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Transgenic Crops IV: v. 4 (Biotechnology in Agriculture and Forestry): Eng Chong Pua, Michael R. Davey:

This volume presents the current knowledge of plant biotechnology as an important tool for crop improvement. It covers cereals, vegetables, root crops, herbs and spices. This volume is an invaluable reference for plant breeders, researchers and graduate students in the fields of plant biotechnology, agronomy, horticulture, genetics and both plant cell and molecular biology.

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PlantBioInnovation
Discovery and Invention Aspects of Plant Biology That Are Interesting, Innovative and Novel !
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Plant-PrAS: A Database of Physicochemical and Structural Properties and Novel Functional Regions in Plant Proteomes

Plant-PrAS: A Database of Physicochemical and Structural Properties and Novel Functional Regions in Plant Proteomes | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Arabidopsis thaliana is an important model species for studies of plant gene functions. Research on Arabidopsis has resulted in the generation of high-quality genome sequences, annotations and related post-genomic studies. The amount of annotation, such as gene-coding regions and structures, is steadily growing in the field of plant research. In contrast to the genomics resource of animals and microorganisms, there are still some difficulties with characterization of some gene functions in plant genomics studies. The acquisition of information on protein structure can help elucidate the corresponding gene function because proteins encoded in the genome possess highly specific structures and functions. In this study, we calculated multiple physicochemical and secondary structural parameters of protein sequences, including length, hydrophobicity, the amount of secondary structure, the number of intrinsically disordered regions (IDRs) and the predicted presence of transmembrane helices and signal peptides, using a total of 208,333 protein sequences from the genomes of six representative plant species, Arabidopsis thaliana, Glycine max (soybean), Populus trichocarpa (poplar), Oryza sativa (rice),Physcomitrella patens (moss) and Cyanidioschyzon merolae (alga). Using the PASS tool and the Rosetta Stone method, we annotated the presence of novel functional regions in 1,732 protein sequences that included unannotated sequences from the Arabidopsis and rice proteomes. These results were organized into the Plant Protein Annotation Suite database (Plant-PrAS), which can be freely accessed online at http://plant-pras.riken.jp/.

 
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The glucosinolate breakdown product indole-3-carbinol acts as an auxin antagonist in roots of Arabidopsis thaliana

Plant J. 2015 Mar 11. doi: 10.1111/tpj.12824. [Epub ahead of print]
Biswapriya Biswavas Misra's insight:

The glucosinolate breakdown product indole-3-carbinol functions in cruciferous vegetables as a protective agent against foraging insects. While the toxic and deterrent effects of glucosinolate breakdown on herbivores and pathogens have been studied extensively, the secondary responses that are induced in the plant by indole-3-carbinol remain relatively uninvestigated. Here we examined the hypothesis that indole-3-carbinol has a role in influencing plant growth and development through manipulating auxin signaling. We show that indole-3-carbinol rapidly and reversibly inhibits root elongation in a dose-dependent manner, and that this inhibition is accompanied by a loss of auxin activity in the root meristem. A direct interaction between indole-3-carbinol and the auxin perception machinery was suggested, as application of indole-3-carbinol rescues auxin-induced root phenotypes. In vitro and yeast-based protein interaction studies show that indole-3-carbinol perturbs the auxin-dependent interaction of TIR1 with Aux/IAA proteins, further supporting the notion that indole-3-carbinol acts as an auxin antagonist. The results indicate that chemicals induced by herbivory, such as indole-3-carbinol, function not only to repel herbivores, but also as signaling molecules that directly compete with auxin to fine tune plant growth and development. This article is protected by copyright. All rights reserved.

 
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Intercellular salicylic acid accumulation during compatible and incompatible Arabidopsis-Pseudomonas syringae interactions

Intercellular salicylic acid accumulation during compatible and incompatible Arabidopsis-Pseudomonas syringae interactions | PlantBioInnovation | Scoop.it
(2014). Intercellular salicylic acid accumulation during compatible and incompatible Arabidopsis-Pseudomonas syringae interactions. Plant Signaling & Behavior: Vol. 9, No. 8, e29362. doi: 10.4161/psb.29362
Biswapriya Biswavas Misra's insight:

The phytohormone salicylic acid (SA) plays an important role in several disease resistance responses. During the Age-Related Resistance (ARR) response that occurs in mature Arabidopsis responding toPseudomonas syringae pv tomato (Pst), SA accumulates in the intercellular space where it may act as an antimicrobial agent. Recently we measured intracellular and intercellular SA levels in young, ARR-incompetent plants responding to virulent and avirulent strains of Pst to determine if intercellular SA accumulation is a component of additional defense responses to Pst. In young plants virulent Pstsuppressed both intra- and intercellular SA accumulation in a coronatine-dependent manner. In contrast, high levels of intra- and intercellular SA accumulated in response to avirulent Pst. Our results support the idea that SA accumulation in the intercellular space is an important component of multiple defense responses. Future research will include understanding how mature plants counteract the effects of coronatine during the ARR response.

