013706Sonenberg, N., & Hinnebusch, A. G. (2009). Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets. Cell, 136(4), 731-745. doi:10.1016/j.cell.2009.01.042Graber, T. E., & Holcik, M. (2007). Cap-independent regulation of gene expression in apoptosis. Molecular BioSystems, 3(12), 825. doi:10.1039/b708867aAl-Fageeh, M. B., & Smales, C. M. (2006). Control and regulation of the cellular responses to cold shock: the responses in yeast and mammalian systems. Biochemical Journal, 397(2), 247-259. doi:10.1042/bj20060166Braunstein, S., Karpisheva, K., Pola, C., Goldberg, J., Hochman, T., Yee, H., … Schneider, R. J. (2007). A Hypoxia-Controlled Cap-Dependent to Cap-Independent Translation Switch in Breast Cancer. Molecular Cell, 28(3), 501-512. doi:10.1016/j.molcel.2007.10.019Castelli, L. M., Lui, J., Campbell, S. G., Rowe, W., Zeef, L. A. H., Holmes, L. E. A., … Ashe, M. P. (2011). Glucose depletion inhibits translation initiation via eIF4A loss and subsequent 48S preinitiation complex accumulation, while the pentose phosphate pathway is coordinately up-regulated. Molecular Biology of the Cell, 22(18), 3379-3393. doi:10.1091/mbc.e11-02-0153Gilbert, W. V., Zhou, K., Butler, T. K., & Doudna, J. A. (2007). Cap-Independent Translation Is Required for Starvation-Induced Differentiation in Yeast. Science, 317(5842), 1224-1227. doi:10.1126/science.1144467Liu, L., & Simon, M. C. (2004). Regulation of Transcription and Translation by Hypoxia. Cancer Biology & Therapy, 3(6), 492-497. doi:10.4161/cbt.3.6.1010Sun, J., Conn, C. S., Han, Y., Yeung, V., & Qian, S.-B. (2010). PI3K-mTORC1 Attenuates Stress Response by Inhibiting Cap-independent Hsp70 Translation. Journal of Biological Chemistry, 286(8), 6791-6800. doi:10.1074/jbc.m110.172882Walsh, D., Mathews, M. B., & Mohr, I. (2012). Tinkering with Translation: Protein Synthesis in Virus-Infected Cells. Cold Spring Harbor Perspectives in Biology, 5(1), a012351-a012351. doi:10.1101/cshperspect.a012351Floris, M., Mahgoub, H., Lanet, E., Robaglia, C., & Menand, B. (2009). Post-transcriptional Regulation of Gene Expression in Plants during Abiotic Stress. International Journal of Molecular Sciences, 10(7), 3168-3185. doi:10.3390/ijms10073168Jackson, R. J., Hellen, C. U. T., & Pestova, T. V. (2010). The mechanism of eukaryotic translation initiation and principles of its regulation. Nature Reviews Molecular Cell Biology, 11(2), 113-127. doi:10.1038/nrm2838Clemens, M. J. (2001). Translational regulation in cell stress and apoptosis. Roles of the eIF4E binding proteins. Journal of Cellular and Molecular Medicine, 5(3), 221-239. doi:10.1111/j.1582-4934.2001.tb00157.xWek, R. C., Jiang, H.-Y., & Anthony, T. G. (2006). Coping with stress: eIF2 kinases and translational control. Biochemical Society Transactions, 34(1), 7-11. doi:10.1042/bst0340007Holcik, M., & Sonenberg, N. (2005). Translational control in stress and apoptosis. Nature Reviews Molecular Cell Biology, 6(4), 318-327. doi:10.1038/nrm1618Muñoz, A., & Castellano, M. M. (2012). Regulation of Translation Initiation under Abiotic Stress Conditions in Plants: Is It a Conserved or Not so Conserved Process among Eukaryotes? Comparative and Functional Genomics, 2012, 1-8. doi:10.1155/2012/406357Hinnebusch, A. G. (2005). TRANSLATIONAL REGULATION OFGCN4AND THE GENERAL AMINO ACID CONTROL OF YEAST. Annual Review of Microbiology, 59(1), 