Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data

Iminosugar inhibitors of carbohydrate-active enzymes that underpin cereal grain germination and endosperm metabolism

Starch is a major energy store in plants. It provides most of the calories in the human diet and, as a bulk commodity, it is used across broad industry sectors. Starch synthesis and degradation are not fully understood, owing to challenging biochemistry at the liquid/solid interface and relatively limited knowledge about the nature and control of starch degradation in plants. Increased societal and commercial demand for enhanced yield and quality in starch crops requires a better understanding of starch metabolism as a whole. Here we review recent advances in understanding the roles of carbohydrate-active enzymes in starch degradation in cereal grains through complementary chemical and molecular genetics. These approaches have allowed us to start dissecting aspects of starch degradation and the interplay with cell-wall polysaccharide hydrolysis during germination. With a view to improving and diversifying the properties and uses of cereal grains, it is possible that starch degradation may be amenable to manipulation through genetic or chemical intervention at the level of cell wall metabolism, rather than simply in the starch degradation pathway per se

Characterization of tomato Cycling Dof Factors reveals conserved and new functions in the control of flowering time and abiotic stress responses

[EN] DNA binding with One Finger (DOF) transcription factors are involved in multiple aspects of plant growth and development but their precise roles in abiotic stress tolerance are largely unknown. Here we report a group of five tomato DOF genes, homologous to Arabidopsis Cycling DOF Factors (CDFs), that function as transcriptional regulators involved in responses to drought and salt stress and flowering-time control in a gene-specific manner. SlCDF15 are nuclear proteins that display specific binding with different affinities to canonical DNA target sequences and present diverse transcriptional activation capacities in vivo. SlCDF15 genes exhibited distinct diurnal expression patterns and were differentially induced in response to osmotic, salt, heat, and low-temperature stresses. Arabidopsis plants overexpressing SlCDF1 or SlCDF3 showed increased drought and salt tolerance. In addition, the expression of various stress-responsive genes, such as COR15, RD29A, and RD10, were differentially activated in the overexpressing lines. Interestingly, overexpression in Arabidopsis of SlCDF3 but not SlCDF1 promotes late flowering through modulation of the expression of flowering control genes such as CO and FT. Overall, our data connect SlCDFs to undescribed functions related to abiotic stress tolerance and flowering time through the regulation of specific target genes and an increase in particular metabolites.This work was supported by grants from Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA; project numbers: 2009-0004-C01, 2012-0008-C01), the Spanish Ministry of Science and Innovation (project number: BIO2010-14871), and the MERIT Project (FP7 ITN2010-264474). ARC was supported by a pre-doctoral fellowship from the INIA. The authors would like to thank Mar Gonzalez and Victor Carrasco for technical assistance and Dr Pablo Gonzalez-Melendi for technical handling of the confocal microscope. We also thank Eugenio Grau for technical assistance with RT-PCR analyses.Corrales, A.; González Nebauer, S.; Carrillo, L.; Fernández Nohales, P.; Marques Signes, J.; Renau Morata, B.; Granell, A.... (2014). Characterization of tomato Cycling Dof Factors reveals conserved and new functions in the control of flowering time and abiotic stress responses. Journal of Experimental Botany. 