8/19/05 (VJC)
Recommendation of new papers for Faculty 1000 March-August 2005.

The mRNA of the Arabidopsis Gene FT Moves from Leaf to Shoot Apex and Induces Flowering
Sciencexpress / www.sciencexpress.org / 11 August 2005 /

Tao Huang, Henrik Böhlenius, Sven Eriksson, François Parcy, Ove Nilsson

Day length controls flowering time in many plants. The day-length signal is perceived in the leaf, but how this signal is transduced to the shoot apex where floral initiation occurs is not known. In Arabidopsis, the daylength response depends on the induction of the FLOWERING LOCUS T (FT) gene. We show here that local induction of FT in a single Arabidopsis leaf is sufficient to trigger flowering. The FT mRNA is transported to the shoot apex, where downstream genes are activated. These data suggest that the FT mRNA is an important component of the elusive “florigen” signal that moves from leaf to shoot apex.

RAC GTPases in Tobacco and Arabidopsis Mediate Auxin-Induced Formation of Proteolytically Active Nuclear Protein Bodies That Contain AUX/IAA Proteins
The Plant Cell, Vol. 17, 2369–2383, August 2005

Li-zhen Tao, Alice Y. Cheung,1 Candida Nibau, and Hen-ming Wu

Auxin signaling relies on ubiquitin ligase SCFTIR1-mediated 26S proteasome-dependent proteolysis of a large family of short-lived transcription regulators, auxin/indole acetic acid (Aux/IAA), resulting in the derepression of auxin-responsive genes. We have shown previously that a subset of Rac GTPases is activated by auxin, and they in turn stimulate auxinresponsive gene expression. We show here that increasing Rac signaling activity promotes Aux/IAA degradation, whereas downregulating that activity results in the reduction of auxin-accelerated Aux/IAA proteolysis. Observations reported here reveal a novel function for these Rac GTPases as regulators for ubiquitin/26S proteasome-mediated proteolysis and further consolidate their role in auxin signaling. Moreover, our study reveals a cellular process whereby auxin induces and Rac GTPases mediate the recruitment of nucleoplasmic Aux/IAAs into proteolytically active nuclear protein bodies, into which components of the SCFTIR1, COP9 signalosome, and 26S proteasome are also recruited.


Stomatal Patterning and Differentiation by Synergistic Interactions of Receptor Kinases
8 JULY 2005 VOL 309 SCIENCE, 290-293

Elena D. Shpak, Jessica Messmer McAbee, Lynn Jo Pillitteri, Keiko U. Torii

Coordinated spacing and patterning of stomata allow efficient gas exchange between plants and the atmosphere. Here we report that three ERECTA (ER)– family leucine-rich repeat–receptor-like kinases (LRR-RLKs) together control stomatal patterning, with specific family members regulating the specification of stomatal stem cell fate and the differentiation of guard cells. Loss-offunction mutations in all three ER-family genes cause stomatal clustering.
Genetic interactions with a known stomatal patterning mutant too many mouths (tmm) revealed stoichiometric epistasis and combination-specific neomorphism. Our findings suggest that the negative regulation of ER-family RLKs by TMM, which is an LRR receptor–like protein, is critical for proper stomatal differentiation.


R gene expression induced by a type-III effector triggers disease resistance in rice
Nature Vol 435|23 June 2005|, 1122-1125

Keyu Gu, Bing Yang, Dongsheng Tian1, Lifang Wu, Dongjiang Wang, Chellamma Sreekala, Fan Yang, Zhaoqing Chu, Guo-Liang Wang, Frank F. White & Zhongchao Yin

Disease resistance (R) genes in plants encode products that specifically recognise incompatible pathogens and trigger a cascade of events leading to disease resistance in the host plant. R-gene specificity is dictated by both host R genes and cognate avirulence (avr) genes in pathogens2,3. However, the basis of gene-for-gene specificity is not well understood. Here, we report the cloning of the R gene Xa27 from rice and the cognate avr gene avrXa27 from Xanthomonas oryzae pv. oryzae. Resistant and susceptible alleles of Xa27 encode identical proteins. However, expression of only the resistant allele occurs when a rice plant is challenged by bacteria harbouring avrXa27, whose product is a nuclear localized type-III effector. Induction of Xa27 occurs only in the immediate vicinity of infected tissue, whereas ectopic expression of Xa27 resulted in resistance to otherwise compatible strains of the pathogen. Thus Xa27 specificity towards incompatible pathogens involves the differential expression of the R gene in the presence of the AvrXa27 effector.


