Adjunct Professor
PhD  Plant Biochemistry    University of California, Los Angeles
B.S.   Plant Physiology    Agricultural University of Athens, Greece

800 Buchanan St.
Albany, California 94710
theo@nature.berkeley.edu
office: 510-559-5911   lab: 510-559-5924   fax:  510-559-5678

Web site         Recent publications     

My laboratory has been involved during the past 20+ years in understanding the molecular aspects of auxin perception (“the auxin project”) and ethylene biosynthesis (“the ethylene project”). More recently (since 1994), the laboratory was involved in Arabidopsis structural genomics as a member of the SSP consortium (Stanford - Ron Davis / Salk - Joe Ecker / PGEC - A. Theologis). Our involvement with Arabidopsis genomics was due to the realization that the two non-genomic projects, “auxin” and “ethylene”, respectively, were not advancing rapidly enough because of the absence of basic molecular resources. With the advent of genomic technology in the early nineties, we decided to participate as part of a consortium in the international effort (AGI) to sequence the Arabidopsis genome. This allowed the development of new molecular tools for advancing our “auxin” and “ethylene” projects. More importantly, however, it provided new resources for the entire plant biology community. I am a strong believer that TECHNOLOGY advances BIOLOGY and vice versa.

After completion of the Arabidopsis genome sequencing project, my laboratory was involved with a second genome project as a member of the same consortium. This project involved the mapping of all the transcriptional units of the Arabidopsis genome. It was a logical consequence of the Arabidopsis genome sequence project. Its purpose was to verify experimentally the annotation of the arabidopsis genome by sequencing full-length cDNAs and by hybridization analysis of whole genome tiling arrays. Concomitantly with the verification of the annotation, the project allowed the construction of ~12K ORF clones for initiating Arabidopsis proteomics. The development of whole genome arrays (WGAs) was the first for any higher eukaryotic organism and provided the community with a tool not only for mapping the transcriptional units, but also for global mapping of DNA binding sites, QTLs, mutations, and small RNAs. In addition, during this project the laboratory produced the first software for analyzing the WGA hybridization data and established a database for Arabidopsis genomic analysis in my lab.

The genomic resources that were developed facilitated the two long-term biology projects of my laboratory. We have been focused on isolating loss of function mutations for a large number of the Aux/IAA and ARF gene family members. These families have 28 and 23 members, respectively. They encode global transcriptional regulators involved in numerous aspects of auxin biology. We are aiming to elucidate their biological function by constructing higher order mutations. The laboratory discovered both groups of genes and has carried out pioneering molecular work with some of them. These factors have the capacity to homo- and heterodimerize with the potential to provide ~4,000 possible homo- and heterodimers. This capacity offers an explanation for the pleiotropic effects of auxin. We are currently attempting to elucidate whether this capacity is detected in planta using bimolecular fluorescence complementation (BiFC). In addition we are constructing the Interactome among the Aux.IAAs,ARFS and TIRs/ARBs (auxin receptors binding proteins) using the yeast two hybrid system.

The availability of WGAs has allowed us to carry out studies on global mapping of the DNA binding sites of one of the ARF proteins, ARF2, using CHiP: Chip experiments. It is not known which type of genes each of the ARF gene family members regulates. Chip:Chip experiments using WAGs have the potential to provide fundamental information for the downstream events in auxin action. Lastly, the laboratory has cloned two auxin hypersensitive mutants, age1 and age2. We isolated both mutations in 1998 by a novel screen. AGE1 encodes the equivalent of RAD3 and XPD in yeast and humans, respectively. AGE1 is one of the nine subunits of the core transcription factor TFIIH. This protein is bifunctional; it has a helicase activity and also participates in DNA repair. AGE2 is a SAM decarboxylase. We are currently characterizing both genes molecularly and genetically.

