Plant Journal

Depletion of leaf-type ferredoxin-NADP(+) oxidoreductase results in permanent induction of photoprotective mechanisms in Arabidopsis chloroplasts.

Publication Date: 2012 Feb 2 PMID: 22300243
Authors: Lintala, M. - Lehtimaki, N. - Philipp Benz, J. - Jungfer, A. - Soll, J. - Aro, E. M. - Bolter, B. - Mulo, P.
Journal: Plant J

Arabidopsis thaliana contains two photosynthetically competent chloroplast-targeted ferredoxin-NADP(+) oxidoreductase (FNR) isoforms which are largely redundant in their function. Nevertheless, the FNR isoforms also display distinct molecular phenotypes as only the FNR1 is able to directly bind to the thylakoid membrane. We report the consequences of depletion of FNR in the F1 (fnr1xfnr2) and F2 (fnr1 fnr2) generation plants of the fnr1 and fnr2 single mutant crossings. The fnr1xfnr2 plants, with a decreased total content of FNR, showed a small and pale green phenotype accompanied with a marked downregulation of photosynthetic pigment-protein complexes. Specifically, when compared to WT, the quantum yield of PSII electron transport was lower, non-photochemical quenching (NPQ) was higher and the rate of P700(+) re-reduction was faster in the mutant plants. The slight overreduction of the plastoquinone pool detected in the mutants resulted in adjustment of the reactive oxygen species (ROS) scavenging systems, as both the content and de-epoxidation state of xanthophylls as well as the content of alpha-tocopherol were higher in the leaves of the mutant plants when compared to WT. The fnr1 fnr2 mutant plants which had no detectable FNR and possessed an extremely downregulated photosynthetic machinery survived only when grown heterotrophically in the presence of sucrose. Intriguingly, the fnr1 fnr2 plants were still capable of sustaining the biogenesis of a few malformed chloroplasts. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Fructokinase is required for carbon partitioning to cellulose in aspen wood.

Publication Date: 2012 Jan 31 PMID: 22288715
Authors: Roach, M. - Gerber, L. - Sandquist, D. - Gorzsas, A. - Hedenstrom, M. - Kumar, M. - Steinhauser, M. C. - Feil, R. - Daniel, G. - Stitt, M. - Sundberg, B. - Niittyla, T.
Journal: Plant J

Sucrose is the main transported form of carbon in several plant species including the model tree aspen. Sucrose metabolism in developing wood is therefore central for carbon partitioning to stem biomass. Half of the sucrose-derived carbon is in the form of fructose, but metabolism of fructose has received little attention as a factor in carbon partitioning to wood cell walls. We show that RNAi mediated reduction of FRK2 activity in developing wood led to accumulation of soluble neutral sugars and a decrease in hexose phosphates and UDP-glucose indicating that carbon flux to the cell wall polysaccharide precursors was decreased. Reduced FRK2 activity also led to thinner fiber cell walls with a reduction in the proportion of cellulose. No pleiotropic effects on stem height or diameter growth were observed. The results establish a central role for the FRK2 activity in carbon flux to wood cellulose. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Putative members of the Arabidopsis Nup107-160 nuclear pore sub-complex contribute to pathogen defense.

Publication Date: 2012 Jan 31 PMID: 22288649
Authors: Wiermer, M. - Cheng, Y. T. - Imkampe, J. - Li, M. - Wang, D. - Lipka, V. - Li, X.
Journal: Plant J

In eukaryotic cells, transduction of external stimuli into the nucleus to induce transcription and export of mRNAs for translation in the cytoplasm is mediated by nuclear pore complexes (NPCs) composed of nucleoporin proteins (Nups). We previously reported that Arabidopsis MOS3, encoding the homolog of vertebrate Nup96, is required for plant immunity and constitutive resistance mediated by the deregulated Toll-Interleukin-1-receptor/nucleotide-binding/leucine-rich-repeat (TNL)-type R gene, snc1. In vertebrates, Nup96 is a member of the conserved Nup107-160 nuclear pore sub-complex and implicated in immunity-related mRNA export. Here, we used a reverse genetics approach to examine the requirement of additional subunits of the predicted Arabidopsis Nup107-160 complex for plant immunity. We show that among eight putative complex members, beside MOS3, only plants with defects in Nup160 or Seh1 are impaired in basal resistance. Constitutive resistance in snc1 and immunity mediated by TNL-type R genes also depend on functional Nup160 and have a partial requirement for Seh1. Conversely, resistance conferred by coiled-coil (CC)-type immune receptors operates largely independently of both genes, demonstrating specific contributions to plant defense signaling. Our functional analysis further revealed that defects of nup160 and seh1 result in nuclear accumulation of poly(A)-mRNA and, in the case of nup160, considerable depletion of EDS1, a key positive regulator of basal and TNL-triggered resistance. These findings suggest that Nup160 is required for nuclear mRNA export and full expression of EDS1-conditioned resistance pathways in Arabidopsis. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Deciphering Energy-Associated Gene Networks Operating in the Response of Arabidopsis Plants to Stress and Nutritional Cues.

Publication Date: 2012 Jan 31 PMID: 22288575
Authors: Avin-Wittenberg, T. - Tzin, V. - Angelovici, R. - Less, H. - Galili, G.
Journal: Plant J

Plants need to continuously adjust their transcriptome in response to various stresses that lead to inhibition of photosynthesis and the deprivation of cellular energy. This adjustment is triggered in part by a coordinated re-programing of the energy-associated transcriptome to slow down photosynthesis and activate other energy-promoting gene networks. Therefore, understanding the stress-related transcriptional networks of genes belonging to energy-associated pathways is of major importance for engineering stress tolerance. In a bioinformatics approach developed by our group, termed "Gene Coordination", we previously divided genes encoding for enzymes and transcription factors in Arabidopsis thaliana to three clusters, displaying altered coordinated transcriptional behaviors in response to multiple biotic and abiotic stresses (Less et al., 2011). Enrichment analysis indicated further that genes controlling energy-associated metabolism operate as a compound network in response to stress. In the present report, we describe in detail the network association of genes belonging to six central energy-associated pathways in each of these three clusters described in our previous report. Our results expose extensive stress-associated intra- and inter-pathway interactions between genes from these pathways, indicating that genes encoding proteins of energy-associated metabolism are expressed in a highly coordinated manner. We also provide an example showing that this approach can be further utilized to elucidate candidate genes for stress tolerance and functions of isozymes. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Tandemly arranged chalcone synthase A genes contribute to the spatially regulated expression of siRNA and the natural bicolor floral phenotype in Petunia hybrida.

Publication Date: 2012 Jan 31 PMID: 22288551
Authors: Morita, Y. - Saito, R. - Ban, Y. - Tanikawa, N. - Kuchitsu, K. - Ando, T. - Yoshikawa, M. - Habu, Y. - Ozeki, Y. - Nakayama, M.
Journal: Plant J

The natural bicolor floral traits of the horticultural petunia (Petunia hybrida) cultivars Picotee and Star are caused by the spatial repression of the chalcone synthase A (CHS-A) gene, which encodes an anthocyanin biosynthetic enzyme. Here we show that Picotee and Star petunias carry the same short interfering RNA (siRNA)-producing locus, consisting of two intact CHS-A copies, PhCHS-A1 and -A2, in a tandem head-to-tail orientation. The precursor CHS mRNAs are transcribed from the two CHS-A copies throughout the bicolored petals, but the mature CHS mRNAs are not found in the white tissues. An analysis of small RNAs revealed the accumulation of siRNAs of 21 nucleotides that originated from the exon 2 region of both CHS-A copies. This accumulation is closely correlated with the disappearance of the CHS mRNAs, indicating that the bicolor floral phenotype is due to the spatially regulated post-transcriptional silencing of both CHS-A genes. Linkage between the tandemly arranged CHS-A allele and the bicolor floral trait indicates that the CHS-A allele is a necessary factor to confer the trait. We suppose that the spatially regulated production of siRNAs in Picotee and Star flowers is triggered by another putative regulatory locus and that the silencing mechanism in this case may be different from other known mechanisms of post-transcriptional gene silencing in plants. A sequence analysis of wild Petunia species indicated that these tandem CHS-A genes originated from P. integrifolia and/or P. inflata, the parental species of P. hybrida, as a result of a chromosomal rearrangement rather than a gene duplication event. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Feedback inhibition by thiols outranks glutathione depletion: a luciferase-based screen reveals glutathione-deficient gamma-ECS and glutathione synthetase mutants impaired in cadmium-induced sulfate assimilation.