 
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ATML1 and PDF2 Play a Redundant and Essential Role in Arabidopsis Embryo Development

The epidermis of shoot organs in plants develops from the outermost layer (L1) of the shoot apical meristem. In Arabidopsis, a pair of homeobox genes, ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1) and PROTODERMAL FACTOR2 (PDF2), plays a role in regulating the expression of L1-specific genes. atml1-1 pdf2-1 double mutants show striking defects in the differentiation of shoot epidermal cells. However, because atml1-1 and pdf2-1 have a T-DNA inserted downstream of respective homeobox sequences, these alleles may not represent null mutations. Here we characterized additional mutant alleles that have a T-DNA insertion at different positions of each gene. Double mutants of a strong atml1-3 allele with each pdf2 allele were found to cause embryonic arrest at the globular stage. Although with low frequency, all double mutant combinations of a weak atml1-1 allele with each pdf2 allele germinated and showed phenotypes defective in shoot epidermal cell differentiation. We further confirmed that transgenic induction of PDF2 fused to the Drosophila Engrailed repressor domain temporarily interferes with epidermal cell differentiation in the wild-type background. These results indicate that ATML1 and PDF2 act redundantly as a positive regulator of shoot epidermal cell differentiation and at least one copy of these genes is essential for embryo development.
Biswapriya Biswavas Misra's insight:

The epidermis of shoot organs in plants develops from the outermost layer (L1) of the shoot apical meristem. In Arabidopsis, a pair of homeobox genes, ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1) and PROTODERMAL FACTOR2 (PDF2), plays a role in regulating the expression of L1-specific genes. atml1-1 pdf2-1 double mutants show striking defects in the differentiation of shoot epidermal cells. However, because atml1-1 and pdf2-1 have a T-DNA inserted downstream of respective homeobox sequences, these alleles may not represent null mutations. Here we characterized additional mutant alleles that have a T-DNA insertion at different positions of each gene. Double mutants of a strong atml1-3 allele with each pdf2 allele were found to cause embryonic arrest at the globular stage. Although with low frequency, all double mutant combinations of a weak atml1-1 allele with each pdf2 allele germinated and showed phenotypes defective in shoot epidermal cell differentiation. We further confirmed that transgenic induction of PDF2 fused to the Drosophila Engrailed repressor domain temporarily interferes with epidermal cell differentiation in the wild-type background. These results indicate that ATML1 and PDF2 act redundantly as a positive regulator of shoot epidermal cell differentiation and at least one copy of these genes is essential for embryo development.

 
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Lateral root initiation in Arabidopsis thaliana: a force awaken

Lateral root initiation in Arabidopsis thaliana: a force awaken | PlantBioInnovation | Scoop.it
Lateral root initiation in Arabidopsis thaliana: a force awakens
Biswapriya Biswavas Misra's insight:

Osmotically driven turgor pressure of plant cells can be higher than that of a car tire. It puts tremendous forces onto cell walls and drives cell growth and changes in cell shape. This has given rise to unique mechanisms to control organ formation compared to metazoans. The fascinating interplay between forces and local cellular reorganization is still poorly understood. Growth of lateral roots is a prominent example of a developmental process in which mechanical forces between neighboring cells are generated and must be dealt with. Lateral roots initiate from a single cell layer that resides deep within the primary root. On their way out, lateral roots grow through the overlying endodermal, cortical, and epidermal cell layers. It was recently demonstrated that endodermal cells actively accommodate lateral root formation. Interfering genetically with these accommodating responses in the endodermis completely blocks cell proliferation in the pericycle. The lateral root system provides a unique opportunity to elucidate the molecular and cellular mechanisms whereby mechanical forces and intercellular communication regulate spatial accommodation during plant development.

 
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A faster Rubisco with potential to increase photosynthesis in crops

