Progress 10/01/02 to 09/30/07

Outputs
OUTPUTS: Our main interest is to understand the molecular mechanism that plants utilize to sense and respond to hormones, and how these molecular pathways are integrated in the cell. To address these general questions several experimental approaches are being employed. Genetic screens are being performed to identify new genes/mutants involved in the response to ethylene (ead1, peo1, wei10, wei11, and wei12), as well as genes that participate in the interaction between ethylene and auxin (wei8, wel1, wel2, and wei9). The genetic, molecular and genomic characterization of these mutants is being carried out. Two graduate students and one postdoctoral fellow as well as several undergraduates are being trained in the context of this project. The results of our studies have been presented at several national and international meetings. -. "Ethylene and auxin signaling and response pathways: a paradigm for hormone interaction". Banbury Center meeting "Integration of Hormonal & Genetic Regulation in Plant Development" Cold Spring Harbor, November 2006. -. "Ethylene and auxin signaling and response pathways: a paradigm for hormone interaction". Department of Biology (Wake Forest University) September 2006 -. " Arabidopsis como modelo experimental". Arabidopsis Workshop "Bases Moleculares para Estudios Funcionales en Arabidopsis". Cinvestav, Campus-Guanajuato (Mexico). September 2006 PARTICIPANTS: Jose M Alonso. PI Anna N. Stepanova (Researcher, NCSU) Jeonga Yun (Graduate Student, NCSU) Vaishali Thanawala (Undergraduate Student, NCSU) Anju Karki (Undergraduate Student from Salem College) TARGET AUDIENCES: - In addition to the aforementioned graduate and undergraduate student training, The PI participates in three graduate training grants and is in the advisory committee of 16 graduate students at NCSU and UNC. - The PI of this grant also serves as a mentor in the HHMI-funded Summer Research Intern Program at NC State University. As mentioned above, in the summer of 2007 a female student from Salem College joined the lab. This outreach activity is directed at stimulating research interest among minority college students around North Carolina.

Impacts
Cloning and molecular characterization of several root specific ethylene resistant mutants (wei8, wel1, wel2, and wei9) is uncovering molecular mechanism utilized by plants to specify the response to this hormone in concrete organs or tissue types. In particular, the activation of auxin production in specific cell types is emerging as key determinant of the tissue-specific response to ethylene. On the other hand, cloning and characterization of ead1, peo1 wei10, wei11 and wei12 is unveiling new points of post-transcriptional regulation of the ethylene and auxin signaling and response pathway. Understanding of the basic molecular mechanisms that control the plant response to these hormones is an essential first step towards an intelligent manipulation of plant traits of key agronomical importance such as fruit ripening, defense against pathogens, and control of biomass production.

Publications

• OMalley RC, Alonso JM, Kim CJ, Leisse TJ, and & Ecker JR. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. Nature Protocols. 2:2910-17 (2007)
• Stepanova AN, Yun J, Likhacheva AV, Alonso JM. Multilevel Interactions between Ethylene and Auxin in Arabidopsis Roots. Plant Cell. 19:2169-85 (2007)
• Li H, He Z, Lu G, Lee SC, Alonso J, Ecker JR, Luan S. A WD40 Domain Cyclophilin Interacts with Histone H3 and Functions in Gene Repression and Organogenesis in Arabidopsis. Plant Cell. 19:2403-16 (2007)

