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PlantBioInnovation
Discovery and Invention Aspects of Plant Biology That Are Interesting, Innovative and Novel !
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Scooped by Biswapriya Biswavas Misra
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A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana

A Functional and Evolutionary Perspective on Transcription Factor Binding in Arabidopsis thaliana | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Understanding the mechanisms underlying gene regulation is paramount to comprehend the translation from genotype to phenotype. The two are connected by gene expression, and it is generally thought that variation in transcription factor (TF) function is an important determinant of phenotypic evolution. We analyzed publicly available genome-wide chromatin immunoprecipitation experiments for 27 TFs in Arabidopsis thaliana and constructed an experimental network containing 46,619 regulatory interactions and 15,188 target genes. We identified hub targets and highly occupied target (HOT) regions, which are enriched for genes involved in development, stimulus responses, signaling, and gene regulatory processes in the currently profiled network. We provide several lines of evidence that TF binding at plant HOT regions is functional, in contrast to that in animals, and not merely the result of accessible chromatin. HOT regions harbor specific DNA motifs, are enriched for differentially expressed genes, and are often conserved across crucifers and dicots, even though they are not under higher levels of purifying selection than non-HOT regions. Distal bound regions are under purifying selection as well and are enriched for a chromatin state showing regulation by the Polycomb repressive complex. Gene expression complexity is positively correlated with the total number of bound TFs, revealing insights in the regulatory code for genes with different expression breadths. The integration of noncanonical and canonical DNA motif information yields new hypotheses on cobinding and tethering between specific TFs involved in flowering and light regulation.

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Characterization of a Novel DWD Protein that Participates in Heat Stress Response in Arabidopsis.

Cullin4-RING ubiquitin ligase (CRL4) is a family of multisubunit E3 ligases. To investigate the possible involvement of CRL4 in heat stress response, we screened T-DNA insertion mutants of putative CRL4 substrate receptors that exhibited altered patterns in response to heat stress. One of the mutants exhibited heat stress tolerance and was named heat stress tolerant DWD1 (htd1). Introduction of HTD1 gene into htd1-1 led to recovery of heat sensitivity to the wild type level, confirming that the decrease of HTD1 transcripts resulted in heat tolerance. Therefore, HTD1 plays a negative role in thermotolerance in Arabidopsis. Additionally, HTD1 directly interacted with DDB1a in yeast two-hybrid assays and associated with DDB1b in vivo, supporting that it could be a part of a CRL4 complex. Various heat-inducible genes such as HSP14.7, HSP21, At2g03020 and WRKY28 were hyper-induced in htd1-1, indicating that HTD1 could function as a negative regulator for the expression of such genes and that these genes might contribute to thermotolerance of htd1-1, at least in part. HTD1 was associated with HSP90-1, a crucial regulator of thermotolerance, in vivo, even though the decrease of HTD1 did not affect the accumulation pattern of HSP90- 1 in Arabidopsis. These findings indicate that a negative role of HTD1 in thermotolerance might be achieved through its association with HSP90-1, possibly by disturbing the action of HSP90-1, not by the degradation of HSP90-1. This study will serve as an important step toward understanding of the functional connection between CRL4-mediated processes and plant heat stress signaling.
Biswapriya Biswavas Misra's insight:

Cullin4-RING ubiquitin ligase (CRL4) is a family of multisubunit E3 ligases. To investigate the possible involvement of CRL4 in heat stress response, we screened T-DNA insertion mutants of putative CRL4 substrate receptors that exhibited altered patterns in response to heat stress. One of the mutants exhibited heat stress tolerance and was named heat stress tolerant DWD1 (htd1). Introduction of HTD1 gene into htd1-1 led to recovery of heat sensitivity to the wild type level, confirming that the decrease of HTD1 transcripts resulted in heat tolerance. Therefore, HTD1 plays a negative role in thermotolerance in Arabidopsis. Additionally, HTD1 directly interacted with DDB1a in yeast two-hybrid assays and associated with DDB1b in vivo, supporting that it could be a part of a CRL4 complex. Various heat-inducible genes such as HSP14.7, HSP21, At2g03020 and WRKY28 were hyper-induced in htd1-1, indicating that HTD1 could function as a negative regulator for the expression of such genes and that these genes might contribute to thermotolerance of htd1-1, at least in part. HTD1 was associated with HSP90-1, a crucial regulator of thermotolerance, in vivo, even though the decrease of HTD1 did not affect the accumulation pattern of HSP90- 1 in Arabidopsis. These findings indicate that a negative role of HTD1 in thermotolerance might be achieved through its association with HSP90-1, possibly by disturbing the action of HSP90-1, not by the degradation of HSP90-1. This study will serve as an important step toward understanding of the functional connection between CRL4-mediated processes and plant heat stress signaling.