A faster Rubisco with potential to increase photosynthesis in crops | PlantBioInnovation | Scoop.it
In photosynthetic organisms, d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating atmospheric CO2 into the biosphere1. Owing to the wasteful oxygenase activity and slow turnover of Rubisco, the enzyme is among the most important targets for improving the photosynthetic efficiency of vascular plants2, 3. It has been anticipated that introducing the CO2-concentrating mechanism (CCM) from cyanobacteria into plants could enhance crop yield4, 5, 6. However, the complex nature of Rubisco’s assembly has made manipulation of the enzyme extremely challenging, and attempts to replace it in plants with the enzymes from cyanobacteria and red algae have not been successful7, 8. Here we report two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942). We knocked out the native tobacco gene encoding the large subunit of Rubisco by inserting the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35, which incorporates three small subunit-like domains9, 10. Se7942 Rubisco and CcmM35 formed macromolecular complexes within the chloroplast stroma, mirroring an early step in the biogenesis of cyanobacterial β-carboxysomes11, 12. Both transformed lines were photosynthetically competent, supporting autotrophic growth, and their respective forms of Rubisco had higher rates of CO2 fixation per unit of enzyme than the tobacco control. These transplastomic tobacco lines represent an important step towards improved photosynthesis in plants and will be valuable hosts for future addition of the remaining components of the cyanobacterial CCM, such as inorganic carbon transporters and the β-carboxysome shell proteins4, 5, 6.
Biswapriya Biswavas Misra's insight:

In photosynthetic organisms, d-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating atmospheric CO2 into the biosphere1. Owing to the wasteful oxygenase activity and slow turnover of Rubisco, the enzyme is among the most important targets for improving the photosynthetic efficiency of vascular plants2, 3. It has been anticipated that introducing the CO2-concentrating mechanism (CCM) from cyanobacteria into plants could enhance crop yield4, 5, 6. However, the complex nature of Rubisco’s assembly has made manipulation of the enzyme extremely challenging, and attempts to replace it in plants with the enzymes from cyanobacteria and red algae have not been successful7, 8. Here we report two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942). We knocked out the native tobacco gene encoding the large subunit of Rubisco by inserting the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35, which incorporates three small subunit-like domains9, 10. Se7942 Rubisco and CcmM35 formed macromolecular complexes within the chloroplast stroma, mirroring an early step in the biogenesis of cyanobacterial β-carboxysomes11, 12. Both transformed lines were photosynthetically competent, supporting autotrophic growth, and their respective forms of Rubisco had higher rates of CO2 fixation per unit of enzyme than the tobacco control. These transplastomic tobacco lines represent an important step towards improved photosynthesis in plants and will be valuable hosts for future addition of the remaining components of the cyanobacterial CCM, such as inorganic carbon transporters and the β-carboxysome shell proteins4, 5, 6.

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Development of a general method for detection and quantification of the P35S promoter based on assessment of existing methods

Development of a general method for detection and quantification of the P35S promoter based on assessment of existing methods | PlantBioInnovation | Scoop.it
The Cauliflower mosaic virus (CaMV) 35S promoter (P35S) is a commonly used target for detection of genetically modified organisms (GMOs). There are currently 24 reported detection methods, targeting different regions of the P35S promoter. Initial assessment revealed that due to the absence of primer binding sites in the P35S sequence, 19 of the 24 reported methods failed to detect P35S in MON88913 cotton, and the other two methods could only be applied to certain GMOs. The rest three reported methods were not suitable for measurement of P35S in some testing events, because SNPs in binding sites of the primer/probe would result in abnormal amplification plots and poor linear regression parameters. In this study, we discovered a conserved region in the P35S sequence through sequencing of P35S promoters from multiple transgenic events, and developed new qualitative and quantitative detection systems targeting this conserved region. The qualitative PCR could detect the P35S promoter in 23 unique GMO events with high specificity and sensitivity. The quantitative method was suitable for measurement of P35S promoter, exhibiting good agreement between the amount of template and Ct values for each testing event. This study provides a general P35S screening method, with greater coverage than existing methods.
Biswapriya Biswavas Misra's insight:

The Cauliflower mosaic virus (CaMV) 35S promoter (P35S) is a commonly used target for detection of genetically modified organisms (GMOs). There are currently 24 reported detection methods, targeting different regions of the P35S promoter. Initial assessment revealed that due to the absence of primer binding sites in the P35S sequence, 19 of the 24 reported methods failed to detect P35S in MON88913 cotton, and the other two methods could only be applied to certain GMOs. The rest three reported methods were not suitable for measurement of P35S in some testing events, because SNPs in binding sites of the primer/probe would result in abnormal amplification plots and poor linear regression parameters. In this study, we discovered a conserved region in the P35S sequence through sequencing of P35S promoters from multiple transgenic events, and developed new qualitative and quantitative detection systems targeting this conserved region. The qualitative PCR could detect the P35S promoter in 23 unique GMO events with high specificity and sensitivity. The quantitative method was suitable for measurement of P35S promoter, exhibiting good agreement between the amount of template and Ct values for each testing event. This study provides a general P35S screening method, with greater coverage than existing methods.

