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Journal Cover Plant Molecular Biology
  [SJR: 1.915]   [H-I: 137]   [9 followers]  Follow
   Hybrid Journal Hybrid journal (It can contain Open Access articles)
   ISSN (Print) 1573-5028 - ISSN (Online) 0167-4412
   Published by Springer-Verlag Homepage  [2335 journals]
  • Elucidating and mining the Tulipa and Lilium transcriptomes
    • Abstract: Abstract Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser ( The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.
      PubDate: 2016-10-01
  • The “putative” role of transcription factors from Hl WRKY family in
           the regulation of the final steps of prenylflavonid and bitter acids
           biosynthesis in hop ( Humulus lupulus L.)
    • Abstract: Abstract Lupulin glands localized in female hop (Humulus lupulus L.) cones are valuable source of bitter acids, essential oils and polyphenols. These compounds are used in brewing industry and are important for biomedical applications. In this study we describe the potential effect of transcription factors from WRKY family in the activation of the final steps of lupulin biosynthesis. In particular, lupulin gland-specific transcription factor HlWRKY1 that shows significant similarity to AtWRKY75, has ability to activate the set of promoters driving key genes of xanthohumol and bitter acids biosynthesis such as chalcone synthase H1, valerophenone synthase, prenyltransferase 1, 1L and 2 and O-methyltransferase-1. When combined with co-factor HlWDR1 and silencing suppressor p19, HlWRKY1 is able to enhance transient expression of gus gene driven by Omt1 and Chs_H1 promoters to significant level as compared to 35S promoter of CaMV in Nicotiana. benthamiana. Transformation of hop with dual Agrobacterium vector bearing HlWRKY1/HlWDR1 led to ectopic overexpression of these transgenes and further activation of lupulin-specific genes expression in hop leaves. It was further showed that (1) HlWRKY1 is endowed with promoter autoactivation; (2) It is regulated by post-transcriptional gene silencing (PTGS) mechanism; (3) It is stimulated by kinase co-expression. Since HlWRKY1 promotes expression of lupulin-specific HlMyb3 gene therefore it can constitute a significant component in hop lupulin regulation network. Putative involvement of HlWRKY1 in the regulation of lupulin biosynthesis may suggest the original physiological function of lupulin components in hop as flower and seed protective compounds.
      PubDate: 2016-10-01
  • Repression of ARF10 by microRNA160 plays an important role in the
           mediation of leaf water loss
    • Abstract: Abstract Solanum lycopersicum auxin response factor 10 (SlARF10) is post-transcriptionally regulated by Sl-miR160. Overexpression of a Sl-miR160-resistant SlARF10 (mSlARF10) resulted in narrower leaflet blades with larger stomata but lower densities. 35S:mSlARF10-6 plants with narrower excised leaves had greater water loss, which was in contrast to the wild type (WT). Further analysis revealed that the actual water loss was not consistent with the calculated stomatal water loss in 35S:mSlARF10-6 and the WT under the dehydration treatment, indicating that there is a difference in hydraulic conductance. Pretreatment with abscisic acid (ABA) and HgCl2 confirmed higher hydraulic conductance in 35S:mSlARF10, which is related to the larger stomatal size and higher activity of aquaporins (AQPs). Under ABA treatment, 35S:mSlARF10-6 showed greater sensitivity, and the stomata closed rapidly. Screening by RNA sequencing revealed that five AQP-related genes, fourteen ABA biosynthesis/signal genes and three stomatal development genes were significantly altered in 35S:mSlARF10-6 plants, and this result was verified by qRT-PCR. The promoter analysis showed that upregulated AQPs contain AuxRE and ABRE, implying that these elements may be responsible for the high expression levels of AQPs in 35S:mSlARF10-6. The three most upregulated AQPs (SlTIP1-1-like, SlPIP2;4 and SlNIP-type-like) were chosen to confirm AuxRE and ABRE function. Promoters transient expression demonstrated that the SlPIP2;4 and SlNIP-type-like AuxREs and SlPIP2;4 and SlTIP1-1-like ABREs could significantly enhance the expression of the GUS reporter in 35S:mSlARF10-6, confirming that AuxRE and ABRE may be the main factors inducing the expression of AQPs. Additionally, two upregulated transcription factors in 35S:mSlARF10-6, SlARF10 and SlABI5-like were shown to directly bind to those elements in an electromobility shift assay and a yeast one-hybrid assay. Furthermore, transient expression of down-regulated ARF10 or up-regulated ABI5 in tomato leaves demonstrated that ARF10 is the direct factor for inducing the water loss in 35S:mSlARF10-6. Here, we show that although SlARF10 increased the ABA synthesis/signal response by regulating stomatal aperture to mitigate water loss, SlARF10 also influenced stomatal development and AQP expression to affect water transport, and both act cooperatively to control the loss of leaf water in tomato. Therefore, this study uncovers a previously unrecognized leaf water loss regulatory factor and a network for coordinating auxin and ABA signalling in this important process. In an evolutionary context, miR160 regulates ARF10 to maintain the water balance in the leaf, thus ensuring normal plant development and environmental adaptation.
