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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  [2351 journals]
  • Heat stress alters genome-wide profiles of circular RNAs in Arabidopsis
    • Authors: Ting Pan; Xiuqiang Sun; Yangxuan Liu; Hui Li; Guangbin Deng; Honghui Lin; Songhu Wang
      Pages: 217 - 229
      Abstract: Key message 1599 novel circRNAs and 1583 heat stress-specific circRNAs were identified in Arabidopsis. Heat stress enhanced accumulation of circRNAs remarkably. Heat stress altered the sizes of circRNAs, numbers of circularized exons and alterative circularization events. A putative circRNA-mediated ceRNA networks under heat stress was established. Heat stress retards plant growth and destabilizes crop yield. The noncoding RNAs were demonstrated to be involved in plant response to heat stress. As a newly-characterized class of noncoding RNAs, circular RNAs (circRNAs) play important roles in transcriptional and post-transcriptional regulation. A few recent investigations indicated that plant circRNAs were differentially expressed under abiotic stress. However, little is known about how heat stress mediates biogenesis of circRNAs in plants. Here, we uncovered 1599 previously-unknown circRNAs and 1583 heat-specific circRNAs, by RNA-sequencing and bioinformatic analysis. Our results indicated that much more circRNAs were expressed under heat stress than in control condition. Besides, heat stress also increased the length of circRNAs, the quantity of circularized exons, and alternative circularization events. Moreover, we observed a positive correlation between expression patterns of some circRNAs and their parental genes. The prediction of ceRNA (competing endogenous RNA) networks indicated that differentially-expressed circRNAs could influence expression of many important genes, that participate in response to heat stress, hydrogen peroxide, and phytohormone signaling pathways, by interacting with the corresponding microRNAs. Together, our observations indicated that heat stress had great impacts on the biogenesis of circRNAs. Heat-induced circRNAs might participate in plant response to heat stress through the circRNA-mediated ceRNA networks.
      PubDate: 2018-02-01
      DOI: 10.1007/s11103-017-0684-7
      Issue No: Vol. 96, No. 3 (2018)
  • Kiwifruit SVP2 controls developmental and drought-stress pathways
    • Authors: Rongmei Wu; Tianchi Wang; Ben A. W. Warren; Susan J. Thomson; Andrew C. Allan; Richard C. Macknight; Erika Varkonyi-Gasic
      Pages: 233 - 244
      Abstract: Key message Genome-wide targets of Actinidia chinensis SVP2 confirm roles in ABA- and dehydration-mediated growth repression and reveal a conservation in mechanism of action between SVP genes of taxonomically distant Arabidopsis and a woody perennial kiwifruit. The molecular mechanisms underlying growth and dormancy in woody perennials are largely unknown. In Arabidopsis, the MADS-box transcription factor SHORT VEGETATIVE PHASE (SVP) plays a key role in the progression from vegetative to floral development, and in woody perennials SVP-like genes are also proposed to be involved in controlling dormancy. During kiwifruit development SVP2 has a role in growth inhibition, with high-chill kiwifruit Actinidia deliciosa transgenic lines overexpressing SVP2 showing suppressed bud outgrowth. Transcriptomic analyses of these plants suggests that SVP2 mimics the well-documented abscisic acid (ABA) effect on the plant dehydration response. To corroborate the growth inhibition role of SVP2 in kiwifruit development at the molecular level, we analysed the genome-wide direct targets of SVP2 using chromatin immunoprecipitation followed by high-throughput sequencing in kiwifruit A. chinensis. SVP2 was found to bind to at least 297 target sites in the kiwifruit genome, and potentially modulates 252 genes that function in a range of biological processes, especially those involved in repressing meristem activity and ABA-mediated dehydration pathways. In addition, our ChIP-seq analysis reveals remarkable conservation in mechanism of action between SVP genes of taxonomically distant plant species.