Publication Date: 2012 Jan 28 PMID: 22283708
Authors: Jobe, T. O. - Sung, D. Y. - Akmakjian, G. - Pham, A. - Komives, E. A. - Mendoza-Cozatl, D. G. - Schroeder, J. I.
Journal: Plant J

Plants exposed to heavy metals rapidly induce changes in gene expression that activate and enhance detoxification mechanisms including toxic-metal chelation and the scavenging of reactive oxygen species. However, the mechanisms mediating toxic heavy metal-induced gene expression remain largely unknown. To genetically elucidate cadmium specific transcriptional responses in Arabidopsis, we designed a genetic screen based on the activation of a cadmium inducible reporter gene. Microarray studies identified a high-affinity sulfate transporter (SULTR1;2) among the most robust and rapid cadmium-inducible transcripts. The SULTR1;2 promoter (2.2 kb) was fused with the firefly luciferase reporter gene to quantitatively report the transcriptional response of plants exposed to cadmium. Stably transformed luciferase reporter lines were EMS mutagenized and stable M2 seedlings were screened for abnormal luciferase response during exposure to cadmium. The screen identified non-allelic mutant lines that fell into one of three categories: 1) super response to cadmium (SRC) mutants, 2) constitutive response to cadmium (CRC) mutants, or 3) non-response and reduced response to cadmium (NRC) mutants. Two nrc mutants, nrc1 and nrc2, were cloned and further characterized. The nrc1 mutation was mapped to the gamma-glutamylcysteine synthetase gene and the nrc2 mutation was identified as the first viable recessive mutant allele in the glutathione synthetase gene. Moreover, genetic, HPLC mass spectrometry, and gene expression analysis of the nrc1 and nrc2 mutants revealed that intracellular glutathione depletion alone would be insufficient to induce gene expression of sulfate uptake and assimilation mechanisms. Our results modify the glutathione-depletion driven model for sulfate assimilation gene induction during cadmium stress and suggest that enhanced oxidative state and depletion of upstream thiols in addition to glutathione depletion are necessary to induce the transcription of sulfate assimilation genes during early cadmium stress. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

RNAi-independent de novo DNA methylation revealed in Arabidopsis mutants of a chromatin remodeling gene DDM1.

Publication Date: 2012 Jan 23 PMID: 22269081
Authors: Sasaki, T. - Kobayashi, A. - Saze, H. - Kakutani, T.
Journal: Plant J

Methylation of histone H3 lysine 9 (H3K9me) and small RNA are associated with constitutively silent chromatin in diverse eukaryotes including plants. In plants, silent transposons are also marked by cytosine methylation, especially at non-CpG sites. The transposon-specific non-CpG methylation in plants is controlled by small RNA and H3K9me. Although it is often assumed that small RNA directs H3K9me, interaction between small RNA and H3K9me has not been directly shown in plants. We have previously shown that a mutation in a chromatin remodeling gene DDM1 (decrease in DNA methylation) induces a global decrease as well as local increase of cytosine methylation and accumulation of small RNA in a locus called BONSAI. Here we show that the de novo BONSAI methylation does not depend on RNAi but depends on H3K9me. Notably, in mutants of H3K9 methyltransferase gene KRYPTONITE or H3K9me-dependent DNA methyltransferase gene CHROMOMETHYALSE3, the ddm1-induced de novo cytosine methylation was abolished for all three contexts, CpG, CpHpG, and CpHpH. Furthermore, RNAi mutants showed strong developmental defects when combined with ddm1 mutation. Our results revealed unexpected interactions of epigenetic modifications, which could be conserved among diverse eukaryotes. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

TGD4 involved in ER-to-chloroplast lipid trafficking is a phosphatidic acid binding protein.

Publication Date: 2012 Jan 23 PMID: 22269056
Authors: Wang, Z. - Xu, C. - Benning, C.
Journal: Plant J

The synthesis of galactoglycerolipids, which are prevalent in photosynthetic membranes, involves enzymes at the Endoplasmic Reticulum (ER) and the chloroplast envelope membranes. Genetic analysis of TGD proteins in Arabidopsis has demonstrated their role in polar lipid transfer from the ER to the chloroplast. The TGD1, 2, and 3 proteins resemble components of a bacterial-type ATP-Binding Cassette (ABC) transporter, with TGD1 representing the permease, TGD2 the substrate binding protein, and TGD3 the ATPase. However, the function of the TGD4 protein in this process is less clear and its location in plant cells remains to be firmly determined. With its predicted C-terminal beta-barrel structure TGD4 is weakly similar to proteins of the outer cell membrane of Gram- negative bacteria. Here, we show that like TGD2, the TGD4 protein fused to DsRED specifically binds phosphatidic acid (PtdOH). As previously shown for tgd1 mutants, tgd4 mutants have elevated PtdOH content, likely in extraplastidic membranes. Using highly purified and specific antibodies to probe different cell fractions, the TGD4 protein was present in the outer envelope membrane of chloroplasts, where it appeared to be deeply buried within the membrane except for the N-terminus, which was found to be exposed to the cytosol. It is proposed that TGD4 is either directly involved in the transfer of polar lipids, possibly PtdOH, from the ER to the outer chloroplast envelope membrane or in the transfer of PtdOH through the outer envelope membrane. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

In vivo visualisation of RNA in plants cells using the lambdaN(22) system and a GATEWAY-compatible vector series for candidate RNAs.

Publication Date: 2012 Jan 23 PMID: 22268772
Authors: Schonberger, J. - Hammes, U. Z. - Dresselhaus, T.
Journal: Plant J

The past decade has seen a tremendous increase in RNA research, which demonstrated that RNAs are involved in many more processes than previously thought. The dynamics of RNA synthesis towards their regulated activity requires the interplay of RNAs with numerous RNA binding proteins (RBPs). Localisation of RNA, a mechanism for controlling translation in a spatial and temporal fashion requires processing and assembly of RNA into transport granules in the nucleus, transport towards cytoplasmic destinations and regulation of its activity. Compared with animal model systems little is known about RNA dynamics and motility in plants. Commonly used methods to study RNA transport and localisation are time-consuming and require expensive equipment and experimental skill. Here, we introduce the lambdaN(22) RNA stem-loop binding system for the in vivo visualization of RNA in plant cells. The lambdaN(22) system consists of two-components, the lambdaN(22) RNA binding peptide and the corresponding boxB stem-loops. We generated fusions of lambdaN(22) to different fluorophores and a GATEWAY vector series for simple fusion of any target RNA 5' or 3' to boxB stem-loops. We show that the lambdaN(22) system can be used to detect RNAs in transient expression assays and that it offers advantages compared to the previously described MS2 system. Furthermore, the lambdaN(22) system can be used in combination with the MS2 system to visualize different RNAs simultaneously in the same cell. The toolbox of vectors generated for both systems is easy to use and promises significant progress in our understanding of RNA transport and localisation in plant cells. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

SoMART, a web server for plant miRNA, tasiRNA and target gene analysis.

Publication Date: 2012 Jan 24 PMID: 22268718
Authors: Li, F. - Orban, R. - Baker, B.
Journal: Plant J

Plant micro(mi)RNAs and trans-acting small interfering (tasi)RNAs play important roles in a variety of biological processes. Bioinformatics prediction and small (s)RNA cloning are the most important approaches for identification of miRNA and tasiRNA and their targets. However these approaches are not readily accessible to every researcher. Here we present SoMART, a web server for miRNA/tasiRNA Analysis Resources and Tools, which is designed for researchers who are interested in identifying miRNAs or tasiRNAs potentially regulating their genes of interest. The server includes four sets of tools: 'Slicer detector' for detecting sRNAs targeting input genes, 'dRNA mapper' for detecting degradome (d)RNA products derived from input genes, 'preMIR detector' for identifying miRNA precursor (MIR) or tasiRNA precursor (TAS) of input sRNAs, and 'sRNA mapper' for mapping sRNAs onto input genes. We also developed a dRNA-seq protocol to achieve longer dRNA reads for better characterization of miRNA precursors by dRNA mapper. To validate the server function and robustness, we installed sRNA, dRNA and collected genomic DNA or transcriptome databases from Arabidopsis and solanaceae plants, and characterized miR172-mediated regulation of APETALA2 gene in potato and showed conservation of MIR390-triggered TAS3 in tomato. More importantly, we predicted a MIR482-triggered TAS5 in tomato. We further tested and confirmed the efficiency and accuracy of the server by analyses of 21 validated miRNA targets and 115 miRNA precursors in Arabidopsis thaliana. SoMART is available at http://somart.ist.berkeley.edu. Published 2012. This article is a US Government work and is in the public domain in the USA.

post to: CiteULike

Peptidyl-prolyl cis-trans isomerase ROF2 modulates intracellular pH homeostasis in Arabidopsis.