407-450. doi:10.1146/annurev.micro.59.031805.133833Harding, H. P., Novoa, I., Zhang, Y., Zeng, H., Wek, R., Schapira, M., & Ron, D. (2000). Regulated Translation Initiation Controls Stress-Induced Gene Expression in Mammalian Cells. Molecular Cell, 6(5), 1099-1108. doi:10.1016/s1097-2765(00)00108-8Ventoso, I., Kochetov, A., Montaner, D., Dopazo, J., & Santoyo, J. (2012). Extensive Translatome Remodeling during ER Stress Response in Mammalian Cells. PLoS ONE, 7(5), e35915. doi:10.1371/journal.pone.0035915Sudhakar, A., Ramachandran, A., Ghosh, S., Hasnain, S. E., Kaufman, R. J., & Ramaiah, K. V. A. (2000). Phosphorylation of Serine 51 in Initiation Factor 2α (eIF2α) Promotes Complex Formation between eIF2α(P) and eIF2B and Causes Inhibition in the Guanine Nucleotide Exchange Activity of eIF2B†. Biochemistry, 39(42), 12929-12938. doi:10.1021/bi0008682García, M. A., Meurs, E. F., & Esteban, M. (2007). The dsRNA protein kinase PKR: Virus and cell control. Biochimie, 89(6-7), 799-811. doi:10.1016/j.biochi.2007.03.001Katze, M. G., He, Y., & Gale, M. (2002). Viruses and interferon: a fight for supremacy. Nature Reviews Immunology, 2(9), 675-687. doi:10.1038/nri888Mohr, I. (2006). Phosphorylation and dephosphorylation events that regulate viral mRNA translation. Virus Research, 119(1), 89-99. doi:10.1016/j.virusres.2005.10.009Zhang, Y., Wang, Y., Kanyuka, K., Parry, M. A. J., Powers, S. J., & Halford, N. G. (2008). GCN2-dependent phosphorylation of eukaryotic translation initiation factor-2α in Arabidopsis. Journal of Experimental Botany, 59(11), 3131-3141. doi:10.1093/jxb/ern169Lageix, S., Lanet, E., Pouch-Pélissier, M.-N., Espagnol, M.-C., Robaglia, C., Deragon, J.-M., & Pélissier, T. (2008). Arabidopsis eIF2α kinase GCN2 is essential for growth in stress conditions and is activated by wounding. BMC Plant Biology, 8(1), 134. doi:10.1186/1471-2229-8-134Bilgin, D. D., Liu, Y., Schiff, M., & Dinesh-Kumar, S. . (2003). P58IPK, a Plant Ortholog of Double-Stranded RNA-Dependent Protein Kinase PKR Inhibitor, Functions in Viral Pathogenesis. Developmental Cell, 4(5), 651-661. doi:10.1016/s1534-5807(03)00125-4Gallie, D. R., Le, H., Caldwell, C., Tanguay, R. L., Hoang, N. X., & Browning, K. S. (1997). The Phosphorylation State of Translation Initiation Factors Is Regulated Developmentally and following Heat Shock in Wheat. Journal of Biological Chemistry, 272(2), 1046-1053. doi:10.1074/jbc.272.2.1046Gingras, A. C., Svitkin, Y., Belsham, G. J., Pause, A., & Sonenberg, N. (1996). Activation of the translational suppressor 4E-BP1 following infection with encephalomyocarditis virus and poliovirus. Proceedings of the National Academy of Sciences, 93(11), 5578-5583. doi:10.1073/pnas.93.11.5578Gingras, A.-C., & Sonenberg, N. (1997). Adenovirus Infection Inactivates the Translational Inhibitors 4E-BP1 and 4E-BP2. Virology, 237(1), 182-186. doi:10.1006/viro.1997.8757Freire, M. A. (2005). Translation initiation factor (iso) 4E interacts with BTF3, the β subunit of the nascent polypeptide-associated complex. Gene, 345(2), 271-277. doi:10.1016/j.gene.2004.11.030Freire, M. A., Tourneur, C., Granier, F., Camonis, J., El Amrani, A., Browning, K. S., & Robaglia, C. (2000). Plant Molecular Biology, 44(2), 129-140. doi:10.1023/a:1006494628892Dreher, T. W., & Miller, W. A. (2006). Translational control in positive strand RNA plant viruses. Virology, 344(1), 185-197. doi:10.1016/j.virol.2005.09.031Thivierge, K., Nicaise, V., Dufresne, P. J., Cotton, S., Laliberté, J.