Unnatural agrochemical ligands for engineered abscisic acid receptors

[EN] Existing agrochemicals can be endowed with new applications through protein engineering of plant receptors. A recent study shows an engineered PYR1 ABA receptor can be activated by mandipropamid. Plants engineered with such PYR1 variant are responsive to this agrochemical, which confers protection against drought through activation of ABA signaling.Rodríguez Egea, PL.; Lozano Juste, J. (2015). Unnatural agrochemical ligands for engineered abscisic acid receptors. Trends in Plant Science. 20(6):330-332. doi:10.1016/j.tplants.2015.04.001S33033220

Nitric oxide sensing in plants is mediated by proteolytic control of group VII ERF transcription factors

Nitric oxide (NO) is an important signaling compound in prokaryotes and eukaryotes. In plants, NO regulates critical developmental transitions and stress responses. Here, we identify a mechanism for NO sensing that coordinates responses throughout development based on targeted degradation of plant-specific transcriptional regulators, the group VII ethylene response factors (ERFs). We show that the N-end rule pathway of targeted proteolysis targets these proteins for destruction in the presence of NO, and we establish them as critical regulators of diverse NO-regulated processes, including seed germination, stomatal closure, and hypocotyl elongation. Furthermore, we define the molecular mechanism for NO control of germination and crosstalk with abscisic acid (ABA) signaling through ERF-regulated expression of ABSCISIC ACID INSENSITIVE5 (ABI5). Our work demonstrates how NO sensing is integrated across multiple physiological processes by direct modulation of transcription factor stability and identifies group VII ERFs as central hubs for the perception of gaseous signals in plants

Tribenuron-methyl metabolism and the rare Pro197Phe double mutation together with 2,4-D metabolism and reduced absorption can evolve in Papaver rhoeas with multiple and cross herbicide resistance to ALS inhibitors and auxin mimics

Multiple resistance mechanisms to ALS inhibitors and auxin mimics in two Papaver rhoeas populations were investigated in wheat fields from Portugal. Dose-response trials, also with malathion (a cytochrome P450 inhibitor), cross-resistance patterns for ALS inhibitors and auxin mimics, alternative herbicides tests, 2,4-D and tribenuron-methyl absorption, translocation and metabolism experiments, together with ALS activity, gene sequencing and enzyme modelling and ligand docking were carried out. Results revealed two different resistant profiles: one population (R1) multiple resistant to tribenuron-methyl and 2,4-D, the second (R2) only resistant to 2,4-D. In R1, several target-site mutations in Pro197 and enhanced metabolism (cytochrome P450-mediated) were responsible of tribenuron-methyl resistance. For 2,4-D, reduced transport was observed in both populations, while cytochrome P450-mediated metabolism was also present in R1 population. Moreover, this is the first P. rhoeas population with enhanced tribenuron-methyl metabolism. This study reports the first case for P. rhoeas of the amino acid substitution Pro197Phe due to a double nucleotide change. This double mutation could cause reduced enzyme sensitivity to most ALS inhibitors according to protein modelling and ligand docking. In addition, this study reports a P. rhoeas population resistant to 2,4-D, apparently, with reduced transport as the sole resistance mechanism.This work has been supported by the Asociacion de Agroquimicos y Medio Ambiente, Spain. Joel Torra acknowledges support from the Spanish Ministry of Science, Innovation, and Universities (grant Ramon y Cajal RYC2018–023866-I) and by the Spanish State Research Agency, Spain (AEI) and the European Regional Development Fund, EU (ERDF) through the projects AGL2017-83325-C4-2-R and PID2020-113229RB- C42. The field surveys made in Portugal were supported by Foundation for Science and Technology through the project UIDB/05064/2020 (VALORIZA). Jorge Lozano-Juste group is funded by grants RYC2020- 029097-I and PID2021-128826OA-I00 from Ministerio de Ciencia e Innovaci ́on (MCIN, Spain), AEI and the ERDF