Publication Date: 2012 Jan 23 PMID: 22268595
Authors: Bissoli, G. - Ninoles, R. - Fresquet, S. - Palombieri, S. - Bueso, E. - Rubio, L. - Garcia-Sanchez, M. J. - Fernandez, J. A. - Mulet, J. M. - Serrano, R.
Journal: Plant J

Intracellular pH must be regulated close to neutrality to be compatible with cellular functions but the mechanisms of pH homeostasis and the responses to intracellular acidification are mostly unknown. We have found in the plant Arabidopsis thaliana that intracellular acid stress, generated by weak organic acids at normal external pH, induces several chaperone genes, including ROF2 encoding a peptidyl-prolyl cis-trans isomerase of the FK506-binding protein class. Loss of function of ROF2, and specially the double mutation of ROF2 and of its closely related gene ROF1 results in acid sensitivity. On the other hand, over-expression of ROF2 confers tolerance to intracellular acidification by increasing proton extrusion from cells. The activation of the plasma membrane proton pump (H(+) -ATPase) is indirect: over-expression of ROF2 activates K(+) uptake, this causes depolarization of the plasma membrane that activates the electrogenic H(+) pump. Depolarization of ROF2-overexpressing plants explains their tolerance to toxic cations such as lithium, norspermidine and hygromycin B, whose uptake is driven by the membrane potential. As ROF2 induction and intracellular acidification are common consequences of many stresses, this mechanism of pH homeostasis may be of general importance for stress tolerance. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Inducible NAD overproduction in Arabidopsis alters metabolic pools and gene expression correlated with increased salicylate content and resistance to Pst-AvrRpm1.

Publication Date: 2012 Jan 23 PMID: 22268572
Authors: Petriacq, P. - de Bont, L. - Hager, J. - Didierlaurent, L. - Mauve, C. - Guerard, F. - Noctor, G. - Pelletier, S. - Renou, J. P. - Tcherkez, G. - Gakiere, B.
Journal: Plant J

Plant development and function are underpinned by redox reactions that depend on cofactors such as nicotinamide adenine dinucleotide (NAD). NAD has recently been shown to be involved in several signalling pathways associated with stress tolerance or defence responses. Still, the mechanisms by which NAD influences plant gene regulation, metabolism and physiology remain unclear. Here, we took advantage of Arabidopsis thaliana lines overexpressing the nadC gene from E. coli, which encodes the NAD biosynthesis enzyme quinolinate phosphoribosyltransferase (QPT). Upon incubation with quinolinate, these lines accumulated NAD and were thus used as inducible systems to elucidate the consequences of an increased NAD content in leaves. Metabolic profiling showed clear changes in several metabolites such as aspartate-derived amino acids and NAD-derived nicotinic acid. Large-scale transcriptomic analyses indicated that NAD promoted the induction of various pathogen-related genes such as the salicylic acid (SA)-responsive defense marker PR1. Extensive comparison with transcriptomic databases further showed that gene expression under high NAD content was similar to that obtained under biotic stress, eliciting conditions or SA treatment. Upon inoculation with the avirulent strain of Pseudomonas syringae pv. tomato Pst-AvrRpm1, the nadC lines showed enhanced resistance to bacterial infection and exhibited a ICS1-dependent build-up of both conjugated and free SA pools. We therefore conclude that higher NAD contents are beneficial for plant immunity by stimulating SA-dependent signalling and pathogen resistance. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Genome-wide identification of SOC1 and SVP targets during the floral transition in Arabidopsis.

Publication Date: 2012 Jan 23 PMID: 22268548
Authors: Tao, Z. - Shen, L. - Liu, C. - Liu, L. - Yan, Y. - Yu, H.
Journal: Plant J

The floral transition in Arabidopsis is tightly controlled by complex genetic regulatory networks in response to endogenous and environmental flowering signals. SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and SHORT VEGETATIVE PHASE (SVP), two key MADS-domain transcription factors, perceive these signals and function as antagonistic flowering regulators. To understand how they mediate the floral transition, we mapped in vivo binding sites of SOC1 and SVP using chromatin immunoprecipitation followed by hybridization to whole-genome tiling arrays (ChIP-chip). Genes encoding proteins with transcription regulator activity and transcription factor activity were the most enriched groups of genes bound by SOC1 and SVP, indicating their central roles in flowering regulatory networks. In combination with gene expression microarray studies, we further identified the genes whose expression was directly controlled by SOC1 or SVP. Among the common direct targets identified, APETALA2 (AP2)-like genes that repress FT and SOC1 expression were downregulated by SOC1, but upregulated by SVP, revealing a complex feedback regulation among key genes determining the integration of flowering signals. SOC1 regulatory regions were also accessed by SOC1 itself and SVP, suggesting that self-activation and repression by SVP contribute to the control of SOC1 expression. In addition, ChIP-chip analysis demonstrated that miR156e and miR172a, which are involved in the regulation of AP2-like genes, were direct targets of SOC1 and SVP, respectively. Taken together, these findings reveal that feedback regulatory loops mediated by SOC1 and SVP are essential components of the gene regulatory networks underpinning the integration of flowering signals during the floral transition. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Visual marker and Agrobacterium-delivered recombinase enable the manipulation of the plastid genome in greenhouse-grown tobacco plants.

Publication Date: 2012 Jan 23 PMID: 22268515
Authors: Tungsuchat-Huang, T. - Maliga, P.
Journal: Plant J

Successful manipulation of the plastid genome (ptDNA) so far has been carried out in tissue culture cells, a limitation that prevents plastid transformation being applied in major agronomic crops. Our objective is to develop a tissue-culture independent protocol that enables manipulation of plastid genomes directly in plants yielding genetically stable seed progeny. We report that in planta excision of a plastid aurea bar gene (bar(au) ) is detectable in greenhouse-grown plants by restoration of the green pigmentation in tobacco leaves. The P1 phage Cre or PhiC31 phage Int site-specific recombinase was delivered on the Agrobacterium T-DNA injected at the axillary bud site, resulting in the excision of the target-site flanked marker gene. Differentiation of new apical meristems was forced by decapitating the plants above the injection site. The new shoot apex differentiating at the injection site contained bar(au) -free plastids in 30% to 40% of the injected plants, of which 7% transmitted the bar(au) -free plastids to the seed progeny. The success of obtaining seed with bar(au) -free plastids depended on repeatedly forcing shoot development from axillary buds, a process that was guided by the size and position of green sectors in the leaves. The success of in planta plastid marker excision proved that manipulation of the plastid genomes is feasible within an intact plant. Extension of the protocol to in planta plastid transformation depends on the development of new protocols for the delivery of transforming DNA encoding visual markers. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Construction of rice minichromosomes by telomere mediated chromosomal truncation.

Publication Date: 2012 Jan 23 PMID: 22268496
Authors: Xu, C. - Cheng, Z. - Yu, W.
Journal: Plant J

Telomere truncation has been shown to be an efficient technology for the creation of minichromosomes, which can be used as artificial chromosome platforms for genetic engineering. Artificial chromosome based genetic engineering is considered to be superior to existing techniques of randomized gene integration by Agrobacterium or biolistic mediated genetic transformation. It organizes multiple transgenes as a unique genetic linkage block for subsequently manipulations in breeding. Telomere truncation technology relies on three components: the telomere sequence that mediates chromosomal truncation, a selection marker that allows the selection of transgenic events, and a site specific recombination system that can be used to accept future genes into the minichromosome by gene targeting. These elements are usually pre-assembled before transformation which is time and labor consuming. We found in this research that the three elements could be mixed to transform plant cells in a biolistic transformation, and produced efficient chromosomal truncations and minichromosomes in rice. This system will allow rapid constructions of minichromosomes with a flexible selection of resistant markers, site specific recombination systems and other desirable elements. In addition, a rice telotrisomic line was used as the starting material for chromosomal truncations. Minichromosomes from the truncations of both the telocentric chromosome and other chromosomes were recovered. The minichromosomes remained stable during two years of subculture. The construction of minichromosomes in rice, an economically important crop, will provide a platform for future artificial chromosome based genetic engineering of rice for the stacking of multiple genes. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Footprints of natural and artificial selection for photoperiod pathway genes in Oryza.

Publication Date: 2012 Jan 23 PMID: 22268451
Authors: Huang, C. L. - Hung, C. Y. - Chiang, Y. C. - Hwang, C. C. - Hsu, T. W. - Huang, C. C. - Hung, K. H. - Tsai, K. C. - Wang, K. H. - Osada, N. - Schaal, B. A. - Chiang, T. Y.
Journal: Plant J

Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigating the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes, divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, revealing a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, reflecting various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31 degrees N in Hd3a, likely resulting from varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, including high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent nonfunctional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

The Non-Random Distribution of Extensive Chromosome Rearrangements in Brassica Napus Depends on Genome Organization.

