An in silico mining of the ammonium transporter gene family in Ananas comosus L.
Keywords:
Bioinformatic analysis; pineapple; ammonium; nitrogen transport.Abstract
Arguably, the nitrogen (N) is an important and essential component for plant growth and development. Among the sources of N available, the ammonium is a major inorganic nitrogen source for plants is mobilized by ammonium transporter (AMT). In this study, data mining revealed that the Ananas comosus L. genome was identified eight genes of the AMT family. Based on this information, we conducted a comprehensive analysis using some bioinformatics tools in order to individually characterize the identified genes. The comprehensive analysis of AMT will provide an important foundation for further investigation of the regulatory mechanisms of AcoAMTs in A. comosus L.
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ALI, H.; LIU, Y.; AZAM, S.M.; PRIYADARSHANI, S.V.G.N.; LI, W., HUANG, X.; HU, B.; XIONG, J.; ALI, U.; QIN, Y. Genomic survey, characterization, and expression profile analysis of the SBP genes in pineapple (Ananas comosus L.). Int J Genom., p. 1–14, 2017. https://doi.org/10.1155/2017/1032846.
ALTSCHUL, S.F.; GISH, W.; MILLER, W.; MYERS, E.W.; LIPMAN, D.J. Basic local alignment search tool. Journal of Molecular Biology, v. 215, n. 3, p. 403-410, 1990. https://doi.org/10.1016/S0022-2836(05)80360-2.
BOWERS, J.E.; CHAPMAN, B.A.; RONG, J.; PATERSON, A.H. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature, v. 422, p. 433–438, 2003.
BLAKEY, D.; LEECH, A.; THOMAS, G.H.; COUTTS, G.; FINDLAY, K.; MERRICK, M. Purification of the Escherichia coli ammonium transporter AmtB reveals a trimeric stoichiometry. Biochemical Journal, v. 364, n. 2, p. 527-535, 2002. https://doi.org /10.1042/BJ20011761.
BLOOM, A.J. The increasing importance of distinguishing among plant nitrogen sources. Current Opinion in Plant Biology., v. 25, p. 10– 16, 2015. https://doi.org/10.1016/j.pbi.2015.03.002.
CASTRO-RODRÍGUEZ, V.; ASSAF-CASALS, I.; PÉREZ-TIENDA, J.; FAN, X.; ÁVILA, C.; MILLER, A.J.; CÁNOVAS, F.M. Deciphering the molecular basis of ammonium uptake and transport in maritime pine. Plant Cell Environ., v. 39, p. 1669–1682, 2016. https://doi.org/10.1111/pce.12692.
CAO, J.; SHI, F. Dynamics of arginase gene evolution in metazoans. J. Biomol. Struct. Dyn., v. 30, p. 407–418, 2012. https://doi.org/10.1080/07391102.2012.682207.
CONANT, G.C.; WOLFE, K.H. Turning a hobby into a job: Howduplicated genes find new functions. Nat. Rev. Genet. v. 9, p. 938–950, 2008.
CHOU, H.C.; SHEN, H.G. Plant-mPLoc: a top-down strategy to augment the power for predicting plant protein subcellular localization. PLoS ONE, v. 5, 2010. https://doi.org/10.1371/journal.pone.0011335.
DOS SANTOS, T.B.; LIMA, J.E.; FELICIO, M.S.; SOARES, J.D.M.; DOMINGUES, D.S. Genome- wide identification, classification and transcriptional analysis of nitrate and ammonium transporters in Coffea. Genet. Mol. Biol., v. 40, p. 346–359, 2017. https://doi.org/10.1590/1678-4685-gmb-2016-0041.
DUAN, J.; TIAN, H.; GAO, Y. Expression of nitrogen transporter genes in roots of winter wheat (Triticum aestivum L.) in response to soil drought with contrasting nitrogen supplies. Crop Pasture Sci., v. 67, n. 2, p. 128–136, 2016. https://doi.org/10.1071/CP15152.
FERREIRA, L. M.; DE SOUZA, V.M.; TAVARES, O.C.H.; ZONTA, E.; SANTA-CATARINA, C.; DE SOUZA, S. R., FERNANDES, M.S.; SANTOS, L. OsAMT1. 3 expression alters rice ammonium uptake kinetics and root morphology. Plant Biotechnology Reports, v. 9, n. 4, p. 221-229, 2015. https://doi.org/ 10.1007/s11816-015-0359-2.
FAN, X.; NAZ, M.; FAN, X.; XUAN, W.; MILLER, A.J.; XU, X. Plant nitrate transporters: from gene function to application. Journal of Experimental Botany, v. 68, p. 2463– 2475, 2017. https://doi.org/10.1093/jxb/erx011.