      PubDate: 2016-10-01
  • De novo transcriptome analysis reveals insights into dynamic homeostasis
           regulation of somatic embryogenesis in upland cotton ( G. hirsutum L.)
    • Abstract: Abstract Plant regeneration via somatic embryogenesis (SE) is the key step for genetic improvement of cotton (Gossypium hirsutum L.) through genetic engineering mediated by Agrobacteria, but the molecular mechanisms underlying SE in cotton is still unclear. Here, RNA-Sequencing was used to analyze the genes expressed during SE and their expression dynamics using RNAs isolated from non-embryogenic callus (NEC), embryogenic callus (EC) and somatic embryos (SEs). A total of 101, 670 unigenes were de novo assembled. The genes differentially expressed (DEGs) amongst NEC, EC and SEs were identified, annotated and classified. More DEGs were found between SEs and EC than between EC and NEC. A significant number of DEGs were related to hormone homeostasis, stress and ROS responses, and metabolism of polyamines. To confirm the expression dynamics of selected DEGs involved in various pathways, experiments were set up to investigate the effects of hormones (Indole-3-butytric acid, IBA; Kinetin, KT), polyamines, H2O2 and stresses on SE. Our results showed that exogenous application of IBA and KT positively regulated the development of EC and SEs, and that polyamines and H2O2 promoted the conversion of EC into SEs. Furthermore, we found that low and moderate stress is beneficial for proliferation of EC and SEs formation. Together, our global analysis of transcriptomic dynamics reveals that hormone homeostasis, polyamines, and stress response synergistically regulating SE in cotton.
      PubDate: 2016-10-01
  • Oral immunisation of mice with transgenic rice calli expressing cholera
           toxin B subunit fused to consensus dengue cEDIII antigen induces
           antibodies to all four dengue serotypes
    • Abstract: Abstract Dengue virus (DENV) infection is an emerging global health threat. DENV consists of four distinct serotypes, necessitating a tetravalent vaccine. In this study, expression of consensus envelope protein domain III (cEDIII) fused to cholera toxin B subunit (CTB) in transgenic rice calli was improved using the luminal binding protein BiP at the N-terminus and the SEKDEL signal sequences at the C-terminus, targeting the recombinant protein to endoplasmic reticulum (ER). We found that the fusion protein showed higher levels of expression when compared to the fusion proteins using rice amylase 3D (RAmy3D) or CTB native signal sequence only. The CTB-cEDIII fusion protein was evaluated as an oral dengue vaccine candidate in mice. Serotype specific systemic IgG antibodies and specific IgA response in feces were detected and furthermore, T cell proliferation and high frequency antibody-secreting B cells were detected in the spleen. These results suggest the possible use of plant-based dengue tetravalent vaccine targeted to the mucosal immune system for induction of systemic and mucosal immune responses to DENV infection.