Highly efficient endogenous human genecorrection using designed zinc-finger nucleases
Nature Vol 435|2 June 2005| 646-651

Fyodor D. Urnov, Jeffrey C. Miller, Ya-Li Lee, Christian M. Beausejour, Jeremy M. Rock, Sheldon Augustus, Andrew C. Jamieson, Matthew H. Porteus2, Philip D. Gregory1 & Michael C. Holmes

Permanent modification of the human genome in vivo is impractical owing to the low frequency of homologous recombination in human cells, a fact that hampers biomedical research and progress towards safe and effective gene therapy. Here we report a general solution using two fundamental biological processes: DNA recognition by C2H2 zinc-finger proteins and homology-directed repair of DNA double-strand breaks. Zinc-finger proteins engineered to recognize a unique chromosomal site can be fused to a nuclease domain, and a double-strand break induced by the resulting zinc-finger nuclease can create specific sequence alterations by stimulating homologous recombination between the chromosome and an extrachromosomal DNA donor. We show that zinc-finger nucleases designed against an X-linked severe combined immune deficiency (SCID) mutation in the IL2Rg gene yielded more than 18% gene-modified human cells without selection. Remarkably, about 7% of the cells acquired the desired genetic modification on both X chromosomes, with cell genotype accurately reflected at the messenger RNA and protein levels. We observe comparably high frequencies in human T cells, raising the possibility of strategies based on zinc-finger nucleases for the treatment of disease.


Autophagy Regulates Programmed Cell Death during the Plant Innate Immune Response
Cell, Vol. 121, 567–577, May 20, 2005

Yule Liu, Michael Schiff, Kirk Czymmek, Zsolt Tallóczy, Beth Levine, and S.P. Dinesh-Kumar

The plant innate immune response includes the hyperpersensitive response (HR), a form of programmed cell death (PCD). PCD must be restricted to infection sites to prevent the HR from playing a pathologic rather than protective role. Here we show that plant BECLIN 1, an ortholog of the yeast and mammalian autophagy gene ATG6/VPS30/beclin 1, functions to restrict HR PCD to infection sites. Initiation of HR PCD is normal in BECLIN 1-deficient plants, but remarkably, healthy uninfected tissue adjacent to HR lesions and leaves distal to the inoculated leaf undergo unrestricted PCD. In the HR PCD response, autophagy is induced in both pathogen-infected cells and distal uninfected cells; this is reduced in BECLIN 1-deficient plants. The restriction of HR PCD also requires orthologs of other autophagy-related genes including PI3K/VPS34, ATG3, and ATG7. Thus, the evolutionarily conserved autophagy pathway plays an essential role in plant innate immunity and negatively regulates PCD.

Induction of Protein Secretory Pathway Is Required for Systemic Acquired Resistance
13 MAY 2005 VOL 308 SCIENCE, 1036-1040

Dong Wang, Natalie D. Weaver, Meenu Kesarwani, Xinnian Dong

In plants, systemic acquired resistance (SAR) is established as a result of NPR1-regulated expression of pathogenesis-related (PR) genes. Using gene expression profiling in Arabidopsis, we found that in addition to controlling the expression of PR genes, NPR1 also directly controls the expression of the protein secretory pathway genes. Up-regulation of these genes is essential for SAR, because mutations in some of them diminished the secretion of PR proteins (for example, PR1), resulting in reduced resistance. We provide evidence that NPR1 coordinately regulates these secretion-related genes through a previously undescribed cis-element. Activation of this cis-element is controlled by a transcription factor that is translocated into the nucleus upon SAR induction.

The F-box protein TIR1 is an auxin receptor
Nature Vol 435|26 May 2005 | 441-115

Nihal Dharmasiri, Sunethra Dharmasiri & Mark Estelle

The plant hormone auxin regulates diverse aspects of plant growth and development. Recent studies indicate that auxin acts by promoting the degradation of the Aux/IAA transcriptional repressors through the action of the ubiquitin protein ligase SCFTIR1. The nature of the signalling cascade that leads to this effect is not known. However, recent studies indicate that the auxin receptor and other signalling components involved in this response are soluble factors. Using an in vitro pull-down assay, we demonstrate that the interaction between transport inhibitor response 1 (TIR1) and Aux/IAA proteins does not require stable modification of either protein. Instead auxin promotes the Aux/IAA–SCFTIR1 interaction by binding directly to SCFTIR1. We further show that the loss of TIR1 and three related F-box proteins eliminates saturable auxin binding in plant extracts. Finally, TIR1 synthesized in insect cells binds Aux/IAA proteins in an uxindependent manner. Together, these results indicate that TIR1 is an auxin receptor that mediates Aux/IAA degradation and auxin-regulated transcription.