      PubDate: 2018-02-01
      DOI: 10.1007/s11103-017-0688-3
      Issue No: Vol. 96, No. 3 (2018)
  • Degradation of the stress-responsive enzyme formate dehydrogenase by the
    • Authors: Daryl McNeilly; Andrew Schofield; Sophia L. Stone
      Pages: 265 - 278
      Abstract: Key message KEG is involved in mediating the proteasome-dependent degradation of FDH, a stress-responsive enzyme. The UPS may function to suppress FDH mediated stress responses under favorable growth conditions. Formate dehydrogenase (FDH) has been studied in bacteria and yeasts for the purpose of industrial application of NADH co-factor regeneration. In plants, FDH is regarded as a universal stress protein involved in responses to various abiotic and biotic stresses. Here we show that FDH abundance is regulated by the ubiquitin proteasome system (UPS). FDH is ubiquitinated in planta and degraded by the 26S proteasome. Interaction assays identified FDH as a potential substrate for the RING-type ubiquitin ligase Keep on Going (KEG). KEG is capable of attaching ubiquitin to FDH in in vitro assays and the turnover of FDH was increased when co-expressed with a functional KEG in planta, suggesting that KEG contributes to FDH degradation. Consistent with a role in regulating FDH abundance, transgenic plants overexpressing KEG were more sensitive to the inhibitory effects of formate. In addition, FDH is a phosphoprotein and dephosphorylation was found to increase the stability of FDH in degradation assays. Based on results from this and previous studies, we propose a model where KEG mediates the ubiquitination and subsequent degradation of phosphorylated FDH and, in response to unfavourable growth conditions, reduction in FDH phosphorylation levels may prohibit turnover allowing the stabilized FDH to facilitate stress responses.
      PubDate: 2018-02-01
      DOI: 10.1007/s11103-017-0691-8
      Issue No: Vol. 96, No. 3 (2018)
  • BPH1, a novel substrate receptor of CRL3, plays a repressive role in ABA
           signal transduction
    • Authors: Og-Geum Woo; Soon-Hee Kim; Seok Keun Cho; Sang-Hoon Kim; Han Nim Lee; Taijoon Chung; Seong Wook Yang; Jae-Hoon Lee
      Abstract: Key message BPH1 acts as a substrate receptor of CRL3 complex and negatively regulates ABA-mediated cellular responses. The study on its function provides information that helps further understand the relationship between ABA signaling and UPS. Abscisic acid (ABA) plays a crucial role in a variety of cellular processes, including seed dormancy, inhibition of seedling growth, and drought resistance in plants. Cullin3-RING E3 ligase (CRL3) complex is a type of multi-subunit E3 ligase, and BTB/POZ protein, a component of CRL3 complex, functions as a receptor to determine a specific substrate. To elucidate the CRL3 complex that participates in ABA-mediated cellular processes, we first investigated ABA-inducible BTB/POZ genes based on data from the AtGenExpress Visualization Tool (AVT). We then isolated an ABA-inducible gene encoding a potential CRL3 substrate receptor in Arabidopsis, BPH1 (BTB/POZ protein hypersensitive to ABA 1). The isolate gene has a BTB/POZ domain and a NPH3 domain within its N-terminal and C-terminal region, respectively. Yeast two-hybrid and co-immunoprecipitation assays showed that BPH1 physically interacted with cullin3a, a scaffold protein of CRL3, suggesting that it functions as an Arabidopsis CRL3 substrate receptor. The functional mutation of BPH1 caused delayed seed germination in response to ABA and enhanced sensitivity by NaCl and mannitol treatments as ABA-related stresses. Moreover, bph1 mutants exhibited enhanced stomatal closure under ABA application and reduced water loss when compared with wild-type, implying their enhanced tolerance to drought stress. Based on the information from microarray/AVT data and expression analysis of various ABA-inducible genes between wild-type and bph1 plants following ABA treatments, we concluded loss of BPH1 resulted in hyper-induction of a large portion of ABA-inducible genes in response to ABA. Taken together, these results show that BPH1 is negatively involved in ABA-mediated cellular events.
      PubDate: 2018-03-21
      DOI: 10.1007/s11103-018-0717-x
  • The wheat TabZIP2 transcription factor is activated by the nutrient
           starvation-responsive SnRK3/CIPK protein kinase
    • Authors: Sukanya Luang; Pradeep Sornaraj; Natalia Bazanova; Wei Jia; Omid Eini; Syed Sarfraz Hussain; Nataliya Kovalchuk; Pradeep K. Agarwal; Maria Hrmova; Sergiy Lopato
      Abstract: Key message The understanding of roles of bZIP factors in biological processes during plant development and under abiotic stresses requires the detailed mechanistic knowledge of behaviour of TFs. Basic leucine zipper (bZIP) transcription factors (TFs) play key roles in the regulation of grain development and plant responses to abiotic stresses. We investigated the role and molecular mechanisms of function of the TabZIP2 gene isolated from drought-stressed wheat plants. Molecular characterisation of TabZIP2 and derived protein included analyses of gene expression and its target promoter, and the influence of interacting partners on the target promoter activation. Two interacting partners of TabZIP2, the 14-3-3 protein, TaWIN1 and the bZIP transcription factor TaABI5L, were identified in a Y2H screen. We established that under elevated ABA levels the activity of TabZIP2 was negatively regulated by the TaWIN1 protein and positively regulated by the SnRK3/CIPK protein kinase WPK4, reported previously to be responsive to nutrient starvation. The physical interaction between the TaWIN1 and the WPK4 was detected. We also compared the influence of homo- and hetero-dimerisation of TabZIP2 and TaABI5L on DNA binding. TabZIP2 gene functional analyses were performed using drought-inducible overexpression of TabZIP2 in transgenic wheat. Transgenic plants grown under moderate drought during flowering, were smaller than control plants, and had fewer spikes and seeds per plant. However, a single seed weight was increased compared to single seed weights of control plants in three of four evaluated transgenic lines. The observed phenotypes of transgenic plants and the regulation of TabZIP2 activity by nutrient starvation-responsive WPK4, suggest that the TabZIP2 could be the part of a signalling pathway, which controls the rearrangement of carbohydrate and nutrient flows in plant organs in response to drought.