65(4):995-1012. https://doi.org/10.1093/jxb/ert451S9951012654AbuQamar, S., Luo, H., Laluk, K., Mickelbart, M. V., & Mengiste, T. (2009). Crosstalk between biotic and abiotic stress responses in tomato is mediated by theAIM1transcription factor. The Plant Journal, 58(2), 347-360. doi:10.1111/j.1365-313x.2008.03783.xAlonso, R., Oñate-Sánchez, L., Weltmeier, F., Ehlert, A., Diaz, I., Dietrich, K., … Dröge-Laser, W. (2009). A Pivotal Role of the Basic Leucine Zipper Transcription Factor bZIP53 in the Regulation of Arabidopsis Seed Maturation Gene Expression Based on Heterodimerization and Protein Complex Formation. The Plant Cell, 21(6), 1747-1761. doi:10.1105/tpc.108.062968Altschul, S. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25(17), 3389-3402. doi:10.1093/nar/25.17.3389An, H. (2004). CONSTANS acts in the phloem to regulate a systemic signal that induces photoperiodic flowering of Arabidopsis. Development, 131(15), 3615-3626. doi:10.1242/dev.01231Artimo, P., Jonnalagedda, M., Arnold, K., Baratin, D., Csardi, G., de Castro, E., … Stockinger, H. (2012). ExPASy: SIB bioinformatics resource portal. Nucleic Acids Research, 40(W1), W597-W603. doi:10.1093/nar/gks400Atherton, J. G., & Harris, G. P. (1986). Flowering. The Tomato Crop, 167-200. doi:10.1007/978-94-009-3137-4_4Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., … Noble, W. S. (2009). MEME SUITE: tools for motif discovery and searching. Nucleic Acids Research, 37(Web Server), W202-W208. doi:10.1093/nar/gkp335Ben-Naim, O., Eshed, R., Parnis, A., Teper-Bamnolker, P., Shalit, A., Coupland, G., … Lifschitz, E. (2006). The CCAAT binding factor can mediate interactions between CONSTANS-like proteins and DNA. The Plant Journal, 46(3), 462-476. doi:10.1111/j.1365-313x.2006.02706.xBEUVE, N., RISPAIL, N., LAINE, P., CLIQUET, J.-B., OURRY, A., & LE DEUNFF, E. (2004). Putative role of gamma -aminobutyric acid (GABA) as a long-distance signal in up-regulation of nitrate uptake in Brassica napus L. Plant, Cell and Environment, 27(8), 1035-1046. doi:10.1111/j.1365-3040.2004.01208.xBlumwald, E. (2000). Sodium transport and salt tolerance in plants. Current Opinion in Cell Biology, 12(4), 431-434. doi:10.1016/s0955-0674(00)00112-5Bombarely, A., Menda, N., Tecle, I. Y., Buels, R. M., Strickler, S., Fischer-York, T., … Mueller, L. A. (2010). The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Research, 39(Database), D1149-D1155. doi:10.1093/nar/gkq866Bressan, R., Bohnert, H., & Zhu, J.-K. (2009). Abiotic Stress Tolerance: From Gene Discovery in Model Organisms to Crop Improvement. Molecular Plant, 2(1), 1-2. doi:10.1093/mp/ssn097Calvert, A. (1959). Effect of the Early Environment on the Development of Flowering in Tomato II. Light and Temperature Interactions. Journal of Horticultural Science, 34(3), 154-162. doi:10.1080/00221589.1959.11513954Carmel-Goren, L., Liu, Y. S., Lifschitz, E., & Zamir, D. (2003). TheSELF-PRUNINGgene family in tomato. Plant Molecular Biology, 52(6), 1215-1222. doi:10.1023/b:plan.0000004333.96451.11Chaves, M. M., Flexas, J., & Pinheiro, C. (2008). Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Annals of Botany, 103(4), 551-560. doi:10.1093/aob/mcn125Claussen, W. (2005). Proline as a measure of stress in tomato plants. Plant Science, 168(1), 241-248. doi:10.1016/j.plantsci.2004.07.039Clough, S. J., & Bent, A. F. (1998). Floral dip: a simplified method forAgrobacterium-mediated transformation ofArabidopsis thaliana. The Plant Journal, 16(6), 735-743. doi:10.1046/j.1365-313x.1998.00343.xCuartero, J., & Fernández-Muñoz, R. (1998). Tomato and salinity. Scientia Horticulturae, 78(1-4), 83-125. doi:10.1016/s0304-4238(98)00191-5Czechowski, T., Stitt, M., Altmann, T., Udvardi, M. K., & Scheible, W.