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Journal Cover Plant Molecular Biology
  [SJR: 1.842]   [H-I: 121]   [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  [2334 journals]
  • Plant hormones in interactions with the environment
    • Authors: Eva Benková
      Pages: 597 - 597
      PubDate: 2016-06-29
      DOI: 10.1007/s11103-016-0501-8
      Issue No: Vol. 91, No. 6 (2016)
  • Hormones and nitrate: a two-way connection
    • Authors: Gabriel Krouk
      Pages: 599 - 606
      Abstract: Abstract During their sessile mode of life, plants need to endure variations in their environment such as a drastic variability in the nutrient concentration in soil solution. It is almost trivial to say that such fluctuations in the soil modify plant growth, development and phase transitions. However, the signaling pathways underlying the connections between nitrogen related signaling and hormonal signaling controlling growth are still poorly documented. This review is meant to present how nitrate/nitrogen controls hormonal pathways. Furthermore, it is very interesting to highlight the increasing evidence that the hormonal signaling pathways themselves seem to feed back control of the nitrate/nitrogen transport and assimilation to adapt nutrition to growth. This thus defines a feed-forward cycle that finely coordinates plant growth and nutrition.
      PubDate: 2016-08-01
      DOI: 10.1007/s11103-016-0463-x
      Issue No: Vol. 91, No. 6 (2016)
  • Hormonal control of sulfate uptake and assimilation
    • Authors: Anna Koprivova; Stanislav Kopriva
      Pages: 617 - 627
      Abstract: Abstract Plant hormones have a plethora of functions in control of plant development, stress response, and primary metabolism, including nutrient homeostasis. In the plant nutrition, the interplay of hormones with responses to nitrate and phosphate deficiency is well described, but relatively little is known about the interaction between phytohormones and regulation of sulfur metabolism. As for other nutrients, sulfate deficiency results in modulation of root architecture, where hormones are expected to play an important role. Accordingly, sulfate deficiency induces genes involved in metabolism of tryptophane and auxin. Also jasmonate biosynthesis is induced, pointing to the need of increase the defense capabilities of the plants when sulfur is limiting. However, hormones affect also sulfate uptake and assimilation. The pathway is coordinately induced by jasmonate and the key enzyme, adenosine 5′-phosphosulfate reductase, is additionally regulated by ethylene, abscisic acid, nitric oxid, and other phytohormones. Perhaps the most intriguing link between hormones and sulfate assimilation is the fact that the main regulator of the response to sulfate starvation, SULFATE LIMITATION1 (SLIM1) belongs to the family of ethylene related transcription factors. We will review the current knowledge of interplay between phytohormones and control of sulfur metabolism and discuss the main open questions.
      PubDate: 2016-08-01
      DOI: 10.1007/s11103-016-0438-y
      Issue No: Vol. 91, No. 6 (2016)
  • ABA and cytokinins: challenge and opportunity for plant stress research
    • Authors: Paul E. Verslues
      Pages: 629 - 640
      Abstract: Abstract Accumulation of the stress hormone abscisic acid (ABA) induces many cellular mechanisms associated with drought resistance. Recent years have seen a rapid advance in our knowledge of how increased ABA levels are perceived by ABA receptors, particularly the PYL/RCAR receptors, but there has been relatively less new information about how ABA accumulation is controlled and matched to stress severity. ABA synthesis and catabolism, conjugation and deconjugation to glucose, and ABA transport all are involved in controlling ABA levels. This highly buffered system of ABA metabolism represents both a challenge and opportunity in developing a mechanistic understanding of how plants detect and respond to drought. Recent data have also shown that direct manipulation of cytokinin levels in transgenic plants has dramatic effect on drought phenotypes and prompted new interest in the role of cytokinins and cytokinin signaling in drought. Both ABA and cytokinins will continue to be major foci of drought research but likely with different trajectories both in terms of basic research and in translational research aimed at increasing plant performance during drought.
      PubDate: 2016-08-01
      DOI: 10.1007/s11103-016-0458-7
      Issue No: Vol. 91, No. 6 (2016)
  • Phytohormone pathways as targets of pathogens to facilitate infection
    • Authors: Ka-Wai Ma; Wenbo Ma
      Pages: 713 - 725
      Abstract: Abstract Plants are constantly threatened by potential pathogens. In order to optimize the output of defense against pathogens with distinct lifestyles, plants depend on hormonal networks to fine-tune specific responses and regulate growth-defense tradeoffs. To counteract, pathogens have evolved various strategies to disturb hormonal homeostasis and facilitate infection. Many pathogens synthesize plant hormones; more importantly, toxins and effectors are produced to manipulate hormonal crosstalk. Accumulating evidence has shown that pathogens exert extensive effects on plant hormone pathways not only to defeat immunity, but also modify habitat structure, optimize nutrient acquisition, and facilitate pathogen dissemination. In this review, we summarize mechanisms by which a wide array of pathogens gain benefits from manipulating plant hormone pathways.