      PubDate: 2018-03-21
      DOI: 10.1007/s11103-018-0713-1
  • Analysis of physiological and miRNA responses to Pi deficiency in alfalfa
           ( Medicago sativa L.)
    • Authors: Zhenyi Li; Hongyu Xu; Yue Li; Xiufu Wan; Zhao Ma; Jing Cao; Zhensong Li; Feng He; Yufei Wang; Liqiang Wan; Zongyong Tong; Xianglin Li
      Abstract: Key message The induction of miR399 and miR398 and the inhibition of miR156, miR159, miR160, miR171, miR2111, and miR2643 were observed under Pi deficiency in alfalfa. The miRNA-mediated genes involved in basic metabolic process, root and shoot development, stress response and Pi uptake. Inorganic phosphate (Pi) deficiency is known to be a limiting factor in plant development and growth. However, the underlying miRNAs associated with the Pi deficiency-responsive mechanism in alfalfa are unclear. To elucidate the molecular mechanism at the miRNA level, we constructed four small RNA (sRNA) libraries from the roots and shoots of alfalfa grown under normal or Pi-deficient conditions. In the present study, alfalfa plants showed reductions in biomass, photosynthesis, and Pi content and increases in their root-to-shoot ratio and citric, malic, and succinic acid contents under Pi limitation. Sequencing results identified 47 and 44 differentially expressed miRNAs in the roots and shoots, respectively. Furthermore, 909 potential target genes were predicted, and some targets were validated by RLM-RACE assays. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed prominent enrichment in signal transducer activity, binding and basic metabolic pathways for carbohydrates, fatty acids and amino acids; cellular response to hormone stimulus and response to auxin pathways were also enriched. qPCR results verified that the differentially expressed miRNA profile was consistent with sequencing results, and putative target genes exhibited opposite expression patterns. In this study, the miRNAs associated with the response to Pi limitation in alfalfa were identified. In addition, there was an enrichment of miRNA-targeted genes involved in biological regulatory processes such as basic metabolic pathways, root and shoot development, stress response, Pi transportation and citric acid secretion.
      PubDate: 2018-03-12
      DOI: 10.1007/s11103-018-0711-3
  • Analysis of the DNA methylation patterns and transcriptional regulation of
           the NB-LRR-encoding gene family in Arabidopsis thaliana
    • Authors: Weiwen Kong; Bin Li; Qianqian Wang; Bin Wang; Xiaoke Duan; Li Ding; Yanke Lu; Li-Wei Liu; Honggui La
      Abstract: Key message The relationships between transcription and methylation were revealed in Arabidopsis thaliana NB-LRR-encoding genes in wild type (Col-0) and different mutants. Plant nucleotide-binding, leucine-rich repeat (NB-LRR) proteins constitute a large family that plays predominant roles in disease resistance. However, the regulation of NB-LRR-encoding genes at the transcriptional level is still poorly understood. Recently, DNA cytosine methylation in eukaryotes has been described as serving an important function in regulating gene expression. Here, we analysed the DNA methylation patterns of NB-LRR-encoding genes in Arabidopsis thaliana in samples from a wild type (Col-0) and ago4, met1, cmt3, drm1/2, and ddm1 mutants. Our results revealed that the vast majority of the NB-LRR-encoding genes in Col-0 were methylated, and the DNA methylation occurred predominantly in the CG sequence context. Moreover, DNA methylation was widely distributed in both the promoters and the bodies of most NB-LRR-encoding genes. Our results also showed that the loss of AGO4, MET1, CMT3, DRM1/2 or DDM1 functions generally led to decreased cytosine methylation in the NB-LRR-encoding genes. Analysis of the available transcriptome data from the wild type and the met1, cmt3, drm1/2 and ddm1 mutants revealed that differences in the transcription levels between the wild type and mutants were statistically significant for 63 of the NB-LRR-encoding genes. Of these genes, 38 were significantly upregulated, and the other 25 were significantly downregulated. Some NB-LRR-encoding genes with differential expression levels, which were revealed by the mRNA-Seq data, were confirmed to be significantly upregulated or downregulated in the mutants compared to the wild type by using quantitative RT-PCR. These data suggest that some Arabidopsis NB-LRR-encoding genes are likely to be regulated by altered DNA methylation patterns.