-R. (2005). Genome-Wide Identification and Testing of Superior Reference Genes for Transcript Normalization in Arabidopsis. Plant Physiology, 139(1), 5-17. doi:10.1104/pp.105.063743Diaz, I., Vicente-Carbajosa, J., Abraham, Z., Martinez, M., Isabel-La Moneda, I., & Carbonero, P. (2002). The GAMYB protein from barley interacts with the DOF transcription factor BPBF and activates endosperm-specific genes during seed development. The Plant Journal, 29(4), 453-464. doi:10.1046/j.0960-7412.2001.01230.xDieleman, J. A., & Heuvelink, E. (1992). Factors affecting the number of leaves preceding the first inflorescence in the tomato. Journal of Horticultural Science, 67(1), 1-10. doi:10.1080/00221589.1992.11516214Farrant, J. M., & Moore, J. P. (2011). Programming desiccation-tolerance: from plants to seeds to resurrection plants. Current Opinion in Plant Biology, 14(3), 340-345. doi:10.1016/j.pbi.2011.03.018Fiehn, O., Kopka, J., Trethewey, R. N., & Willmitzer, L. (2000). Identification of Uncommon Plant Metabolites Based on Calculation of Elemental Compositions Using Gas Chromatography and Quadrupole Mass Spectrometry. Analytical Chemistry, 72(15), 3573-3580. doi:10.1021/ac991142iFornara, F., Panigrahi, K. C. S., Gissot, L., Sauerbrunn, N., Rühl, M., Jarillo, J. A., & Coupland, G. (2009). Arabidopsis DOF Transcription Factors Act Redundantly to Reduce CONSTANS Expression and Are Essential for a Photoperiodic Flowering Response. Developmental Cell, 17(1), 75-86. doi:10.1016/j.devcel.2009.06.015Gaquerel, E., Heiling, S., Schoettner, M., Zurek, G., & Baldwin, I. T. (2010). Development and Validation of a Liquid Chromatography−Electrospray Ionization−Time-of-Flight Mass Spectrometry Method for Induced Changes inNicotiana attenuataLeaves during Simulated Herbivory. Journal of Agricultural and Food Chemistry, 58(17), 9418-9427. doi:10.1021/jf1017737Gardiner, J., Sherr, I., & Scarpella, E. (2010). Expression of DOF genes identifies early stages of vascular development in Arabidopsis leaves. The International Journal of Developmental Biology, 54(8-9), 1389-1396. doi:10.1387/ijdb.093006jgGong, P., Zhang, J., Li, H., Yang, C., Zhang, C., Zhang, X., … Ye, Z. (2010). Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato. Journal of Experimental Botany, 61(13), 3563-3575. doi:10.1093/jxb/erq167Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R. D., Fazo, J., … Rokhsar, D. S. (2011). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40(D1), D1178-D1186. doi:10.1093/nar/gkr944Gualberti, G., Papi, M., Bellucci, L., Ricci, I., Bouchez, D., Camilleri, C., … Vittorioso, P. (2002). Mutations in the Dof Zinc Finger Genes DAG2 and DAG1 Influence with Opposite Effects the Germination of Arabidopsis Seeds. The Plant Cell, 14(6), 1253-1263. doi:10.1105/tpc.010491Guindon, S., & Gascuel, O. (2003). A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood. Systematic Biology, 52(5), 696-704. doi:10.1080/10635150390235520Gullberg, J., Jonsson, P., Nordström, A., Sjöström, M., & Moritz, T. (2004). Design of experiments: an efficient strategy to identify factors influencing extraction and derivatization of Arabidopsis thaliana samples in metabolomic studies with gas chromatography/mass spectrometry. Analytical Biochemistry, 331(2), 283-295. doi:10.1016/j.ab.2004.04.037Guo, Y., Qin, G., Gu, H., & Qu, L.