-F., Le Gall, O., & Fortin, M. G. (2005). Plant Virus RNAs. Coordinated Recruitment of Conserved Host Functions by (+) ssRNA Viruses during Early Infection Events: Figure 1. Plant Physiology, 138(4), 1822-1827. doi:10.1104/pp.105.064105Deprost, D., Yao, L., Sormani, R., Moreau, M., Leterreux, G., Nicolaï, M., … Meyer, C. (2007). The Arabidopsis TOR kinase links plant growth, yield, stress resistance and mRNA translation. EMBO reports, 8(9), 864-870. doi:10.1038/sj.embor.7401043Manjunath, S., Williams, A. J., & Bailey-Serres, J. (1999). Oxygen deprivation stimulates Ca2+-mediated phosphorylation of mRNA cap-binding protein eIF4E in maize roots. The Plant Journal, 19(1), 21-30. doi:10.1046/j.1365-313x.1999.00489.xRausell, A., Kanhonou, R., Yenush, L., Serrano, R., & Ros, R. (2003). The translation initiation factor eIF1A is an important determinant in the tolerance to NaCl stress in yeast and plants. The Plant Journal, 34(3), 257-267. doi:10.1046/j.1365-313x.2003.01719.xSanan-Mishra, N., Pham, X. H., Sopory, S. K., & Tuteja, N. (2005). Pea DNA helicase 45 overexpression in tobacco confers high salinity tolerance without affecting yield. Proceedings of the National Academy of Sciences, 102(2), 509-514. doi:10.1073/pnas.0406485102Kim, T.-H., Kim, B.-H., Yahalom, A., Chamovitz, D. A., & von Arnim, A. G. (2004). Translational Regulation via 5′ mRNA Leader Sequences Revealed by Mutational Analysis of the Arabidopsis Translation Initiation Factor Subunit eIF3h. The Plant Cell, 16(12), 3341-3356. doi:10.1105/tpc.104.026880Schepetilnikov, M., Kobayashi, K., Geldreich, A., Caranta, C., Robaglia, C., Keller, M., & Ryabova, L. A. (2011). Viral factor TAV recruits TOR/S6K1 signalling to activate reinitiation after long ORF translation. The EMBO Journal, 30(7), 1343-1356. doi:10.1038/emboj.2011.39Mayberry, L. K., Allen, M. L., Nitka, K. R., Campbell, L., Murphy, P. A., & Browning, K. S. (2011). Plant Cap-binding Complexes Eukaryotic Initiation Factors eIF4F and eIFISO4F. Journal of Biological Chemistry, 286(49), 42566-42574. doi:10.1074/jbc.m111.280099Carberry, S. E., Goss, D. J., & Darzynkiewicz, E. (1991). A comparison of the binding of methylated cap analogs to wheat germ protein synthesis initiation factors 4F and (iso) 4F. Biochemistry, 30(6), 1624-1627. doi:10.1021/bi00220a026Lellis, A. D., Allen, M. L., Aertker, A. W., Tran, J. K., Hillis, D. M., Harbin, C. R., … Browning, K. S. (2010). Deletion of the eIFiso4G subunit of the Arabidopsis eIFiso4F translation initiation complex impairs health and viability. Plant Molecular Biology, 74(3), 249-263. doi:10.1007/s11103-010-9670-zDinkova, T. D., Zepeda, H., Martínez-Salas, E., Martínez, L. M., Nieto-Sotelo, J., & Jiménez, E. S. (2005). Cap-independent translation of maize Hsp101. The Plant Journal, 41(5), 722-731. doi:10.1111/j.1365-313x.2005.02333.xHutvagner, G. (2002). A microRNA in a Multiple-Turnover RNAi Enzyme Complex. Science, 297(5589), 2056-2060. doi:10.1126/science.1073827Voinnet, O. (2009). Origin, Biogenesis, and Activity of Plant MicroRNAs. Cell, 136(4), 669-687. doi:10.1016/j.cell.2009.01.046Brodersen, P., Sakvarelidze-Achard, L., Bruun-Rasmussen, M., Dunoyer, P., Yamamoto, Y. Y., Sieburth, L., & Voinnet, O. (2008). Widespread Translational Inhibition by Plant miRNAs and siRNAs. Science, 320(5880), 1185-1190. doi:10.1126/science.1159151Sunkar, R., Li, Y.