The second project is the understanding of ethylene biosynthesis at the level of ACC synthase. The completion of the Arabidopsis genome sequence revealed the presence of 9 ACS genes. Eight of them are enzymatically active, and one inactive. We are investigating why plants such as Arabidopsis encode nine isozymes for producing ethylene. This question has been raised for numerous multigene families since the discovery of the Arabidopsis genome sequencing revealed that many proteins are encoded by multigene families. The ACS family is relatively small enough to carry out studies with the entire family. We hypothesize that each isozyme is expressed in cells/tissues that have the appropriate biochemical environment for its optimum function. For example, low Km (high affinity) isozymes may be expressed in tissues with a low SAM concentration and vice versa. Biochemical characterization of all Arabidopsis ACS isozymes shows a high degree of biochemical diversity. ACS is a homodimer with shared active sites. We recently discovered that the 9 ACS polypeptides can heterodimerize. The analysis was carried out by intermolecular complementation experiments and showed that active heterodimers are formed only among the ACS isozymes that belong to the same phylogenetic branch. The inactivity of certain heterodimers is not due to the absence of heterodimers but rather to the inactivity of shared active sites. We found that the 9 ACS polypeptides encoded by the At genome have the capacity to form 25 active homo- and heterodimers. Experiments are in progress for searching the formation of ACS heterodimers in planta using BiFC. The possible formation of ACS heterodimers is also supported by our tissue-specific expression experiments that indicate overlapping expression patterns among the various ACS genes. Do the heterodimers have distinct biochemical properties? We are currently determining the biochemical properties of the ACS heterodimers. In the near future, we plan to use nano-technological approaches to determine solute concentration in individual plant cells, for example, to determine SAM concentrations in individual cells. Furthermore X-ray crystallographic studies are currently in progress for understanding the inactivity of certain heterodimers at the structural level.

Okushima, Y., Fukaki, H., Onada,M., Theologis, A. and Tasaka, M., 2007. ARF7 and ARF19 Regulate Lateral Root Formation via Direct Activation of LBD/ASL Genes in Arabidopsis. Plant Cell, 19: 118-130. pdf1578k

Overvoorde, P. J , Okushima, Y.,.Alonso, J. M., Chan, A., Chang, C., Ecker, J. R., Hughes, B., Lui, A., Nguyen, D., Onodera, C., Quach, H., Smith, A., Yu, G., and Theologis, A. 2005. Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) Gene Family Members in Arabidopsis thaliana. Plant Cell, 17: 3282-3300. pdf1061k

Fukaki, H., Nakao, Y., Okushima Y., Theologis, A., Tasaka, M., 2005. Tissue specific expression of stabilized SOLITARY-ROOT/IAA14 alters lateral root development in Arabidopsis, Plant J.,44, 382-395. pdf617k

Okushima, Y., Mitina, I., Quach, H. and Theologis, A. 2005. AUXIN RESPONSE FACTOR 2 (ARF2): a pleiotropic developmental regulator. Plant J., 43:29-46. pdf1404k

Okushima, Y., Overvoorde, P. J., Arima, K., Alonso, J. M., Chan, A., Chang, C., Ecker, J. R., Hughes, B., Lui, A., Nguyen, D., Onodera, C., Quach, H., Smith, A., Yu, G., and Theologis A., 2005, Functional Genomic Analysis of the AUXIN RESPONSE FACTOR (ARF) Gene Family Members in Arabidopsis thaliana: Unique and Overlapping Functions of ARF7 and ARF19. Plant Cell, 17: 444-463. pdf1334k

Tsuchisaka, A. and Theologis, A. 2004. Unique and Overlapping Expression Patterns among the Arabidopsis 1-Amino-Cyclopropane-1-Carboxylate Synthase Gene Family Members. Plant Physiology, 136: 2982–3000. pdf1055k

Armstrong, J. I., Yuan, S., Dale, J. M., Tanner, V. N. and Theologis, A. 2004. Identification of inhibitors of auxin transcriptional activation by means of chemical genetics in Arabidopsis. Proc. Natl. Acad. Sci. USA 101: 14978-14983. pdf481k

Tsuchisaka, A., and Theologis, A. 2004. Heterodimeric interactions among the 1-amino-cyclopropane-1-carboxylate synthase polypeptides encoded by the Arabidopsis gene family. Proc. Natl. Acad. Sci. USA, 101: 2275-2280. pdf642k