-J. (2009). Dof5.6/HCA2, a Dof Transcription Factor Gene, Regulates Interfascicular Cambium Formation and Vascular Tissue Development in Arabidopsis. The Plant Cell, 21(11), 3518-3534. doi:10.1105/tpc.108.064139Haupt-Herting, S., Klug, K., & Fock, H. P. (2001). A New Approach to Measure Gross CO2 Fluxes in Leaves. Gross CO2 Assimilation, Photorespiration, and Mitochondrial Respiration in the Light in Tomato under Drought Stress. Plant Physiology, 126(1), 388-396. doi:10.1104/pp.126.1.388Hernando-Amado, S., González-Calle, V., Carbonero, P., & Barrero-Sicilia, C. (2012). The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling. BMC Plant Biology, 12(1), 202. doi:10.1186/1471-2229-12-202Hoekstra, F. A., Golovina, E. A., & Buitink, J. (2001). Mechanisms of plant desiccation tolerance. Trends in Plant Science, 6(9), 431-438. doi:10.1016/s1360-1385(01)02052-0Hoffman, N. E., Ko, K., Milkowski, D., & Pichersky, E. (1991). Isolation and characterization of tomato cDNA and genomic clones encoding the ubiquitin gene ubi3. Plant Molecular Biology, 17(6), 1189-1201. doi:10.1007/bf00028735Huang, Z., Zhang, Z., Zhang, X., Zhang, H., Huang, D., & Huang, R. (2004). Tomato TERF1 modulates ethylene response and enhances osmotic stress tolerance by activating expression of downstream genes. FEBS Letters, 573(1-3), 110-116. doi:10.1016/j.febslet.2004.07.064HUSSEY, G. (1963). Growth and Development in the Young Tomato: I. THE EFFECT OF TEMPERATURE AND LIGHT INTENSITY ON GROWTH OF THE SHOOT APEX AND LEAF PRIMORDIA. Journal of Experimental Botany, 14(2), 316-325. doi:10.1093/jxb/14.2.316Imaizumi, T. (2005). FKF1 F-Box Protein Mediates Cyclic Degradation of a Repressor of CONSTANS in Arabidopsis. Science, 309(5732), 293-297. doi:10.1126/science.1110586IWAMOTO, M., HIGO, K., & TAKANO, M. (2009). Circadian clock- and phytochrome-regulated Dof-like gene,Rdd1, is associated with grain size in rice. Plant, Cell & Environment, 32(5), 592-603. doi:10.1111/j.1365-3040.2009.01954.xJang, S., Marchal, V., Panigrahi, K. C. S., Wenkel, S., Soppe, W., Deng, X.-W., … Coupland, G. (2008). Arabidopsis COP1 shapes the temporal pattern of CO accumulation conferring a photoperiodic flowering response. The EMBO Journal, 27(8), 1277-1288. doi:10.1038/emboj.2008.68Jones, M. L. (2013). Mineral nutrient remobilization during corolla senescence in ethylene-sensitive and -insensitive flowers. AoB Plants, 5(0), plt023-plt023. doi:10.1093/aobpla/plt023Karimi, M., Depicker, A., & Hilson, P. (2007). Recombinational Cloning with Plant Gateway Vectors. Plant Physiology, 145(4), 1144-1154. doi:10.1104/pp.107.106989Kerepesi, I., & Galiba, G. (2000). Osmotic and Salt Stress-Induced Alteration in Soluble Carbohydrate Content in Wheat Seedlings. Crop Science, 40(2), 482. doi:10.2135/cropsci2000.402482xKinet, J. M. (1977). Effect of light conditions on the development of the inflorescence in tomato. Scientia Horticulturae, 6(1), 15-26. doi:10.1016/0304-4238(77)90074-7Kirby, J., & Kavanagh, T. A. (2002). NAN fusions: a synthetic sialidase reporter gene as a sensitive and versatile partner for GUS. The Plant Journal, 32(3), 391-400. doi:10.1046/j.1365-313x.2002.01422.xKloosterman, B., Abelenda, J. A., Gomez, M. del M. C., Oortwijn, M., de Boer, J. M., Kowitwanich, K., … Bachem, C. W. B. (2013). Naturally occurring allele diversity allows potato cultivation in northern latitudes. Nature, 495(7440), 246-250. doi:10.1038/nature11912Konishi, M., & Yanagisawa, S. (2007). Sequential activation of two Dof transcription factor gene promoters during vascular development in Arabidopsis thaliana. Plant Physiology and Biochemistry, 45(8), 623-629. doi:10.1016/j.plaphy.2007.05.001Krohn, N. M., Yanagisawa, S., & Grasser, K. D. (2002). Specificity of the Stimulatory Interaction between Chromosomal HMGB Proteins and the Transcription Factor Dof2 and Its Negative Regulation by Protein Kinase CK2-mediated Phosphorylation. Journal of Biological Chemistry, 277(36), 32438-32444. doi:10.1074/jbc.m203814200Kurai, T., Wakayama, M., Abiko, T., Yanagisawa, S., Aoki, N., & Ohsugi, R. (2011). Introduction of the ZmDof1 gene into rice enhances carbon and nitrogen assimilation under low-nitrogen conditions. Plant Biotechnology Journal, 9(8), 826-837. doi:10.1111/j.1467-7652.2011.00592.xKushwaha, H., Gupta, S., Singh, V. K., Rastogi, S., & Yadav, D. (2010). Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis. Molecular Biology Reports, 38(8), 5037-5053. doi:10.1007/s11033-010-0650-9Lakhssassi, N., Doblas, V. G., Rosado, A., del Valle, A. E., Posé, D., Jimenez, A. J., … Botella, M. A. (2012). The Arabidopsis TETRATRICOPEPTIDE THIOREDOXIN-LIKE Gene Family Is Required for Osmotic Stress Tolerance and Male Sporogenesis. Plant Physiology, 158(3), 1252-1266. doi:10.1104/pp.111.188920Lee, H. E., Shin, D., Park, S. R., Han, S.-E., Jeong, M.-J., Kwon, T.-R., … Byun, M.-O. (2007). Ethylene responsive element binding protein 1 (StEREBP1) from Solanum tuberosum increases tolerance to abiotic stress in transgenic potato plants. Biochemical and Biophysical Research Communications, 353(4), 863-868. doi:10.1016/j.bbrc.2006.12.095Lijavetzky, D., Carbonero, P., & Vicente-Carbajosa, J. (2003). BMC Evolutionary Biology, 3(1), 17. doi:10.1186/1471-2148-3-17Livak, K. J., & Schmittgen, T. D. (2001). Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method. Methods, 25(4), 402-408. doi:10.1006/meth.2001.1262Mackay, J. P., & Crossley, M. (1998). Zinc fingers are sticking together. Trends in Biochemical Sciences, 23(1), 1-4. doi:10.1016/s0968-0004(97)01168-7Mena, M., Vicente-Carbajosa, J., Schmidt, R. J., & Carbonero, P. (1998). An endosperm-specific DOF protein from barley, highly conserved in wheat, binds to and activates transcription from the prolamin-box of a native B-hordein promoter in barley endosperm. The Plant Journal, 16(1), 53-62. doi:10.1046/j.1365-313x.1998.00275.xMizoguchi, T., Wright, L., Fujiwara, S., Cremer, F., Lee, K., Onouchi, H., … Coupland, G. (2005). Distinct Roles of GIGANTEA in Promoting Flowering and Regulating Circadian Rhythms in Arabidopsis. The Plant Cell, 17(8), 2255-2270. doi:10.1105/tpc.105.033464Moreno-Risueno, M. Á., Martínez, M., Vicente-Carbajosa, J., & Carbonero, P. (2006). The family of DOF transcription factors: from green unicellular algae to vascular plants. Molecular Genetics and Genomics, 277(4), 379-390. doi:10.1007/s00438-006-0186-9Moreno-Risueno, M. Á., Díaz, I., Carrillo, L., Fuentes, R., & Carbonero, P. (2007). The HvDOF19 transcription factor mediates the abscisic acid-dependent repression of hydrolase genes in germinating barley aleurone. The Plant Journal, 51(3), 352-365. doi:10.1111/j.1365-313x.2007.03146.xMurashige, T., & Skoog, F. (1962). A Revised Medium for Rapid Growth and Bio Assays with Tobacco Tissue Cultures. Physiologia Plantarum, 15(3), 473-497. doi:10.1111/j.1399-3054.1962.tb08052.xNakagawa, T., Kurose, T., Hino, T., Tanaka, K., Kawamukai, M., Niwa, Y., … Kimura, T. (2007). Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. Journal of Bioscience and Bioengineering, 104(1), 34-41. doi:10.1263/jbb.104.34Oñate-Sánchez, L., & Vicente-Carbajosa, J. (2008). DNA-free RNA isolation protocols for Arabidopsis thaliana, including seeds and siliques. BMC Research Notes, 1(1), 93. doi:10.1186/1756-0500-1-93ORELLANA, S., YAÑEZ, M., ESPINOZA, A., VERDUGO, I., GONZÁLEZ, E., RUIZ-LARA, S., & CASARETTO, J. A. (2010). The transcription factor SlAREB1 confers drought, salt stress tolerance and regulates biotic and abiotic stress-related genes in tomato. Plant, Cell & Environment, 33(12), 2191-2208. doi:10.1111/j.1365-3040.2010.02220.xPapi, M., Sabatini, S., Altamura, M. M., Hennig, L., Schäfer, E., Costantino, P., & Vittorioso, P. (2002). Inactivation