-F., & Jagadeeswaran, G. (2012). Functions of microRNAs in plant stress responses. Trends in Plant Science, 17(4), 196-203. doi:10.1016/j.tplants.2012.01.010Dong, Z., Shi, L., Wang, Y., Chen, L., Cai, Z., Wang, Y., … Li, X. (2013). Identification and Dynamic Regulation of microRNAs Involved in Salt Stress Responses in Functional Soybean Nodules by High-Throughput Sequencing. International Journal of Molecular Sciences, 14(2), 2717-2738. doi:10.3390/ijms14022717Srivastava, S., Srivastava, A. K., Suprasanna, P., & D’Souza, S. F. (2012). Identification and profiling of arsenic stress-induced microRNAs inBrassica juncea. Journal of Experimental Botany, 64(1), 303-315. doi:10.1093/jxb/ers333Dugas, D. V., & Bartel, B. (2008). Sucrose induction of Arabidopsis miR398 represses two Cu/Zn superoxide dismutases. Plant Molecular Biology, 67(4), 403-417. doi:10.1007/s11103-008-9329-1Aukerman, M. J., & Sakai, H. (2003). Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes. The Plant Cell, 15(11), 2730-2741. doi:10.1105/tpc.016238Chen, X. (2004). A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development. Science, 303(5666), 2022-2025. doi:10.1126/science.1088060Park, W., Li, J., Song, R., Messing, J., & Chen, X. (2002). CARPEL FACTORY, a Dicer Homolog, and HEN1, a Novel Protein, Act in microRNA Metabolism in Arabidopsis thaliana. Current Biology, 12(17), 1484-1495. doi:10.1016/s0960-9822(02)01017-5Gu, S., & Kay, M. A. (2010). How do miRNAs mediate translational repression? Silence, 1(1), 11. doi:10.1186/1758-907x-1-11Lanet, E., Delannoy, E., Sormani, R., Floris, M., Brodersen, P., Crété, P., … Robaglia, C. (2009). Biochemical Evidence for Translational Repression by Arabidopsis MicroRNAs. The Plant Cell, 21(6), 1762-1768. doi:10.1105/tpc.108.063412Olsthoorn, R. C. L. (1999). A conformational switch at the 3’ end of a plant virus RNA regulates viral replication. The EMBO Journal, 18(17), 4856-4864. doi:10.1093/emboj/18.17.4856Smirnyagina, E. V., Morozov, S. Y., Rodionova, N. P., Miroshnichenko, N. A., Solovyev, A. G., Fedorkin, O. N., & Atabekov, J. G. (1991). Translational efficiency and competitive ability of mRNAs with 5′-untranslated αβ-leader of potato virus X RNA. Biochimie, 73(5), 587-598. doi:10.1016/0300-9084(91)90027-xThanaraj, T. A., & Pandit, M. W. (1990). Translation-Initiation Promoting Site on Transcripts of Highly Expressed Genes FromSaccharomyces cerevisiaeand the Role of Hairpin Stems to Position the Site Near the Initiation Codon. Journal of Biomolecular Structure and Dynamics, 7(6), 1279-1289. doi:10.1080/07391102.1990.10508565Tomashevskaya, O. L., Solovyev, A. G., Karpova, O. V., Fedorkin, O. N., Rodionova, N. P., Morozov, S. Y., & Atabekov, J. G. (1993). Effects of sequence elements in the potato virus X RNA 5’ non-translated  beta-leader on its translation enhancing activity. Journal of General Virology, 74(12), 2717-2724. doi:10.1099/0022-1317-74-12-2717Belkum, A. van, Abrahams, J. P., Pleij, C. W. A., & Bosch, L. (1985). Five pseudoknots are present at the 204 nucleotides long 3’ noncoding region of tobacco mosak virus RNA. Nucleic Acids Research, 13(21), 7673-7686. doi:10.1093/nar/13.21.7673Gallie, D. R. (2002). The 5’-leader of tobacco mosaic virus promotes translation through enhanced recruitment of eIF4F. Nucleic Acids Research, 30(15), 3401-3411. doi:10.1093/nar/gkf457Wells, D. R., Tanguay, R. L., Le, H., & Gallie, D. R. (1998). HSP101 functions as a specific translational regulatory protein whose activity is regulated by nutrient status. Genes & Development, 12(20), 3236-3251. doi:10.1101/gad.12.20.3236Leonard, S., Plante, D., Wittmann, S., Daigneault, N., Fortin, M. G., & Laliberte, J.