FILIZ, E.; AKBUDAK, M.A. Ammonium transporter 1 (AMT1) gene family in tomato (Solanum lycopersicum L.): Bioinformatics, physiological and expression analyses under drought and salt stresses. Genomics, 2020. https://doi.org/10.1016/j.ygeno.2020.04.009.
GASTEIGER, E.; GATTIKER, A.; HOOGLAND, C.; IVANYI, I.; APPEL, R.D.; BAIROCH, A. ExPASy—the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res, v. 31, p. 3784–3788, 2003. https://doi.org/10.1093/nar/gkg563.
GOODSTEIN, D.M.; SHU, S.; HOWSON, R.; NEUPANE, R.; HAYES, R.D.; FAZO, J.; ROKHSAR, D.S. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, v. 40, n. D1, p. 1178-1186, 2012. https://doi.org/10.1093/nar/gkr944.
GU, R.; DUAN, F.; AN, X.; ZHANG, F.; VON WIRÉN, N.; YUAN, L. Characterization of AMT-mediated high-affinity ammonium uptake in roots of maize (Zea mays L.). Plant Cell Physiol., v. 54, p. 1515–1524, 2013. https://doi.org/10.1093/pcp/pct099.
GUETHER, M.; NEUHÄUSER, B.; BALESTRINI, R.; DYNOWSKI, M.; LUDEWIG, U.; BONFANTE, P. A mycorrhizal-specific ammonium transporter from Lotus japonicus acquires nitrogen released by arbuscular mycorrhizal fungi. Plant Physiology, v. 150, n. 1, p. 73-83, 2009. https://doi.org/10.1104/pp.109.136390.
HAO, D.L.; ZHOU, J.Y.; YANG, S.Y.; QI, W.; YANG, K.J.; SU, Y.H. Function and Regulation of Ammonium Transporters in Plants. International Journal of Molecular Sciences, v. 21, n. 10, p. 3557, 2020. https://doi.org/10.3390/ijms21103557.
HU, B.; JIN, J.; GUO, A.Y.; ZHANG, H.; LUO, J.; GAO, G. 2015. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, v. 31, n. 8, p. 1296–1297, 2015. https://doi.org/10.1093/bioinformatics/btu817.
HUANG, L.; ZHANG, H.; ZHANG, H.; DENG, X.W.; WEI, N. HY5 regulates nitrite reductase 1 (NIR1) and ammonium transporter1; 2 (AMT1; 2) in Arabidopsis seedlings. Plant Science, v. 238, p. 330-339, 2015. https://doi.org/10.1016/j.plantsci.2015.05.004.
KROGH, A.; LARSSON, B.; VON HEIJNE, G.; SONNHAMMER, E.L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol., v. 305, p. 567-580, 2001. https://doi.org/10.1006/jmbi.2000.4315.
KRZYWINSKI, M.; SCHEIN, J.; BIROL, I.; CONNORS, J.; GASCOYNE, R.; HORSMAN, D., JONES, S.J.; MARRA, M.A. Circos: an information aesthetic for comparative genomics. Genome Research, v. 19, n. 9, p. 1639-1645, 2009. https://doi.org/10.1101/gr.092759.109.
KUMAR, S.; STECHER, G.; TAMURA, K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, v. 33, n. 7, p. 1870-1874, 2016. https://doi.org/10.1093/molbev/msw054.
LOQUÉ, D.; VON WIRÉN, N. Regulatory levels for the transport of ammonium in plant roots. Journal of Experimental Botany, v. 55, p. 1293– 1305, 2004. https://doi.org/10.1093/jxb/erh147.
LUDEWIG, U.; NEUHÄUSER, B.; DYNOWSKI, M. Molecular mechanisms of ammonium transport and accumulation in plants. FEBS Lett., v. 581, p. 2301–2308, 2007. https://doi.org/10.1016/j.febslet.2007.03.034.
LUDEWIG, U.; WILKEN, S.; WU, B.; JOST, W.; OBRDLIK, P.; EL BAKKOURY, M.; MARINI, A.M.; ANDRÉ, B.; HAMACHER, T.; BOLES, E.; VON WIRÉN, N. Homo-and hetero-oligomerization of ammonium transporter-1 uniporters. Journal of Biological Chemistry, v. 278, n. 46, p. 45603-45610, 2003. https://doi.org// 10.1074/jbc.M307424200.
MARINI, A.M.; SOUSSI-BOUDEKOU, S.; VISSERS, S.D.; ANDRÉ, B. A family of ammonium transporters in Saccharomyces cerevisiae. Mol. Cell. Boil., v. 17, p. 4282–4293, 1997. https://doi.org//doi: 10.1128/MCB.17.8.4282.