Publication Date: 2012 Jan 23 PMID: 22268419
Authors: Nicolas, S. D. - Monod, H. - Eber, F. - Chevre, A. M. - Jenczewski, E.
Journal: Plant J

Chromosome rearrangements are common, but their dynamics over time, mechanisms of occurrence and the genomic features that shape their distribution and rate are still poorly understood. We used allohaploid Brassica napus (AC, 2n=19) as a model to analyze the effect of different genomic features on the formation and diversity of meiotically-driven chromosome rearrangements. We showed that allohaploid B. napus meiosis drives extensive new structural diversity. Almost every allohaploid offspring carried a unique combination of multiple rearrangements throughout the genome and was thus structurally differentiated from both its haploid parent and its sister plants. This large amount of genome reshuffling was remarkably well-tolerated in the heterozygous state since both male and female fertility were not strongly reduced and in most cases meiosis behavior was normal. We also used quantitative statistical model, which accounted for 75% of the observed variation in rearrangement rates, to show that the distribution of meiotically-driven chromosome rearrangements was not random but shaped by three principal genomic features. In descending order of importance the rate of marker loss increased strongly with the genetic distance from the centromere, the degree of collinearity between chromosomes, and the genome of origin (A
post to: CiteULike

Reconstruction of a human mitochondrial complex I mutation in the unicellular green alga Chlamydomonas.

Publication Date: 2012 Jan 23 PMID: 22268373
Authors: Larosa, V. - Coosemans, N. - Motte, P. - Bonnefoy, N. - Remacle, C.
Journal: Plant J

Defects in complex I (NADH:ubiquinone oxidoreductase) are the most frequent cause of human respiratory disorders. The pathogenicity of a given human mitochondrial mutation can be difficult to demonstrate because the mitochondrial genome harbors large numbers of polymorphic base changes that have no pathogenic significance. In addition, mitochondrial mutations are usually found in the heteroplasmic state, which could hide the biochemical effect of the mutation. We propose that the unicellular green alga Chlamydomonas could be used to study such mutations because (1) respiratory-deficient mutants are viable and mitochondrial mutations are found in the homoplasmic state, (2) transformation of the mitochondrial genome is feasible, (3) Chlamydomonas complex I is close to that of humans. To illustrate that, we have introduced a Leu157Pro substitution in the Chlamydomonas ND4 subunit of complex I of two different recipient strains by biolistic transformation, demonstrating that site-directed mutagenesis of the Chlamydomonas mitochondrial genome is possible. This substitution did not lead to any respiratory enzyme defect when it is present in the heteroplasmic state in a patient presenting chronic progressive external ophthalmoplegia. When present in the homoplasmic state in the alga, the mutation does not prevent the assembly of the 950 kDa whole complex I which conserves nearly all the NADH dehydrogenase activity of the peripheral arm. However, the NADH:duroquinone oxidoreductase activity is strongly reduced, suggesting that the substitution could affect ubiquinone fixation to the membrane domain. The in vitro defects are correlated in vivo with a decrease in dark respiration and growth rate. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Potato CONSTANS is involved in photoperiodic tuberisation in a graft-transmissible manner.

Publication Date: 2012 Jan 19 PMID: 22260207
Authors: Gonzalez-Schain, N. D. - Diaz-Mendoza, M. - Zurczak, M. - Suarez-Lopez, P.
Journal: Plant J

CONSTANS (CO) is involved in the photoperiodic control of plant developmental processes, including flowering in several species and seasonal growth cessation and bud set in trees. It has been proposed that CO could also affect the daylength regulation of tuber induction in potato, a plant of great agricultural relevance. To address this question, we examined the role of CO in potato. A potato CO-like gene, StCO, was identified and found to be highly similar to a previously reported potato gene of unknown function. Potato plants overexpressing StCO tuberised later than wild-type plants under a weakly inductive photoperiod. StCO silencing promoted tuberisation under both repressive and weakly inductive photoperiods, but did not have any effect under strongly inductive short days, demonstrating that StCO represses tuberisation in a photoperiod-dependent manner. The effect of StCO on tuber induction was transmitted through grafts. In addition, StCO affected the mRNA levels of StBEL5 - a tuberisation promoter whose mRNA moves long distances in potato plants - and StFT/StSP6A, a protein highly similar to FLOWERING LOCUS T (FT), which is a key component of systemic flowering signals in other species. We also found that StFT/StSP6A transcript levels correlate with the induction of tuber formation in wild-type plants. These results show that StCO plays an important role in photoperiodic tuberisation and, together with the recent demonstration that StFT/StSP6A promotes tuberisation, indicate that the CO/FT module participates in controlling this process. Moreover, they support the notion that StCO is involved in the expression of long-distance regulatory signals in potato, as CO does in other species. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Maternal control of seed size by EOD3/CYP78A6 in Arabidopsis thaliana.

Publication Date: 2012 Jan 17 PMID: 22251317
Authors: Fang, W. - Wang, Z. - Cui, R. - Li, J. - Li, Y.
Journal: Plant J

Seed size in higher plants is coordinately determined by the growth of the embryo, endosperm and maternal tissue, but relatively little is known about the genetic and molecular mechanisms that set final seed size. We have previously demonstrated that Arabidopsis DA1 acts maternally to control seed size, with the da1-1 mutant producing larger seeds than wild type. Through an activation tagging screen for modifiers of da1-1, we have identified an enhancer of da1-1 (eod3-1D) in seed size. EOD3 encodes the Arabidopsis cytochrome P450/CYP78A6 and is expressed in most plant organs. Overexpression of EOD3 dramatically increases seed size of wild-type plants, while eod3-ko loss-of-function mutants form small seeds. The disruption of CYP78A9, the most closely related family member, synergistically enhances the seed size phenotype of eod3-ko mutants, indicating that EOD3 functions redundantly with CYP78A9 to affect seed growth. Reciprocal cross experiments show that EOD3 acts maternally to promote seed growth. eod3-ko cyp78a9-ko double mutants have smaller cells in the maternal integuments of developing seeds, whereas eod3-1D forms more and larger cells in the integuments. Genetic analyses suggest that EOD3 functions independently of maternal factors DA1 and TTG2 to influence seed growth. Collectively, our findings identify EOD3 as a factor of seed size control and give insight into how plants control their seed size. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

The cyclin L homolog MOS12 and the MOS4-associated complex are required for proper splicing of plant resistance genes.

Publication Date: 2012 Jan 16 PMID: 22248079
Authors: Xu, F. - Xu, S. - Wiermer, M. - Zhang, Y. - Li, X.
Journal: Plant J

Plant resistance (R) proteins protect cells from infections through recognizing effector molecules produced by pathogens and initiating downstream defense cascades. Expression of R genes has to be tightly controlled transcriptionally and post-transcriptionally to mount proper immune responses. Intriguingly, alternative splicing of R genes of the NB-LRR-type was observed in different plant species, but its regulatory mechanism remains elusive. Here, we report the positional cloning and functional analysis of modifier of snc1, 12 (mos12-1), a partial loss-of-function mutant that can suppress the constitutive defense responses conferred by the gain-of-function R gene mutant snc1 (suppressor of npr1-1, constitutive 1). MOS12 encodes an arginine-rich protein homologous to human cyclin L. A null allele of mos12-2 is lethal, suggesting its vital role in plant growth and development. MOS12 localizes to the nucleus and the mos12-1 mutation results in altered splicing patterns of SNC1 and RPS4, indicate that MOS12 is required for proper splicing of target R genes. MOS12 co-immunoprecipitates with MOS4, indicating that MOS12 associates with the MOS4-associated complex (MAC). Accordingly, splicing patterns of SNC1 and RPS4 are changed in most MAC core mutants. Our study highlights the contribution of MOS12 and the MAC in alternative splicing of R genes, providing regulatory details on how alternative splicing is used to fine-tune R gene expression in plant immunity. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Functional disruption of the pentatricopeptide protein SLG1 affects mitochondrial RNA editing, plant development, and responses to abiotic stresses in Arabidopsis.

Publication Date: 2012 Jan 16 PMID: 22248025
Authors: Yuan, H. - Liu, D.
Journal: Plant J

Land plants contain a large family of genes that encode for pentatricopeptide (PPR) proteins. To date, few of these PPR proteins have been functionally characterized. In this study, we have analyzed an Arabidopsis mutant, slg1, which exhibits slow growth and delayed development. In addition, slg1 shows an enhanced response to ABA and increased tolerance to drought stress. The SLG1 gene encodes a PPR protein that is localized in mitochondria. In the slg1 mutant, RNA editing in a single site of the mitochondrial transcript nad3 is abolished. nad3 is a subunit of complex I of the electron transport chain in mitochondria. As a consequence, the NADH dehydrogenase activity of complex I in slg1 is strongly impaired and production of ATP is reduced. When responding to ABA treatment, slg1 accumulates more H(2) O(2) in its guard cells than the wild type. The slg1 mutant also has an increased expression of genes involved in the alternative respiratory pathway, which may compensate for the disrupted function of complex I and help scavenge the excess accumulation of H(2) O(2) . Our functional characterization of the slg1 mutant revealed a putative link between mitochondrial RNA editing and plant responses to abiotic stress.

post to: CiteULike

Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis.