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BcRISP1, isolated from non-heading Chinese cabbage, decreases the seed set of transgenic Arabidopsis

BcRISP1, isolated from non-heading Chinese cabbage, decreases the seed set of transgenic Arabidopsis | PlantBioInnovation | Scoop.it
Horticulture Research, Published online: 10 December 2014; | doi:10.1038/hortres.2014.62
Biswapriya Biswavas Misra's insight:

Mitochondria are the energy sources of plant cells and are involved in regulating cell development. Ubiquinol–cytochrome c reductase iron-sulfur protein, which is necessary for mitochondrial respiration, is a subunit of mitochondrial electron transport chain multimeric enzyme complexes. To better understand the biological function of the ubiquinol–cytochrome c reductase iron–sulfur protein, the full-length cDNA of BcRISP1 was cloned; it was found to contain 810 base pairs and encode 269 amino acids. Unusually, high expression of the BcRISP1 gene in the archesporial cell stages was determined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis of cytoplasmic male sterile lines and maintainer lines. The seed set was affected by the overexpression of BcRISP1, and shorter siliques with lower seed sets were observed in 35S::BcRISP1 Arabidopsis plants. These characteristics may have resulted from the reduced formation of pollen and impaired pollen tube growth. qRT-PCR results revealed that in 35S::BcRISP1 plants, the expression levels of the mitochondrial respiratory chain-related genes, COX10 and RIP1, were enhanced, whereas the expression levels of QCR7 and SDH2-1 were reduced. This result implies that overexpression of BcRISP1 in transgenic Arabidopsis plants may disrupt the mitochondrial electron transport chain by affecting the expression of mitochondrial respiratory chain-related genes and therefore, reducing the seed set.

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A maize wall-associated kinase confers quantitative resistance to head smut

A maize wall-associated kinase confers quantitative resistance to head smut | PlantBioInnovation | Scoop.it
Mingliang Xu and colleagues show that a wall-associated kinase, ZmWAK, confers resistance to maize head smut, a systemic fungal disease in maize.
Biswapriya Biswavas Misra's insight:

Head smut is a systemic disease in maize caused by the soil-borne fungus Sporisorium reilianum that poses a grave threat to maize production worldwide. A major head smut quantitative resistance locus, qHSR1, has been detected on maize chromosome bin2.09. Here we report the map-based cloning of qHSR1 and the molecular mechanism of qHSR1-mediated resistance. Sequential fine mapping and transgenic complementation demonstrated that ZmWAK is the gene within qHSR1 conferring quantitative resistance to maize head smut. ZmWAK spans the plasma membrane, potentially serving as a receptor-like kinase to perceive and transduce extracellular signals. ZmWAK was highly expressed in the mesocotyl of seedlings where it arrested biotrophic growth of the endophytic S. reilianum. Impaired expression in the mesocotyl compromised ZmWAK-mediated resistance. Deletion of the ZmWAK locus appears to have occurred after domestication and spread among maize germplasm, and the ZmWAK kinase domain underwent functional constraints during maize evolution.

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The inheritance of resistance to bacterial leaf spot of lettuce caused by Xanthomonas campestris pv. vitians in three lettuce cultivars

The inheritance of resistance to bacterial leaf spot of lettuce caused by Xanthomonas campestris pv. vitians in three lettuce cultivars | PlantBioInnovation | Scoop.it
Horticulture Research, Published online: 24 December 2014; | doi:10.1038/hortres.2014.66
Biswapriya Biswavas Misra's insight:

Lettuce yields can be reduced by the disease bacterial leaf spot (BLS) caused by the pathogen Xanthomonas campestris pv. vitians (Xcv) and host resistance is the most feasible method to reduce disease losses. The cultivars La Brillante, Pavane and Little Gem express an incompatible host–pathogen interaction as a hypersensitive response (HR) to California strains of Xcv resulting in resistance. Little was known about the inheritance of resistance; however, resistance to other lettuce pathogens is often determined by resistance gene candidates (RGCs) encoding nucleotide-binding leucine-rich repeat (NB-LRR) proteins. Therefore, we determined the inheritance of BLS resistance in the cultivars La Brillante, Little Gem and Pavane and mapped it relative to RGCs. The reaction to Xcv was analyzed in nine F1, F2 and recombinant inbred line populations of lettuce from HR×compatible or HR×HR crosses. The HR in La Brillante, Pavane and Little Gem is conditioned by single dominant genes, which are either allelic or closely linked genes. The resistance gene in La Brillante was designated Xanthomonas resistance 1 (Xar1) and mapped to lettuce linkage group 2. Xar1 is present in a genomic region that contains numerous NB-LRR encoding RGCs and functional pathogen resistance loci in the RGC2 family. The Xar1 gene confers a high level of BLS resistance in the greenhouse and field that can be introgressed into commercial lettuce cultivars to reduce BLS losses using molecular markers.