Theologis, A. and Davis, R. W., 2004.To Give or Not to Give? That Is the Question. Plant Physiol., 135: 4-9, 2004 pdf81k

Yamagami, T., Tsuchisaka, A., Yamada, K., Haddon, W. F., Harden, L. A. and Theologis, A. 2003. Biochemical Diversity among the 1-Amino-cyclopropane-1-Carboxylate Synthase Isozymes Encoded by the Arabidopsis Gene Family. J. Biol. Chem., 278: 49102-49112. pdf1405k

Yamada, K., Lim, J., Dale, J. M. et al. 2003. Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome, Science, 302: 842-846. pdf1378k

Theologis, A. 2001. Goodbye to ‘one by one’ genetics. Genome Biology, 2:2004.1-2004.9. pdf129k

Ouellet, F., Overvoorde, P. and Theolgis, A. 2001. IAA17/AXR3: Biochemical insight into an auxin mutant phenotype. Plant Cell, 13: 829-841. pdf3200k

Theologis, A., Ecker, J. R., Palm, C. J. et al. 2000. Sequence and analysis of chromosome 1 of the plant arabidopsis thaliana. Nature, 408:816-820. pdf279k

Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant arabidopsis thaliana. Nature, 408:796-815. pdf403k

Cho, R. J., Mindrinos, M., Richards, D. R., Sapolsky, R. J., Anderson, M., Drenkard, E., Dewdney, L., Reuber, T. L., Stammers, M., Federspiel, N., Theologis, A., Yang, W. H., Hubbell, E., Au, M., Chung, E. Y., Lashkari, D., Lemieux, B., Dean, C., Lipshutz, R. J., Ausubel, F. M., Davis, R. W. and Oefner, P. J. 1999. Genome-wide mapping with biallelic markers in arabidopsis thaliana. Nature Genetics, 23:203-207. pdf161k

Morgan, K. E., Zarembinski, T. I., Theologis, A. and Abel, S. 1999. Biochemical characterization of recombinant polypeptides corresponding to the predicted βαα fold in Aux/IAA proteins. FEBS Letters, 454:283-287. pdf436k

Theologis, A. 1998. Ethylene signaling: Redundant receptors all have their say. Curr. Biol., 8:R875-R878. pdf91k

Oono, Y., Chen, Q. G., Overvoorde, P. J., Köhler, C. and Theologis, A. 1998. age mutants of Arabidopsis exhibit altered auxin-regulated gene expression. Plant Cell, 10:1649-1662.

Tarun, A. S., Lee, J. S. and Theologis, A. 1998. Random Mutagenesis of 1-Aminocyclopropane-1-Carboxylate Synthase: A Key Enzyme in Ethylene Biosynthesis. Proc. Natl. Acad. Sci. USA, 95:9796-9801. pdf417k

Vogel, J. P., Woeste, K E., Theologis, A., Kieber, J. J. 1998. Recessive and dominant mutations in the ethylene biosynthetic gene ACS5 of Arabidopsis confer cytokinin insensitivity and ethylene overproduction, respectively. Proc. Natl. Acad. Sci. USA, 95:4766-4771. pdf259k

Tarun, A. S. and Theologis, A. 1998. Complementation analysis of mutants of 1-aminocyclopropane-1-carboxylate synthase reveals the enzyme is a dimer with shared active sites. J. Biol. Chem., 273:12509-12514. pdf617k

Kim, J., Harter, K. and Theologis, A. 1997. Protein-protein interactions among the Aux/IAA proteins. Proc. Natl. Acad. Sci. USA, 94:11786-11791. pdf4220k

Zarembinski, T. and Theologis, A. 1997. Expression characteristics of OS-ACS1 and OS-ACS2, two members of the 1-aminocyclopropane-1-carboxylate synthase gene family in rice (oryza sativa L. cv. Habiganj Aman II.) during partial submergence. Plant Mol. Biol., 33:71-77. pdf2895k