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The roles of histone acetylation in seed performance and plant development

The roles of histone acetylation in seed performance and plant development | PlantBioInnovation | Scoop.it
HATs
Biswapriya Biswavas Misra's insight:

Histone acetylation regulates gene transcription by chromatin modifications and plays a crucial role in the plant development and response to environment cues. The homeostasis of histone acetylation is controlled by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in different plant tissues and development stages. The vigorous knowledge of the function and co-factors about HATs (e.g. GCN5) and HDACs (e.g. HDA19, HDA6) has been obtained from model plant Arabidopsis. However, understanding individual role of other HATs and HDACs require more work, especially in the major food crops such as rice, maize and wheat. Many co-regulators have been recently identified to function as a component of HAT or HDAC complex in some specific developmental processes. The described findings show a distinctive and interesting epigenetic regulation network composed of HATs, HDACs and co-regulators playing crucial roles in the seed performance, flowering time, plant morphogenesis, plant response to stresses etc. In this review, we summarized the recent progresses and suggested the perspective of histone acetylation research, which might provide us a new window to understand the epigenetic code of plant development and to improve the crop production and quality.

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Coming of age: orphan genes in plants:

Coming of age: orphan genes in plants: | PlantBioInnovation | Scoop.it
importance
Biswapriya Biswavas Misra's insight:

Sizable minorities of protein-coding genes from every sequenced eukaryotic and prokaryotic genome are unique to the species. These so-called ‘orphan genes’ may evolve de novo from non-coding sequence or be derived from older coding material. They are often associated with environmental stress responses and species-specific traits or regulatory patterns. However, difficulties in studying genes where comparative analysis is impossible, and a bias towards broadly conserved genes, have resulted in underappreciation of their importance. We review here the identification, possible origins, evolutionary trends, and functions of orphans with an emphasis on their role in plant biology. We exemplify several evolutionary trends with an analysis of Arabidopsis thaliana and present QQS as a model orphan gene.

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Plant biotechnology for lignocellulosic biofuel production

Plant biotechnology for lignocellulosic biofuel production | PlantBioInnovation | Scoop.it

Lignocelluloses from plant cell walls are attractive resources for sustainable biofuel production. However, conversion of lignocellulose to biofuel is more expensive than other current technologies, due to the costs of chemical pretreatment and enzyme hydrolysis for cell wall deconstruction. Recalcitrance of cell walls to deconstruction has been reduced in many plant species by modifying plant cell walls through biotechnology. These results have been achieved by reducing lignin content and altering its composition and structure. Reduction of recalcitrance has also been achieved by manipulating hemicellulose biosynthesis and by overexpression of bacterial enzymes in plants to disrupt linkages in the lignin–carbohydrate complexes. These modified plants often have improved saccharification yield and higher ethanol production. Cell wall-degrading (CWD) enzymes from bacteria and fungi have been expressed at high levels in plants to increase the efficiency of saccharification compared with exogenous addition of cellulolytic enzymes. In planta expression of heat-stable CWD enzymes from bacterial thermophiles has made autohydrolysis possible. Transgenic plants can be engineered to reduce recalcitrance without any yield penalty, indicating that successful cell wall modification can be achieved without impacting cell wall integrity or plant development. A more complete understanding of cell wall formation and structure should greatly improve lignocellulosic feedstocks and reduce the cost of biofuel production.


Via Pierre-André Marechal
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Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis

Abstract

Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by a wide range of plant-associated microorganisms. They are best known for their cytotoxicity in dicot plants that leads to the induction of rapid tissue necrosis and plant immune responses. The biotrophic downy mildew pathogenHyaloperonospora arabidopsidis encodes 10 different noncytotoxic NLPs (HaNLPs) that do not cause necrosis. We discovered that these noncytotoxic NLPs, however, act as potent activators of the plant immune system in Arabidopsis thaliana. Ectopic expression of HaNLP3 in Arabidopsis triggered resistance to H. arabidopsidis, activated the expression of a large set of defense-related genes, and caused a reduction of plant growth that is typically associated with strongly enhanced immunity. N- and C-terminal deletions of HaNLP3, as well as amino acid substitutions, pinpointed to a small central region of the protein that is required to trigger immunity, indicating the protein acts as a microbe-associated molecular pattern (MAMP). This was confirmed in experiments with a synthetic peptide of 24 aa, derived from the central part of HaNLP3 and corresponding to a conserved region in type 1 NLPs that induces ethylene production, a well-known MAMP response. Strikingly, corresponding 24-aa peptides of fungal and bacterial type 1 NLPs were also able to trigger immunity in Arabidopsis. The widespread phylogenetic distribution of type 1 NLPs makes this protein family (to our knowledge) the first proteinaceous MAMP identified in three different kingdoms of life.