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Fast sampling method for mammalian cell metabolic analyses using liquid chromatography–mass spectrometry

Metabolomics has emerged as a powerful tool for addressing biological questions. Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used for metabolic characterization, including targeted and untargeted approaches. Despite recent innovations, a crucial aspect of this technique is the sample preparation for accurate data analyses. In this protocol, we present a robust and adaptable workflow for metabolic analyses of mammalian cells from adherent cell cultures, which is particularly suited for qualitative and quantitative central metabolite characterization by LC-MS. Each sample consists of 600,000 mammalian cells grown on cover glasses, allowing for fast and complete transfer of the cells for metabolite extraction or medium exchange, e.g., for labeling experiments. The sampling procedure includes a fast and efficient washing step in liquid flow in water, which reduces cross-contamination and matrix effects while minimizing perturbation of the metabolic steady state of the cells; it is followed by quenching cell metabolism. The latter is achieved by using a −20 °C cold methanol acetonitrile mixture acidified with formic acid, followed by freeze drying, metabolite extraction and LC-MS. The protocol requires 2 s for cell sampling until quenching, and the entire protocol takes a total of 1.5 h per sample when the provided nanoscale LC-MS method is applied.
Biswapriya Biswavas Misra's insight:

Metabolomics has emerged as a powerful tool for addressing biological questions. Liquid chromatography coupled with mass spectrometry (LC-MS) is widely used for metabolic characterization, including targeted and untargeted approaches. Despite recent innovations, a crucial aspect of this technique is the sample preparation for accurate data analyses. In this protocol, we present a robust and adaptable workflow for metabolic analyses of mammalian cells from adherent cell cultures, which is particularly suited for qualitative and quantitative central metabolite characterization by LC-MS. Each sample consists of 600,000 mammalian cells grown on cover glasses, allowing for fast and complete transfer of the cells for metabolite extraction or medium exchange, e.g., for labeling experiments. The sampling procedure includes a fast and efficient washing step in liquid flow in water, which reduces cross-contamination and matrix effects while minimizing perturbation of the metabolic steady state of the cells; it is followed by quenching cell metabolism. The latter is achieved by using a −20 °C cold methanol acetonitrile mixture acidified with formic acid, followed by freeze drying, metabolite extraction and LC-MS. The protocol requires 2 s for cell sampling until quenching, and the entire protocol takes a total of 1.5 h per sample when the provided nanoscale LC-MS method is applied.

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Biomass conversion: Lignin up for break-down

Lignin is an abundant renewable resource, but its intrinsic recalcitrant nature has so far hampered its conversion into higher value chemicals. Now, a two-step strategy, oxidation followed by bond cleavage, has been shown to deconstruct lignin into high yields of low-molecular-weight aromatics.
Biswapriya Biswavas Misra's insight:

Lignin is an abundant renewable resource, but its intrinsic recalcitrant nature has so far hampered its conversion into higher value chemicals. Now, a two-step strategy, oxidation followed by bond cleavage, has been shown to deconstruct lignin into high yields of low-molecular-weight aromatics.

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Wheat rescued from fungal disease

Knockout of all six alleles of a gene in the large wheat genome confers resistance to powdery mildew.
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Knockout of all six alleles of a gene in the large wheat genome confers resistance to powdery mildew.

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Focus issue on plant immunity: from model systems to crop species.

Focus issue on plant immunity: from model systems to crop species.
Biswapriya Biswavas Misra's insight:

One of the largest challenges of our time is to enhance agricultural production to feed a growing population in the midst of a changing climate. According to estimates, the global population will increase from 7 to 9 billion people by 2050 requiring a 60% increase in food in order to meet demand (Alexandratos et al., 2012). Only the combination of reduction of food waste together with an increase in food productivity will enable us to meet this daunting challenge (Godfray et al., 2010). Advancements in agricultural practices, technology, food transport, and crop yields on marginal lands will be required to address this looming food production challenge. Crop losses due to plant disease significantly impact agriculture, with ~15% of global crop production lost due to preharvest plant disease (Pinstrup-Andersen, 2001; Oerke, 2006). Studies of model plants, such as Arabidopsis, have significantly enhanced our understanding of plant innate immune perception and signaling. For example, the identification of classical plant resistant genes in Arabidopsis and other model dicots facilitated the successful cloning of multiple wheat rust resistant genes (Ellis et al., 2014; Wulff and Moscou, 2014). With advancements in genome sequencing and analyses, we are now at a stage to exploit the basic knowledge gained in plant model species at a full genome scale in crops (Piquerez et al., 2014). 