      PubDate: 2018-03-10
      DOI: 10.1007/s11103-018-0715-z
  • Comprehensive transcriptome analyses correlated with untargeted metabolome
           reveal differentially expressed pathways in response to cell wall
    • Authors: Nathan T. Reem; Han-Yi Chen; Manhoi Hur; Xuefeng Zhao; Eve Syrkin Wurtele; Xu Li; Ling Li; Olga Zabotina
      Abstract: Key message This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes. Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.
      PubDate: 2018-03-03
      DOI: 10.1007/s11103-018-0714-0
  • Genome-wide genetic variation and comparison of fruit-associated traits
           between kumquat ( Citrus japonica ) and Clementine mandarin ( Citrus
           clementina )
    • Authors: Tian-Jia Liu; Yong-Ping Li; Jing-Jing Zhou; Chun-Gen Hu; Jin-Zhi Zhang
      Abstract: Key message The comprehensive genetic variation of two citrus species were analyzed at genome and transcriptome level. A total of 1090 differentially expressed genes were found during fruit development by RNA-sequencing. Fruit size (fruit equatorial diameter) and weight (fresh weight) are the two most important components determining yield and consumer acceptability for many horticultural crops. However, little is known about the genetic control of these traits. Here, we performed whole-genome resequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Citrus japonica) and Clementine mandarin (Citrus clementina). In total, 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertions/deletions (InDels) were identified in the two citrus species. Based on integrative analysis of genome and transcriptome of fruit, 640,801 SNPs and 20,733 InDels were identified. The features, genomic distribution, functional effect, and other characteristics of these genetic variations were explored. RNA-sequencing identified 1090 differentially expressed genes (DEGs) during fruit development of kumquat and Clementine mandarin. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. In addition, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reports were also identified. A global survey identified 24,237 specific alternative splicing events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing. These genome variation data provide a foundation for further exploration of citrus diversity and gene–phenotype relationships and for future research on molecular breeding to improve kumquat, Clementine mandarin and related species.
      PubDate: 2018-02-26
      DOI: 10.1007/s11103-018-0712-2
  • Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in
           Arabidopsis and its prevention
    • Authors: Qiang Zhang; Hui-Li Xing; Zhi-Ping Wang; Hai-Yan Zhang; Fang Yang; Xue-Chen Wang; Qi-Jun Chen
      Abstract: Key message We present novel observations of high-specificity SpCas9 variants, sgRNA expression strategies based on mutant sgRNA scaffold and tRNA processing system, and CRISPR/Cas9-mediated T-DNA integrations. Specificity of CRISPR/Cas9 tools has been a major concern along with the reports of their successful applications. We report unexpected observations of high frequency off-target mutagenesis induced by CRISPR/Cas9 in T1 Arabidopsis mutants although the sgRNA was predicted to have a high specificity score. We also present evidence that the off-target effects were further exacerbated in the T2 progeny. To prevent the off-target effects, we tested and optimized two strategies in Arabidopsis, including introduction of a mCherry cassette for a simple and reliable isolation of Cas9-free mutants and the use of highly specific mutant SpCas9 variants. Optimization of the mCherry vectors and subsequent validation found that fusion of tRNA with the mutant rather than the original sgRNA scaffold significantly improves editing efficiency. We then examined the editing efficiency of eight high-specificity SpCas9 variants in combination with the improved tRNA-sgRNA fusion strategy. Our results suggest that highly specific SpCas9 variants require a higher level of expression than their wild-type counterpart to maintain high editing efficiency. Additionally, we demonstrate that T-DNA can be inserted into the cleavage sites of CRISPR/Cas9 targets with high frequency. Altogether, our results suggest that in plants, continuous attention should be paid to off-target effects induced by CRISPR/Cas9 in current and subsequent generations, and that the tools optimized in this report will be useful in improving genome editing efficiency and specificity in plants and other organisms.