      PubDate: 2016-10-01
  • Nitrogen assimilation system in maize is regulated by developmental and
           tissue-specific mechanisms
    • Abstract: Key message We found metabolites, enzyme activities and enzyme transcript abundances vary significantly across the maize lifecycle, but weak correlation exists between the three groups. We identified putative genes regulating nitrate assimilation. Progress in improving nitrogen (N) use efficiency (NUE) of crop plants has been hampered by the complexity of the N uptake and utilisation systems. To understand this complexity we measured the activities of seven enzymes and ten metabolites related to N metabolism in the leaf and root tissues of Gaspe Flint maize plants grown in 0.5 or 2.5 mM NO3 − throughout the lifecycle. The amino acids had remarkably similar profiles across the lifecycle except for transient responses, which only appeared in the leaves for aspartate or in the roots for asparagine, serine and glycine. The activities of the enzymes for N assimilation were also coordinated to a certain degree, most noticeably with a peak in root activity late in the lifecycle, but with wide variation in the activity levels over the course of development. We analysed the transcriptional data for gene sets encoding the measured enzymes and found that, unlike the enzyme activities, transcript levels of the corresponding genes did not exhibit the same coordination across the lifecycle and were only weakly correlated with the levels of various amino acids or individual enzyme activities. We identified gene sets which were correlated with the enzyme activity profiles, including seven genes located within previously known quantitative trait loci for enzyme activities and hypothesise that these genes are important for the regulation of enzyme activities. This work provides insights into the complexity of the N assimilation system throughout development and identifies candidate regulatory genes, which warrant further investigation in efforts to improve NUE in crop plants.
      PubDate: 2016-10-01
  • Deciphering the role of the AT-rich interaction domain and the HMG-box
           domain of ARID-HMG proteins of Arabidopsis thaliana
    • Abstract: Abstract ARID-HMG DNA-binding proteins represent a novel group of HMG-box containing protein family where the AT-rich interaction domain (ARID) is fused with the HMG-box domain in a single polypeptide chain. ARID-HMG proteins are highly plant specific with homologs found both in flowering plants as well as in moss such as Physcomitrella. The expression of these proteins is ubiquitous in plant tissues and primarily localises in the cell nucleus. HMGB proteins are involved in several nuclear processes, but the role of ARID-HMG proteins in plants remains poorly explored. Here, we performed DNA-protein interaction studies with Arabidopsis ARID-HMG protein HMGB11 (At1g55650) to understand the functionality of this protein and its individual domains. DNA binding assays revealed that AtHMGB11 can bind double-stranded DNA with a weaker affinity (Kd = 475 ± 17.9 nM) compared to Arabidopsis HMGB1 protein (Kd = 39.8 ± 2.68 nM). AtHMGB11 also prefers AT-rich DNA as a substrate and shows structural bias for supercoiled DNA. Molecular docking of the DNA-AtHMGB11 complex indicated that the protein interacts with the DNA major groove, mainly through its ARID domain and the junction region connecting the ARID and the HMG-box domain. Also, predicted by the docking model, mutation of Lys85 from the ARID domain and Arg199 & Lys202 from the junction region affects the DNA binding affinity of AtHMGB11. In addition, AtHMGB11 and its truncated form containing the HMG-box domain can not only promote DNA mini-circle formation but are also capable of inducing negative supercoils into relaxed plasmid DNA suggesting the involvement of this protein in several nuclear events. Overall, the study signifies that both the ARID and the HMG-box domain contribute to the optimal functioning of ARID-HMG protein in vivo.
      PubDate: 2016-10-01
  • Intron sequences that stimulate gene expression in Arabidopsis
    • Abstract: Key message Related motifs strongly increase gene expression when added to an intron located in coding sequences. Many introns greatly increase gene expression through a mechanism that remains elusive. An obstacle to understanding intron-mediated enhancement (IME) has been the difficulty of locating the specific intron sequences responsible for boosting expression because they are redundant, dispersed, and degenerate. Previously we used the IMEter algorithm in two independent ways to identify two motifs (CGATT and TTNGATYTG) that are candidates for involvement in IME in Arabidopsis. Here we show that both motifs are sufficient to increase expression. An intron that has little influence on expression was converted into one that increased mRNA accumulation 24-fold and reporter enzyme activity 40-fold relative to the intronless control by introducing 11 copies of the more active TTNGATYTG motif. This degree of stimulation is twice as large as that of the strongest of 15 natural introns previously tested in the same reporter gene. Even though the CGATT and TTNGATYTG motifs each increased expression, and CGATT matches the NGATY core of the longer motif, combining the motifs to make TTCGATTTG reduced the stimulating ability of the TTNGATYTG motif. Additional substitutions were used to test the contribution to IME of other residues in the TTNGATYTG motif. The verification that these motifs are active in IME will improve our ability to predict the stimulating ability of introns, to engineer any intron to increase expression to a desired level, and to explore the mechanism of IME by seeking factors that might interact with these sequences.