-F. (2000). Complex Formation between Potyvirus VPg and Translation Eukaryotic Initiation Factor 4E Correlates with Virus Infectivity. Journal of Virology, 74(17), 7730-7737. doi:10.1128/jvi.74.17.7730-7737.2000Wittmann, S., Chatel, H., Fortin, M. G., & Laliberté, J.-F. (1997). Interaction of the Viral Protein Genome Linked of Turnip Mosaic Potyvirus with the Translational Eukaryotic Initiation Factor (iso) 4E ofArabidopsis thalianaUsing the Yeast Two-Hybrid System. Virology, 234(1), 84-92. doi:10.1006/viro.1997.8634Robaglia, C., & Caranta, C. (2006). Translation initiation factors: a weak link in plant RNA virus infection. Trends in Plant Science, 11(1), 40-45. doi:10.1016/j.tplants.2005.11.004WANG, A., & KRISHNASWAMY, S. (2012). Eukaryotic translation initiation factor 4E-mediated recessive resistance to plant viruses and its utility in crop improvement. Molecular Plant Pathology, 13(7), 795-803. doi:10.1111/j.1364-3703.2012.00791.xLellis, A. D., Kasschau, K. D., Whitham, S. A., & Carrington, J. C. (2002). Loss-of-Susceptibility Mutants of Arabidopsis thaliana Reveal an Essential Role for eIF(iso)4E during Potyvirus Infection. Current Biology, 12(12), 1046-1051. doi:10.1016/s0960-9822(02)00898-9Duprat, A., Caranta, C., Revers, F., Menand, B., Browning, K. S., & Robaglia, C. (2002). The Arabidopsis eukaryotic initiation factor (iso)4E is dispensable for plant growth but required for susceptibility to potyviruses. The Plant Journal, 32(6), 927-934. doi:10.1046/j.1365-313x.2002.01481.xSato, M., Nakahara, K., Yoshii, M., Ishikawa, M., & Uyeda, I. (2005). Selective involvement of members of the eukaryotic initiation factor 4E family in the infection ofArabidopsis thalianaby potyviruses. FEBS Letters, 579(5), 1167-1171. doi:10.1016/j.febslet.2004.12.086Ruffel, S., Dussault, M.-H., Palloix, A., Moury, B., Bendahmane, A., Robaglia, C., & Caranta, C. (2002). A natural recessive resistance gene against potato virus Y in pepper corresponds to the eukaryotic initiation factor 4E (eIF4E). The Plant Journal, 32(6), 1067-1075. doi:10.1046/j.1365-313x.2002.01499.xNicaise, V., German-Retana, S., Sanjuán, R., Dubrana, M.-P., Mazier, M., Maisonneuve, B., … LeGall, O. (2003). The Eukaryotic Translation Initiation Factor 4E Controls Lettuce Susceptibility to the Potyvirus Lettuce mosaic virus. Plant Physiology, 132(3), 1272-1282. doi:10.1104/pp.102.017855Ruffel, S., Gallois, J. L., Lesage, M. L., & Caranta, C. (2005). The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. Molecular Genetics and Genomics, 274(4), 346-353. doi:10.1007/s00438-005-0003-xKhan, M. A., Miyoshi, H., Gallie, D. R., & Goss, D. J. (2007). Potyvirus Genome-linked Protein, VPg, Directly Affects Wheat Germin VitroTranslation. Journal of Biological Chemistry, 283(3), 1340-1349. doi:10.1074/jbc.m703356200Cotton, S., Dufresne, P. J., Thivierge, K., Ide, C., & Fortin, M. G. (2006). The VPgPro protein of Turnip mosaic virus: In vitro inhibition of translation from a ribonuclease activity. Virology, 351(1), 92-100. doi:10.1016/j.virol.2006.03.019Grzela, R., Strokovska, L., Andrieu, J.