Recent Publications

Selected Publications

Lee KH, Minami A, Marshall RS, Book AJ, Farmer LM, Walker JM, Vierstra RD. (2011) The RPT2 subunit of the 26S proteasome directs complex assembly, histone dynamics, and gametophyte and sporophyte development in Arabidopsis. Plant Cell. 12:4298-317.

Suttangkakul A, Li F, Chung T, Vierstra RD. (2011) The ATG1/ATG13 protein kinase complex is both a regulator and a target of autophagic recycling in Arabidopsis. Plant Cell. 10:3761-79.

Hua Z, Zou C, Shiu SH, Vierstra RD. (2011) Phylogenetic comparison of F-Box (FBX) gene superfamily within the plant kingdom reveals divergent evolutionary histories indicative of genomic drift. PLoS ONE. 6(1): e16219.

Miller MJ, Barrett-Wilt GA, Hua Z, Vierstra RD. (2010) Proteomic analyses identify a diverse array of nuclear processes affected by small ubiquitin-like modifier conjugation in Arabidopsis. Proc Natl Acad Sci U S A. 38:16512-7.

Li H, Zhang J, Vierstra RD, Li H (2010) Quaternary organization of a phytochrome dimer as revealed by cryoelectron microscopy. Proc Natl Acad Sci U S A. 24:10872-7.

Book AJ, Gladman NP, Lee SS, Scalf M, Smith LM, Vierstra RD (2010) Affinity purification of the Arabidopsis 26 S proteasome reveals a diverse array of plant proteolytic complexes. J. Biol. Chem. 33:25554-69.

Chung T, Phillips AR, Vierstra RD (2010) ATG8 lipidation and ATG8-mediated autophagy in Arabidopsis require ATG12 expressed from the differentially controlled ATG12A AND ATG12B loci. Plant J. 3:483-93.

Farmer LM, Book AJ, Lee KH, Lin YL, Fu H, Vierstra RD (2010) The RAD23 Family Provides an Essential Connection between the 26S Proteasome and Ubiquitylated Proteins in Arabidopsis. Plant Cell 1:124-42.

Ulijasz AT, Cornilescu G, Cornilescu CC, Zhang J, Rivera M, Markley JL, Vierstra RD (2010) Stuctural basis for the photoconversion of a phytochrome to the activated Pfr form. Nature 463:250-254

Ulijasz, A.T., G. Cornilescu, D. von Stetten, C. Cornilescu, F. Velazquez, J. Zhang, R.J. Stankey, M. Rivera, P. Hildebrandt, and R.D. Vierstra (2009) Cyanochromes:blue-green light photoreversible phytochromes defined by a stable double cysteine linkage to a phycoviolobilin-type chromophore. J. Biol. Chem. 284: 29757-72

Vierstra, R.D. (2009) The ubiquitin/26S proteasome system at the nexus of plant development. Nat. Rev. Mol. Cell Biol. 10: 385-397.

Saracco, S.A., M. Hansson, M. Scalf, J.M. Walker, L.M. Smith, and R.D. Vierstra (2009) Tandem affinity purification and mass spectrometric analysis of ubiquitylated proteins in Arabidopsis. Plant J. 59: 344-358.

Book, A.J., J. Smalle, K.H. Lee, P. Yang, J.M. Walker, S. Casper, J.H. Holmes L.R. Russo, Z.W. Buzzinotti, P.D. Jenik, and R.D. Vierstra (2009) The RPN5 subunit of the 26S proteasome is essential for gametogenesis, sporophyte development, and complex assembly in Arabidopsis. Plant Cell 21: 460-478.

Christians, M.J., D.J. Gingerich, M. Hansen, B.M. Binder, J. J. Kieber, and R.D. Vierstra (2009) The BTB ubiquitin ligases ETO1, EOL1 and EOL2 act collectively to regulate ethylene biosynthesis in Arabidopsis by controlling type-2 ACC synthase levels.Plant J. 57: 332-345.