      PubDate: 2018-02-23
      DOI: 10.1007/s11103-018-0709-x
  • A banana NAC transcription factor ( MusaSNAC1 ) impart drought tolerance
           by modulating stomatal closure and H 2 O 2 content
    • Authors: Sanjana Negi; Himanshu Tak; T. R. Ganapathi
      Abstract: Key message MusaSNAC1 function in H2O2 mediated stomatal closure and promote drought tolerance by directly binding to CGT[A/G] motif in regulatory region of multiple stress-related genes. Drought is a abiotic stress-condition, causing reduced plant growth and diminished crop yield. Guard cells of the stomata control photosynthesis and transpiration by regulating CO2 exchange and water loss, thus affecting growth and crop yield. Roles of NAC (NAM, ATAF1/2 and CUC2) protein in regulation of stress-conditions has been well documented however, their control over stomatal aperture is largely unknown. In this study we report a banana NAC protein, MusaSNAC1 which induced stomatal closure by elevating H2O2 content in guard cells during drought stress. Overexpression of MusaSNAC1 in banana resulted in higher number of stomata closure causing reduced water loss and thus elevated drought-tolerance. During drought, expression of GUS (β-glucuronidase) under P MusaSNAC1 was remarkably elevated in guard cells of stomata which correlated with its function as a transcription factor regulating stomatal aperture closing. MusaSNAC1 is a transcriptional activator belonging to SNAC subgroup and its 5′-upstream region contain multiple Dof1 elements as well as stress-associated cis-elements. Moreover, MusaSNAC1 also regulate multiple stress-related genes by binding to core site of NAC-proteins CGT[A/G] in their 5′-upstream region. Results indicated an interesting mechanism of drought tolerance through stomatal closure by H2O2 generation in guard cells, regulated by a NAC-protein in banana.
      PubDate: 2018-02-22
      DOI: 10.1007/s11103-018-0710-4
  • An intronless form of the tobacco extensin gene terminator strongly
           enhances transient gene expression in plant leaves
    • Authors: Sun Hee Rosenthal; Andrew G. Diamos; Hugh S. Mason
      Abstract: Key message We have found interesting features of a plant gene (extensin) 3′ flanking region, including extremely efficient polyadenylation which greatly improves transient expression of transgenes when an intron is removed. Its use will greatly benefit studies of gene expression in plants, research in molecular biology, and applications for recombinant proteins. Plants are a promising platform for the production of recombinant proteins. To express high-value proteins in plants efficiently, the optimization of expression cassettes using appropriate regulatory sequences is critical. Here, we characterize the activity of the tobacco extensin (Ext) gene terminator by transient expression in Nicotiana benthamiana, tobacco, and lettuce. Ext is a member of the hydroxyproline-rich glycoprotein (HRGP) superfamily and constitutes the major protein component of cell walls. The present study demonstrates that the Ext terminator with its native intron removed increased transient gene expression up to 13.5-fold compared to previously established terminators. The enhanced transgene expression was correlated with increased mRNA accumulation and reduced levels of read-through transcripts, which could impair gene expression. Analysis of transcript 3′-ends found that the majority of polyadenylated transcripts were cleaved at a YA dinucleotide downstream from a canonical AAUAAA motif and a UG-rich region, both of which were found to be highly conserved among related extensin terminators. Deletion of either of these regions eliminated most of the activity of the terminator. Additionally, a 45 nt polypurine sequence ~ 175 nt upstream from the polyadenylation sites was found to also be necessary for the enhanced expression. We conclude that the use of Ext terminator has great potential to benefit the production of recombinant proteins in plants.
      PubDate: 2018-02-10
      DOI: 10.1007/s11103-018-0708-y
  • Longevity in vivo of primary cell wall cellulose synthases
    • Authors: Joseph Lee Hill; Cooper Josephs; William J. Barnes; Charles T. Anderson; Ming Tien
      Abstract: Key message Our work focuses on understanding the lifetime and thus stability of the three main cellulose synthase (CESA) proteins involved in primary cell wall synthesis of Arabidopsis. It had long been thought that a major means of CESA regulation was via their rapid degradation. However, our studies here have uncovered that AtCESA proteins are not rapidly degraded. Rather, they persist for an extended time in the plant cell. Plant cellulose is synthesized by membrane-embedded cellulose synthase complexes (CSCs). The CSC is composed of cellulose synthases (CESAs), of which three distinct isozymes form the primary cell wall CSC and another set of three isozymes form the secondary cell wall CSC. We determined the stability over time of primary cell wall (PCW) CESAs in Arabidopsis thaliana seedlings, using immunoblotting after inhibiting protein synthesis with cycloheximide treatment. Our work reveals very slow turnover for the Arabidopsis PCW CESAs in vivo. Additionally, we show that the stability of all three CESAs within the PCW CSC is altered by mutations in individual CESAs, elevated temperature, and light conditions. Together, these results suggest that CESA proteins are very stable in vivo, but that their lifetimes can be modulated by intrinsic and environmental cues.