      PubDate: 2016-10-01
  • In vitro promoter recognition by the catalytic subunit of plant phage-type
           RNA polymerases
    • Abstract: Key message We identified sequence motifs, which enhance or reduce the ability of the Arabidopsis phage-type RNA polymerases RPOTm (mitochondrial RNAP), RPOTp (plastidial RNAP), and RPOTmp (active in both organelles) to recognize their promoters in vitro with help of a ‘specificity loop’. The importance of this data for the evolution and function of the organellar RNA polymerases is discussed. The single-subunit RNA polymerase (RNAP) of bacteriophage T7 is able to perform all steps of transcription without additional transcription factors. Dicotyledonous plants possess three phage-type RNAPs, RPOTm—the mitochondrial RNAP, RPOTp—the plastidial RNAP, and RPOTmp—an RNAP active in both organelles. RPOTm and RPOTp, like the T7 polymerase, are able to recognize promoters, while RPOTmp displays no significant promoter specificity in vitro. To find out which promoter motifs are crucial for recognition by the polymerases we performed in vitro transcription assays with recombinant Arabidopsis RPOTm and RPOTp enzymes. By comparing different truncated and mutagenized promoter constructs, we observed the same minimal promoter sequence supposed to be needed in vivo for transcription initiation. Moreover, we identified elements of core and flanking sequences, which are of critical importance for promoter recognition and activity in vitro. We further intended to reveal why RPOTmp does not efficiently recognize promoters in vitro and if promoter recognition is based on a structurally defined specificity loop of the plant enzymes as described for the yeast and T7 RNAPs. Interestingly, the exchange of only three amino acids within the putative specificity loop of RPOTmp enabled the enzyme for specific promoter transcription in vitro. Thus, also in plant phage-type RNAPs the specificity loop is engaged in promoter recognition. The results are discussed with respect to their relevance for transcription in organello and to the evolution of RPOT enzymes including the divergence of their functions.
      PubDate: 2016-10-01
  • Stability and localization of 14-3-3 proteins are involved in salt
           tolerance in Arabidopsis
    • Abstract: Key message Salt stress induces the degradation of 14-3-3 proteins, and affects the localization of 14-3-3 λ. Both the modulation of 14-3-3 protein stability and the subcellular localization of these proteins are involved in salt tolerance in plants. Salt tolerance in plants is regulated by multiple signaling pathways, including the salt overly sensitive (SOS) pathway, of which the SOS2 protein is a key component. SOS2 is activated under salt stress to enhance salt tolerance in plants. We previously identified 14-3-3 λ and κ as important regulators of salt tolerance. Both proteins interact with SOS2 to inhibit its kinase activity under normal growth conditions. In response to salt stress, 14-3-3 proteins dissociate from SOS2, releasing its activity and activating the SOS pathway to confer salt tolerance (Zhou et al. Plant Cell 26:1166–1182, 2014). Here we report that salt stress promotes the degradation of 14-3-3 λ and κ, at least in part via the actions of SOS3-like calcium binding protein 8/calcineurin-B-like10, and also decreases the plasma membrane (PM) localization of 14-3-3 λ. Salt stress also partially represses the interaction of SOS2 and 14-3-3 λ at the PM, but activates PM-localized SOS2. Together, these results suggest that, in plants, both the modulation of 14-3-3 stability and the subcellular localization of these proteins in response to salt stress are important for SOS2 activation and salt tolerance. These data provide new insights into the biological roles of 14-3-3 proteins in modulating salt tolerance.