Publication Date: 2012 Jan 16 PMID: 22247970
Authors: Yang, X. - Zhang, H. - Li, L.
Journal: Plant J

MicroRNAs (miRNAs) represent an important class of sequence-specific, trans-acting endogenous small RNA molecules that modulate gene expression at the post-transcriptional level. They function by binding to partial complementary cis-regulatory sites (miRNA binding sites) in their target mRNAs. Based on two recent observations from plant genome studies, namely that alternative splicing is a common phenomenon and that miRNA regulates a significant proportion of the transcriptome, we hypothesize that there may be a mechanism for gene regulation that involves both processes. In the present study, we performed a systemic search in the model plant Arabidopsis thaliana using annotated gene models as well as publically available high-throughput RNA sequencing data with a total of 570 million reads. Of the 354 high-confidence miRNA binding sites identified in Arabidopsis, at least 44 (12.4%) were affected by alternative splicing such that mRNA isoforms of the same miRNA target gene differ in the sequences encoding the miRNA binding sites. By simulation, we found that the frequency of alternative splicing at miRNA binding sites is significantly higher than at other regions. Comparative and functional analyses further indicated that the alternative splicing events are important for target gene expression and miRNA action. Together our results show that alternative splicing of miRNA binding sites is a plausible mechanism for attenuating miRNA-mediated gene regulation.

post to: CiteULike

An additional role of O-acetylserine as a sulphur status independent regulator during plant growth.

Publication Date: 2012 Jan 13 PMID: 22243437
Authors: Hubberten, H. M. - Klie, S. - Caldana, C. - Degenkolbe, T. - Willmitzer, L. - Hoefgen, R.
Journal: Plant J

O-acetylserine (OAS) is one of the most prominent metabolites changing upon sulphur starvation. Its putative role as a signaling molecule in higher plants has however been controversially discussed. This work provides further evidence for OAS being a signaling molecule based on the one hand on computational analysis of time-series experiments and on the other hand on transgenic plants conditionally displaying increased OAS levels. Transcripts correlating to a transient and specific increase of OAS levels observed in leaves of Arabidopsis thaliana plants 5 to 10 minutes after transfer to darkness and to a diurnal oscillation of the OAS content displaying a characteristic peak during the night were determined. Further, transgenic A. thaliana plants expressing a serine-O-acetyltransferase (SERAT) gene under the control of an inducible promoter were constructed. Induction of SERAT resulted in a specific time-dependent increase of OAS levels. Monitoring the transcriptome response in time-points where no changes in sulphur-related metabolites except OAS were observed and correlating this to the light dark transition and diurnal experiments resulted in the identification of six highly OAS correlated genes (adenosine-5'-phosphosulfate-reductase 3, sulphur-deficiency-induced 1, sulphur-deficiency-induced 2, low-sulphur-induced 1, serine hydroxymethyltransferase 7, and ChaC-like-protein). These data suggest that OAS on the one hand displays a signalling function leading to changes in transcript levels of a specific gene set irrespective of the sulphur status of the plant. On the other hand a role for OAS for a specific part of the sulphate response can be inferred. (c) 2012 The Authors. The Plant Journal(c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Mutations defective in ribonucleotide reductase activity interfere with pollen plastid DNA degradation mediated by DPD1 exonuclease.

Publication Date: 2012 Jan 12 PMID: 22239102
Authors: Tang, L. Y. - Matsushima, R. - Sakamoto, W.
Journal: Plant J

Organelle DNAs in mitochondria and plastids are present in multiple copies and make up a substantial fraction of total cellular DNA despite their limited genetic capacity. We recently demonstrated that organelle DNA degradation (ODD) proceeds during pollen maturation, mediated by the Mg(2+) -dependent organelle exonuclease DPD1. To understand ODD further, we characterized a distinct mutant (dpd2) in this study. In contrast to dpd1 which retains both plastid and mitochondrial DNAs, dpd2 showed a specific accumulation of plastid DNAs. Multiple abnormalities in vegetative and reproductive tissues of dpd2 were also detected. DPD2 encodes the large subunit of ribonucleotide reductase (RNR), an enzyme which functions at the rate-limiting step of de novo nucleotide biosynthesis. We demonstrated that the defects in RNR indirectly compromise the activity of DPD1 nuclease in plastids, thus supporting a different regulation of ODD in pollen. Several lines of evidence provided in this study reinforced our previous conclusion that the DPD1 exonuclease plays a central role in ODD that functions for DNA salvage, rather than maternal inheritance during pollen development. (c) 2012 The Authors. The Plant Journal(c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Stable integration of an engineered megabase repeat array into the maize genome.

Publication Date: 2012 Jan 10 PMID: 22233334
Authors: Zhang, H. - Phan, B. H. - Wang, K. - Artelt, B. J. - Jiang, J. - Parrott, W. A. - Dawe, R. K.
Journal: Plant J

Plant genome engineering as a practical matter will require stable introduction of long and complex segments of DNA sequence into plant genomes. Here we show that it is possible to synthetically engineer and introduce centromere-sized satellite repeat arrays into maize. We designed a synthetic repeat monomer of 156 bp that contains five DNA-binding motifs (LacO, TetO, Gal4, LexA, and CENPB), and extended it into tandem arrays using an overlapping PCR method similar to that commonly used in gene synthesis. The PCR products were then directly transformed into maize using biolistic transformation. We identified three resulting insertion sites (arrayed binding sites), the longest of which is at least 1100 kb. The LacI DNA-binding module is sufficient to efficiently tether YFP to the arrayed binding sites. We conclude that synthetic repeats can be delivered into plant cells by omitting passage through Escherichia coli, that they generally insert into one locus, and that great lengths may be achieved. It is anticipated that these experimental approaches will be useful for future applications in artificial chromosome design.

post to: CiteULike

Alternative splicing of the auxin biosynthesis gene YUCCA4 determines its subcellular compartmentation.

Publication Date: 2012 Jan 10 PMID: 22233288
Authors: Kriechbaumer, V. - Wang, P. - Hawes, C. - Abell, B. M.
Journal: Plant J

Auxin is a major growth hormone in plants, and recent studies have elucidated many of the molecular mechanisms underlying its action, including transport, perception and signal transduction. However, major gaps remain in our knowledge of auxin biosynthetic control, partly due to the complexity and probable redundancy of multiple pathways that involve the YUCCA family of flavin-dependent mono-oxygenases. This study reveals the differential localization of YUCCA4 alternative splice variants to the endoplasmic reticulum and the cytosol, which depends on tissue-specific splicing. One isoform is restricted to flowers, and is anchored to the cytosolic face of the endoplasmic reticulum membrane via a hydrophobic C-terminal transmembrane domain. The other isoform is present in all tissues and is distributed throughout the cytosol. These findings are consistent with previous observations of yucca4 phenotypes in flowers, and suggest a role for intracellular compartmentation in auxin biosynthesis.

post to: CiteULike

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis.

Publication Date: 2012 Jan 9 PMID: 22229385
Authors: Matsuda, F. - Okazaki, Y. - Oikawa, A. - Kusano, M. - Nakabayashi, R. - Kikuchi, J. - Yonemaru, J. I. - Ebana, K. - Yano, M. - Saito, K.
Journal: Plant J

A comprehensive and large scale metabolome quantitative trait loci (mQTL) analysis was performed to investigate the genetic backgrounds associated with metabolic phenotypes in rice grains. The metabolome dataset consisted of 759 metabolite signals was obtained from the grains of 85 lines of rice (Oryza sativa, Sasanishiki x Habataki back-crossed inbred lines). Metabolome analysis was performed using 4 different mass spectrometry pipelines to enhance detection of different classes of metabolites. mQTL analysis of a wide range of metabolites highlighted an uneven distribution of 802 mQTLs around the rice genome, as well as different modes of metabolomic trait (m-trait) control among various types of metabolites. The levels of most metabolites within rice grains were highly sensitive to environmental factors, but only weakly associated with mQTLs. Coordinated control was observed for several groups of metabolites, such as amino acids that linked to the mQTL hotspot on chromosome 3. For flavonoids, m-trait variation among the experimental lines was tightly governed by genetic factors that alter the glycosylation of flavones. Many loci affecting m-trait levels were detected by QTL analysis and plausible gene candidates were evaluated by in silico analysis. There were several mQTLs that profoundly influenced metabolite levels, providing insight into the control of rice metabolism. The genomic region and genes potentially responsible for the biosynthesis of apigenin-6,8-di-C-alpha-l-arabinoside are presented as an example of a critical mQTL identified by the analysis. (c) 2012 The Authors. The Plant Journal(c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Abiotic Stress-Inducible Receptor-Like Kinases Negatively Control ABA Signaling in Arabidopsis.