Pre-mRNA splicing repression triggers abiotic stress signaling in plants

[EN] Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work has shown that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various inhibitors of AS. Here, we show that the macrolide pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA sequencing (RNA-seq) data revealed that PB mimics abiotic stress signals including salt, drought and abscisic acid (ABA). PB activates the abiotic stress-and ABA-responsive reporters RD29A::LUC and MAPKKK18::uidA in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2C phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling and post-transcriptional regulation in plants.We wish to thank members of the Laboratory for Genome Engineering at King Abdullah University of Science and Technology for helpful discussions and comments on the manuscript. We wish to thank Moussa Benhamed for helpful discussions and suggestions and for providing key materials. We wish to thank Sean Cutler for providing Arabidopsis seeds of MAKPKKK18-uidA. This study was supported by King Abdullah University of Science and Technology. Work in PR's laboratory was funded by grant BIO2014-52537-R from MINECO. Work in PD's laboratory is funded by grant PTDC/BIA-PLA/1084/2014 from FCT. The authors declare no conflicts of interest.Ling, Y.; Alshareef, S.; Butt, H.; Lozano Juste, J.; Li, L.; Galal, AA.; Moustafa, A.... (2017). Pre-mRNA splicing repression triggers abiotic stress signaling in plants. The Plant Journal. 89(2):291-309. https://doi.org/10.1111/tpj.13383S29130989

Abscisic acid mimic-fluorine derivative 4 alleviates water deficit stress by regulating ABA-responsive genes, proline accumulation, CO2 assimilation, water use efficiency and better nutrient uptake in tomato plants

Water deficit represents a serious limitation for agriculture and both genetic and chemical approaches are being used to cope with this stress and maintain plant yield. Next-generation agrochemicals that control stomatal aperture are promising for controlling water use efficiency. For example, chemical control of abscisic acid (ABA) signaling through ABA-receptor agonists is a powerful method to activate plant adaptation to water deficit. Such agonists are molecules able to bind and activate ABA receptors and, although their development has experienced significant advances in the last decade, few translational studies have been performed in crops. Here, we describe protection by the ABA mimic-fluorine derivative 4 (AMF4) agonist of the vegetative growth in tomato plants subjected to water restriction. Photosynthesis in mock-treated plants is markedly impaired under water deficit conditions, whereas AMF4 treatment notably improves CO2 assimilation, the relative plant water content and growth. As expected for an antitranspirant molecule, AMF4 treatment diminishes stomatal conductance and transpiration in the first phase of the experiment; however, when photosynthesis declines in mock-treated plants as stress persists, higher photosynthetic and transpiration parameters are recorded in agonist-treated plants. Additionally, AMF4 increases proline levels over those achieved in mock-treated plants in response to water deficit. Thus water deficit and AMF4 cooperate to upregulate P5CS1 through both ABA-independent and ABA-dependent pathways, and therefore, higher proline levels are produced Finally, analysis of macronutrients reveals higher levels of Ca, K and Mg in AMF4- compared to mock-treated plants subjected to water deficit. Overall, these physiological analyses reveal a protective effect of AMF4 over photosynthesis under water deficit and enhanced water use efficiency after agonist treatment. In summary, AMF4 treatment is a promising approach for farmers to protect the vegetative growth of tomatoes under water deficit stress

Structure-guided engineering of a receptor-agonist pair for inducible activation of the ABA adaptive response to drought

Strategies to activate abscisic acid (ABA) receptors and boost ABA signaling by small molecules that act as ABA receptor agonists are promising biotechnological tools to enhance plant drought tolerance. Protein structures of crop ABA receptors might require modifications to improve recognition of chemical ligands, which in turn can be optimized by structural information. Through structure-based targeted design, we have combined chemical and genetic approaches to generate an ABA receptor agonist molecule (iSB09) and engineer a CsPYL1 ABA receptor, named CsPYL15m, which efficiently binds iSB09. This optimized receptor-agonist pair leads to activation of ABA signaling and marked drought tolerance. No constitutive activation of ABA signaling and hence growth penalty was observed in transformed Arabidopsis thaliana plants. Therefore, conditional and efficient activation of ABA signaling was achieved through a chemical-genetic orthogonal approach based on iterative cycles of ligand and receptor optimization driven by the structure of ternary receptor-ligand-phosphatase complexes

Involvement of nitric oxide (NO) and auxin in signal transduction of copper induced morphological responses in Arabidopsis seedlings