      PubDate: 2018-01-31
      DOI: 10.1007/s11103-017-0695-4
  • Physiological and RNA-seq analyses provide insights into the response
           mechanism of the Cf-10 -mediated resistance to Cladosporium fulvum
           infection in tomato
    • Authors: Guan Liu; Junfang Liu; Chunli Zhang; Xiaoqing You; Tingting Zhao; Jingbin Jiang; Xiuling Chen; He Zhang; Huanhuan Yang; Dongye Zhang; Chong Du; Jingfu Li; Xiangyang Xu
      Abstract: Key message Based on the physiological and RNA-seq analysis, some progress has been made in elucidating the Cf-10-mediated resistance responses to C. fulvum infection in tomato. GO and KEGG enrichment analysis revealed that the DEGs were significantly associated with defense-signaling pathways like oxidation-reduction processes, oxidoreductase activity and plant hormone signal transduction. Leaf mold, caused by the fungus Cladosporium fulvum, is one of the most common diseases affecting tomatoes worldwide. Cf series genes including Cf-2, Cf-4, Cf-5, Cf-9 and Cf-10 play very important roles in resisting tomato leaf mold. Understanding the molecular mechanism of Cf gene-mediated resistance is thus the key to facilitating genetic engineering of resistance to C. fulvum infection. Progress has been made in elucidating two Cf genes, Cf -19 and Cf -12, and how they mediate resistance responses to C. fulvum infection in tomato. However, the mechanism of the Cf-10- mediated resistance response is still unclear. In the present study, RNA-seq was used to analyze changes in the transcriptome at different stages of C. fulvum infection. A total of 2,242 differentially expressed genes (DEGs) responsive to C. fulvum between 0 and 16 days post infection (dpi) were identified, including 1,501 upregulated and 741 downregulated genes. The majority of DEGs were associated with defense-signaling pathways including oxidation–reduction processes, oxidoreductase activity and plant hormone signal transduction. Four DEGs associated with plant-pathogen interaction were uniquely activated in Cf-10 tomato and validated by qRT-PCR. In addition, physiological indicators including reactive oxygen species (ROS), superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were measured at 0–21 dpi, and hormone expression [Jasmonic acid (JA) and salicylic acid (SA)] was estimated at 0 and 16 dpi to elucidate the mechanism of the Cf-10-mediated resistance response. C. fulvum infection induced the activities of POD, CAT and SOD, and decreased ROS levels. JA was determined to participate in the resistance response to C. fulvum during the initial infection period. The results of this study provide accountable evidence for the physiological and transcriptional regulation of the Cf-10-mediated resistance response to C. fulvum infection, facilitating further understanding of the molecular mechanism of Cf-10-mediated resistance to C. fulvum infection.
      PubDate: 2018-01-30
      DOI: 10.1007/s11103-018-0706-0
  • Correction to: Heat stress alters genome-wide profiles of circular RNAs in
    • Authors: Ting Pan; Xiuqiang Sun; Yangxuan Liu; Hui Li; Guangbing Deng; Honghui Lin; Songhu Wang
      Abstract: Due to an unfortunate turn of events, the first name of the fifth author appeared incorrectly in the original publication and should have read Guangbing. The correct representation of the authors’ names and their affiliation is listed here and should be treated as definitive.