MASCLAUX-DAUBRESSE, C.; DANIEL-VEDELE, F.; DECHORGNAT, J.; CHARDON, F.; GAUFICHON, L.; SUZUKI, A. Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture. Ann. Bot., V. 105, p. 1141–1157, 2010. https://doi.org/10.1093/aob/mcq028.
McDONALD, T.R.; WARD, J.M. Evolution of Electrogenic Ammonium Transporters (AMTs). Front. Plant Sci., v. 7, p. 352, 2016. https://doi.org/10.3389/fpls.2016.00352.
MING, R.; VANBUREN, R.; WAI, C.M.; TANG, H.; SCHATZ, M.C.; BOWERS, J.E.; LYONS, E.; WANG, M.L.; CHEN, J.; BIGGERS, E. The pineapple genome and the evolution of CAM photosynthesis. Nat. Genet., v. 47, n. 12, p. 1435–42, 2015. https://doi.org doi:10.1038/ng.3435.
NACRY, P.; BOUGUYON, E.; GOJON, A. Nitrogen acquisition by roots: physiological and developmental mechanisms ensuring plant adaptation to a fluctuating resource. Plant and Soil, v. 370, p. 1– 29, 2013. https://doi.org//10.1007/s11104-013-1645-9.
NINNEMANN, O.; JAUNIAUX J.C.; FROMMER, W.B. Identification of a High Affinity NH4+ Transporter from Plants. The EMBO Journal, v. 13, n. 15, p. 3464–71, 1994. https://doi.org/10.1002/j.1460-2075.1994.tb06652.x.
SIMON-ROSIN, U.; WOOD, C.; UDVARDI, M.K. Molecular and cellular characterisation of LjAMT2;1, an ammonium transporter from the model legume Lotus japonicus. Plant Mol. Biol., v. 51, p. 99–108, 2003.
SUN, Y.; SHENG, S.; FAN, T.; LIU, L.; KE, J.; WANG, D.; HUA, J.; LIU, L.; CAO, F. Molecular identification and functional characterization of GhAMT1.3 in ammonium transport with a high affinity from cotton (Gossypium hirsutum L.). Physiol. Plantarum, v. 167, p. 217–231, 2018. https://doi.org/10.1111/ppl.12882.
TEGEDER, M.; MASCLAUX-DAUBRESSE, C. Source and sink mechanisms of nitrogen transport and use. New Phytol., v. 217, p. 5–53, 2018. https://doi.org/10.1111/nph.14876.
VON WITTGENSTEIN, N. J.; LE, C. H.; HAWKINS, B. J.; EHLTING, J. Evolutionary classification of ammonium, nitrate, and peptide transporters in land plants. BMC Evolutionary Biology, v. 14, n. 1, p. 1-17, 2014.
VON WIRÉN, N.; MERRICK, M. Regulation and function of ammonium carriers in bacteria, fungi, and plants. In Molecular Mechanisms Controlling Transmembrane Transport, Springer: Berlin/Heidelberg, Germany, pp. 95–120, 2004. https://doi.org//doi:10.1007/b95775.
VOORRIPS, R. E. MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, v. 93, n. 1, p. 77-78, 2002. https://doi.org/10.1093/jhered/93.1.77.
XIE, T.; CHEN, C.; LI, C.; LIU, J.; LIU, C.; HE, Y. Genome-wide investigation of WRKY gene family in pineapple: evolution and expression profiles during development and stress. BMC Genomics, v. 19, n. 1, p. 490, 2018. https://doi.org/ 10.1186/s12864-018-4880-x.
XU, G.; FAN, X.; MILLER, A.J. Plant nitrogen assimilation and use efficiency. Annu Rev Plant Biol, v. 63, p. 153–182. 2012. https://doi.org/10.1146/annurev-arplant-042811-105532.
YUAN, L.; LOQUÉ, D.; KOJIMA, S.; RAUCH, S.; ISHIYAMA, K.; INOUE, E.; TAKAHASHI, H.; VON WIRÉN N. The organization of high-affinity ammonium uptake in Arabidopsis roots depends on the spatial arrangement and biochemical properties of AMT1-type transporters. The Plant Cell, v.19, p. 2636–2652, 2007. https://doi.org/10.1105/tpc.107.052134.
ZHANG, Z.; LI, J.; ZHAO, X. Q.; WANG, J.; WONG, G. K. S.; YU, J. KaKs_Calculator: calculating Ka and Ks through model selection and model averaging. Genomics, Proteomics & Bioinformatics, v. 4, n. 4, p. 259-263, 2006. https://doi.org/10.1016/S1672-0229(07)60007-2.
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