Via Pierre-Marc Delaux
Biswapriya Biswavas Misra's insight:

Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by a wide range of plant-associated microorganisms. They are best known for their cytotoxicity in dicot plants that leads to the induction of rapid tissue necrosis and plant immune responses. The biotrophic downy mildew pathogenHyaloperonospora arabidopsidis encodes 10 different noncytotoxic NLPs (HaNLPs) that do not cause necrosis. We discovered that these noncytotoxic NLPs, however, act as potent activators of the plant immune system in Arabidopsis thaliana. Ectopic expression of HaNLP3 in Arabidopsis triggered resistance to H. arabidopsidis, activated the expression of a large set of defense-related genes, and caused a reduction of plant growth that is typically associated with strongly enhanced immunity. N- and C-terminal deletions of HaNLP3, as well as amino acid substitutions, pinpointed to a small central region of the protein that is required to trigger immunity, indicating the protein acts as a microbe-associated molecular pattern (MAMP). This was confirmed in experiments with a synthetic peptide of 24 aa, derived from the central part of HaNLP3 and corresponding to a conserved region in type 1 NLPs that induces ethylene production, a well-known MAMP response. Strikingly, corresponding 24-aa peptides of fungal and bacterial type 1 NLPs were also able to trigger immunity in Arabidopsis. The widespread phylogenetic distribution of type 1 NLPs makes this protein family (to our knowledge) the first proteinaceous MAMP identified in three different kingdoms of life.

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Origin of plant auxin biosynthesis in charophyte algae

Origin of plant auxin biosynthesis in charophyte algae | PlantBioInnovation | Scoop.it
The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA flavin monooxygenase (YUC) pathway is the main auxin biosynthesis pathway in plants [1]. The origin of plant auxin biosynthesis remains unclear and controversial. Recently Yue et al. addressed this issue by performing phylogenetic analysis of TAA and YUC proteins [2]. They found that land plant TAA proteins are most closely related to proteins from non-plant eukaryotes (such as Choanoflagellida and Haptophyta). Moreover, by searching against expressed sequence tag (EST) database, Yue et al.
Biswapriya Biswavas Misra's insight:

The TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA)/YUCCA flavin monooxygenase (YUC) pathway is the main auxin biosynthesis pathway in plants [1]. The origin of plant auxin biosynthesis remains unclear and controversial. Recently Yue et al. addressed this issue by performing phylogenetic analysis of TAA and YUC proteins [2]. They found that land plant TAA proteins are most closely related to proteins from non-plant eukaryotes (such as Choanoflagellida and Haptophyta). Moreover, by searching against expressed sequence tag (EST) database, Yue et al.

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Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus

Systematic Analysis of Zn2Cys6 Transcription Factors Required for Development and Pathogenicity by High-Throughput Gene Knockout in the Rice Blast Fungus | PlantBioInnovation | Scoop.it
From molecules to physiology
Biswapriya Biswavas Misra's insight:

Because of great challenges and workload in deleting genes on a large scale, the functions of most genes in pathogenic fungi are still unclear. In this study, we developed a high-throughput gene knockout system using a novel yeast-Escherichia-Agrobacterium shuttle vector, pKO1B, in the rice blast fungus Magnaporthe oryzae. Using this method, we deleted 104 fungal-specific Zn2Cys6 transcription factor (TF) genes in M. oryzae. We then analyzed the phenotypes of these mutants with regard to growth, asexual and infection-related development, pathogenesis, and 9 abiotic stresses. The resulting data provide new insights into how this rice pathogen of global significance regulates important traits in the infection cycle through Zn2Cys6TF genes. A large variation in biological functions of Zn2Cys6TF genes was observed under the conditions tested. Sixty-one of 104 Zn2Cys6 TF genes were found to be required for fungal development. In-depth analysis of TF genes revealed that TF genes involved in pathogenicity frequently tend to function in multiple development stages, and disclosed many highly conserved but unidentified functional TF genes of importance in the fungal kingdom. We further found that the virulence-required TF genes GPF1 and CNF2 have similar regulation mechanisms in the gene expression involved in pathogenicity. These experimental validations clearly demonstrated the value of a high-throughput gene knockout system in understanding the biological functions of genes on a genome scale in fungi, and provided a solid foundation for elucidating the gene expression network that regulates the development and pathogenicity of M. oryzae.