      PubDate: 2016-08-01
      DOI: 10.1007/s11103-016-0452-0
      Issue No: Vol. 91, No. 6 (2016)
  • How plants handle multiple stresses: hormonal interactions underlying
           responses to abiotic stress and insect herbivory
    • Authors: Duy Nguyen; Ivo Rieu; Celestina Mariani; Nicole M. van Dam
      Pages: 727 - 740
      Abstract: Abstract Adaptive plant responses to specific abiotic stresses or biotic agents are fine-tuned by a network of hormonal signaling cascades, including abscisic acid (ABA), ethylene, jasmonic acid (JA) and salicylic acid. Moreover, hormonal cross-talk modulates plant responses to abiotic stresses and defenses against insect herbivores when they occur simultaneously. How such interactions affect plant responses under multiple stresses, however, is less understood, even though this may frequently occur in natural environments. Here, we review our current knowledge on how hormonal signaling regulates abiotic stress responses and defenses against insects, and discuss the few recent studies that attempted to dissect hormonal interactions occurring under simultaneous abiotic stress and herbivory. Based on this we hypothesize that drought stress enhances insect resistance due to synergistic interactions between JA and ABA signaling. Responses to flooding or waterlogging involve ethylene signaling, which likely reduces plant resistance to chewing herbivores due to its negative cross-talk with JA. However, the outcome of interactions between biotic and abiotic stress signaling is often plant and/or insect species-dependent and cannot simply be predicted based on general knowledge on the involvement of signaling pathways in single stress responses. More experimental data on non-model plant and insect species are needed to reveal general patterns and better understand the molecular mechanisms allowing plants to optimize their responses in complex environments.
      PubDate: 2016-08-01
      DOI: 10.1007/s11103-016-0481-8
      Issue No: Vol. 91, No. 6 (2016)
  • Precision breeding for RNAi suppression of a major 4-coumarate:coenzyme A
           ligase gene improves cell wall saccharification from field grown sugarcane
    • Abstract: Abstract Sugarcane (Saccharum spp. hybrids) is a major feedstock for commercial bioethanol production. The recent integration of conversion technologies that utilize lignocellulosic sugarcane residues as well as sucrose from stem internodes has elevated bioethanol yields. RNAi suppression of lignin biosynthetic enzymes is a successful strategy to improve the saccharification of lignocellulosic biomass. 4-coumarate:coenzyme A ligase (4CL) is a key enzyme in the biosynthesis of phenylpropanoid metabolites, such as lignin and flavonoids. Identifying a major 4CL involved in lignin biosynthesis among multiple isoforms with functional divergence is key to manipulate lignin biosynthesis. In this study, two full length 4CL genes (Sh4CL1 and Sh4CL2) were isolated and characterized in sugarcane. Phylogenetic, expression and RNA interference (RNAi) analysis confirmed that Sh4CL1 is a major lignin biosynthetic gene. An intragenic precision breeding strategy may facilitate the regulatory approval of the genetically improved events and was used for RNAi suppression of Sh4CL1. Both, the RNAi inducing cassette and the expression cassette for the mutated ALS selection marker consisted entirely of DNA sequences from sugarcane or the sexually compatible species Sorghum bicolor. Field grown sugarcane with intragenic RNAi suppression of Sh4CL1 resulted in reduction of the total lignin content by up to 16.5 % along with altered monolignol ratios without reduction in biomass yield. Mature, field grown, intragenic sugarcane events displayed 52–76 % improved saccharification efficiency of lignocellulosic biomass compared to wild type (WT) controls. This demonstrates for the first time that an intragenic approach can add significant value to lignocellulosic feedstocks for biofuel and biochemical production.