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PHABULOSA Controls the Quiescent Center-Independent Root Meristem Activities in Arabidopsis thaliana

PLoS Genet. 2015 Mar 2;11(3):e1004973. doi: 10.1371/journal.pgen.1004973. eCollection 2015.
Biswapriya Biswavas Misra's insight:

Plant growth depends on stem cell niches in meristems. In the root apical meristem, the quiescent center (QC) cells form a niche together with the surrounding stem cells. Stem cells produce daughter cells that are displaced into a transit-amplifying (TA) domain of the root meristem. TA cells divide several times to provide cells for growth. SHORTROOT (SHR) and SCARECROW (SCR) are key regulators of the stem cell niche. Cytokinin controls TA cell activities in a dose-dependent manner. Although the regulatory programs in each compartment of the root meristem have been identified, it is still unclear how they coordinate one another. Here, we investigate how PHABULOSA (PHB), under the posttranscriptional control of SHR and SCR, regulates TA cell activities. The root meristem and growth defects in shr or scr mutants were significantly recovered in the shr phb or scr phb double mutant, respectively. This rescue in root growth occurs in the absence of a QC. Conversely, when the modified PHB, which is highly resistant to microRNA, was expressed throughout the stele of the wild-type root meristem, root growth became very similar to that observed in the shr; however, the identity of the QC was unaffected. Interestingly, a moderate increase in PHB resulted in a root meristem phenotype similar to that observed following the application of high levels of cytokinin. Our protoplast assay and transgenic approach using ARR10 suggest that the depletion of TA cells by high PHB in the stele occurs via the repression of B-ARR activities. This regulatory mechanism seems to help to maintain the cytokinin homeostasis in the meristem. Taken together, our study suggests that PHB can dynamically regulate TA cell activities in a QC-independent manner, and that the SHR-PHB pathway enables a robust root growth system by coordinating the stem cell niche and TA domain.

  
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Trehalose-6-phosphate synthase 1 is not the only active TPS in Arabidopsis thalian

Biswapriya Biswavas Misra's insight:

Trehalose metabolism is essential for normal growth and development in higher plants. It is synthesized in a two-step pathway catalysed by TPS (trehalose-6-phosphate synthase) and trehalose phosphatase. Arabidopsis thalianahas 11 TPS or TPS-like proteins, which belong to two distinct clades: class I (AtTPS1–AtTPS4) and class II (AtTPS5–AtTPS11). Only AtTPS1 has previously been shown to have TPS activity. A. thaliana tps1∆ mutants fail to complete embryogenesis and rescued lines have stunted growth and delayed flowering, indicating that AtTPS1 is important throughout the life cycle. In the present study, we show that expression of AtTPS2 or AtTPS4 enables the yeast tps1∆tps2∆ mutant to grow on glucose and accumulate Tre6P (trehalose 6-phosphate) and trehalose. Class II TPS genes did not complement the yeast mutant. Thus A. thaliana has at least three catalytically active TPS isoforms, suggesting that loss of Tre6P production might not be the only reason for the growth defects of A. thaliana tps1mutants.

 
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Dual role of tree florigen activation complex component FD in photoperiodic growth control and adaptive response pathways

Dual role of tree florigen activation complex component FD in photoperiodic growth control and adaptive response pathways | PlantBioInnovation | Scoop.it
Perennial plants display seasonal cycles of growth. For example, in the trees of boreal temperate forests, growth must cease prior to the advent of winter and cold hardiness must be acquired to survive extreme low temperature. Growth cessation and activation of transcriptional programs underlying adaptive responses associated with cold hardiness are photoperiodically controlled. We show that the evolutionarily conserved protein FD implicated in the control of flowering mediates photoperiodic control of seasonal growth in trees by forming a complex with FLOWERING LOCUS T (FT) protein. FD genes of hybrid aspen display neofunctionalization and, in contrast to Arabidopsis, have evolved functions that are independent of their interaction with FT, such as transcriptional control of the adaptive response and bud maturation pathways in trees.
Biswapriya Biswavas Misra's insight:

Perennial plants display seasonal cycles of growth. For example, in the trees of boreal temperate forests, growth must cease prior to the advent of winter and cold hardiness must be acquired to survive extreme low temperature. Growth cessation and activation of transcriptional programs underlying adaptive responses associated with cold hardiness are photoperiodically controlled. We show that the evolutionarily conserved protein FD implicated in the control of flowering mediates photoperiodic control of seasonal growth in trees by forming a complex with FLOWERING LOCUS T (FT) protein. FD genes of hybrid aspen display neofunctionalization and, in contrast to Arabidopsis, have evolved functions that are independent of their interaction with FT, such as transcriptional control of the adaptive response and bud maturation pathways in trees.