Chung, T., A. Suttangkakul, and R.D. Vierstra (2009) The ATG autophagic conjugation system in maize: Atg transcripts and abundance of the ATG8-lipid adduct are regulated by development and nutrient availability. Plant Physiol. 149: 220-234.

Cornilescu, G., A.T. Ulijasz, C. Cornilescu, J.L. Markley, and R.D. Vierstra (2008) The solution structure of a cyanobacterial phytochrome GAF domain in the red light-absorbing ground state. J. Mol. Biol. 383: 403-413.

Ulijasz, A.T., G. Cornilescu, D. von Stetten, S. Kaminski, M.A. Mroginski, J. Zhang, D. Bhaya, P. Hildebrandt, and R.D. Vierstra (2008) Characterization of two thermostable cyanobacterial phytochromes reveals global movements in the chromophore binding domain during photoconversion. J. Biol. Chem. 283: 21251-21266.

Phillips, A.R., A, Suttangkakul, and R.D. Vierstra (2008) The ATG12-conjugating enzyme ATG10 is essential for autophagic vesicle formation in Arabidopsis thaliana. Genetics. 178: 1339-1353.

Wagner, J.R., J. Zhang, D. von Stetten, M. Gunter, D.H. Murida, M.A. Mroginski, J.R. Walker, K.T. Forest, P. Hildebrandt, and R.D. Vierstra (2008) Mutational analysis of Deinococcus radiodurans bacteriophytochrome reveals key amino acids necessary for the photochromicity and proton exchange cycle of phytochromes. J. Biol. Chem. 283: 12212-12226.

Gingerich, D.J., K. Hanada, S.H. Shiu, and R.D. Vierstra (2007) Large-scale, lineage-specific expansion of the Bric-a Brac/Tramtrack/Broad Complex (BTB) ubiquitin-ligase gene family in rice. Plant Cell. 19: 2329-2348.

Doelling, J. H., A.R. Phillips, G. Soyler-Ogretim, J. Wise, J. Chandler, J. Callis, M. Otegui, and R.D. Vierstra (2007) The ubiquitin-specific protease subfamily UBP3/UBP4 is essential for pollen development and transmission in Arabidopsis thaliana. Plant Physiol. 145: 801-183.

Saracco, S.A., M. J. Miller, M. Kurepa, and R.D. Vierstra (2007) Genetic analysis of the SUMOylation in Arabidopsis: conjugation of SUMO1 and 2 to nuclear proteins is essential. Plant. Physiol. 145: 119-134.

Domagalska, M.A., F.M. Schomburg, R.M. Amasino, R.D. Vierstra, F. Nagy, and S.J. Davis (2007) Attenuation of brassinosteriod signaling enhances FLC expression and delays flowering. Development 134: 2841-2850. (paper featured on front cover)

Yang, P. J. Smalle, S.-S. Lee, N. Yan, T.J. Emborg, and R.D. Vierstra (2007) Ubiquitin carboxy-terminal hydrolase 1 and 2 affect shoot architecture in Arabidopsis. Plant J. 51: 441-457.

Wagner, J.M., J. Zhang, J.S. Brunzelle, R.D. Vierstra, and K.T. Forest (2007) High resolution structure of Deinococcus bacteriophytochrome yields new insights in phytochrome architecture and evolution. J. Biol. Chem. 282: 12298-12309.

Walker, J.M., and R.D. Vierstra (2007) Ubiquitin-based vectors for the stoichiometric production of multiple proteins in plants. Plant Biotech. J. 5: 413-421

Binder, B.M., J.M. Gagne, J.M. Walker, T.J. Emborg, G. Hemmann, A.B. Bleecker, and R.D. Vierstra (2007) The Arabidopsis EIN3-binding F-box proteins, EBF1 and EBF2 have distinct but overlapping roles in the control of ethylene signaling. Plant Cell 19: 509-523.