      PubDate: 2016-08-22
      DOI: 10.1007/s11103-016-0527-y
  • Repression of ARF10 by microRNA160 plays an important role in the
           mediation of leaf water loss
    • Authors: Xin Liu; Xiufen Dong; Zihan Liu; Zihang Shi; Yun Jiang; Mingfang Qi; Tao Xu; Tianlai Li
      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: 2016-08-19
      DOI: 10.1007/s11103-016-0514-3
  • Nutritional functions of the funiculus in Brassica napus seed maturation
           revealed by transcriptome and dynamic metabolite profile analyses
    • Authors: Helin Tan; Xiaoe Xiang; Jie Tang; Xingchun Wang
      Abstract: Abstract The funiculus provides the sole channel of communication between the seed and the parent plant; however, little is known about its role in nutrient supply during seed maturation. Here, we investigated the dynamic metabolite profiles of the funiculus during seed maturation in Brassica napus. The funiculus was fully developed at 21 days after flowering (DAF), but the levels of nutrients, including carbohydrates, fatty acids, and amino acids, increased rapidly from 21 to 35 DAF. Orthogonal partial least squares discriminant analysis and correlation analysis identified 37 metabolites that correlated closely with seed fresh weight. To determine the influence of silique wall photosynthesis on the metabolites in the funiculus, we also covered the siliques of intact plants with aluminum foil; in these plants, the funiculus and silique wall had lower metabolite levels, compared with control. RNA-sequencing analysis of the funiculi in the dark-treated and light-exposed siliques showed that the expression of genes encoding nutrient transporters significantly increased in the funiculi in the dark-treated siliques. Furthermore, the transcripts encoding primary metabolic enzymes for amino acid synthesis, fatty acid synthesis and triacylglycerol assembly, and sucrose-starch metabolism, were also markedly up-regulated, despite the decline in metabolite levels of funiculi in the dark-treated silique. These results provide new insights into funiculus function in seed growth and synthesis of storage reserves in seeds, at the metabolic and transcriptional levels. The identification of these metabolites and genes also provides useful information for creating genetically enhanced oilseed crops with improved seed properties.
      PubDate: 2016-08-18
      DOI: 10.1007/s11103-016-0530-3
  • Regulation of transcription by the Arabidopsis UVR8 photoreceptor involves
           a specific histone modification
    • Authors: Christos N. Velanis; Pawel Herzyk; Gareth I. Jenkins
      Abstract: Abstract The photoreceptor UV RESISTANCE LOCUS 8 (UVR8) specifically mediates photomorphogenic responses to UV-B wavelengths. UVR8 acts by regulating transcription of a set of genes, but the underlying mechanisms are unknown. Previous research indicated that UVR8 can associate with chromatin, but the specificity and functional significance of this interaction are not clear. Here we show, by chromatin immunoprecipitation, that UV-B exposure of Arabidopsis increases acetylation of lysines K9 and/or K14 of histone H3 at UVR8-regulated gene loci in a UVR8-dependent manner. The transcription factors HY5 and/or HYH, which mediate UVR8-regulated transcription, are also required for this chromatin modification, at least for the ELIP1 gene. Furthermore, sequencing of the immunoprecipitated DNA revealed that all UV-B-induced enrichments in H3K9,14diacetylation across the genome are UVR8-dependent, and approximately 40 % of the enriched loci contain known UVR8-regulated genes. In addition, inhibition of histone acetylation by anacardic acid reduces the UV-B induced, UVR8 mediated expression of ELIP1 and CHS. No evidence was obtained in yeast 2-hybrid assays for a direct interaction between either UVR8 or HY5 and several proteins involved in light-regulated histone modification, nor for the involvement of these proteins in UVR8-mediated responses in plants, although functional redundancy between proteins could influence the results. In summary, this study shows that UVR8 regulates a specific chromatin modification associated with transcriptional regulation of a set of UVR8-target genes.