      PubDate: 2018-01-22
      DOI: 10.1007/s11103-018-0705-1
  • Interaction network of core ABA signaling components in maize
    • Authors: Ying-Ge Wang; Feng-Ling Fu; Hao-Qiang Yu; Tao Hu; Yuan-Yuan Zhang; Yi Tao; Jian-Kang Zhu; Yang Zhao; Wan-Chen Li
      Abstract: Key message We defined a comprehensive core ABA signaling network in monocot maize, including the gene expression, subcellular localization and interaction network of ZmPYLs, ZmPP2Cs, ZmSnRK2s and the putative substrates. The phytohormone abscisic acid (ABA) plays an important role in plant developmental processes and abiotic stress responses. In Arabidopsis, ABA is sensed by the PYL ABA receptors, which leads to binding of the PP2C protein phosphatase and activation of the SnRK2 protein kinases. These components functioning diversely and redundantly in ABA signaling are little known in maize. Using Arabidopsis pyl112458 and snrk2.2/3/6 mutants, we identified several ABA-responsive ZmPYLs and ZmSnRK2s, and also ZmPP2Cs. We showed the gene expression, subcellular localization and interaction network of ZmPYLs, ZmPP2Cs, and ZmSnRK2s, and the isolation of putative ZmSnRK2 substrates by mass spectrometry in monocot maize. We found that the ABA dependency of PYL-PP2C interactions is contingent on the identity of the PP2Cs. Among 238 candidate substrates for ABA-activated protein kinases, 69 are putative ZmSnRK2 substrates. Besides homologs of previously reported putative AtSnRK2 substrates, 23 phosphoproteins have not been discovered in the dicot Arabidopsis. Thus, we have defined a comprehensive core ABA signaling network in monocot maize and shed new light on ABA signaling.
      PubDate: 2018-01-17
      DOI: 10.1007/s11103-017-0692-7
  • RFAthM6A: a new tool for predicting m 6 A sites in Arabidopsis thaliana
    • Authors: Xiaofeng Wang; Renxiang Yan
      Abstract: Key message We curated a reliable dataset of m6A sites in Arabidopsis thaliana, built competitive models for predicting m6A sites, extracted predominant rules from the prediction models and analyzed the most important features. In biological RNA, approximately 150 chemical modifications have been discovered, of which N6-methyladenine (m6A) is the most prevalent and abundant. This modification plays an essential role in a myriad of biological mechanisms and regulates RNA localization, nuclear export, translation, stability, alternative splicing, and other processes. However, m6A-seq and other wet-lab techniques do not easily facilitate accurate and complete determination of m6A sites across the transcriptome. Therefore, the use of computational methods to establish accurate models for predicting m6A sites is essential. In this work, we manually curated a reliable dataset of m6A sites and non-m6A sites and developed a new tool called RFAthM6A for predicting m6A sites in Arabidopsis thaliana. Briefly, RFAthM6A consists of four independent models named RFPSNSP, RFPSDSP, RFKSNPF and RFKNF and strict benchmarks show that the AUC values of the four models reached 0.894, 0.914, 0.920 and 0.926, respectively in a fivefold cross validation and the prediction performance of RFPSDSP, RFKSNPF and RFKNF exceeded that of three previously reported models (AthMethPre, M6ATH and RAM-NPPS). Linear combination of the prediction scores of RFPSDSP, RFKSNPF and RFKNF improved the prediction performance. We also extracted several predominant rules that underlie the m6A site identification from the trained models. Furthermore, the most important features of the predictors for the m6A site identification were also analyzed in depth. To facilitate use of our proposed models by interested researchers, all the source codes and datasets are publicly deposited at
      PubDate: 2018-01-16
      DOI: 10.1007/s11103-018-0698-9
  • The novel transcription factor TRP interacts with ZFP5, a trichome
           initiation-related transcription factor, and negatively regulates trichome
           initiation through gibberellic acid signaling
    • Authors: Soo Youn Kim; Sujin Hyoung; Won Mi So; Jeong Sheop Shin
      Abstract: Key message The trichome-related protein (TRP) is a novel transcription factor (TF) that negatively regulates trichome initiation-related TFs through gibberellin (GA) signaling. Trichomes, which are outgrowths of leaf epidermal cells, provide the plant with a first line of defense against damage from herbivores and reduce transpiration. The initiation and development of trichomes are regulated by a network of positively or negatively regulating transcription factors (TFs). However, little information is currently available on transcriptional regulation related to trichome formation. Here, we report a novel TF Trichome-Related Protein (TRP) that was observed to negatively regulate the trichome initiation-related TFs through gibberellic acid (GA) signaling. ProTRP:GUS revealed that TRP was only expressed in the trichome. The TRP loss-of-function mutant (trp) had an increased number of trichomes on the flower, cauline leaves, and main inflorescence stems compared to the wild-type. In contrast, TRP overexpression lines (TRP-Ox) exhibited a decreased number of trichomes on cauline leaves and main inflorescence stem following treatment with exogenous GA. Moreover, the expressions of trichome initiation regulators (GIS, GIS2, ZFP8, GL1, and GL3) increased in trp plants but decreased in TRP-Ox lines after GA treatment. TRP was observed to physically interact with ZFP5, a C2H2 TF that controls trichome cell development through GA signaling, both in vivo and in vitro. Based on these results, we suggest that TRP functions upstream of the trichome initiation regulators and represses the binding of ZFP5 to the ZFP8 promoter.