Progress 10/01/05 to 09/30/06

Outputs
Our main research interest is to understand (1) how plants sense and respond to hormones and (2) what the role of these hormones is in the integration of developmental and environmental signals. Towards these goals, genetic screens have been performed and mutants affected in these hormone-related processes have been identified. Characterization of ein2-9 suppressors: To better understand the molecular function of the essential ethylene-signaling component EIN2, a suppressor screen was performed. Characterization and cloning of seven ein2-9 suppressors provides additional support for the key role of protein stability in ethylene signaling. Characterization of wei8, wel1, and wel2: The analysis of a root-specific ethylene insensitive mutant wei8 has uncovered a novel genetic element involved in a key step of auxin biosynthesis. Mutant alleles of paralogous genes WEL1 and WEL2 have been identified allowing for the generation of the triple wei8 wel1 wel2 mutants. Characterization of the triple mutant combinations confirms the crucial role of this small gene family in the control of auxin production in plants. An in-depth study of these genes will be critical to establishing not only how, but also when and where, auxin is synthesized. Characterization of sur2 suppressors: In order to find new elements in the control of auxin biosynthesis, a suppressor screen of the auxin overproducer sur2 has been carried out. Two of the sur2 suppressors, rus1 and rus2 have been characterized in detail. rus1 and rus2 not only suppress the high auxin morphology of sur2 in seedling and adults, but also the high levels of expression of the auxin reporter DR5::GUS. RUS1 has been recently cloned and its role in auxin biosynthesis is now being investigated. Characterization of ead1 and peo1: Identification and characterization of ead1 and peo1 mutants clearly indicates that the physical interaction previously observed in vitro between EAD1 and PEO1 is biologically relevant. Phenotypic and molecular characterization of these mutants indicates that the EAD1 and PEO1 function is required for normal ethylene and auxin responses. The potential role of these proteins in the control of protein translation of putative targets is currently being tested. Protocol setup for BAC tagging using recombineering approaches: We have shown that tags can be precisely and easily fused to a gene of choice present in a large artificial chromosome by employing newly developed highly efficient homologous recombination systems in E. coli. These recent technical advances are making it possible to easily manipulate and modify large DNA molecules such as BACs without the need for restriction enzymes and classical cloning techniques.

Impacts
1) Identification and characterization of the ein2 suppressors has opened a new niche in the discovery of novel elements of the ethylene signaling pathway. The importance of this hormone in a multitude of critical agronomic traits, such as pathogen resistance or post-harvest durability, broadens the impact of this research beyond basic hormone biology. 2) The wei8, wel1, wel2 studies are revealing a previously unknown point of interaction between ethylene responses and auxin biosynthesis. Understanding how hormones interact is critical not only for the basic knowledge of how hormones work in plants, but also for our ability to manipulate plants in an intelligent way for the benefit of agriculture. Likewise, characterization of the sur2 suppressors is providing new insights into auxin biosynthesis and its regulation. Relevance of the auxin biosynthesis research to basic as well as applied plant sciences is enormous. 3) The EAD1 project is unveiling a previously uncharacterized molecular mechanism of post-trancriptional regulation of gene expression common to all eukaryotic species. The recent report of the role of the human orthologue of EAD1 in cancer further expands the impact of plant-based studies far beyond plant biology. 4) Finally, the development of a simple strategy to modify very precisely and efficiently large genomic clones is opening the possibility of generating a whole-genome collection of tagged genes that will facilitate the enormous task of understanding the function of the over 30,000 genes present in the Arabidopsis genome.