      PubDate: 2016-08-17
      DOI: 10.1007/s11103-016-0522-3
  • Split-ubiquitin yeast two-hybrid interaction reveals a novel interaction
           between a natural resistance associated macrophage protein and a membrane
           bound thioredoxin in Brassica juncea
    • Authors: Ananya Marik; Haraprasad Naiya; Madhumanti Das; Gairik Mukherjee; Soumalee Basu; Chinmay Saha; Rajdeep Chowdhury; Kankan Bhattacharyya; Anindita Seal
      Abstract: Abstract Natural resistance associated macrophage proteins (NRAMPs) are evolutionarily conserved metal transporters involved in the transport of essential and nonessential metals in plants. Fifty protein interactors of a Brassica juncea NRAMP protein was identified by a Split-Ubiquitin Yeast-Two-Hybrid screen. The interactors were predicted to function as components of stress response, signaling, development, RNA binding and processing. BjNRAMP4.1 interactors were particularly enriched in proteins taking part in photosynthetic or light regulated processes, or proteins predicted to be localized in plastid/chloroplast. Further, many interactors also had a suggested role in cellular redox regulation. Among these, the interaction of a photosynthesis-related thioredoxin, homologous to Arabidopsis HCF164 (High-chlorophyll fluorescence164) was studied in detail. Homology modeling of BjNRAMP4.1 suggested that it could be redox regulated by BjHCF164. In yeast, the interaction between the two proteins was found to increase in response to metal deficiency; Mn excess and exogenous thiol. Excess Mn also increased the interaction in planta and led to greater accumulation of the complex at the root apoplast. Network analysis of Arabidopsis homologs of BjNRAMP4.1 interactors showed enrichment of many protein components, central to chloroplastic/cellular ROS signaling. BjNRAMP4.1 interacted with BjHCF164 at the root membrane and also in the chloroplast in accordance with its proposed function related to photosynthesis, indicating that this interaction occurred at different sub-cellular locations depending on the tissue. This may serve as a link between metal homeostasis and chloroplastic/cellular ROS through protein–protein interaction.
      PubDate: 2016-08-17
      DOI: 10.1007/s11103-016-0528-x
  • Variation of 45S rDNA intergenic spacers in Arabidopsis thaliana
    • Authors: Kateřina Havlová; Martina Dvořáčková; Ramon Peiro; David Abia; Iva Mozgová; Lenka Vansáčová; Crisanto Gutierrez; Jiří Fajkus
      Abstract: Abstract Approximately seven hundred 45S rRNA genes (rDNA) in the Arabidopsis thaliana genome are organised in two 4 Mbp-long arrays of tandem repeats arranged in head-to-tail fashion separated by an intergenic spacer (IGS). These arrays make up 5 % of the A. thaliana genome. IGS are rapidly evolving sequences and frequent rearrangements inside the rDNA loci have generated considerable interspecific and even intra-individual variability which allows to distinguish among otherwise highly conserved rRNA genes. The IGS has not been comprehensively described despite its potential importance in regulation of rDNA transcription and replication. Here we describe the detailed sequence variation in the complete IGS of A. thaliana WT plants and provide the reference/consensus IGS sequence, as well as genomic DNA analysis. We further investigate mutants dysfunctional in chromatin assembly factor-1 (CAF-1) (fas1 and fas2 mutants), which are known to have a reduced number of rDNA copies, and plant lines with restored CAF-1 function (segregated from a fas1xfas2 genetic background) showing major rDNA rearrangements. The systematic rDNA loss in CAF-1 mutants leads to the decreased variability of the IGS and to the occurrence of distinct IGS variants. We present for the first time a comprehensive and representative set of complete IGS sequences, obtained by conventional cloning and by Pacific Biosciences sequencing. Our data expands the knowledge of the A. thaliana IGS sequence arrangement and variability, which has not been available in full and in detail until now. This is also the first study combining IGS sequencing data with RFLP analysis of genomic DNA.
      PubDate: 2016-08-16
      DOI: 10.1007/s11103-016-0524-1
  • The catalytic subunit of magnesium-protoporphyrin IX monomethyl ester
           cyclase forms a chloroplast complex to regulate chlorophyll biosynthesis
           in rice
    • Authors: Weiyi Kong; Xiaowen Yu; Haiyuan Chen; Linglong Liu; Yanjia Xiao; Yunlong Wang; Chaolong Wang; Yun Lin; Yang Yu; Chunming Wang; Ling Jiang; Huqu Zhai; Zhigang Zhao; Jianmin Wan
      Abstract: Key message YGL8 has the dual functions in Chl biosynthesis: one as a catalytic subunit of MgPME cyclase, the other as a core component of FLU-YGL8-LCAA-POR complex in Chl biosynthesis. Magnesium-protoporphyrin IX monomethyl ester (MgPME) cyclase is an essential enzyme involved in chlorophyll (Chl) biosynthesis. However, its roles in regulating Chl biosynthesis are not fully explored. In this study, we isolated a rice mutant yellow-green leaf 8 (ygl8) that exhibited chlorosis phenotype with abnormal chloroplast development in young leaves. As the development of leaves, the chlorotic plants turned green accompanied by restorations in Chl content and chloroplast ultrastructure. Map-based cloning revealed that the ygl8 gene encodes a catalytic subunit of MgPME cyclase. The ygl8 mutation caused a conserved amino acid substitution (Asn182Ser), which was related to the alterations of Chl precursor content. YGL8 was constitutively expressed in various tissues, with more abundance in young leaves and panicles. Furthermore, we showed that expression levels of some nuclear genes associated with Chl biosynthesis were affected in both the ygl8 mutant and YGL8 RNA interference lines. By transient expression in rice protoplasts, we found that N-terminal 40 amino acid residues were enough to localize the YGL8 protein to chloroplast. In vivo experiments demonstrated a physical interaction between YGL8 and a rice chloroplast protein, low chlorophyll accumulation A (OsLCAA). Moreover, bimolecular fluorescence complementation assays revealed that YGL8 also interacted with the other two rice chloroplast proteins, viz. fluorescent (OsFLU1) and NADPH:protochlorophyllide oxidoreductase (OsPORB). These results provide new insights into the roles of YGL8, not only as a subunit with catalytic activity, but as a core component of FLU–YGL8–LCAA–POR complex required for Chl biosynthesis.