      PubDate: 2018-01-16
      DOI: 10.1007/s11103-018-0697-x
  • Volatile compounds from beneficial or pathogenic bacteria differentially
           regulate root exudation, transcription of iron transporters, and defense
           signaling pathways in Sorghum bicolor
    • Authors: Erasto Hernández-Calderón; Maria Elizabeth Aviles-Garcia; Diana Yazmín Castulo-Rubio; Lourdes Macías-Rodríguez; Vicente Montejano Ramírez; Gustavo Santoyo; José López-Bucio; Eduardo Valencia-Cantero
      Abstract: Key message Our results show that Sorghum bicolor is able to recognize bacteria through its volatile compounds and differentially respond to beneficial or pathogens via eliciting nutritional or defense adaptive traits. Plants establish beneficial, harmful, or neutral relationships with bacteria. Plant growth promoting rhizobacteria (PGPR) emit volatile compounds (VCs), which may act as molecular cues influencing plant development, nutrition, and/or defense. In this study, we compared the effects of VCs produced by bacteria with different lifestyles, including Arthrobacter agilis UMCV2, Bacillus methylotrophicus M4-96, Sinorhizobium meliloti 1021, the plant pathogen Pseudomonas aeruginosa PAO1, and the commensal rhizobacterium Bacillus sp. L2-64, on S. bicolor. We show that VCs from all tested bacteria, except Bacillus sp. L2-64, increased biomass and chlorophyll content, and improved root architecture, but notheworthy A. agilis induced the release of attractant molecules, whereas P. aeruginosa activated the exudation of growth inhibitory compounds by roots. An analysis of the expression of iron-transporters SbIRT1, SbIRT2, SbYS1, and SbYS2 and genes related to plant defense pathways COI1 and PR-1 indicated that beneficial, pathogenic, and commensal bacteria could up-regulate iron transporters, whereas only beneficial and pathogenic species could induce a defense response. These results show how S. bicolor could recognize bacteria through their volatiles profiles and highlight that PGPR or pathogens can elicit nutritional or defensive traits in plants.
      PubDate: 2018-01-12
      DOI: 10.1007/s11103-017-0694-5
  • Salt tolerance of two perennial grass Brachypodium sylvaticum accessions
    • Authors: Nir Sade; Maria del Mar Rubio Wilhelmi; Xiaojuan Ke; Yariv Brotman; Matthew Wright; Imran Khan; Wagner De Souza; Elias Bassil; Christian M. Tobias; Roger Thilmony; John P. Vogel; Eduardo Blumwald
      Abstract: Key message We studied the salt stress tolerance of two accessions isolated from different areas of the world (Norway and Tunisia) and characterized the mechanism(s) regulating salt stress in Brachypodium sylvaticum Osl1 and Ain1. Perennial grasses are widely grown in different parts of the world as an important feedstock for renewable energy. Their perennial nature that reduces management practices and use of energy and agrochemicals give these biomass crops advantages when dealing with modern agriculture challenges such as soil erosion, increase in salinized marginal lands and the runoff of nutrients. Brachypodium sylvaticum is a perennial grass that was recently suggested as a suitable model for the study of biomass plant production and renewable energy. However, its plasticity to abiotic stress is not yet clear. We studied the salt stress tolerance of two accessions isolated from different areas of the world and characterized the mechanism(s) regulating salt stress in B. sylvaticum Osl1, originated from Oslo, Norway and Ain1, originated from Ain-Durham, Tunisia. Osl1 limited sodium transport from root to shoot, maintaining a better K/Na homeostasis and preventing toxicity damage in the shoot. This was accompanied by higher expression of HKT8 and SOS1 transporters in Osl1 as compared to Ain1. In addition, Osl1 salt tolerance was accompanied by higher abundance of the vacuolar proton pump pyrophosphatase and Na+/H+ antiporters (NHXs) leading to a better vacuolar pH homeostasis, efficient compartmentation of Na+ in the root vacuoles and salt tolerance. Although preliminary, our results further support previous results highlighting the role of Na+ transport systems in plant salt tolerance. The identification of salt tolerant and sensitive B. sylvaticum accessions can provide an experimental system for the study of the mechanisms and regulatory networks associated with stress tolerance in perennials grass.
      PubDate: 2018-01-10
      DOI: 10.1007/s11103-017-0696-3
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