      PubDate: 2016-10-01
  • Genome-wide identification and characterization of tRNA-derived RNA
           fragments in land plants
    • Abstract: Key message The manuscript by Alves et al. entitled “Genome-wide identification and characterization of tRNA-derived RNA fragments in land plants” describes the identification and characterization of tRNAderived sRNA fragments in plants. By combining bioinformatic analysis and genetic and molecular approaches, we show that tRF biogenesis does not rely on canonical microRNA/siRNA processing machinery (i.e., independent of DICER-LIKE proteins). Moreover, we provide evidences that the Arabidopsis S-like Ribonuclease 1 (RNS1) might be involved in the biogenesis of tRFs. Detailed analyses showed that plant tRFs are sorted into different types of ARGONAUTE proteins and that they have potential target candidate genes. Our work advances the understanding of the tRF biology in plants by providing evidences that plant and animal tRFs shared common features and raising the hypothesis that an interplay between tRFs and other sRNAs might be important to fine-tune gene expression and protein biosynthesis in plant cells. Small RNA (sRNA) fragments derived from tRNAs (3′-loop, 5′-loop, anti-codon loop), named tRFs, have been reported in several organisms, including humans and plants. Although they may interfere with gene expression, their biogenesis and biological functions in plants remain poorly understood. Here, we capitalized on small RNA sequencing data from distinct species such as Arabidopsis thaliana, Oryza sativa, and Physcomitrella patens to examine the diversity of plant tRFs and provide insight into their properties. In silico analyzes of 19 to 25-nt tRFs derived from 5′ (tRF-5s) and 3′CCA (tRF-3s) tRNA loops in these three evolutionary distant species showed that they are conserved and their abundance did not correlate with the number of genomic copies of the parental tRNAs. Moreover, tRF-5 is the most abundant variant in all three species. In silico and in vivo expression analyses unraveled differential accumulation of tRFs in Arabidopsis tissues/organs, suggesting that they are not byproducts of tRNA degradation. We also verified that the biogenesis of most Arabidopsis 19–25 nt tRF-5s and tRF-3s is not primarily dependent on DICER-LIKE proteins, though they seem to be associated with ARGONAUTE proteins and have few potential targets. Finally, we provide evidence that Arabidopsis ribonuclease RNS1 might be involved in the processing and/or degradation of tRFs. Our data support the notion that an interplay between tRFs and other sRNAs might be important to fine tune gene expression and protein biosynthesis in plant cells.
      PubDate: 2016-09-28
  • Salinity-mediated transcriptional and post-translational regulation of the
           Arabidopsis aquaporin PIP2;7
    • Abstract: Key message Salt stress triggers a simultaneous transcriptional repression and aquaporin internalization to modify root cell water conductivity. Plasma membrane intrinsic proteins (PIPs) are involved in the adjustment of plant water balance in response to changing environmental conditions. In this study, Arabidopsis wild-type (Col-0) and transgenic lines overexpressing PIP2;7 were used to investigate and compare their response to salt stress. Hydraulic conductivity measurements using a high-pressure flowmeter (HPFM) revealed that overexpression of PIP2;7 induced a sixfold increase in root hydraulic conductivity of four week-old Arabidopsis thaliana plants compared to WT. Exposure to a high salt stress (150 mM NaCl) triggered a rapid repression of overall aquaporin activity in both genotypes. Response to salt stress was also investigated in 8 day-old seedlings. Exposure to salt led to a repression of PIP2;7 promoter activity and a significant decrease in PIP2;7 mRNA abundance within 2 h. Concomitantly, a rapid internalization of fluorescently-tagged PIP2;7 proteins was observed but removal from the cell membrane was not accompanied by further degradation of the protein within 4 h of exposure to salinity stress. These data suggest that PIP transcriptional repression and channel internalization act in concert during salt stress conditions to modulate aquaporin activity, thereby significantly altering the plant hydraulic parameters in the short term.