 
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Enabling plant synthetic biology through genome engineering

Enabling plant synthetic biology through genome engineering | PlantBioInnovation | Scoop.it
Synthetic biology seeks to create new biological systems, including user-designed plants and plant cells. These systems can be employed for a variety of purposes, ranging from producing compounds of industrial or therapeutic value, to reducing crop losses by altering cellular responses to pathogens or climate change. To realize the full potential of plant synthetic biology, techniques are required that provide control over the genetic code – enabling targeted modifications to DNA sequences within living plant cells. Such control is now within reach owing to recent advances in the use of sequence-specific nucleases to precisely engineer genomes. We discuss here the enormous potential provided by genome engineering for plant synthetic biology.
Biswapriya Biswavas Misra's insight:

Synthetic biology seeks to create new biological systems, including user-designed plants and plant cells. These systems can be employed for a variety of purposes, ranging from producing compounds of industrial or therapeutic value, to reducing crop losses by altering cellular responses to pathogens or climate change. To realize the full potential of plant synthetic biology, techniques are required that provide control over the genetic code – enabling targeted modifications to DNA sequences within living plant cells. Such control is now within reach owing to recent advances in the use of sequence-specific nucleases to precisely engineer genomes. We discuss here the enormous potential provided by genome engineering for plant synthetic biology.

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Tissue-specific clocks in Arabidopsis show asymmetric coupling

Tissue-specific clocks in Arabidopsis show asymmetric coupling | PlantBioInnovation | Scoop.it
tissues
Biswapriya Biswavas Misra's insight:

Many organisms rely on a circadian clock system to adapt to daily and seasonal environmental changes. The mammalian circadian clock consists of a central clock in the suprachiasmatic nucleus that has tightly coupled neurons and synchronizes other clocks in peripheral tissues1, 2. Plants also have a circadian clock, but plant circadian clock function has long been assumed to be uncoupled3. Only a few studies have been able to show weak, local coupling among cells4, 5, 6, 7. Here, by implementing two novel techniques, we have performed a comprehensive tissue-specific analysis of leaf tissues, and show that the vasculature and mesophyll clocks asymmetrically regulate each other in Arabidopsis. The circadian clock in the vasculature has characteristics distinct from other tissues, cycles robustly without environmental cues, and affects circadian clock regulation in other tissues. Furthermore, we found that vasculature-enriched genes that are rhythmically expressed are preferentially expressed in the evening, whereas rhythmic mesophyll-enriched genes tend to be expressed in the morning. Our results set the stage for a deeper understanding of how the vasculature circadian clock in plants regulates key physiological responses such as flowering time.

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A Y-chromosome–encoded small RNA acts as a sex determinant in persimmons

In plants, multiple lineages have evolved sex chromosomes independently, providing a powerful comparative framework, but few specific determinants controlling the expression of a specific sex have been identified. We investigated sex determinants in the Caucasian persimmon, Diospyros lotus, a dioecious plant with heterogametic males (XY). Male-specific short nucleotide sequences were used to define a male-determining region. A combination of transcriptomics and evolutionary approaches detected a Y-specific sex-determinant candidate, OGI, that displays male-specific conservation among Diospyros species. OGI encodes a small RNA targeting the autosomal MeGI gene, a homeodomain transcription factor regulating anther fertility in a dosage-dependent fashion. This identification of a feminizing gene suppressed by a Y-chromosome–encoded small RNA contributes to our understanding of the evolution of sex chromosome systems in higher plants.
Biswapriya Biswavas Misra's insight:

In plants, multiple lineages have evolved sex chromosomes independently, providing a powerful comparative framework, but few specific determinants controlling the expression of a specific sex have been identified. We investigated sex determinants in the Caucasian persimmon, Diospyros lotus, a dioecious plant with heterogametic males (XY). Male-specific short nucleotide sequences were used to define a male-determining region. A combination of transcriptomics and evolutionary approaches detected a Y-specific sex-determinant candidate, OGI, that displays male-specific conservation among Diospyros species. OGI encodes a small RNA targeting the autosomal MeGI gene, a homeodomain transcription factor regulating anther fertility in a dosage-dependent fashion. This identification of a feminizing gene suppressed by a Y-chromosome–encoded small RNA contributes to our understanding of the evolution of sex chromosome systems in higher plants.