The Arabidopsis F-box protein TIR1 is an auxin receptor
Nature Vol 435 | 26 May 2005 | 446-451

Stefan Kepinski & Ottoline Leyser

Despite 100 years of evidence showing a pivotal role for indole-3-acetic acid (IAA or auxin) in plant development, the mechanism of auxin perception has remained elusive. Central to auxin response are changes in gene expression, brought about by auxin-induced interaction between the Aux/IAA transcriptional repressor proteins and the ubiquitin–ligase complex SCFTIR1, thus targeting for them proteolysis. Regulated SCF-mediated protein degradation is a widely occurring signal transduction mechanism. Target specificity is conferred by the F-box protein subunit of the SCF (TIR1 in the case of Aux/IAAs) and there are multiple F-box protein genes in all eukaryotic genomes examined so far. Although SCF–target interaction is usually regulated by signal-induced modification of the target, we have previously shown that auxin signalling involves the modification of SCFTIR1. Here we show that this modification involves the direct binding of auxin to TIR1 and thus that TIR1 is an auxin receptor mediating transcriptional responses to auxin.


Activation of a Phytopathogenic Bacterial Effector Protein by a Eukaryotic Cyclophilin
22 APRIL 2005 VOL 308 SCIENCE, 548-550

Gitta Coaker, Arnold Falick, Brian Staskawicz

Innate immunity in higher plants invokes a sophisticated surveillance system capable of recognizing bacterial effector proteins. In Arabidopsis, resistance to infection by strains of Pseudomonas syringae expressing the effector AvrRpt2 requires the plant resistance protein RPS2. AvrRpt2 was identified as a putative cysteine protease that results in the elimination of the Arabidopsis protein RIN4. RIN4 cleavage serves as a signal to activate RPS2-mediated resistance.
AvrRpt2 is delivered into the plant cell, where it is activated by a eukaryotic factor that we identify as cyclophilin. This activation of AvrRpt2 is necessary for protease activity. Active AvrRpt2 can then directly cleave RIN4.


BZR1 Is a Transcriptional Repressor with Dual Roles in Brassinosteroid Homeostasis and Growth Responses
11 MARCH 2005 VOL 307 SCIENCE, 1634-1638

Jun-Xian He, Joshua M. Gendron, Yu Sun, Srinivas S. L. Gampala, Nathan Gendron, Catherine Qing Sun, Zhi-Yong Wang

Brassinosteroid (BR) homeostasis and signaling are crucial for normal growth and development of plants. BR signaling through cell-surface receptor kinases and intracellular components leads to dephosphorylation and accumulation of the nuclear protein BZR1. How BR signaling regulates gene expression, however, remains unknown. Here we show that BZR1 is a transcriptional repressor that has a previously unknown DNA binding domain and binds directly to the promoters of feedback-regulated BR biosynthetic genes. Microarray analyses identified additional potential targets of BZR1 and illustrated, together with physiological studies, that BZR1 coordinates BR homeostasis and signaling by playing dual roles in regulating BR biosynthesis and downstream growth responses.


SREBP Pathway Responds to Sterols and Functions as an Oxygen Sensor in Fission Yeast
Cell, Vol. 120, 831–842, March 25, 2005

Adam L. Hughes, Bridget L. Todd, and Peter J. Espenshade

Cholesterol and fatty acid synthesis in mammals are controlled by SREBPs, a family of membrane bound transcription factors. Our studies identified homologs of SREBP, its binding partner SCAP, and the ER retention protein Insig in Schizosaccharomyces pombe, named sre1+, scp1+, and ins1+. Like SREBP, Sre1 is cleaved and activated in response to sterol depletion in a Scp1-dependent manner. Microarray analysis revealed that Sre1 activates sterol biosynthetic enzymes as in mammals, and, surprisingly, Sre1 also stimulates transcription of genes required for adaptation to hypoxia. Furthermore, Sre1 rapidly activates target genes in response to low oxygen and is itself required for anaerobic growth. Based on these findings, we propose and test a model in which Sre1 and Scp1 monitor oxygen-dependent sterol synthesis as an indirect measure of oxygen supply and mediate a hypoxic response in fission yeast.