Background and Aims Plants are able to adapt to the environment dynamically through regulation of their growth and development. Excess copper (Cu2+ ), a toxic heavy metal, induces morphological alterations in plant organs; however, the underlying mechanisms are still unclear. With this in mind, the multiple signalling functions of nitric oxide (NO) in plant cells and its possible regulatory role and relationship with auxin were examined during Cu2+ -induced morphological responses. Methods Endogenous auxin distribution was determined by microscopic observation of X-Gluc-stained DR5::GUS arabidopsis, and the levels of NO, superoxide and peroxynitrite were detected by ¿uorescence microscopy. As well as wild-type, NO-overproducer (nox1) and -de¿cient (nia1nia2 and nia1nia2noa1-2) arabidopsis plants were used. Key Results Cu2+ at a concentration of 50mM resulted in a large reduction in cotyledon area and hypocotyl and primary root lengths, accompanied by an increase in auxin levels. In cotyledons, a low Cu2+ concentration promoted NO accumulation, which was arrested by nitric oxide synthase or nitrate reductase inhibitors. The 5-mM Cu2+ -induced NO synthesis was not detectable in nia1nia2 or nia1nia2noa1-2 plants. In roots, Cu2+ caused a decrease of the NO level which was not associated with superoxide and peroxynitrite formation. Inhibition of auxin transport resulted in an increase in NO levels, while exogenous application of an NO donor reduced DR5::GUS expression. The elongation processes of nox1 were not sensitive to Cu2+ , but NO-de¿cient plants showed diverse growth responses. ConclusionsIn plant organs, Cu2+ excess results in severe morphological responses during which the endogenous hormonal balance and signal transduction are affected. Auxin and NO negatively regulate each other¿s level and NO intensi¿es the metal-induced cotyledon expansion, but mitigates elongation processes under Cu2+ exposurePetó, A.; Lehotai, N.; Lozano Juste, J.; Leon Ramos, J.; Tari, I.; Erdei, L.; Kolbert, Z. (2011). Involvement of nitric oxide (NO) and auxin in signal transduction of copper induced morphological responses in Arabidopsis seedlings. Annals of Botany. 108(3):449-457. doi:10.1093/aob/mcr176S449457108

Pre-mRNA splicing repression triggers abiotic stress signaling in plants

Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work showed that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various AS inhibitors. Here, we show that the macrolide Pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA-seq data revealed that PB mimics abiotic stress signals including salt, drought, and abscisic acid (ABA). PB activates the abiotic stress- and ABA-responsive reporters RD29A::LUC and MAPKKK18::GUS in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2Cs phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling, and post-transcriptional regulation in plants.</p

PYL8 mediates ABA perception in the root through non-cell-autonomous and ligand-stabilization-based mechanisms