of the Phloem-Specific Dof Zinc Finger GeneDAG1 Affects Response to Light and Integrity of the Testa of Arabidopsis Seeds. Plant Physiology, 128(2), 411-417. doi:10.1104/pp.010488Pinheiro, C., & Chaves, M. M. (2010). Photosynthesis and drought: can we make metabolic connections from available data? Journal of Experimental Botany, 62(3), 869-882. doi:10.1093/jxb/erq340Pnueli, L. (2001). Tomato SP-Interacting Proteins Define a Conserved Signaling System That Regulates Shoot Architecture and Flowering. THE PLANT CELL ONLINE, 13(12), 2687-2702. doi:10.1105/tpc.13.12.2687Rajasekaran, L. R., Aspinall, D., & Paleg, L. G. (2000). Physiological mechanism of tolerance of Lycopersicon spp. exposed to salt stress. Canadian Journal of Plant Science, 80(1), 151-159. doi:10.4141/p99-003Rizhsky, L., Liang, H., Shuman, J., Shulaev, V., Davletova, S., & Mittler, R. (2004). When Defense Pathways Collide. The Response of Arabidopsis to a Combination of Drought and Heat Stress. Plant Physiology, 134(4), 1683-1696. doi:10.1104/pp.103.033431Rueda-López, M., Crespillo, R., Cánovas, F. M., & Ávila, C. (2008). Differential regulation of two glutamine synthetase genes by a single Dof transcription factor. The Plant Journal, 56(1), 73-85. doi:10.1111/j.1365-313x.2008.03573.xSawa, M., Nusinow, D. A., Kay, S. A., & Imaizumi, T. (2007). FKF1 and GIGANTEA Complex Formation Is Required for Day-Length Measurement in Arabidopsis. Science, 318(5848), 261-265. doi:10.1126/science.1146994Seki, M., Umezawa, T., Urano, K., & Shinozaki, K. (2007). Regulatory metabolic networks in drought stress responses. Current Opinion in Plant Biology, 10(3), 296-302. doi:10.1016/j.pbi.2007.04.014Shannon, M. C., & Grieve, C. M. (1998). Tolerance of vegetable crops to salinity. Scientia Horticulturae, 78(1-4), 5-38. doi:10.1016/s0304-4238(98)00189-7Shaw, L. M., McIntyre, C. L., Gresshoff, P. M., & Xue, G.-P. (2009). Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation. Functional & Integrative Genomics, 9(4), 485-498. doi:10.1007/s10142-009-0130-2Shelp, B. J., Bown, A. W., & Faure, D. (2006). Extracellular γ-Aminobutyrate Mediates Communication between Plants and Other Organisms. Plant Physiology, 142(4), 1350-1352. doi:10.1104/pp.106.088955Shelp, B. (1999). Metabolism and functions of gamma-aminobutyric acid. Trends in Plant Science, 4(11), 446-452. doi:10.1016/s1360-1385(99)01486-7Skirycz, A., Jozefczuk, S., Stobiecki, M., Muth, D., Zanor, M. I., Witt, I., & Mueller-Roeber, B. (2007). Transcription factor AtDOF4;2 affects phenylpropanoid metabolism in Arabidopsis thaliana. New Phytologist, 175(3), 425-438. doi:10.1111/j.1469-8137.2007.02129.xSkirycz, A., Reichelt, M., Burow, M., Birkemeyer, C., Rolcik, J., Kopka, J., … Witt, I. (2006). DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. The Plant Journal, 47(1), 10-24. doi:10.1111/j.1365-313x.2006.02767.xSuárez-López, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F., & Coupland, G. (2001). CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature, 410(6832), 1116-1120. doi:10.1038/35074138Sun, S.-J., Guo, S.-Q., Yang, X., Bao, Y.-M., Tang, H.-J., Sun, H., … Zhang, H.-S. (2010). Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. Journal of Experimental Botany, 61(10), 2807-2818. doi:10.1093/jxb/erq120Takada, S., & Goto, K. (2003). TERMINAL FLOWER2, an Arabidopsis Homolog of HETEROCHROMATIN PROTEIN1, Counteracts the Activation of FLOWERING LOCUS T by CONSTANS in the Vascular Tissues of Leaves to Regulate Flowering Time. The Plant Cell, 15(12), 2856-2865. doi:10.1105/tpc.016345Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution, 28(10), 2731-2739. doi:10.1093/molbev/msr121Thompson, J. (1997). The CLUSTAL_X windows