      PubDate: 2016-08-11
      DOI: 10.1007/s11103-016-0513-4
  • De novo transcriptome analysis reveals insights into dynamic homeostasis
           regulation of somatic embryogenesis in upland cotton ( G. hirsutum L.)
    • Authors: Wen-Han Cheng; Hua-Guo Zhu; Wen-Gang Tian; Shou-Hong Zhu; Xian-Peng Xiong; Yu-Qiang Sun; Qian-Hao Zhu; Jie Sun
      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: 2016-08-10
      DOI: 10.1007/s11103-016-0511-6
  • Nitrogen assimilation system in maize is regulated by developmental and
           tissue-specific mechanisms
    • Authors: Darren Plett; Luke Holtham; Ute Baumann; Elena Kalashyan; Karen Francis; Akiko Enju; John Toubia; Ute Roessner; Antony Bacic; Antoni Rafalski; Kanwarpal S. Dhugga; Mark Tester; Trevor Garnett; Brent N. Kaiser
      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: 2016-08-10
      DOI: 10.1007/s11103-016-0512-5
  • 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 Mukhobadhyay; Shubho Chaudhuri
      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: 2016-08-09
      DOI: 10.1007/s11103-016-0519-y
  • GH32 family activity: a topological approach through protein contact
    • Authors: Sara Cimini; Luisa Di Paola; Alessandro Giuliani; Alessandra Ridolfi; Laura De Gara
      Abstract: Key message The application of Protein Contact Networks methodology allowed to highlight a novel response of border region between the two domains to substrate binding. Glycoside hydrolases (GH) are enzymes that mainly hydrolyze the glycosidic bond between two carbohydrates or a carbohydrate and a non-carbohydrate moiety. These enzymes are involved in many fundamental and diverse biological processes in plants. We have focused on the GH32 family, including enzymes very similar in both sequence and structure, each having however clear specificities of substrate preferences and kinetic properties. Structural and topological differences among proteins of the GH32 family have been here identified by means of an emerging approach (Protein Contact network, PCN) based on the formalization of 3D structures as contact networks among amino-acid residues. The PCN approach proved successful in both reconstructing the already known functional domains and in identifying the structural counterpart of the properties of GH32 enzymes, which remain uncertain, like their allosteric character. The main outcome of the study was the discovery of the activation upon binding of the border (cleft) region between the two domains. This reveals the allosteric nature of the enzymatic activity for all the analyzed forms in the GH32 family, a character yet to be highlighted in biochemical studies. Furthermore, we have been able to recognize a topological signature (graph energy) of the different affinity of the enzymes towards small and large substrates.
      PubDate: 2016-08-08
      DOI: 10.1007/s11103-016-0515-2
  • Stability and localization of 14-3-3 proteins are involved in salt
           tolerance in Arabidopsis
    • Authors: Tinghong Tan; Jingqing Cai; Erbao Zhan; Yongqing Yang; Jinfeng Zhao; Yan Guo; Huapeng Zhou
      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: 2016-08-08
      DOI: 10.1007/s11103-016-0520-5
  • In vitro promoter recognition by the catalytic subunit of plant phage-type
           RNA polymerases
    • Authors: Alexandra-Viola Bohne; Marlene Teubner; Karsten Liere; Andreas Weihe; Thomas Börner
      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: 2016-08-06
      DOI: 10.1007/s11103-016-0518-z
  • Intron sequences that stimulate gene expression in Arabidopsis
    • Authors: Alan B. Rose; Amanda Carter; Ian Korf; Noah Kojima
      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: 2016-08-05
      DOI: 10.1007/s11103-016-0516-1
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