Publication Date: 2012 Jan 7 PMID: 22225700
Authors: Tanaka, H. - Osakabe, Y. - Katsura, S. - Mizuno, S. - Maruyama, K. - Kusakabe, K. - Mizoi, J. - Shinozaki, K. - Yamaguchi-Shinozaki, K.
Journal: Plant J

Membrane-anchored receptor-like protein kinases (RLKs) recognize extracellular signals at the cell surface and activate the downstream signaling pathway by phosphorylating specific target proteins. We analyzed a receptor-like cytosolic kinase (RLCK), ARCK1, whose expression was induced by abiotic stress. ARCK1 belongs to the cysteine-rich repeat (CRR)-RLK subfamily and encodes a cytosolic protein kinase. The arck1 mutant showed higher sensitivity than the wild-type to ABA and osmotic stress during the postgerminative growth phase. CRK36, an abiotic stress-inducible RLK belonging to the CRR-RLK subfamily, was screened as an interacting factor with ARCK1 by co-expression analyses and a yeast two-hybrid system. CRK36 physically interacted with ARCK1 in plant cells and the kinase domain of CRK36 phosphorylated ARCK1 in vitro. We generated CRK36 RNAi transgenic plants and the transgenic plants with suppressed CRK36 expression showed higher sensitivity than arck1-2 to ABA and osmotic stress during the postgerminative growth phase. Microarray analysis using CRK36 RNAi plants revealed that the suppression of CRK36 up-regulates several ABA-responsive genes, such as LEAs, oleosin, ABI4, and ABI5. These results suggest that CRK36 and ARCK1 form a complex and negatively control ABA and osmotic stress signal transduction. (c) 2012 The Authors. The Plant Journal(c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Functional disruption of the PPR protein SLG1 affects mitochondrial RNA editing, plant development, and responses to abiotic stresses in Arabidopsis.

Publication Date: 2012 Jan 5 PMID: 22221074
Authors: Yuan, H. - Liu, D.
Journal: Plant J

Land plants contain a large family of genes that encode for pentatricopeptide (PPR) proteins. To date, few of these PPR proteins have been functionally characterized. In this study, we have analyzed an Arabidopsis mutant, slg1, which exhibits slow growth and delayed development. In addition, slg1 shows enhanced response to ABA and increased tolerance to drought stress. The SLG1 gene encodes a PPR protein that is localized in mitochondria. In the slg1 mutant, RNA editing in a single site of the mitochondrial transcript nad3 is abolished. nad3 is a subunit of complex I of the electron transport chain in mitochondria. As a consequence, the NADH dehydrogenase activity of complex I in slg1 is strongly impaired and ATP production is reduced. When responding to ABA treatment, slg1 accumulates more H(2) O(2) in its guard cells than the WT. slg1 also has an increased expression of the genes involved in the alternative respiratory pathway, which may compensate for the disrupted function of the complex I and help scavenge the excess accumulation of H(2) O(2) . Our functional characterization of the slg1 mutant revealed a putative link between mitochondrial RNA editing and plant responses to abiotic stress. (c) 2012 The Authors. The Plant Journal(c) 2012 Blackwell Publishing Ltd.

post to: CiteULike

Two AP2 family genes, SUPERNUMERARY BRACT (SNB) and OsINDETERMINATE SPIKELET 1 (OsIDS1), synergistically control inflorescence architecture and floral meristem establishment in rice.

Publication Date: 2012 Feb PMID: 22003982
Authors: Lee, D. Y. - An, G.
Journal: Plant J

Meristem identity is crucial in determining the inflorescence architecture of grass species. We previously reported that SUPERNUMERARY BRACT (SNB) regulates the transition of spikelet meristems into floral meristems in rice (Oryza sativa). Here we demonstrated that SNB and Oryza sativa INDETERMINATE SPIKELET 1 (OsIDS1) together play important roles in inflorescence architecture and the establishment of floral meristems. In snb osids1 double mutants, the numbers of branches and spikelets within a panicle are significantly decreased, and the transition to a floral meristem is further delayed compared with the snb single mutant. Expression analyses showed that SNB and OsIDS1 are required for spatio-temporal expression of B- and E-function floral organ identity genes in the lodicules. In addition, the AP2 family genes are important for determining the degree of ramification in branch meristems, regulating the spatio-temporal expression of spikelet meristem genes, such as FRIZZY PANICLE (FZP). Furthermore, overexpression of microRNA172 (miR172) causes reductions in SNB and OsIDS1 transcript levels, and phenotypes of the transgenic plants are more severe than for snb osids1. This indicates that additional gene(s) participate in the development of branch and floral meristems. Preferential expression of mature miR172s in the area around the spikelet meristems implies that depletion of the AP2 family genes in those meristems via miR172 is an important step in controlling inflorescence branching and the formation of floral organs.

post to: CiteULike

Cold acclimation induces changes in Arabidopsis tonoplast protein abundance and activity and alters phosphorylation of tonoplast monosaccharide transporters.

Publication Date: 2012 Feb PMID: 21988472
Authors: Schulze, W. X. - Schneider, T. - Starck, S. - Martinoia, E. - Trentmann, O.
Journal: Plant J

Because they are immotile organisms, higher plants have developed efficient strategies for adaptation to temperature changes. During cold acclimation, plants accumulate specific types of solutes to enhance freezing tolerance. The vacuole is a major solute storage organelle, but until now the role of tonoplast proteins in cold acclimation has not been investigated. In a comparative tonoplast proteome analysis, we identified several membrane proteins with altered abundance upon cold acclimation. We found an increased protein abundance of the tonoplast pyrophosphatase and subunits of the vacuolar V-ATPase and a significantly increased V-ATPase activity. This was accompanied by increased vacuolar concentrations of dicarbonic acids and soluble sugars. Consistently, the abundance of the tonoplast dicarbonic acid transporter was also higher in cold-acclimatized plants. However, no change in the protein abundance of tonoplast monosaccharide transporters was detectable. However, a generally higher cold-induced phosphorylation of members of this sugar transporter sub-group was observed. Our results indicate that cold-induced solute accumulation in the vacuole is mediated by increased acidification of this organelle. Thus solute transport activity is either modulated by increased protein amounts or by modification of proteins via phosphorylation.

post to: CiteULike

Direct mapping of morphological distribution of syringyl and guaiacyl lignin in the xylem of maple by time-of-flight secondary ion mass spectrometry.

Publication Date: 2012 Feb PMID: 21978273
Authors: Saito, K. - Watanabe, Y. - Shirakawa, M. - Matsushita, Y. - Imai, T. - Koike, T. - Sano, Y. - Funada, R. - Fukazawa, K. - Fukushima, K.
Journal: Plant J

Lignin, one of the main structural polymer of plant cell walls, varies in amount and monomeric composition among tissue and cell types, as well as among plant species. However, few analytical methods are available that can conveniently and accurately determine the morphological distribution of lignin units at the cellular level. In this report, we used time-of-flight secondary ion mass spectrometry (TOF-SIMS) to directly map guaiacyl (G) and syringyl (S) lignin units in several successive growth rings of the maple xylem. TOF-SIMS imaging and a semiquantitative approach revealed clear difference in the annual distribution of lignins between the fiber and vessel. While the vessel walls were constantly G-rich with varied S/G ratios through a growth ring, the fibers showed fairly regular annual distribution of lignins in which the earlywood was S-rich with an almost constant S/G ratio and the latewood was G-rich resulting from a decrease of the S unit. The reliability of TOF-SIMS results was demonstrated by its high correlation with the results of thioacidolysis on radial distribution of the S/G ratio in several contiguous tree rings and also in the latewood and earlywood of each ring. These results indicate that TOF-SIMS allows direct visualization of lignin composition in plant tissues.

post to: CiteULike

Arbuscule-containing and non-colonized cortical cells of mycorrhizal roots undergo extensive and specific reprogramming during arbuscular mycorrhizal development.

Publication Date: 2012 Feb PMID: 21978245
Authors: Gaude, N. - Bortfeld, S. - Duensing, N. - Lohse, M. - Krajinski, F.
Journal: Plant J

Most vascular plants form a mutualistic association with arbuscular mycorrhizal (AM) fungi, known as AM symbiosis. The development of AM symbiosis is an asynchronous process, and mycorrhizal roots therefore typically contain several symbiotic structures and various cell types. Hence, the use of whole-plant organs for downstream analyses can mask cell-specific variations in gene expression. To obtain insight into cell-specific reprogramming during AM symbiosis, comparative analyses of various cell types were performed using laser capture microdissection combined with microarray hybridization. Remarkably, the most prominent transcriptome changes were observed in non-arbuscule-containing cells of mycorrhizal roots, indicating a drastic reprogramming of these cells during root colonization that may be related to subsequent fungal colonization. A high proportion of transcripts regulated in arbuscule-containing cells and non-arbuscule-containing cells encode proteins involved in transport processes, transcriptional regulation and lipid metabolism, indicating that reprogramming of these processes is of particular importance for AM symbiosis.

post to: CiteULike

Next-generation sequencing and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content.