Stone, S.L., L. Williams, L.M. Farmer, R.D. Vierstra, and J. Callis (2006) KEEP ON GOING, a RING E3 ligase essential for Arabidopsis growth and development, is involved in abscisic acid signaling. Plant Cell. 18: 3415-3428.

Potuschak, T., A. Vansiri, B.M. Binder, E. Lechner, R.D. Vierstra, and P. Genschik (2006) The exonuclease XRN4 is a component of the ethylene response pathway in Arabidopsis. Plant Cell 18: 3047-3057.

Downes, B, S.A. Sarracco, S.-S. Lee, D.N. Crowell, and R.D. Vierstra (2006) MUBs, a family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation. J. Biol. Chem. 281: 27145-27157. (paper featured on front cover)

Emborg, T, J.M. Walker, B. Noh, and R.D. Vierstra (2006) Multiple heme oxygenase family members contribute to the biosynthesis of the phytochrome chromophore in Arabidopsis. Plant Physiol. 140: 856-868.

Froehlich, A.C. B. Noh, R.D. Vierstra, J. Loros, and J.C. Dunlap (2005) Genetic and molecular analysis of phytochromes from the filamentous fungus Neurospora crassa. Eukaroytic Cell 4: 2140-2152.

Karniol, B., and R.D. Vierstra (2005) Functional analysis of bacteriophytochromes In: Photomorphogenesis in Plant and Bacteria: Function and Signal Transduction Mechanisms (E. Schafer ed) Kulwer Academic Publishers, Dordrecht, The Netherlands. pgs 65-98..

Wagner, J.R., J.S. Brunzelle, K.T. Forest, and R.D. Vierstra (2005) A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438: 325-331. (article featured by The Plant Cell)

Karniol, B., J. Wagner, J. M. Walker, and R.D. Vierstra (2005) Phylogenetic analysis of thephytochrome superfamily reveals distinct subfamilies of microbial photoreceptors. Biochem.J. 392: 103-116.

Thompson, A.R., J.H. Doelling, A, Suttangkakul, and R.D. Vierstra (2005) Autophagic nutrient recycling in Arabidopsis thaliana directed by the ATG8 and ATG12 conjugation pathways. Plant Physiol. 138: 2097-2110.

Book, A.J., P. Yang, M. Scarf, L.M. Smith, and R.D. Vierstra (2005) Tripeptidyl peptidase (TPP)-II, an oligomeric protease complex from Arabidopsis. Plant Physiol. 138: 1046-1057.

Gingerich, D.J., J.M. Gagne, H. Helleman, M. Estelle, L. Ma, and R.D. Vierstra (2005) Cullin 3A and B assemble with members of the broad complex/tramtrack/bric-a-brac (BTB) protein family to form essential ubiquitin-protein ligases in Arabidopsis. J. Biol Chem. 280: 18810-18821.

Thompson, A.R., and R.D. Vierstra (2005) Autophagic recycling: lessons from yeast help define the process in plants. Curr. Opin. Plant Biol. . 8: 165-173.

Vierstra R.D., and B. Karniol (2005) Phytochromes in microorganisms. In: Handbook of Photosensory Receptors (W.R. Briggs and J.L. Spudich, eds). Wiley-VCH Press, Wehiheim Germany. pp 171-195.

Gagne, J.M., J. Smalle, D. J. Gingerich, J.M. Walker, S.-D. Yoo, S. Yanagisawa, and R.D. Vierstra (2004) Arabidopsis EIN3-binding F-box 1 and 2 form ubiquitin-protein ligases that repress ethylene action and promote growth by directing EIN3 degradation. Proc.Natl. Acad. Sci. USA 101: 6803-6808.

Yang, P., H. Fu, J. M. Walker, C. M. Papa, J. Smalle, Y.-M. Ju, and R. D. Vierstra (2004) Purification of the Arabidopsis 26S proteasome: biochemical and molecular analyses revealed the presence multiple isoforms. J. Biol. Chem. 279: 6401-6413.

