TY - JOUR ID - 1469 TI - S-RNase-like Sequences in Styles of Coffea (Rubiaceae). Evidence for S-RNase Based Gametophytic Self-Incompatibility? JO - Trop. Plant Biol. PY - 2011 SP - 237-249 AU - Asquini, E. AU - Gerdol, M. AU - Gasperini, D. AU - Igic, B. AU - Graziosi, G. AU - Pallavicini, A. AU - VL - 4 UR - DO - 10.1007/s12042-011-9085-2 AB - Although RNase-based self-incompatibility (SI) is suspected to operate in a wide group of plant families, it has been characterized as the molecular genetic basis of SI in only three distantly related families, Solanaceae, Plantaginaceae, and Rosaceae, all described over a decade ago. Previous studies found that gametophytic SI, controlled by a multi-allelic S-locus, operates in the coffee family (Rubiaceae). The molecular genetic basis of this mechanism remains unknown, despite the immense importance of coffee as an agricultural commodity. Here, we isolated ten sequences with features of T2-S-type RNases from two Coffea species. While three of the sequences were identified in both species and clearly do not appear to be S-locus products, our data suggest that six sequences may be S-alleles in the self-incompatible C. canephora, and one may be a relict in the self-compatible C. arabica. We demonstrate that these sequences show style-specific expression, display polymorphism in C. canephora, and cluster with S-locus products in a phylogenetic analysis that includes other plant families with RNase-based SI. Although our results are not definitive, in part because the available plant materials were limited and data patterns relatively complex, our results strongly hint that RNase-based SI mechanism operates in the Rubiaceae family. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1468 TI - Phosphate sensing in root development JO - Curr. Opin. Plant Biol. PY - 2011 SP - 303-309 AU - Abel, S. AU - VL - 14 UR - DO - 10.1016/j.pbi.2011.04.007 AB - Phosphate (Pi) and its anhydrides constitute major nodes in metabolism. Thus, plant performance depends directly on Pi nutrition. Inadequate Pi availability in the rhizosphere is a common challenge to plants, which activate metabolic and developmental responses to maximize Pi usage and acquisition. The sensory mechanisms that monitor environmental Pi and transmit the nutritional signal to adjust root development have increasingly come into focus. Recent transcriptomic analyses and genetic approaches have highlighted complex antagonistic interactions between external Pi and Fe bioavailability and have implicated the stem cell niche as a target of Pi sensing to regulate root meristem activity. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1520 TI - Nitric oxide influences auxin signaling through S-nitrosylation of the Arabidopsis TRANSPORT INHIBITOR RESPONSE 1 auxin receptor JO - Plant J. PY - 2011 SP - 492-500 AU - Terrile, M. C. AU - París, R. AU - Calderón-Villalobos, L. I. A. AU - Iglesias, M. J. AU - Lamattina, L. AU - Estelle, M. AU - Casalongué, C. A. AU - VL - 70 UR - DO - 10.1111/j.1365-313X.2011.04885.x AB - Previous studies have demonstrated that auxin (indole‐3‐acetic acid) and nitric oxide (NO) are plant growth regulators that coordinate several plant physiological responses determining root architecture. Nonetheless, the way in which these factors interact to affect these growth and developmental processes is not well understood. The Arabidopsis thaliana F‐box proteins TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F‐BOX (TIR1/AFB) are auxin receptors that mediate degradation of AUXIN/INDOLE‐3‐ACETIC ACID (Aux/IAA) repressors to induce auxin‐regulated responses. A broad spectrum of NO‐mediated protein modifications are known in eukaryotic cells. Here, we provide evidence that NO donors increase auxin‐dependent gene expression while NO depletion blocks Aux/IAA protein degradation. NO also enhances TIR1‐Aux/IAA interaction as evidenced by pull‐down and two‐hybrid assays. In addition, we provide evidence for NO‐mediated modulation of auxin signaling through S‐nitrosylation of the TIR1 auxin receptor. S‐nitrosylation of cysteine is a redox‐based post‐translational modification that contributes to the complexity of the cellular proteome. We show that TIR1 C140 is a critical residue for TIR1–Aux/IAA interaction and TIR1 function. These results suggest that TIR1 S‐nitrosylation enhances TIR1–Aux/IAA interaction, facilitating Aux/IAA degradation and subsequently promoting activation of gene expression. Our findings underline the importance of NO in phytohormone signaling pathways. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1518 TI - Molecular Evolution and Selection Patterns of Plant F-Box Proteins with C-Terminal Kelch Repeats JO - Plant Physiol. PY - 2011 SP - 835-850 AU - Schumann, N. AU - Navarro-Quezada, A. AU - Ullrich, K. AU - Kuhl, C. AU - Quint, M. AU - VL - 155 UR - DO - 10.1104/pp.110.166579 AB - The F-box protein superfamily represents one of the largest families in the plant kingdom. F-box proteins phylogenetically organize into numerous subfamilies characterized by their carboxyl (C)-terminal protein-protein interaction domain. Among the largest F-box protein subfamilies in plant genomes are those with C-terminal kelch repeats. In this study, we analyzed the phylogeny and evolution of F-box kelch proteins/genes (FBKs) in seven completely sequenced land plant genomes including a bryophyte, a lycophyte, monocots, and eudicots. While absent in prokaryotes, F-box kelch proteins are widespread in eukaryotes. Nonplant eukaryotes usually contain only a single FBK gene. In land plant genomes, however, FBKs expanded dramatically. Arabidopsis thaliana, for example, contains at least 103 F-box genes with well-conserved C-terminal kelch repeats. The construction of a phylogenetic tree based on the full-length amino acid sequences of the FBKs that we identified in the seven species enabled us to classify FBK genes into unstable/stable/superstable categories. In contrast to superstable genes, which are conserved across all seven species, kelch domains of unstable genes, which are defined as lineage specific, showed strong signatures of positive selection, indicating adaptational potential. We found evidence for conserved protein features such as binding affinities toward A. thaliana SKP1-like adaptor proteins and subcellular localization among closely related FBKs. Pseudogenization seems to occur only rarely, but differential transcriptional regulation of close relatives may result in subfunctionalization. A2 - C1 - Molecular Signal Processing; Biochemistry of Plant Interactions ER - TY - JOUR ID - 1500 TI - Chemoenzymatic synthesis of diverse thiohydroximates from glucosinolate-utilizing enzymes from Helix pomatia and Caldicellulosiruptor saccharolyticus JO - Biotechnol. Lett. PY - 2011 SP - 1039-1046 AU - Kopycki, J. AU - Schmidt, J. AU - Abel, S. AU - Grubb, C. D. AU - VL - 33 UR - DO - 10.1007/s10529-011-0530-y AB - Thiohydroximates comprise a diverse class of compounds important in both biological and industrial chemistry. Their syntheses are generally limited to simple alkyl and aryl compounds with few stereocenters and a narrow range of functional groups. We hypothesized that sequential action of two recombinant enzymes, a sulfatase from Helix pomatia and a β-O-glucosidase from Caldicellulosiruptor saccharolyticus, on glucosinolates would allow synthesis of thiohydroximates from a structurally broad array of abundant precursors. We report successful synthesis of thiohydroximates of varied chemical classes, including from homochiral compounds of demonstrated biological activity. The chemoenzymatic synthetic route reported here should allow access to many, if not all, of the thiohydroximate core structures of the ~200 known naturally occurring glucosinolates. The enrichment of this group for compounds with possible pharmacological potential is discussed. A2 - C1 - Molecular Signal Processing; Bioorganic Chemistry ER - TY - JOUR ID - 1485 TI - Rolling-circle replication of viroids, viroid-like satellite RNAs and hepatitis delta virus: Variations on a theme JO - RNA Biol. PY - 2011 SP - 200-206 AU - Flores, R. AU - Grubb, D. AU - Elleuch, A. AU - Nohales, M.-?. AU - Delgado, S. AU - Gago, S. AU - VL - 8 UR - DO - 10.4161/rna.8.2.14238 AB - Viroids and viroid-like satellite RNAs from plants, and the human hepatitis delta virus (HDV) RNA share some properties that include small size, circularity and replication through a rolling-circle mechanism. Replication occurs in different cell compartments (nucleus, chloroplast and membrane-associated cytoplasmatic vesicles) and has three steps: RNA polymerization, cleavage and ligation. The first step generates oligomeric RNAs that result from the reiterative transcription of the circular templates of one or both polarities, and is catalyzed by either the RNA-dependent RNA polymerase of the helper virus on which viroid-like satellite RNAs are functionally dependent, or by host DNA-dependent RNA polymerases that, remarkably, viroids and HDV redirect to transcribe RNA templates. Cleavage is mediated by host enzymes in certain viroids and viroid-like satellite RNAs, while in others and in HDV is mediated by cis-acting ribozymes of three classes. Ligation appears to be catalyzed mainly by host enzymes. Replication most likely also involves many other non-catalytic proteins of host origin and, in HDV, the single virus-encoded protein. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1481 TI - Expression level polymorphisms: heritable traits shaping natural variation JO - Trends Plant Sci. PY - 2011 SP - 481-488 AU - Delker, C. AU - Quint, M. AU - VL - 16 UR - DO - 10.1016/j.tplants.2011.05.009 AB - Natural accessions of many species harbor a wealth of genetic variation visible in a large array of phenotypes. Although expression level polymorphisms (ELPs) in several genes have been shown to contribute to variation in diverse traits, their general impact on adaptive variation has likely been underestimated. At present, ELPs have predominantly been correlated to quantitative trait loci (eQTLs) that occupy central hubs in signaling networks, which pleiotropically affect numerous traits. To increase the sensitivity of detecting minor effect eQTLs or those that act in a trait-specific manner, we emphasize the need for more systematic approaches. This requires, but is not limited to, refining experimental designs such as reduction of tissue complexity and combinatorial methods including a priori defined networks. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1479 TI - Phosphorus and nitrogen interaction: loss of QC identity in response to P or N limitation is antecipated in pdr23 mutant JO - Braz. J. Plant Physiol. PY - 2011 SP - 219-229 AU - Costa, C. T. AU - Strieder, M. L. AU - Abel, S. AU - Delatorre, C. A. AU - VL - 23 UR - DO - 10.1590/S1677-04202011000300006 AB - Changes in root architecture are an important adaptive strategy used by plants in response to limited nutrient availability to increase the odds of acquiring them. The quiescent center (QC) plays an important role by altering the meristem activity causing differentiation and therefore, inducing a determinate growth program. The arabidopsis mutant pdr23 presents primary short root in the presence of nitrate and is inefficient in the use of nucleic acids as a source of phosphorus. In this study the effect of the pdr23 mutation on the QC maintenance under low phosphorus (P) and/or nitrogen is evaluated. QC identity is maintained in wild-type in the absence of nitrate and/or phosphate if nucleic acids can be used as an alternative source of these nutrients, but not in pdr23. The mutant is not able to use nucleic acids efficiently for substitute Pi, determinate growth is observed, similar to wild-type in the total absence of P. In the absence of N pdr23 loses the expression of QC identity marker earlier than wild-type, indicating that not only the response to P is altered, but also to N. The data suggest that the mutation affects a gene involved either in the crosstalk between these nutrients or in a pathway shared by both nutrients limitation response. Moreover loss of QC identity is also observed in wild-type in the absence of N at longer limitation. Less drastic symptoms are observed in lateral roots of both genotypes. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 1477 TI - Trans-cleaving hammerhead ribozymes with tertiary stabilizing motifs: in vitro and in vivo activity against a structured viroid RNA JO - Nucleic Acids Res. PY - 2011 SP - 2432-2444 AU - Carbonell, A. AU - Flores, R. AU - Gago, S. AU - VL - 39 UR - DO - 10.1093/nar/gkq1051 AB - Trans -cleaving hammerheads with discontinuous or extended stem I and with tertiary stabilizing motifs (TSMs) have been tested previously against short RNA substrates in vitro at low Mg 2+ concentration. However, the potential of these ribozymes for targeting longer and structured RNAs in vitro and in vivo has not been examined. Here, we report the in vitro cleavage of short RNAs and of a 464-nt highly structured RNA from potato spindle tuber viroid (PSTVd) by hammerheads with discontinuous and extended formats at submillimolar Mg 2+ . Under these conditions, hammerheads derived from eggplant latent viroid and peach latent mosaic viroid (PLMVd) with discontinuous and extended formats, respectively, where the most active. Furthermore, a PLMVd-derived hammerhead with natural TSMs showed activity in vivo against the same long substrate and interfered with systemic PSTVd infection, thus reinforcing the idea that this class of ribozymes has potential to control pathogenic RNA replicons. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 2474 TI - Intracellular Localization of Jasmonate-Induced Proteins in Barley Leaves JO - Bot. Acta PY - 1994 SP - 333-341 AU - Hause, B. AU - zur Nieden, U. AU - Lehmann, J. AU - Wasternack, C. AU - Parthier, B. AU - VL - 107 UR - DO - 10.1111/j.1438-8677.1994.tb00804.x AB - The plant growth substance jasmonic acid and its methyl ester (JA‐Me) induce a set of proteins (jasmonate‐induced proteins, JIPs) when applied to leaf segments of barley (Hordeum vulgare L. cv. Salome). Most of these JIPs could be localized within different cell compartments by using a combination of biochemical and histochemical methods. Isolation and purification of various cell organelles of barley mesophyll cells, the separation of their proteins by one‐dimensional polyacrylamide gel electrophoresis and the identification of the major abundant JIPs by Western blot analysis, as well as the immuno‐gold labelling of JIPs in ultrathin sections were performed to localize JIPs intracellularly. JIP‐23 was found to be in vacuoles, peroxisomes, and in the granular parts of the nucleus as well as within the cytoplasm; JIP‐37 was detected in vacuoles and in the nucleoplasm; JIP‐66 is a cytosolic protein. Some less abundant JIPs were also localized within different cell compartments: JIP‐100 was found within the stromal fraction of chloroplasts; JIP‐70 is present in the peroxisome and the nucleus; JIP‐50 and JIP‐6 accumulate in vacuoles. The location of JIP‐66 and JIP‐6 confirms their possible physiological role deduced from molecular analysis of their cDNA. A2 - C1 - Molecular Signal Processing; Cell and Metabolic Biology ER - TY - JOUR ID - 2470 TI - Transient transformation of Arabidopsis leaf protoplasts: a versatile experimental system to study gene expression JO - Plant J. PY - 1994 SP - 421-427 AU - Abel, S. AU - Theologis, A. AU - VL - 5 UR - DO - 10.1111/j.1365-313X.1994.00421.x AB - An improved protocol is reported to isolate and transiently transform mesophyll protoplasts of Arabidopsis thaliana. Transfected leaf protoplasts support high levels of expression of the bacterial reporter gene coding for β‐glucuronidase (GUS), under the control of the cauliflower mosaic virus (CaMV) 35S promoter. Transient expression of GUS activity was monitored spectrophotometrically and reached a maximum between 18 and 48 h after polyethylene glycol (PEG)‐mediated DNA uptake. Histochemical staining for GUS activity revealed reproducible transformation frequencies between 40 and 60%, based on the number of protoplasts survived. To demonstrate the applicability of the transient expression system, the subcellular localization of GUS proteins tagged with different nuclear polypeptides was studied in transfected mesophyll protoplasts, revealing nuclear compartmentalization of the chimeric GUS enzymes. Furthermore, Arabidopsis mesophyll protoplasts support auxin‐mediated induction of chloramphenicol acetyl‐transferase (CAT) activity when transfected with a transcriptional fusion between the CAT reporter gene and the early auxin‐inducible PS‐IAA4/5 promoter. Hence, the method allows in vivo analysis of promoter activity and subcellular localization of fusion proteins in a homologous transformation system. A2 - C1 - Molecular Signal Processing ER - TY - JOUR ID - 2469 TI - Early auxin-induced genes encode short-lived nuclear proteins. JO - Proc. Natl. Acad. Sci. U.S.A. PY - 1994 SP - 326-330 AU - Abel, S. AU - Oeller, P. W. AU - Theologis, A. AU - VL - 91 UR - DO - 10.1073/pnas.91.1.326 AB - The plant growth hormone indoleacetic acid (IAA) transcriptionally activates gene expression in plants. Some of the genes whose expression is induced by IAA encode a family of proteins in pea (PS-IAA4 and PS-IAA6) and Arabidopsis (IAA1 and IAA2) that contain putative nuclear localization signals that direct a beta-glucuronidase reporter protein into the nucleus. Pulse-chase and immunoprecipitation experiments have defined the t1/2 of the PS-IAA4 and PS-IAA6 proteins to be 8 and 6 min, respectively. Their most prominent feature is the presence of a beta alpha alpha motif similar to the beta-sheet DNA-binding domain found in prokaryotic repressors of the Arc family. Based on these data, we suggest that plant tissues express short-lived nuclear proteins as a primary response to IAA. We propose that these proteins act as activators or repressors of genes responsible for mediating the various auxin responses. A2 - C1 - Molecular Signal Processing ER -