Publications

• Mason MG, Mathews DE, Argyros DA, Maxwell BB, Kieber JJ, Alonso JM, Ecker JR, Schaller GE. Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. Plant Cell. 17:3007-18 (2005).
• Stepanova AN and Alonso JM. PCR-based screening for insertional mutants. In Arabidopsis Protocols. Salinas J and Sanchez-Serrano, J.J. (Eds). Humana Press Totawa New Jersey. Methods Mol Biol. 323:163-72. (2006)
• Larissa M. Benavente and Jose M. Alonso. Molecular mechanisms of ethylene signaling in Arabidopsis. Mol. BioSyst., 2:165-173 (2006)
• Alonso JM, Ecker JR. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Nat. Rev. Genet. 7: 524-536 (2006)
• Rudella A, Friso G, Alonso JM, Ecker JR, van Wijk KJ. Downregulation of ClpR2 Leads to Reduced Accumulation of the ClpPRS Protease Complex and Defects in Chloroplast Biogenesis in Arabidopsis. Plant Cell. 18: 1704-1721 (2006)
• Chen JG, Ullah H, Temple B, Liang J, Guo J, Alonso JM, Ecker JR, Jones AM. RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis. J Exp Bot. 57: 2697-2708 (2006)
• Lariguet P, Schepens I, Hodgson D, Pedmale UV, Trevisan M, Kami C, de Carbonnel M, Alonso JM, Ecker JR, Liscum E, Fankhauser C. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism.. Proc Natl Acad Sci U S A. 103: 10134-9 (2006)
• Mori IC, Murata Y, Yang Y, Munemasa S, Wang YF, Andreoli S, Tiriac H, Alonso JM, Harper JF, Ecker JR, Kwak JM, Schroeder JI. CDPKs CPK6 and CPK3 Function in ABA Regulation of Guard Cell S-Type Anion- and Ca(2+)- Permeable Channels and Stomatal Closure. PLoS Biol. 4: 1749-1762 (2006)
• Sun A. Kim, Tracy Punshon, Antonio Lanzirotti, Liangtao Li, Jose M. Alonso, Joseph R. Ecker, Jerry Kaplan, and Mary Lou Guerinot.Localization of Iron in Arabidopsis Seed Requires the Vacuolar Membrane Transporter VIT1. Science 314:1295-1298 (2006)
• Hutchison CE, Li J, Argueso C, Gonzalez M, Lee E, Lewis MW, Maxwell BB, Perdue TD, Schaller GE, Alonso JM, Ecker JR, Kieber JJ The Arabidopsis Histidine Phosphotransfer Proteins Are Redundant Positive Regulators of Cytokinin Signaling. Plant Cell. 2006

Progress 10/01/04 to 09/30/05

Outputs
Our main research interest is to understand (1) how plants sense and respond to hormones and (2) what the role of these hormones is in the integration of developmental and environmental signals. Towards these goals, genetic screens have been performed and mutants affected in these hormone-related processes have been identified. Characterization of ein2-9 suppressors Although the ethylene signaling pathway is one of the best understood in plants, there are still some key aspects that remain obscure. The function of the essential signaling element EIN2 is still unknown. A genetic approach has been taken to elucidate the function of this gene. Suppressor screening have been carried out and more than 100 putative suppressors have been identified. So far, 7 suppressors have been characterized. These initial studies indicate that the genetic approach utilized is working as expected and new insights on the ethylene signaling pathway are to be gained. Characterization of wei8 and wel2 The analysis of these root-specific ethylene insensitive mutants has uncovered the genetic elements involved in a key step of auxin biosynthesis. This is not only supported by the phenotypic anlaysis of these mutants, but also by the low levels of expression of the DR5::GUS auxin reporter. To further examine the role of these genes in auxin biosynthesis, a procedure has been established in the lab that allows for the quantification of auxin biosynthetic rates. Finally, transcriptional and translational fusions have been generated to study the expression patterns of these genes and the subcellular localization of the corresponding proteins. Characterization of ead1 Cloning and initial characterization of ead1, a mutant that shows both auxin and ethylene defects, has uncovered an additional level of regulation in the response to these hormones. Molecular characterization of ead1, as well as the identification and characterization of an EAD1-interacting protein PEO1, uncovered an unexpected role for translational control in the plant response to ethylene and auxin. Genetic interaction with other ethylene and auxin mutants as well as further molecular characterization are being deployed to investigate the mechanism of action and to identify potential targets of these new translation regulatory elements.