      PubDate: 2016-09-26
  • Altered levels of AtHSCB disrupts iron translocation from roots to shoots
    • Authors: Laura Leaden; María A. Pagani; Manuel Balparda; María V. Busi; Diego F. Gomez-Casati
      Abstract: Key message Plants overexpressing AtHSCB and hscb knockdown mutants showed altered iron homeostasis. The overexpression of AtHSCB led to activation of the iron uptake system and iron accumulation in roots without concomitant transport to shoots, resulting in reduced iron content in the aerial parts of plants. By contrast, hscb knockdown mutants presented the opposite phenotype, with iron accumulation in shoots despite the reduced levels of iron uptake in roots. AtHSCB play a key role in iron metabolism, probably taking part in the control of iron translocation from roots to shoots. Many aspects of plant iron metabolism remain obscure. The most known and studied homeostatic mechanism is the control of iron uptake in the roots by shoots. Nevertheless, this mechanism likely involves various unknown sensors and unidentified signals sent from one tissue to another which need to be identified. Here, we characterized Arabidopsis thaliana plants overexpressing AtHSCB, encoding a mitochondrial cochaperone involved in [Fe–S] cluster biosynthesis, and hscb knockdown mutants, which exhibit altered shoot/root Fe partitioning. Overexpression of AtHSCB induced an increase in root iron uptake and content along with iron deficiency in shoots. Conversely, hscb knockdown mutants exhibited increased iron accumulation in shoots and reduced iron uptake in roots. Different experiments, including foliar iron application, citrate supplementation and iron deficiency treatment, indicate that the shoot-directed control of iron uptake in roots functions properly in these lines, implying that [Fe–S] clusters are not involved in this regulatory mechanism. The most likely explanation is that both lines have altered Fe transport from roots to shoots. This could be consistent with a defect in a homeostatic mechanism operating at the root-to-shoot translocation level, which would be independent of the shoot control over root iron deficiency responses. In summary, the phenotypes of these plants indicate that AtHSCB plays a role in iron metabolism.
      PubDate: 2016-09-21
      DOI: 10.1007/s11103-016-0537-9
  • Arabidopsis acyl-CoA-binding protein ACBP6 localizes in the phloem and
           affects jasmonate composition
    • Abstract: Abstract Arabidopsis thaliana ACYL-COA-BINDING PROTEIN6 (AtACBP6) encodes a cytosolic 10-kDa AtACBP. It confers freezing tolerance in transgenic Arabidopsis, possibly by its interaction with lipids as indicated by the binding of acyl-CoA esters and phosphatidylcholine to recombinant AtACBP6. Herein, transgenic Arabidopsis transformed with an AtACBP6 promoter-driven β-glucuronidase (GUS) construct exhibited strong GUS activity in the vascular tissues. Immunoelectron microscopy using anti-AtACBP6 antibodies showed AtACBP6 localization in the phloem especially in the companion cells and sieve elements. Also, the presence of gold grains in the plasmodesmata indicated its potential role in systemic trafficking. The AtACBP6 protein, but not its mRNA, was found in phloem exudate of wild-type Arabidopsis. Fatty acid profiling using gas chromatography-mass spectrometry revealed an increase in the jasmonic acid (JA) precursor, 12-oxo-cis,cis-10,15-phytodienoic acid (cis-OPDA), and a reduction in JA and/or its derivatives in acbp6 phloem exudates in comparison to the wild type. Quantitative real-time PCR showed down-regulation of COMATOSE (CTS) in acbp6 rosettes suggesting that AtACBP6 affects CTS function. AtACBP6 appeared to affect the content of JA and/or its derivatives in the sieve tubes, which is consistent with its role in pathogen-defense and in its wound-inducibility of AtACBP6pro::GUS. Taken together, our results suggest the involvement of AtACBP6 in JA-biosynthesis in Arabidopsis phloem tissues.
      PubDate: 2016-09-19
      DOI: 10.1007/s11103-016-0541-0
  • Multidimensional patterns of metabolic response in abiotic stress-induced
           growth of Arabidopsis thaliana
    • Abstract: Key message Contextualization of specific transcriptional responses of Arabidopsis within the stress–tissue–time perspective provides a simplified representation of the cellular transcriptional response pathways to abiotic stress, while reducing the dimensions in gene-oriented response description. Crops resistant to abiotic stresses are a long-term goal of many research programs, thus understanding the progression of stress responses is of great interest. We reanalyzed the AtGenExpress transcription dataset to go beyond gene-level characterization, and to contextualize the discrete information into (1) a process-level signature of stress-specific, time-specific, and tissue-specific responses and (2) identify patterns of response progression across a time axis. To gain a functional perspective, ∼1000 pathways associated with the differentially-expressed genes were characterized across all experiments. We find that the global response of pathways to stress is multi-dimensional and does not obviously cluster according to stress, time or tissue. The early response to abiotic stress typically involves induction of genes involved in transcription, hormone synthesis and signaling modules; a later response typically involves metabolism of amino acids and secondary metabolites. By linking specific primary and secondary response pathways, we outline possible stress-associated routes of response progression. The contextualization of specific processes within stress–tissue–time perspective provides a simplified representation of cellular response while reducing the dimensions in gene-oriented response description. Such simplified representation allows finding stress-specific markers based on process-combinations pointing whether a stress-specific response was invoked as well as provide a reference point for the conductance of comparative inter-plant study of stress response, bypassing the need in detailed orthologous mapping.