Publication Date: 2012 Feb PMID: 21974774
Authors: Hernandez, P. - Martis, M. - Dorado, G. - Pfeifer, M. - Galvez, S. - Schaaf, S. - Jouve, N. - Simkova, H. - Valarik, M. - Dolezel, J. - Mayer, K. F.
Journal: Plant J

Wheat is the third most important crop for human nutrition in the world. The availability of high-resolution genetic and physical maps and ultimately a complete genome sequence holds great promise for breeding improved varieties to cope with increasing food demand under the conditions of changing global climate. However, the large size of the bread wheat (Triticum aestivum) genome (approximately 17 Gb/1C) and the triplication of genic sequence resulting from its hexaploid status have impeded genome sequencing of this important crop species. Here we describe the use of mitotic chromosome flow sorting to separately purify and then shotgun-sequence a pair of telocentric chromosomes that together form chromosome 4A (856 Mb/1C) of wheat. The isolation of this much reduced template and the consequent avoidance of the problem of sequence duplication, in conjunction with synteny-based comparisons with other grass genomes, have facilitated construction of an ordered gene map of chromosome 4A, embracing >/=85% of its total gene content, and have enabled precise localization of the various translocation and inversion breakpoints on chromosome 4A that differentiate it from its progenitor chromosome in the A genome diploid donor. The gene map of chromosome 4A, together with the emerging sequences of homoeologous wheat chromosome groups 4, 5 and 7, represent unique resources that will allow us to obtain new insights into the evolutionary dynamics between homoeologous chromosomes and syntenic chromosomal regions.

post to: CiteULike

A dual regulatory role of Arabidopsis calreticulin-2 in plant innate immunity.

Publication Date: 2012 Feb PMID: 21974727
Authors: Qiu, Y. - Xi, J. - Du, L. - Roje, S. - Poovaiah, B. W.
Journal: Plant J

Calreticulin (CRT) is an endoplasmic reticulum-resident calcium-binding molecular chaperone that is highly conserved in multi-cellular eukaryotes. Higher plants contain two distinct groups of CRTs: CRT1/CRT2 and CRT3 isoforms. Previous studies have shown that bacterial elongation factor Tu receptor (EFR), a pattern-recognition receptor that is responsible for pathogen-associated molecular pattern-triggered immunity, is a substrate for Arabidopsis CRT3, suggesting a role for CRT3 in regulating plant defense against pathogens. Here we report that Arabidopsis CRT2 is another regulator of plant innate immunity. Despite significantly increased salicylic acid levels and constitutive expression of the systemic acquired resistance-associated marker genes PR1, PR2 and PR5, transgenic plants over-expressing CRT2 displayed reduced resistance to virulent Pseudomonas syringae pv. tomato DC3000 (PstDC3000). A (45) Ca(2+) overlay assay and a domain-swapping experiment further demonstrated that the negatively charged C-terminal tail of CRT2 is responsible for its high calcium-binding capacity and function in regulating the endogenous salicylic acid level. In addition, over-expression of the His173 mutant of CRT2 greatly enhanced plant defense against PstDC3000, supporting the existence of a self-inhibition mechanism that can counteract the effects of salicylic acid-dependent immune responses. These results suggest that CRT2 functions through its N-terminal domain(s) as a self-modulator that can possibly prevent the salicylic acid-mediated runaway defense responses triggered by its C-terminal calcium-buffering activity in response to pathogen invasion.

post to: CiteULike

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis.

Publication Date: 2012 Feb PMID: 21973320
Authors: Song, X. - Li, P. - Zhai, J. - Zhou, M. - Ma, L. - Liu, B. - Jeong, D. H. - Nakano, M. - Cao, S. - Liu, C. - Chu, C. - Wang, X. J. - Green, P. J. - Meyers, B. C. - Cao, X.
Journal: Plant J

Higher plants have evolved multiple proteins in the RNase III family to produce and regulate different classes of small RNAs with specialized molecular functions. In rice (Oryza sativa), numerous genomic clusters are targeted by one of two microRNAs (miRNAs), miR2118 and miR2275, to produce secondary small interfering RNAs (siRNAs) of either 21 or 24 nucleotides in a phased manner. The biogenesis requirements or the functions of the phased small RNAs are completely unknown. Here we examine the rice Dicer-Like (DCL) family, including OsDCL1, -3a, -3b and -4. By deep sequencing of small RNAs from different tissues of the wild type and osdcl4-1, we revealed that the processing of 21-nucleotide siRNAs, including trans-acting siRNAs (tasiRNA) and over 1000 phased small RNA loci, was largely dependent on OsDCL4. Surprisingly, the processing of 24-nucleotide phased small RNA requires the DCL3 homolog OsDCL3b rather than OsDCL3a, suggesting functional divergence within DCL3 family. RNA ligase-mediated 5' rapid amplification of cDNA ends and parallel analysis of RNA ends (PARE)/degradome analysis confirmed that most of the 21- and 24-nucleotide phased small RNA clusters were initiated from the target sites of miR2118 and miR2275, respectively. Furthermore, the accumulation of the two triggering miRNAs requires OsDCL1 activity. Finally, we show that phased small RNAs are preferentially produced in the male reproductive organs and are likely to be conserved in monocots. Our results revealed significant roles of OsDCL4, OsDCL3b and OsDCL1 in the 21- and 24-nucleotide phased small RNA biogenesis pathway in rice.

post to: CiteULike

Polar development of preprophase bands and cell plates in the Arabidopsis leaf epidermis.

Publication Date: 2012 Feb PMID: 21972819
Authors: Lucas, J. R. - Sack, F. D.
Journal: Plant J

Preprophase bands are belts of cortical microtubules that appear at the end of interphase and predict where cell plates will fuse with parental walls during division. Phragmoplasts are microtubule-rich arrays that orchestrate the growth and guidance of cell plates during cytokinesis. Descriptions of the development of these arrays often assume non-polar formation, with preprophase bands developing more or less simultaneously around the cell circumference. Phragmoplasts are often described as initiating at the cell center and then expanding evenly outwards until fusion with parent cell walls. We analyzed the spatio-temporal development of both arrays because initial observations of array growth in the Arabidopsis leaf epidermis revealed directional variability. Almost all preprophase bands formed in a polar fashion, with initiation and maturation occurring first in the cell cortex near the inside of the leaf, and later in the outer cell cortex. A similar polarity developed in phragmoplasts and cell plates, raising the possibility that polarized division is common in plants. Together, these findings identify additional polar features of the epidermis, and thereby provide a visually accessible system for identifying new proteins and subcellular components involved in the development of cell division and the previously formed division site.

post to: CiteULike

The turbulent life of Sirevirus retrotransposons and the evolution of the maize genome: more than ten thousand elements tell the story.

Publication Date: 2012 Feb PMID: 21967390
Authors: Bousios, A. - Kourmpetis, Y. A. - Pavlidis, P. - Minga, E. - Tsaftaris, A. - Darzentas, N.
Journal: Plant J

Sireviruses are one of the three genera of Copia long terminal repeat (LTR) retrotransposons, exclusive to and highly abundant in plants, and with a unique, among retrotransposons, genome structure. Yet, perhaps due to the few references to the Sirevirus origin of some families, compounded by the difficulty in correctly assigning retrotransposon families into genera, Sireviruses have hardly featured in recent research. As a result, analysis at this key level of classification and details of their colonization and impact on plant genomes are currently lacking. Recently, however, it became possible to accurately assign elements from diverse families to this genus in one step, based on highly conserved sequence motifs. Hence, Sirevirus dynamics in the relatively obese maize genome can now be comprehensively studied. Overall, we identified >10 600 intact and approximately 28 000 degenerate Sirevirus elements from a plethora of families, some brought into the genus for the first time. Sireviruses make up approximately 90% of the Copia population and it is the only genus that has successfully infiltrated the genome, possibly by experiencing intense amplification during the last 600 000 years, while being constantly recycled by host mechanisms. They accumulate in chromosome-distal gene-rich areas, where they insert in between gene islands, mainly in preferred zones within their own genomes. Sirevirus LTRs are heavily methylated, while there is evidence for a palindromic consensus target sequence. This work brings Sireviruses in the spotlight, elucidating their lifestyle and history, and suggesting their crucial role in the current genomic make-up of maize, and possibly other plant hosts.

post to: CiteULike

The F-box protein CPR1/CPR30 negatively regulates R protein SNC1 accumulation.