Impacts
1) Identification and characterization of ein2 suppressors has opened a new niche in the discovery of novel elements of the ethylene signaling pathway. The importance of this hormone in a multitude of critical agronomic traits, such as pathogen resistance or post-harvest durability, broadens the impact of this research beyond basic hormone biology. 2) The wei8 and wel2 studies are revealing a previously unknown point of interaction between ethylene responses and auxin biosynthesis. Understanding how hormones interact is critical not only for the basic knowledge of how hormones work in plants, but also for our ability to manipulate plants in an intelligent way for the benefit of agriculture. On the other hand, the relevance of auxin biosynthesis studies to basic as well as applied plant sciences is enormous. The identification of the genes involved in auxin biosynthesis represents the first step towards understanding how this hormone is produced and, therefore, this research is vital to our ability to manipulate auxin levels for the purpose of improving crop yields. 3) Finally, the EAD1 project is unveiling a previously uncharacterized molecular mechanism of post-trancriptional regulation of gene expression common to all eukaryotic species. The recent report of the role of the human orthologue of EAD1 in cancer further expands the impact of plant-based studies far beyond plant biology.

Publications

• -. Prigge MJ, Otsuga D, Alonso JM, Ecker JR, Drews GN, Clark SE. (2005). Class III Homeodomain-Leucine Zipper Gene Family Members Have Overlapping, Antagonistic, and Distinct Roles in Arabidopsis Development. Plant Cell. 17:61-76.
• -. Stepanova AN, Hoyt JM, Hamilton AA, Alonso JM. (2005). A Link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis. Plant Cell. 17:2230-42.
• -. Wilmoth JC, Wang S, Tiwari SB, Joshi AD, Hagen G, Guilfoyle TJ, Alonso JM, Ecker JR, Reed JW. (2005). NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. Plant J. 43:118-30.
• -. Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker JR, Reed JW. (2005). Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Development. 132:4107-18.
• -. Stepanova AN, Alonso JM. (2005). Arabidopsis ethylene signaling pathway. Sci STKE: 2005(276):cm3.
• -. Stepanova, A.N. and Alonso, J.M. (2005)Ethylene signaling and response pathway: A unique signaling cascade with a multitude of inputs and outputs. Physiol. Plant. 123: 195-206.
• -. Ryu JS, Kim JI, Kunkel T, Kim BC, Cho DS, Hong SH, Kim SH, Fernandez AP, Kim Y, Alonso JM, Ecker JR, Nagy F, Lim PO, Song PS, Schafer E, Nam HG. (2005). Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer. Cell: 120:395-406.
• -. Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D, Onodera C, Quach H, Smith A, Yu G, Theologis A. (2005). Functional Genomic Analysis of the AUXIN RESPONSE FACTOR Gene Family Members in Arabidopsis thaliana: Unique and Overlapping Functions of ARF7 and ARF19. Plant Cell. 17:444-463.
• -. Liu G, Holub EB, Alonso JM, Ecker JR, Fobert PR. (2005). An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance. Plant J. 41: 304-18.

Progress 10/01/03 to 09/30/04

Outputs
Our main research interest is to understand (1) how plants sense and respond to hormones and (2) what the role of these hormones is in the integration of developmental and environmental signals. Toward these goals, genetic screens have been performed and mutants affected, and these hormone-related processes have been identified. Characterization of wei2 and wei7: Cloning and characterization of the two root-specific, ethylene-insensitive mutants, wei2 and wei7, have unveiled a new point of interaction between ethylene responses and auxin biosynthesis. We have shown that these genes are required for an ethylene-mediated increase in auxin levels in Arabidopsis root tips. Analysis of the expression patterns of WEI2 and WEI7 indicates that these two genes are transcriptionally regulated be ethylene and are co-expressed in the same cells. We have recently shown that mutations in either one of these two genes suppress the auxin overproduction defects of sur1 and sur2 both in seedlings and adults. Remarkably, the double mutants wei2 sur1 and wei7 sur1 are viable and produce seeds, whereas sur1 is completely sterile. Characterization of wei8 and wel2: Cloning and characterization of wei8 suggests that this root-specific, ethylene-insensitive mutant represents a key step in auxin biosynthesis. Phenotypic analysis of a double mutant between wei8 and the closely related wel2 gene supports this idea. We have shown that the moderate ethylene insensitivity of wei8, as well as the strong ethylene insensitivity of wei8 wel2 double mutant, can be suppressed by low levels of exogenous auxin. Moreover, the adult wei8 wel2 double-mutant plants show a number of characteristics expected of an auxin-deficient mutant, such as reduced apical dominance, increased inflorescence branching, and flower organ alterations. Purified WEI8 protein can catalyze the conversion of tryptophan into indole-3-piruvic acid. Although strong biochemical evidences indicate that this biosynthetic step plays a mayor role in the de novo synthesis of IAA, the genetic elements catalyzing the respective reaction have been elusive until now. Characterization of ead1: In order to further understand the molecular nature of the interaction between the ethylene and auxin signaling/response pathways, we had previously identified a new class of mutants that shows both ethylene and auxin defects (ead mutants). Cloning of EAD1 indicates that this single-copy gene in Arabidopsis is conserved in all eukaryotes, expanding the impact of this research beyond plant biology. Preliminary evidences indicate that EAD1, together with PEO1 (an EAD1 interacting protein), are involved in the regulation of auxin transport and general ethylene responses. Analysis of the expression of EAD1 indicates that this protein is expressed in all plant tissues and cells, with the highest levels observed in meristematic regions. The molecular nature of EAD1 and PEO1 suggests that they are involved in the posttranscriptional regulation of specific types of genes. We are currently investigating the molecular phenotypes of ead1 and peo1 and trying to identify the molecular mechanisms responsible for these defects.