      PubDate: 2016-09-15
      DOI: 10.1007/s11103-016-0539-7
  • The germin-like protein OsGLP2-1 enhances resistance to fungal blast and
           bacterial blight in rice
    • Authors: Qing Liu; Jianyuan Yang; Shijuan Yan; Shaohong Zhang; Junliang Zhao; Wenjuan Wang; Tifeng Yang; Xiaofei Wang; Xingxue Mao; Jingfang Dong; Xiaoyuan Zhu; Bin Liu
      Abstract: Key message This is the first report that GLP gene (OsGLP2-1) is involved in panicle blast and bacterial blight resistance in rice. In addition to its resistance to blast and bacterial blight, OsGLP2-1 has also been reported to co-localize with a QTLs for sheath blight resistance in rice. These suggest that the disease resistance provided by OsGLP2-1 is quantitative and broad spectrum. Its good resistance to these major diseases in rice makes it to be a promising target in rice breeding. Rice (Oryza sativa) blast caused by Magnaporthe oryzae and bacterial blight caused by Xanthomonas oryzae pv. oryzae are the two most destructive rice diseases worldwide. Germin-like protein (GLP) gene family is one of the important defense gene families which have been reported to be involved in disease resistance in plants. Although GLP proteins have been demonstrated to positively regulate leaf blast resistance in rice, their involvement in resistance to panicle blast and bacterial blight, has not been reported. In this study, we reported that one of the rice GLP genes, OsGLP2-1, was significantly induced by blast fungus. Overexpression of OsGLP2-1 quantitatively enhanced resistance to leaf blast, panicle blast and bacterial blight. The temporal and spatial expression analysis revealed that OsGLP2-1is highly expressed in leaves and panicles and sub-localized in the cell wall. Compared with empty vector transformed (control) plants, the OsGLP2-1 overexpressing plants exhibited higher levels of H2O2 both before and after pathogen inoculation. Moreover, OsGLP2-1 was significantly induced by jasmonic acid (JA). Overexpression of OsGLP2-1 induced three well-characterized defense-related genes which are associated in JA-dependent pathway after pathogen infection. Higher endogenous level of JA was also identified in OsGLP2-1 overexpressing plants than in control plants both before and after pathogen inoculation. Together, these results suggest that OsGLP2-1 functions as a positive regulator to modulate disease resistance. Its good quantitative resistance to the two major diseases in rice makes it to be a promising target in rice breeding.
      PubDate: 2016-09-15
      DOI: 10.1007/s11103-016-0521-4
  • ER-localized adenine nucleotide transporter ER-ANT1: an integrator of
           energy and stress signaling in rice
    • Authors: Xiangqian Zhang; Xu Zheng; Shanwen Ke; Haitao Zhu; Fang Liu; Zemin Zhang; Xinxiang Peng; Lin Guo; Ruizhen Zeng; Pei Hou; Ziqiang Liu; Suowei Wu; Meifang Song; Jianping Yang; Guiquan Zhang
      Abstract: Abstract Most environmental perturbations have a direct or indirect deleterious impact on photosynthesis, and, in consequence, the overall energy status of the cell. Despite our increased understanding of convergent energy and stress signals, the connections between photosynthesis, energy and stress signals through putative common nodes are still unclear. Here we identified an endoplasmic reticulum (ER)-localized adenine nucleotide transporter1 (ER-ANT1), whose deficiency causes seedling lethality in air but viable under high CO2, exhibiting the typical photorespiratory phenotype. Metabolic analysis suggested that depletion of ER-ANT1 resulted in circadian rhythm disorders in sucrose synthesis and induced sucrose signaling pathways, indicating that the ER is involved in the regulation of vital energy metabolism in plants. In addition, the defect of ER-ANT1 triggers ER stress and activates the unfolded protein response in plant cells, suggesting ER stress and photorespiration are closely linked. These findings provide an important evidence for a key role of ER-localized ER-ANT1 in convergent energy and stress signals in rice. Our findings support the idea that ATP is a central signal involved in the plant response to a variety of stresses.