[EN] The phytohormone abscisic acid (ABA) plays a key role regulating root growth, root system architecture, and root adaptive responses, such as hydrotropism. The molecular and cellular mechanisms that regulate the action of core ABA signaling components in roots are not fully understood. ABA is perceived through receptors from the PYR/PYL/RCAR family and PP2C coreceptors. PYL8/RCAR3 plays a nonredundant role in regulating primary and lateral root growth. Here we demonstrate that ABA specifically stabilizes PYL8 compared with other ABA receptors and induces accumulation of PYL8 in root nuclei. This requires ABA perception by PYL8 and leads to diminished ubiquitination of PYL8 in roots. The ABA agonist quinabactin, which promotes root ABA signaling through dimeric receptors, fails to stabilize the monomeric receptor PYL8. Moreover, a PYL8 mutant unable to bind ABA and inhibit PP2C is not stabilized by the ligand, whereas a PYL85KR mutant is more stable than PYL8 at endogenous ABA concentrations. The PYL8 transcript was detected in the epidermis and stele of the root meristem; however, the PYL8 protein was also detected in adjacent tissues. Expression of PYL8 driven by tissue-specific promoters revealed movement to adjacent tissues. Hence both inter- and intracellular trafficking of PYL8 appears to occur in the root apical meristem. Our findings reveal a non-cell-autonomous mechanism for hormone receptors and help explain the nonredundant role of PYL8-mediated root ABA signaling.Work in the P.L.R. and F.M. laboratories was supported by the Ministerio de Ciencia e Innovacion, Fondo Europeo de Desarrollo Regional and Consejo Superior de Investigaciones Cientificas Grants BIO2014-52537-R and BIO2017-82503-R (to P.L.R.) and BIO2015-64307-R (to F.M.). J.L.-J. was supported by a Juan de la Cierva contract from Ministerio de Economia y Competitividad (MINECO) and by the Marie Sklodowska-Curie Action H2020-MSCA-IF-2015-707477. B.B.-P. was funded by Programa VALi+d GVA APOSTD/2017/039. J.J. was supported by a FPI contract from MINECO and M.A.F. by a Formacion de Profesorado Universitario contract from MINECO. D.D. and M.J.B. were supported by Biotechnology and Biological Sciences Research Council Grant BB/M002136/1 and Leverhulme Trust Grant RPG-2016-409.Belda-Palazón, B.; Gonzalez-Garcia, M.; Lozano Juste, J.; Coego Gonzalez, A.; Antoni-Alandes, R.; Julian-Valenzuela, J.; Peirats-Llobet, M.... (2018). PYL8 mediates ABA perception in the root through non-cell-autonomous and ligand-stabilization-based mechanisms. Proceedings of the National Academy of Sciences of the United States of America (Online). 115(50):E11857-E11863. https://doi.org/10.1073/pnas.1815410115SE11857E1186311550Ubeda-Tomás, S., Beemster, G. T. S., & Bennett, M. J. (2012). Hormonal regulation of root growth: integrating local activities into global behaviour. Trends in Plant Science, 17(6), 326-331. doi:10.1016/j.tplants.2012.02.002Bao, Y., Aggarwal, P., Robbins, N. E., Sturrock, C. J., Thompson, M. C., Tan, H. Q., … Dinneny, J. R. (2014). Plant roots use a patterning mechanism to position lateral root branches toward available water. Proceedings of the National Academy of Sciences, 111(25), 9319-9324. doi:10.1073/pnas.1400966111Dietrich, D., Pang, L., Kobayashi, A., Fozard, J. A., Boudolf, V., Bhosale, R., … Bennett, M. J. (2017). Root hydrotropism is controlled via a cortex-specific growth mechanism. Nature Plants, 3(6). doi:10.1038/nplants.2017.57Harris, J. (2015). Abscisic Acid: Hidden Architect of Root System Structure. Plants, 4(3), 548-572. doi:10.3390/plants4030548Spollen, W. G., LeNoble, M. E., Samuels, T. D., Bernstein, N., & Sharp, R. E. (2000). Abscisic Acid Accumulation Maintains Maize Primary Root Elongation at Low Water Potentials by Restricting Ethylene Production. Plant Physiology, 122(3), 967-976. doi:10.1104/pp.122.3.967Sharp, R. E. (2004). Root growth maintenance during water deficits: physiology to functional genomics. Journal of Experimental Botany, 55(407), 2343-2351. doi:10.1093/jxb/erh276Deak, K. I., & Malamy, J. (2005). Osmotic regulation of root system architecture. The Plant Journal, 43(1), 17-28. doi:10.1111/j.1365-313x.2005.02425.xGonzalez-Guzman, M., Pizzio, G. A., Antoni, R., Vera-Sirera, F., Merilo, E., Bassel, G. W., … Rodriguez, P. L. (2012). Arabidopsis PYR/PYL/RCAR Receptors Play a Major Role in Quantitative Regulation of Stomatal Aperture and Transcriptional Response to Abscisic Acid. The Plant Cell, 24(6), 2483-2496. doi:10.1105/tpc.112.098574Duan, L., Dietrich, D., Ng, C. H., Chan, P. M. Y., Bhalerao, R., Bennett, M. J., & Dinneny, J. R. (2013). Endodermal ABA Signaling Promotes Lateral Root Quiescence during Salt Stress in Arabidopsis Seedlings. The Plant Cell, 25(1), 324-341. doi:10.1105/tpc.112.107227Feng, W., Lindner, H., Robbins, N. E., & Dinneny, J. R. (2016). Growing Out of Stress: The Role of Cell- and Organ-Scale Growth Control in Plant Water-Stress Responses. The Plant Cell, 28(8), 1769-1782. doi:10.1105/tpc.16.00182Geng, Y., Wu, R., Wee, C. W., Xie, F., Wei, X., Chan, P. M. Y., … Dinneny, J. R. (2013). A Spatio-Temporal Understanding of Growth Regulation during the Salt Stress