Impacts
Our research is making a significant impact in three different areas: (1) The wei2, wei7, and wei8 studies are revealing a previously unknown point of interaction between ethylene responses and auxin biosynthesis. Understanding how hormones interact is critical not only for the basic knowledge of how hormones work in plants but also for our ability to manipulate plants in an intelligent way for the benefit of agriculture. (2) In addition to advancing the hormone interaction field, the characterization of wei2, wei7, and wei8 is uncovering new genetic elements in the largely unknown auxin biosynthetic pathway. The relevance of auxin studies to basic as well as applied plant sciences is enormous. However, the essential knowledge of how, when, and where this hormone is synthesized is still lacking. The identification of the genes involved in auxin biosynthesis represents the first step toward understanding how this hormone is produced, and, therefore, this research is vital to our ability to manipulate auxin levels for the purpose of improving crop yields. (3) Finally, the characterization of EAD1 is unveiling a previously uncharacterized molecular mechanism of posttranscriptional regulation of gene expression common to all eukaryote species. The recent report of the role of the human orthologue of EAD1 in cancer further expands the impact of these studies far beyond basic plant biology.

Publications

• Pfund, C., Tans-Kersten, J., Dunning, F.M., Alonso, J.M., Ecker, J.R., Allen, C. and Bent, A.F. 2004. Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana. Mol. Plant Microbe Interact. 17:696-706.
• Chen, J.G., Pandey, S., Huang, J., Alonso, J.M., Ecker, J.R., Assmann, S.M. and Jones, A.M. 2004. GCR1 can act independently of heterotrimeric G-protein in response to brassinosteroids and gibberellins in Arabidopsis seed germination. Plant Physiol. 135:907-915.
• Tyler, L., Thomas, S.G., Hu, J., Dill, A., Alonso, J.M., Ecker, J.R. and Sun, T.P. 2004. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Plant Physiol. 135:1008-1019.
• Page, M.L., Hamel, P.P., Gabilly, S.T., Zegzouti, H., Perea, J.V., Alonso, J.M., Ecker, J.R., Theg, S.M., Christensen, S.K. and Merchant, S. 2004. A homolog of prokaryotic thiol-disulfide transporter CcdA is required for the assembly of the cytochrome b6f complex in Arabidopsis chloroplasts. J. Biol. Chem. 279:32474-32482.
• Li, H., Johnson, P., Stepanova, A., Alonso, J.M. and Ecker, J.R. 2004. Convergence of signaling pathways in the control of differential cell growth in Arabidopsis. Dev. Cell 7:193-204.
• Mockler, T.C., Yu, X., Shalitin, D., Parikh, D., Michael, T.P., Liou, J., Huang, J., Smith, Z., Alonso, J.M., Ecker, J.R., Chory, J. and Lin, C. 2004. Regulation of flowering time in Arabidopsis by K homology domain proteins. PNAS 101:12759-12764.
• Alonso, J.M. and Stepanova, A.N. The ethylene signaling pathway. 2004. Science 306:1513-1515.
• To, J.P.C., Haberer, G., Ferreira, F.J., Deruere, J., Mason, M.G., Schaller, G.E., Alonso, J.M., Ecker, J.R. and Kieber, J.J. 2004. Type-A ARRs are partially redundant negative regulators of cytokinin signaling in Arabidopsis. Plant Cell 16:658-671.
• Novillo, F., Alonso, J.M., Ecker, J.R. and Salinas, J. 2004. CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. PNAS 101:3985-3990.