Plant protein-coding gene families: emerging bioinformatics approaches

Protein-coding gene families are sets of similar genes with a shared evolutionary origin and, generally, with similar biological functions. In plants, the size and role of gene families has been only partially addressed. However, suitable bioinformatics tools are being developed to cluster the enormous number of sequences currently available in databases. Specifically, comparative genomic databases promise to become powerful tools for gene family annotation in plant clades. In this review, I evaluate the data retrieved from various gene family databases, the ease with which they can be extracted and how useful the extracted information is

Cytokinin acts through the auxin influx carrier AUX1 to regulate cell elongation in the root

Hormonal interactions are critical for plant development. In Arabidopsis, cytokinins inhibit root growth through effects on cell proliferation and cell elongation. Here we define key mechanistic elements in a regulatory network by which cytokinin inhibits root cell elongation in concert with the hormones auxin and ethylene. The auxin importer AUX1 functions as a positive regulator of cytokinin responses in the root, AUX1 mutants specifically affecting the ability of cytokinin to inhibit cell elongation but not cell proliferation. AUX1 is required for cytokinin-dependent changes of auxin activity in the lateral root cap associated with the control of cell elongation. Cytokinin regulates root cell elongation through ethylene-dependent and independent mechanisms, both hormonal signals converging on AUX1 as a regulatory hub. An autoregulatory circuit is identified involving the control of ARR10 and AUX1 expression by cytokinin and auxin, this circuit potentially functioning as an oscillator to integrate the effects of these two hormones. Taken together, our results uncover several regulatory circuits controlling interactions of cytokinin with auxin and ethylene, and support a model in which cytokinin regulates shootward auxin transport to control cell elongation and root growth

The Maltase Involved in Starch Metabolism in Barley Endosperm Is Encoded by a Single Gene

During germination and early seedling growth of barley (Hordeum vulgare), maltase is responsible for the conversion of maltose produced by starch degradation in the endosperm to glucose for seedling growth. Despite the potential relevance of this enzyme for malting and the production of alcoholic beverages, neither the nature nor the role of maltase is fully understood. Although only one gene encoding maltase has been identified with certainty, there is evidence for the existence of other genes and for multiple forms of the enzyme. It has been proposed that maltase may be involved directly in starch granule degradation as well as in maltose hydrolysis. The aim of our work was to discover the nature of maltase in barley endosperm. We used ion exchange chromatography to fractionate maltase activity from endosperm of young seedlings, and we partially purified activity for protein identification. We compared maltase activity in wild-type barley and transgenic lines with reduced expression of the previously-characterised maltase gene Agl97, and we used genomic and transcriptomic information to search for further maltase genes. We show that all of the maltase activity in the barley endosperm can be accounted for by a single gene, Agl97. Multiple forms of the enzyme most likely arise from proteolysis and other post-translational modifications

Global Landscape of a Co-Expressed Gene Network in Barley and its Application to Gene Discovery in Triticeae Crops

Accumulated transcriptome data can be used to investigate regulatory networks of genes involved in various biological systems. Co-expression analysis data sets generated from comprehensively collected transcriptome data sets now represent efficient resources that are capable of facilitating the discovery of genes with closely correlated expression patterns. In order to construct a co-expression network for barley, we analyzed 45 publicly available experimental series, which are composed of 1,347 sets of GeneChip data for barley. On the basis of a gene-to-gene weighted correlation coefficient, we constructed a global barley co-expression network and classified it into clusters of subnetwork modules. The resulting clusters are candidates for functional regulatory modules in the barley transcriptome. To annotate each of the modules, we performed comparative annotation using genes in Arabidopsis and Brachypodium distachyon. On the basis of a comparative analysis between barley and two model species, we investigated functional properties from the representative distributions of the gene ontology (GO) terms. Modules putatively involved in drought stress response and cellulose biogenesis have been identified. These modules are discussed to demonstrate the effectiveness of the co-expression analysis. Furthermore, we applied the data set of co-expressed genes coupled with comparative analysis in attempts to discover potentially Triticeae-specific network modules. These results demonstrate that analysis of the co-expression network of the barley transcriptome together with comparative analysis should promote the process of gene discovery in barley. Furthermore, the insights obtained should be transferable to investigations of Triticeae plants. The associated data set generated in this analysis is publicly accessible at http://coexpression.psc.riken.jp/barley/

Branching out in roots: uncovering form, function, and regulation

Root branching is critical for plants to secure anchorage and ensure the supply of water, minerals, and nutrients. To date, research on root branching has focused on lateral root development in young seedlings. However, many other programs of postembryonic root organogenesis exist in angiosperms. In cereal crops, the majority of the mature root system is composed of several classes of adventitious roots that include crown roots and brace roots. In this Update, we initially describe the diversity of postembryonic root forms. Next, we review recent advances in our understanding of the genes, signals, and mechanisms regulating lateral root and adventitious root branching in the plant models Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). While many common signals, regulatory components, and mechanisms have been identified that control the initiation, morphogenesis, and emergence of new lateral and adventitious root organs, much more remains to be done. We conclude by discussing the challenges and opportunities facing root branching research