Response in Arabidopsis. The Plant Cell, 25(6), 2132-2154. doi:10.1105/tpc.113.112896Takahashi, N., Goto, N., Okada, K., & Takahashi, H. (2002). Hydrotropism in abscisic acid, wavy, and gravitropic mutants of Arabidopsis thaliana. Planta, 216(2), 203-211. doi:10.1007/s00425-002-0840-3Antoni, R., Gonzalez-Guzman, M., Rodriguez, L., Peirats-Llobet, M., Pizzio, G. A., Fernandez, M. A., … Rodriguez, P. L. (2012). PYRABACTIN RESISTANCE1-LIKE8 Plays an Important Role for the Regulation of Abscisic Acid Signaling in Root. Plant Physiology, 161(2), 931-941. doi:10.1104/pp.112.208678Barberon, M., Vermeer, J. E. M., De Bellis, D., Wang, P., Naseer, S., Andersen, T. G., … Geldner, N. (2016). Adaptation of Root Function by Nutrient-Induced Plasticity of Endodermal Differentiation. Cell, 164(3), 447-459. doi:10.1016/j.cell.2015.12.021Ondzighi-Assoume, C. A., Chakraborty, S., & Harris, J. M. (2016). Environmental Nitrate Stimulates Abscisic Acid Accumulation in Arabidopsis Root Tips by Releasing It from Inactive Stores. The Plant Cell, 28(3), 729-745. doi:10.1105/tpc.15.00946Irigoyen, M. L., Iniesto, E., Rodriguez, L., Puga, M. I., Yanagawa, Y., Pick, E., … Rubio, V. (2014). Targeted Degradation of Abscisic Acid Receptors Is Mediated by the Ubiquitin Ligase Substrate Adaptor DDA1 in Arabidopsis. The Plant Cell, 26(2), 712-728. doi:10.1105/tpc.113.122234Bueso, E., Rodriguez, L., Lorenzo-Orts, L., Gonzalez-Guzman, M., Sayas, E., Muñoz-Bertomeu, J., … Rodriguez, P. L. (2014). The single-subunit RING-type E3 ubiquitin ligase RSL1 targets PYL4 and PYR1 ABA receptors in plasma membrane to modulate abscisic acid signaling. The Plant Journal, 80(6), 1057-1071. doi:10.1111/tpj.12708Knoblich, J. A. (2005). Pins for spines. Nature Cell Biology, 7(12), 1057-1058. doi:10.1038/ncb1205-1057Zhang, H., Han, W., De Smet, I., Talboys, P., Loya, R., Hassan, A., … Wang, M.-H. (2010). ABA promotes quiescence of the quiescent centre and suppresses stem cell differentiation in the Arabidopsis primary root meristem. The Plant Journal, 64(5), 764-774. doi:10.1111/j.1365-313x.2010.04367.xBelda-Palazon, B., Rodriguez, L., Fernandez, M. A., Castillo, M.-C., Anderson, E. M., Gao, C., … Rodriguez, P. L. (2016). FYVE1/FREE1 Interacts with the PYL4 ABA Receptor and Mediates Its Delivery to the Vacuolar Degradation Pathway. The Plant Cell, 28(9), 2291-2311. doi:10.1105/tpc.16.00178Yu, F., Lou, L., Tian, M., Li, Q., Ding, Y., Cao, X., … Xie, Q. (2016). ESCRT-I Component VPS23A Affects ABA Signaling by Recognizing ABA Receptors for Endosomal Degradation. Molecular Plant, 9(12), 1570-1582. doi:10.1016/j.molp.2016.11.002Santiago, J., Rodrigues, A., Saez, A., Rubio, S., Antoni, R., Dupeux, F., … Rodriguez, P. L. (2009). Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs. The Plant Journal, 60(4), 575-588. doi:10.1111/j.1365-313x.2009.03981.xSzostkiewicz, I., Richter, K., Kepka, M., Demmel, S., Ma, Y., Korte, A., … Grill, E. (2010). Closely related receptor complexes differ in their ABA selectivity and sensitivity. The Plant Journal, 61(1), 25-35. doi:10.1111/j.1365-313x.2009.04025.xOkamoto, M., Peterson, F. C., Defries, A., Park, S.-Y., Endo, A., Nambara, E., … Cutler, S. R. (2013). Activation of dimeric ABA receptors elicits guard cell closure, ABA-regulated gene expression, and drought tolerance. Proceedings of the National Academy of Sciences, 110(29), 12132-12137. doi:10.1073/pnas.1305919110Cao, M., Liu, X., Zhang, Y., Xue, X., Zhou, X. E., Melcher, K., … Xu, Y. (2013). An ABA-mimicking ligand that reduces water loss and promotes drought resistance in plants. Cell Research, 23(8), 1043-1054. doi:10.1038/cr.2013.95Castillo, M.-C., Lozano-Juste, J., González-Guzmán, M., Rodriguez, L., Rodriguez, P. L., & León, J. (2015). Inactivation of PYR/PYL/RCAR ABA receptors by tyrosine nitration may enable rapid inhibition of ABA signaling by nitric oxide in plants. Science Signaling, 8(392), ra89-ra89. doi:10.1126/scisignal.aaa7981Wu, S., & Gallagher, K. L. (2014). The movement of the non-cell-autonomous transcription factor, SHORT-ROOT relies on the endomembrane system. 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Chemical Genetics Reveals Negative Regulation of Abscisic Acid Signaling by a Plant Immune Response Pathway. Current Biology, 21(11), 990-997. doi:10.1016/j.cub.2011.04.045Waadt, R., Hitomi, K., Nishimura, N., Hitomi, C., Adams, S. R., Getzoff, E. D., & Schroeder, J. I. (2014). FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis. eLife, 3. doi:10.7554/elife.01739Jones, A. M., Danielson, J. Å., ManojKumar, S. N., Lanquar, V., Grossmann, G., & Frommer, W. B. (2014). Abscisic acid dynamics in roots detected with genetically encoded FRET sensors. eLife, 3. doi:10.7554/elife.01741Zhao, Y., Xing, L., Wang, X., Hou, Y.-J., Gao, J., Wang, P., … Zhu, J.-K. (2014). The ABA Receptor PYL8 Promotes Lateral Root Growth by Enhancing MYB77-Dependent Transcription of Auxin-Responsive Genes. Science Signaling, 7(328), ra53-ra53. doi:10.1126/scisignal.2005051Peirats-Llobet, M., Han, S.-K., Gonzalez-Guzman, M., Jeong, C. 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In vivo protein tyrosine nitration in Arabidopsis thaliana