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A comparative study on genetic effects of artificial and natural habitat fragmentation on Loropetalum chinense (Hamamelidaceae) in Southeast China

An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
Biswapriya Biswavas Misra's insight:

Elucidating the demographic and landscape features that determine the genetic effects of habitat fragmentation has become fundamental to research in conservation and evolutionary biology. Land-bridge islands provide ideal study areas for investigating the genetic effects of habitat fragmentation at different temporal and spatial scales. In this context, we compared patterns of nuclear microsatellite variation between insular populations of a shrub of evergreen broad-leaved forest, Loropetalum chinense, from the artificially created Thousand-Island Lake (TIL) and the Holocene-dated Zhoushan Archipelago of Southeast China. Populations from the TIL region harboured higher levels of genetic diversity than those from the Zhoushan Archipelago, but these differences were not significant. There was no correlation between genetic diversity and most island features, excepting a negative effect of mainland–island distance on allelic richness and expected heterozygosity in the Zhoushan Archipelago. In general, levels of gene flow among island populations were moderate to high, and tests of alternative models of population history strongly favoured a gene flow-drift model over a pure drift model in each region. In sum, our results showed no obvious genetic effects of habitat fragmentation due to recent (artificial) or past (natural) island formation. Rather, they highlight the importance of gene flow (most likely via seed) in maintaining genetic variation and preventing inter-population differentiation in the face of habitat ‘insularization’ at different temporal and spatial scales.

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A Widespread Glutamine-Sensing Mechanism in the Plant Kingdom

A Widespread Glutamine-Sensing Mechanism in the Plant Kingdom | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Glutamine is the primary metabolite of nitrogen assimilation from inorganic nitrogen sources in microorganisms and plants. The ability to monitor cellular nitrogen status is pivotal for maintaining metabolic homeostasis and sustaining growth. The present study identifies a glutamine-sensing mechanism common in the entire plant kingdom except Brassicaceae. The plastid-localized PII signaling protein controls, in a glutamine-dependent manner, the key enzyme of the ornithine synthesis pathway, N-acetyl-l-glutamate kinase (NAGK), that leads to arginine and polyamine formation. Crystal structures reveal that the plant-specific C-terminal extension of PII, which we term the Q loop, forms a low-affinity glutamine-binding site. Glutamine binding alters PII conformation, promoting interaction and activation of NAGK. The binding motif is highly conserved in plants except Brassicaceae. A functional Q loop restores glutamine sensing in a recombinant Arabidopsis thaliana PII protein, demonstrating the modular concept of the glutamine-sensing mechanism adopted by PII proteins during the evolution of plant chloroplasts.

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Chrysanthemyl Diphosphate Synthase Operates in Planta as a Bifunctional Enzyme with Chrysanthemol Synthase Activity

Biswapriya Biswavas Misra's insight:

Chrysanthemyl diphosphate synthase (CDS) is the first pathway-specific enzyme in the biosynthesis of pyrethrins, the most widely used plant-derived pesticide. CDS catalyzes c1′-2-3 cyclopropanation reactions of two molecules of dimethylallyl diphosphate (DMAPP) to yield chrysanthemyl diphosphate (CPP). Three proteins are known to catalyze this cyclopropanation reaction of terpene precursors. Two of them, phytoene and squalene synthase, are bifunctional enzymes with both prenyltransferase and terpene synthase activity. CDS, the other member, has been reported to perform only the prenyltransferase step. Here we show that the NDXXD catalytic motif of CDS, under the lower substrate conditions prevalent in plants, also catalyzes the next step, converting CPP into chrysanthemol by hydrolyzing the diphosphate moiety. The enzymatic hydrolysis reaction followed conventional Michaelis-Menten kinetics, with a Km value for CPP of 196 μm. For the chrysanthemol synthase activity, DMAPP competed with CPP as substrate. The DMAPP concentration required for half-maximal activity to produce chrysanthemol was ∼100 μm, and significant substrate inhibition was observed at elevated DMAPP concentrations. The N-terminal peptide of CDS was identified as a plastid-targeting peptide. Transgenic tobacco plants overexpressing CDS emitted chrysanthemol at a rate of 0.12–0.16 μg h−1 g−1 fresh weight. We propose that CDS should be renamed a chrysanthemol synthase utilizing DMAPP as substrate.

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Plant genomics: High-throughput phenotyping of rice growth traits

A high-throughput phenotyping tool enables the study of rice traits during the growth period and after harvest. Yang et al. combined imaging techniques with a yield traits scorer to automatically screen for 15 agronomic traits, including two newly defined traits — plant compactness and grain-projected area — that cannot be identified by…
Biswapriya Biswavas Misra's insight:

A high-throughput phenotyping tool enables the study of rice traits during the growth period and after harvest. Yang et al. combined imaging techniques with a yield traits scorer to automatically screen for 15 agronomic traits, including two newly defined traits — plant compactness and grain-projected area — that cannot be identified by…

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Cell walls: Cellulose snakes along

Biswapriya Biswavas Misra's insight:

Cellulose polymers found in plant cell walls are synthesized by cellulose synthase complexes (CESA), but the mechanism for conversion of individual polymers into microfibrils remains unclear. COBRA is coexpressed with CESA, and mutations of COBRA are linked to changes in cellulose, but its specific function is unknown.…

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