An auxin-regulable oscillatory circuit drives the root clock in Arabidopsis

CSIC - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)In Arabidopsis, the root clock regulates the spacing of lateral organs along the primary root through oscillating gene expression. The core molecular mechanism that drives the root clock periodicity and how it is modified by exogenous cues such as auxin and gravity remain unknown. We identified the key elements of the oscillator (AUXIN RESPONSE FACTOR 7, its auxin-sensitive inhibitor IAA18/POTENT, and auxin) that form a negative regulatory loop circuit in the oscillation zone. Through multilevel computer modeling fitted to experimental data, we explain how gene expression oscillations coordinate with cell division and growth to create the periodic pattern of organ spacing. Furthermore, gravistimulation experiments based on the model predictions show that external auxin stimuli can lead to entrainment of the root clock. Our work demonstrates the mechanism underlying a robust biological clock and how it can respond to external stimuli.This work was funded by the Ministerio de Economía y Competitividad of Spain (MINECO) and/or the ERDF (BFU2016-80315-P to M.A.M.-R., BIO2017-82209-R to J.C.d.P., and TIN2016-81079-R to A.R.-P.), the Comunidad de Madrid and/or ERDF and ESF (2017-T1/BIO-5654 to K.W. and S2017/BMD-3691 to A.R.-P.), the Howard Hughes Medical Institute and the NIH (R35-GM131725 to P.N.B.), the Fonds Wetenschappelijk Onderzoek (FWO Flanders) (G022516N, G020918N, and G024118N to T.B.), and the “Severo Ochoa Program for Centres of Excellence in R&D” from the Agencia Estatal de Investigacion of Spain [SEV-2016-0672 (2017–2021)] to K.W., P.P.-G., and M.A.M.-R. through CBGP. M.M. was supported by a postdoctoral contract associated to SEV-2016-0672, E.B.-A. by Ayudante de Investigacion contract PEJ-2017-AI/BIO-7360 from the Comunidad de Madrid, A.S.-C. and L.S.-R. by FPI contracts from MINECO (BES-2014-068852 and BES-2017-080155, respectively), J.C. by a Juan de la Cierva contract from MINECO (FJCI-2016-28607), P.P.-G. by a Juan de la Cierva contract from MINECO (FJCI-2015-24905) and Programa Atraccion Talento from Comunidad Madrid (2017-T2/BIO-3453), A.S. by a Torres Quevedo contract from MINECO (PTQ-15-07915), and K.W. by program PGC2018-093387-A-I00 from the Ministerio de Ciencia e Innovacion (MICIU)Peer reviewe

Plant roots use a patterning mechanism to position lateral root branches toward available water

[EN] The architecture of the branched root system of plants is a major determinant of vigor. Water availability is known to impact root physiology and growth; however, the spatial scale at which this stimulus influences root architecture is poorly understood. Here we reveal that differences in the availability of water across the circumferential axis of the root create spatial cues that determine the position of lateral root branches. We show that roots of several plant species can distinguish between a wet surface and air environments and that this also impacts the patterning of root hairs, anthocyanins, and aerenchyma in a phenomenon we describe as hydropatterning. This environmental response is distinct from a touch response and requires available water to induce lateral roots along a contacted surface. X-ray microscale computed tomography and 3D reconstruction of soil-grown root systems demonstrate that such responses also occur under physiologically relevant conditions. Using early-stage lateral root markers, we show that hydropatterning acts before the initiation stage and likely determines the circumferential position at which lateral root founder cells are specified. Hydro-patterning is independent of endogenous abscisic acid signaling, distinguishing it from a classic water-stress response. Higher water availability induces the biosynthesis and transport of the lateral root-inductive signal auxin through local regulation of TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 and PIN-FORMED 3, both of which are necessary for normal hydropatterning. Our work suggests that water availability is sensed and interpreted at the suborgan level and locally patterns a wide variety of developmental processes in the root.We thank Jose Alonso, Fred Berger, Eva Benkova, Matt Evans, Annemarie Meijer, Ben Scheres, and Jian Xu for providing materials, and the J.R.D. laboratory for comments on the manuscript. Funding was provided by a Carnegie Institution for Science endowment, the National Research Foundation of Singapore, a National Science Foundation Graduate Research Fellowship under Grant DGE-1147470 (to N.E.R.), European Research Council FUTUREROOTS (C.J.S., M.C.T., S.J.M., and M.J.B.), and Biotechnology and Biological Sciences Research Council (C.J.S., S.J.M., and M.J.B.).Bao, Y.; Aggarwal, P.; Robbins, NEI.; Sturrock, CJ.; Thompson, MC.; Tan, HQ.; Tham, C.... (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. https://doi.org/10.1073/pnas.1400966111S931993241112