Publication Date: 2012 Feb PMID: 21967323
Authors: Gou, M. - Shi, Z. - Zhu, Y. - Bao, Z. - Wang, G. - Hua, J.
Journal: Plant J

Disease resistance (R) proteins, as central regulators of plant immunity, are tightly regulated for effective defense responses and to prevent constitutive defense activation under non-pathogenic conditions. Here we report the identification of an F-box protein CPR1/CPR30 as a negative regulator of an R protein SNC1 likely through SCF (Skp1-cullin-F-box) mediated protein degradation. The cpr1-2 (cpr30-1) loss-of-function mutant has constitutive defense responses, and it interacts synergistically with a gain-of function mutant snc1-1 and a bon1-1 mutant where SNC1 is upregulated. The loss of SNC1 function suppresses the mutant phenotypes of cpr1-2 and cpr1-2 bon1-1, while overexpression of CPR1 rescues mutant phenotypes of both bon1-1 and snc1-1. Furthermore, the amount of SNC1 protein is upregulated in the cpr1-2 mutant and down-regulated when CPR1 is overexpressed. The regulation of SNC1 by CPR1 is dependent on the 26S proteosome as a protease inhibitor MG132 stabilizes SNC1 and reverses the effect of CPR1 on SNC1. Interestingly, CPR1 is induced after infection of both virulent and avirulent pathogens similarly to the other negative defense regulator BON1. Thus, this study reveals a new mechanism in R protein regulation likely through protein degradation and suggests negative regulation as a critical component in fine control of plant immunity.

post to: CiteULike

Quantitative analysis of venation patterns of Arabidopsis leaves by supervised image analysis.

Publication Date: 2012 Feb PMID: 21955023
Authors: Dhondt, S. - Van Haerenborgh, D. - Van Cauwenbergh, C. - Merks, R. M. - Philips, W. - Beemster, G. T. - Inze, D.
Journal: Plant J

The study of transgenic Arabidopsis lines with altered vascular patterns has revealed key players in the venation process, but details of the vascularization process are still unclear, partly because most lines have only been assessed qualitatively. Therefore, quantitative analyses are required to identify subtle perturbations in the pattern and to test dynamic modeling hypotheses using biological measurements. We developed an online framework, designated Leaf Image Analysis Interface (LIMANI), in which venation patterns are automatically segmented and measured on dark-field images. Image segmentation may be manually corrected through use of an interactive interface, allowing supervision and rectification steps in the automated image analysis pipeline and ensuring high-fidelity analysis. This online approach is advantageous for the user in terms of installation, software updates, computer load and data storage. The framework was used to study vascular differentiation during leaf development and to analyze the venation pattern in transgenic lines with contrasting cellular and leaf size traits. The results show the evolution of vascular traits during leaf development, suggest a self-organizing mechanism for leaf venation patterning, and reveal a tight balance between the number of end-points and branching points within the leaf vascular network that does not depend on the leaf developmental stage and cellular content, but on the leaf position on the rosette. These findings indicate that development of LIMANI improves understanding of the interaction between vascular patterning and leaf growth.

post to: CiteULike

Maternal control of seed oil content in Brassica napus: the role of silique wall photosynthesis.

Publication Date: 2012 Feb PMID: 21954986
Authors: Hua, W. - Li, R. J. - Zhan, G. M. - Liu, J. - Li, J. - Wang, X. F. - Liu, G. H. - Wang, H. Z.
Journal: Plant J

Seed oil content is an important agronomic trait in rapeseed. However, our understanding of the regulatory processes controlling oil accumulation is still limited. Using two rapeseed lines (zy036 and 51070) with contrasting oil content, we found that maternal genotype greatly affects seed oil content. Genetic and physiological evidence indicated that difference in the local and tissue-specific photosynthetic activity in the silique wall (a maternal tissue) was responsible for the different seed oil contents. This effect was mimicked by in planta manipulation of silique wall photosynthesis. Furthermore, the starch content and expression of the important lipid synthesis regulatory gene WRINKLED1 in developing seeds were linked with silique wall photosynthetic activity. 454 pyrosequencing was performed to explore the possible molecular mechanism for the difference in silique wall photosynthesis between zy036 and 51070. Interestingly, the results suggested that photosynthesis-related genes were over-represented in both total silique wall expressed genes and genes that were differentially expressed between genotypes. A potential regulatory mechanism for elevated photosynthesis in the zy036 silique wall is proposed on the basis of knowledge from Arabidopsis. Differentially expressed ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)-related genes were used for further investigations. Oil content correlated closely with BnRBCS1A expression levels and Rubisco activities in the silique wall, but not in the leaf. Taken together, our results highlight an important role of silique wall photosynthesis in the regulation of seed oil content in terms of maternal effects.

post to: CiteULike

Raa4 is a trans-splicing factor that specifically binds chloroplast tscA intron RNA.

Publication Date: 2012 Feb PMID: 21954961
Authors: Glanz, S. - Jacobs, J. - Kock, V. - Mishra, A. - Kuck, U.
Journal: Plant J

During trans-splicing of discontinuous organellar introns, independently transcribed coding sequences are joined together to generate a continuous mRNA. The chloroplast psaA gene from Chlamydomonas reinhardtii encoding the P(700) core protein of photosystem I (PSI) is split into three exons and two group IIB introns, which are both spliced in trans. Using forward genetics, we isolated a novel PSI mutant, raa4, with a defect in trans-splicing of the first intron. Complementation analysis identified the affected gene encoding the 112.4 kDa Raa4 protein, which shares no strong sequence identity with other known proteins. The chloroplast localization of the protein was confirmed by confocal fluorescence microscopy, using a GFP-tagged Raa4 fusion protein. RNA-binding studies showed that Raa4 binds specifically to domains D2 and D3, but not to other conserved domains of the tripartite group II intron. Raa4 may play a role in stabilizing folding intermediates or functionally active structures of the split intron RNA.

post to: CiteULike

Plastid stromules are induced by stress treatments acting through abscisic acid.

Publication Date: 2012 Feb PMID: 21951173
Authors: Gray, J. C. - Hansen, M. R. - Shaw, D. J. - Graham, K. - Dale, R. - Smallman, P. - Natesan, S. K. - Newell, C. A.
Journal: Plant J

Stromules are highly dynamic stroma-filled tubules that extend from the surface of all plastid types in all multi-cellular plants examined to date. The stromule frequency (percentage of plastids with stromules) has generally been regarded as characteristic of the cell and tissue type. However, the present study shows that various stress treatments, including drought and salt stress, are able to induce stromule formation in the epidermal cells of tobacco hypocotyls and the root hairs of wheat seedlings. Application of abscisic acid (ABA) to tobacco and wheat seedlings induced stromule formation very effectively, and application of abamine, a specific inhibitor of ABA synthesis, prevented stromule induction by mannitol. Stromule induction by ABA was dependent on cytosolic protein synthesis, but not plastid protein synthesis. Stromules were more abundant in dark-grown seedlings than in light-grown seedlings, and the stromule frequency was increased by transfer of light-grown seedlings to the dark and decreased by illumination of dark-grown seedlings. Stromule formation was sensitive to red and far-red light, but not to blue light. Stromules were induced by treatment with ACC (1-aminocyclopropane-1-carboxylic acid), the first committed ethylene precursor, and by treatment with methyl jasmonate, but disappeared upon treatment of seedlings with salicylate. These observations indicate that abiotic, and most probably biotic, stresses are able to induce the formation of stromules in tobacco and wheat seedlings.

post to: CiteULike

Exclusion of plastid nucleoids and ribosomes from stromules in tobacco and Arabidopsis.

Publication Date: 2012 Feb PMID: 21951134
Authors: Newell, C. A. - Natesan, S. K. - Sullivan, J. A. - Jouhet, J. - Kavanagh, T. A. - Gray, J. C.
Journal: Plant J

Stromules are stroma-filled tubules that extend from the surface of plastids and allow the transfer of proteins as large as 550 kDa between interconnected plastids. The aim of the present study was to determine if plastid DNA or plastid ribosomes are able to enter stromules, potentially permitting the transfer of genetic information between plastids. Plastid DNA and ribosomes were marked with green fluorescent protein (GFP) fusions to LacI, the lac repressor, which binds to lacO-related sequences in plastid DNA, and to plastid ribosomal proteins Rpl1 and Rps2, respectively. Fluorescence from GFP-LacI co-localised with plastid DNA in nucleoids in all tissues of transgenic tobacco (Nicotiana tabacum L.) examined and there was no indication of its presence in stromules, not even in hypocotyl epidermal cells, which contain abundant stromules. Fluorescence from Rpl1-GFP and Rps2-GFP was also observed in a punctate pattern in chloroplasts of tobacco and Arabidopsis [Arabidopsis thaliana (L.) Heynh.], and fluorescent stromules were not detected. Rpl1-GFP was shown to assemble into ribosomes and was co-localised with plastid DNA. In contrast, in hypocotyl epidermal cells of dark-grown Arabidopsis seedlings, fluorescence from Rpl1-GFP was more evenly distributed in plastids and was observed in stromules on a total of only four plastids (<0.02% of the plastids observed). These observations indicate that plastid DNA and plastid ribosomes do not routinely move into stromules in tobacco and Arabidopsis, and suggest that transfer of genetic information by this route is likely to be a very rare event, if it occurs at all.

post to: CiteULike