-P., Dublet, B., Zagorski, W., & Chroboczek, J. (2006). Potyvirus terminal protein VPg, effector of host eukaryotic initiation factor eIF4E. Biochimie, 88(7), 887-896. doi:10.1016/j.biochi.2006.02.012Kneller, E. L. P., Rakotondrafara, A. M., & Miller, W. A. (2006). Cap-independent translation of plant viral RNAs. Virus Research, 119(1), 63-75. doi:10.1016/j.virusres.2005.10.010Zeenko, V., & Gallie, D. R. (2005). Cap-independent Translation of Tobacco Etch Virus Is Conferred by an RNA Pseudoknot in the 5′-Leader. Journal of Biological Chemistry, 280(29), 26813-26824. doi:10.1074/jbc.m503576200Miller, W. A., & White, K. A. (2006). Long-Distance RNA-RNA Interactions in Plant Virus Gene Expression and Replication. Annual Review of Phytopathology, 44(1), 447-467. doi:10.1146/annurev.phyto.44.070505.143353Wang, S., Browning, K. S., & Miller, W. A. (1997). A viral sequence in the 3′-untranslated region mimics a 5′ cap in facilitating translation of uncapped mRNA. The EMBO Journal, 16(13), 4107-4116. doi:10.1093/emboj/16.13.4107Gao, F., Kasprzak, W., Stupina, V. A., Shapiro, B. A., & Simon, A. E. (2012). A Ribosome-Binding, 3′ Translational Enhancer Has a T-Shaped Structure and Engages in a Long-Distance RNA-RNA Interaction. Journal of Virology, 86(18), 9828-9842. doi:10.1128/jvi.00677-12Wang, Z., Treder, K., & Miller, W. A. (2009). Structure of a Viral Cap-independent Translation Element That Functions via High Affinity Binding to the eIF4E Subunit of eIF4F. Journal of Biological Chemistry, 284(21), 14189-14202. doi:10.1074/jbc.m808841200Gazo, B. M., Murphy, P., Gatchel, J. R., & Browning, K. S. (2004). A Novel Interaction of Cap-binding Protein Complexes Eukaryotic Initiation Factor (eIF) 4F and eIF(iso)4F with a Region in the 3′-Untranslated Region of Satellite Tobacco Necrosis Virus. Journal of Biological Chemistry, 279(14), 13584-13592. doi:10.1074/jbc.m311361200Mardanova, E. S., Zamchuk, L. A., Skulachev, M. V., & Ravin, N. V. (2008). The 5′ untranslated region of the maize alcohol dehydrogenase gene contains an internal ribosome entry site. Gene, 420(1), 11-16. doi:10.1016/j.gene.2008.04.00

Genomic Analysis of Intrinsically Disordered Proteins in the Genus Camelus

Intrinsically disordered proteins/regions (IDPs/IDRs) fail to fold completely into 3D structures, but have major roles in determining protein function. While natively disordered proteins/regions have been found to fulfill a wide variety of primary cellular roles, the functions of many disordered proteins in numerous species remain to be uncovered. Here, we perform the first large-scale study of IDPs/IDRs in the genus Camelus, one of the most important mammalians in Asia and North Africa, in order to explore the biological roles of these proteins. The study includes the prediction of disordered proteins/regions in Camelus species and in humans using multiple state-of-the-art prediction tools. Additionally, we provide a comparative analysis of Camelus and Homo sapiens IDPs/IDRs for the sake of highlighting the distinctive use of disorder in each genus. Our findings indicate that the human proteome is more disordered than the Camelus proteome. Gene Ontology analysis also revealed that Camelus IDPs are enriched in glutathione catabolism and lactose biosynthesis