Nitration of tyrosine (Y) residues of proteins is a low abundant post-translational modification that modulates protein function or fate in animal systems. However, very little is known about the in vivo prevalence of this modification and its corresponding targets in plants. Immunoprecipitation, based on an anti-3-nitroY antibody, was performed to pull-down potential in vivo targets of Y nitration in the Arabidopsis thaliana proteome. Further shotgun liquid chromatography–mass spectrometry (LC-MS/MS) proteomic analysis of the immunoprecipitated proteins allowed the identification of 127 proteins. Around 35% of them corresponded to homologues of proteins that have been previously reported to be Y nitrated in other non-plant organisms. Some of the putative in vivo Y-nitrated proteins were further confirmed by western blot with specific antibodies. Furthermore, MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) analysis of protein spots, separated by two-dimensional electrophoresis from immunoprecipitated proteins, led to the identification of seven nitrated peptides corresponding to six different proteins. However, in vivo nitration sites among putative targets could not be identified by MS/MS. Nevertheless, an MS/MS spectrum with 3-aminoY318 instead of the expected 3-nitroY was found for cytosolic glyceraldehyde-3-phosphate dehydrogenase. Reduction of nitroY to aminoY during MS-based proteomic analysis together with the in vivo low abundance of these modifications made the identification of nitration sites difficult. In turn, in vitro nitration of methionine synthase, which was also found in the shotgun proteomic screening, allowed unequivocal identification of a nitration site at Y287