Smalle, J., and R.D. Vierstra (2004) The ubiquitin 26S proteasome proteolytic pathway. Ann. Rev. Plant Biol. 55: 555-590.

Karniol, B. and R. D. Vierstra (2004) The HWE histidine kinases, a new family of bacterial two-component sensor kinases with potentially diverse roles in environmental signaling. J. Bactertiol. 186: 445-453 (paper was chosen as the feature article).

Vierstra, R.D. (2003) The ubiquitin/26S proteasome pathway, the complex last chapter in the life of many plant proteins. Trends Plant Sci. 8: 135-142

Newbigin, E., and R. D. Vierstra (2003) Plant reproduction–sex and self denial. Nature 423: 229-230.

Downes, B. P., R. M. Stupar, D. J. Gingerich, and R. D. Vierstra (2003) The HECT ubiquitin-protein ligase family in Arabidopsis: UPL3 has a specific role in trichome development. Plant J. 35: 729-742.

Smalle, J., M. Kurepa, P. Yang, T. Emborg, E. Babyichuk, S. Kushnir, and R.D. Vierstra (2003) The pleiotropic role in the 26S proteasome subunit RPN10 in Arabidopsis thaliana growth and development supports a substrate-specific function in abscisic acid signaling. Plant Cell 15: 965-980.

Karniol, B. and R. D. Vierstra (2003) The pair of bacteriophytochrome from Agrobacteriumtumefaciens are histidine kinases with opposing photobiological properties. Proc. Natl. Acad. Sci. USA 100: 2807-2812.

Kurepa, J., J. M. Walker, J. Smalle, M. M. Gosink, S. J. Davis, and R.D. Vierstra (2003) Small ubiquitin-like modifier (SUMO) protein modification system in Arabidopsis: accumulation of SUMO conjugates is increased by stress. J. Biol. Chem. 278: 6862-6872.

Gagne, J., B. P. Downes, S.-H. Shiu, A. M. Durski and R. D. Vierstra (2002) The F-Box subunit of the SCF E3 complex is encoded by a diverse superfamily of genes in Arabidopsis. Proc. Natl. Acad. Sci USA 99: 11519-11524.

Doelling, J.N., J.M. Walker, E.M. Friedman, A.R. Thompson, and R.D. Vierstra (2002) The APG12/8-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana. J. Biol. Chem. 277: 33105-33114.

Smalle, J, M. Kurepa, P. Yang, E. Babyichuk, S. Kushnir, A. Durski, and R.D. Vierstra (2002) The cytokinin response of Arabidopsis involves the 26S proteasome subunit RPN12a. Plant Cell 14: 17-32.

Fu, H.-Y., N. Reiss, M.H. Glickman, Y. Lee, and R.D. Vierstra (2001) Mapping subunit interactions within the regulatory particle of the 26S proteasome and the COP9-signalosome: comparisons reveal a conserved core structure. EMBO J. 24: 7096-7107.

Bhoo, S.-H., S.J. Davis, J.M. Walker, B. Karniol, and R.D. Vierstra (2001) Bacterio-phytochromes are photochromic histidine kinases using a biliverdin chromophore. Nature 414:776-779.

Vener, A.V., A. Harms, M.R. Sussman, and R.D. Vierstra (2001) Mass spectrometric resolutionof reversible phosphorylation in photosynthetic membranes of Arabidopsis thaliana. J. Biol. Chem. 276: 6959-6966.

Davis, S.J., A. Vener, and R.D. Vierstra (1999) Bacteriophytochromes, phytochrome-like photoreceptors from non-photosynthetic eubacteria. Science 286: 2517-2520.

Davis, S.J., J. Kurepa, and R.D. Vierstra (1999) The Arabidopsis thaliana HY1 locus, required for phytochrome chromophore biosynthesis, encodes a protein related to heme oxygenases. Proc. Natl. Acad. Sci. USA. 96: 6541-6546.

All Publications (Pubmed)