Progress 10/01/02 to 09/30/03

Outputs
The main goal of this project is to understand how plants sense and respond to the plant hormone ethylene and how the ethylene pathway interacts with other signals to produce the desired response. Toward this general goal, we have identified and are in the process of characterizing five new ethylene-insensitive mutants. Characterization of wei2: Previously, we have identified and cloned a new root-specific ethylene-insensitive mutant referred to as wei2. Phenotypic characterization indicated that WEI2 could be involved in an ethylene-mediated regulation of auxin biosynthesis. The ethylene-insensitive phenotype of wei2 could be complemented by low levels of exogenous auxin reinforcing the idea that this gene is involved in auxin biosynthesis. Using a combination of molecular and genetic techniques, we have shown that WEI2 is activated at the transcriptional level by ethylene. Interestingly, this induction is restricted to the root tip where high levels of auxin accumulate. Using an auxin reporter construct (DR5::GUS), we have also demonstrated that ethylene alters the levels and distribution of auxin in roots and that these changes are dependent on the WEI2 activity. We are currently doing direct measurements of changes in the auxin biosynthetic rates in response to ethylene and examining the role of WEI2 in those changes. Cloning of wei7: A new mutant, wei7, with a phenotype very similar to that of wei2 was identified. Complementation analysis showed that wei7, for which we have found three different mutant alleles, is not allelic to wei2. Using a map-based approach, we have cloned wei7. Sequence analysis indicates that this gene encodes a protein that works in conjunction with WEI2 in the biosynthesis of auxin. We have constructed transgenic lines in which the promoter of WEI7 has been fused to the reporter gene GUS. These lines will be used to determine the spatial/temporal pattern of expression of WEI7 as well as its regulation by ethylene. An approach similar to the one described for wei2 is being utilized to determine the role of WEI7 in the regulation of auxin biosynthesis by ethylene. Cloning of wei8: Another root-specific, ethylene-insensitive mutant not allelic to either wei2 or wei7 was identified. This mutant was named wei8. Phenotypic analysis suggested that WEI8 could also be involved in auxin biosynthesis/transport because its ethylene insensitivity could be complemented by low levels of exogenous auxin. We are in the final steps of cloning WEI8. Identification of ead1: In the search for mutants involved in the crosstalk between ethylene and auxin, we have identified a new mutant loci referred to as ethylene and auxin defects (ead1). This mutant shows ethylene insensitivity as well as certain auxin defects. Characterization of the ead1 mutant shows that in addition to failing to produce the triple-response phenotype in the presence of ethylene it also displays a large array of auxin-related defects, such as loss of apical dominance, pin-formed inflorescences, reduced venation, and so forth. Our current experiments are directed at understanding the molecular nature of EAD1 and its role in plant responses to ethylene and auxin.