      PubDate: 2016-09-10
      DOI: 10.1007/s11103-016-0540-1
  • Trichome patterning control involves TTG1 interaction with SPL
           transcription factors
    • Authors: Eugenia Ioannidi; Stamatis Rigas; Dikran Tsitsekian; Gerasimos Daras; Anastasios Alatzas; Antonis Makris; Georgia Tanou; Anagnostis Argiriou; Dimitrios Alexandrou; Scott Poethig; Polydefkis Hatzopoulos; Angelos K. Kanellis
      Abstract: Abstract Epidermal cell differentiation is a paramount and conserved process among plants. In Arabidopsis, a ternary complex formed by MYB, bHLH transcription factors and TTG1 modulates unicellular trichome morphogenesis. The formation of multicellular glandular trichomes of the xerophytic shrub Cistus creticus that accumulate labdane-type diterpenes, has attained much attention renowned for its medicinal properties. Here, we show that C. creticus TTG1 (CcTTG1) interacts with the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPLA/B) proteins, putative homologs of AtSPL4/5 that in turn interact with AtTTG1. These interactions occur between proteins from evolutionarily distant species supporting the conserved function of TTG1-SPL complex. Overexpression of AtSPL4 and AtSPL5 decreased the expression of GLABRA2 (AtGL2), the major regulator of trichome morphogenesis, resulting in trichome reduction on the adaxial surface of cauline leaves, thereby illuminating the significance of TTG1-SPLs interactions in trichome formation control. AtGL2 and AtSPL4 have opposite expression patterns during early stages of leaf development. We postulate an antagonistic effect between SPLs and the heterogeneous MYB-bHLH factors binding to TTG1. Hence, the SPLs potentially rearrange the complex, attenuating its transcriptional activity to control trichome distribution.
      PubDate: 2016-09-08
      DOI: 10.1007/s11103-016-0538-8
  • AINTEGUMENTA-LIKE6 can functionally replace AINTEGUMENTA but alters
           Arabidopsis flower development when misexpressed at high levels
    • Authors: Han Han; Beth A. Krizek
      Abstract: Key message Expression differences underlie the functional differences between two related transcription factors: AINTEGUMENTA and AINTEGUMENTA-LIKE6. Ectopic expression of AINTEGUMENTA-LIKE6 at high levels alters floral organ initiation, growth and identity specification. AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6 (AIL6) encode related transcription factors with partially overlapping roles in floral organ development in Arabidopsis thaliana. To investigate whether the functional differences between ANT and AIL6 are a consequence of differences in gene expression and/or protein activity, we made transgenic plants in which a genomic copy of AIL6 was expressed under the control of the ANT promoter. ANT:gAIL6 can rescue the floral organ size defects of ant mutants when AIL6 is expressed at similar levels as ANT in wild type. Thus, the functional differences between ANT and AIL6 result primarily from gene expression differences. However, lines that express AIL6 at higher levels display additional phenotypes that include reduced numbers of floral organs and the production of mosaic floral organs. These phenotypes were also observed in two different inducible AIL6 transgenic lines but not in 35S:ANT, suggesting that AIL6 protein may have activities distinct from ANT, although the in vivo relevance of such differences is not clear. Similar to 35S:ANT plants, overexpression of AIL6 in the inducible lines also results in the production of larger flowers. The distinct phenotypes resulting from AIL6 misexpression in the transgenic lines described here and those previously characterized appear to result from different levels and patterns of AIL6 expression.
      PubDate: 2016-09-07
      DOI: 10.1007/s11103-016-0535-y
  • Erratum to: Deciphering the role of the AT-rich interaction domain and the
           HMG-box domain of ARID-HMG proteins of Arabidopsis thaliana
    • Authors: Adrita Roy; Arkajyoti Dutta; Dipan Roy; Payel Ganguly; Ritesh Ghosh; Rajiv K. Kar; Anirban Bhunia; Jayanta Mukhopadhyay; Shubho Chaudhuri
      PubDate: 2016-09-05
      DOI: 10.1007/s11103-016-0534-z
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