Impacts
The characterization and cloning of WEI2, WEI7, WEI8, and EAD1 have unveiled several possible interaction points between the ethylene signaling and auxin response pathways. In the last decade, molecular genetic studies in the plant reference system Arabidopsis thaliana have uncovered many of the main components in the biosynthesis, signaling, and response pathways of several plant hormones. An emerging challenge in hormone biology is to understand how these different hormonal pathways interact among themselves and with other internal and external cues to produce the appropriate responses. The requirement of auxin sensitivity and transport for a normal ethylene response suggests that auxin levels in specific cell types are essential for a normal ethylene response. Our findings suggest that this regulation may involve the initial steps of the auxin biosynthetic pathway as well as new shared signaling components.

Publications

• Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., Stevenson, D.K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C., Heller, C., Jeske, A., Koesema, E., Meyers, C.C., Parker, H., Prednis, L., Ansari, Y., Choy, N., Deen, H., Geralt, M., Hazari, N., Hom, E., Karnes, M., Mulholland, C., Ndubaku, R., Schmidt, I., Guzman, P., Aguilar-Henonin, L., Schmid, M., Weigel, D., Carter, D.E., Marchand, T., Risseeuw, E., Brogden, D., Zeko, A., Crosby, W.L., Berry, C.C. and Ecker, J.R. 2003. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657.
• Monte, E., Alonso, J.M., Ecker, J.R., Zhang, Y., Li, X., Young, J., Austin-Phillips, S. and Quail, P.H. 2003. Isolation and characterization of phyC mutants in Arabidopsis reveals complex crosstalk between phytochrome signaling pathways. Plant Cell 15: 1962-1980.
• Michael, T.P., Salome, P.A., Yu, H.J., Spencer, T.R., Sharp, E.L., McPeek, M.A., Alonso, J.M., Ecker, J.R. and McClung, C.R. 2003. Enhanced fitness conferred by naturally occurring variation in the circadian clock. Science 7: 1049-1053.
• Lariguet, P., Boccalandro, H.E., Alonso, J.M., Ecker, J.R., Chory, J., Casal, J.J. and Fankhauser, C. 2003. The balance between phytochrome kinase substrate1 and PKS2 provides homeostasis for phytochrome A signaling in Arabidopsis. Plant Cell 15: 2966-2978.
• Catala, R., Santos, E., Alonso, J.M., Ecker, J.R., Martinez-Zapater, J.M. and Salinas, J. 2003. Mutations in the Ca2+/H+ transporter CAX1 increase CBF/DREB1 expression and the cold-acclimation response in Arabidopsis. Plant Cell 15: 2940-2951.
• Yoshida, R., Hobo, T., Ichimura, K., Mizoguchi, T., Takahashi, F., Alonso, J., Ecker, J.R. and Shinozaki, K. 2002. ABA-activated SnRK2 protein kinase is required for dehydration, stress signaling in Arabidopsis. Plant Cell Physiol. 43: 1473-1483.
• Strand, A., Asami, T., Alonso, J., Ecker, J.R. and Chory, J. 2003. Mg-protoporphyrinIX is a signalling molecule involved in retrograde communication between the chloroplast and nucleus. Nature 421: 79-83.
• Ullah, H., Chen, J.-G., Temple, B., Boyes, D.C., Alonso, J.M., Davis, K.R., Ecker, J.R. and Jones, A.M. 2003. The alpha-subunit of the Arabidopsis G protein negatively regulates auxin-induced cell division and affects multiple developmental processes. Plant Cell 15: 393-409.
• Alonso, J.M., Stepanova, A.N., Solano, R., Wisman, E., Ferrari, S., Ausubel, F.M. and Ecker, J.R. 2003. Five components of the ethylene-response pathway identified in a screening for weak ethylene-insensitive mutants in Arabidopsis. PNAS 100: 2992-2997.
• Larkin, R.M., Alonso, J., Ecker, J. and Chory, J. 2003. GUN4, a regulator of chlorophyll synthesis and intracellular signaling. Science 299: 902-906.
• Mackey, D., Belkhadir, Y., Alonso, J.M., Ecker, J.R. and Dangl, J.L. 2003. Arabidopsis RIN4 is a target of the Type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance. Cell 112: 379-389.