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Phenotypic diversity of diploid and haploid Emiliania huxleyi cells and of cells in different growth phases revealed by comparative metabolomics

In phytoplankton a high species diversity of microalgae co-exists at a given time. But diversity is not only reflected by the species composition. Within these species different life phases as well as different metabolic states can cause additional diversity. One important example is the coccolithophore Emiliania huxleyi. Diploid cells play an important role in marine ecosystems since they can form massively abundant algal blooms but in addition the less abundant haploid life phase of E. huxleyi occurs in lower quantities. Both life phases may fulfill different functions in the plankton. We hypothesize that in addition to the functional diversity caused by this life phase transition the growth stage of cells can also influence the metabolic composition and thus the ecological impact of E. huxleyi. Here we introduce a metabolomic survey in dependence of life phases as well as different growth phases to reveal such changes. The comparative metabolomic approach is based on the extraction of intracellular metabolites from intact microalgae, derivatization and analysis by gas chromatography coupled to mass spectrometry (GC-MS). Automated data processing and statistical analysis using canonical analysis of principal coordinates (CAP) revealed unique metabolic profiles for each life phase. Concerning the correlations of metabolites to growth phases, complex patterns were observed. As for example the saccharide mannitol showed its highest concentration in the exponential phase, whereas fatty acids were correlated to stationary and sterols to declining phase. These results are indicative for specific ecological roles of these stages of E. huxleyi and are discussed in the context of previous physiological and ecological studies.
Biswapriya Biswavas Misra's insight:

In phytoplankton a high species diversity of microalgae co-exists at a given time. But diversity is not only reflected by the species composition. Within these species different life phases as well as different metabolic states can cause additional diversity. One important example is the coccolithophore Emiliania huxleyi. Diploid cells play an important role in marine ecosystems since they can form massively abundant algal blooms but in addition the less abundant haploid life phase of E. huxleyi occurs in lower quantities. Both life phases may fulfill different functions in the plankton. We hypothesize that in addition to the functional diversity caused by this life phase transition the growth stage of cells can also influence the metabolic composition and thus the ecological impact of E. huxleyi. Here we introduce a metabolomic survey in dependence of life phases as well as different growth phases to reveal such changes. The comparative metabolomic approach is based on the extraction of intracellular metabolites from intact microalgae, derivatization and analysis by gas chromatography coupled to mass spectrometry (GC-MS). Automated data processing and statistical analysis using canonical analysis of principal coordinates (CAP) revealed unique metabolic profiles for each life phase. Concerning the correlations of metabolites to growth phases, complex patterns were observed. As for example the saccharide mannitol showed its highest concentration in the exponential phase, whereas fatty acids were correlated to stationary and sterols to declining phase. These results are indicative for specific ecological roles of these stages of E. huxleyi and are discussed in the context of previous physiological and ecological studies.

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Transcriptome analysis of a Ustilago maydis ust1 deletion mutant uncovers involvement of laccase and polyketide synthase genes in spore development

Transcriptome analysis of a Ustilago maydis ust1 deletion mutant uncovers involvement of laccase and polyketide synthase genes in spore development | PlantBioInnovation | Scoop.it
polyketide
Biswapriya Biswavas Misra's insight:

Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.

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‘Fukusensor:’ a genetically engineered plant for reporting DNA damage in response to gamma radiation

‘Fukusensor:’ a genetically engineered plant for reporting DNA damage in response to gamma radiation | PlantBioInnovation | Scoop.it
Transgenic plants can be designed to be ‘phytosensors’ for detection of environmental contaminants and pathogens. In this study, we describe the design and testing of a radiation phytosensor in the form of green fluorescence protein (GFP)-transgenic Arabidopsis plant utilizing a DNA repair deficiency mutant background as a host. Mutant lines of Arabidopsis AtATM (At3g48190), which are hypersensitive to gamma irradiation, were used to generate stable GFP transgenic plants in which a gfp gene was under the control of a strong constitutive CaMV 35S promoter. Mutant and nonmutant genetic background transgenic plants were treated with 0, 1, 5, 10 and 100 Gy radiation doses, respectively, using a Co-60 source. After 1 week, the GFP expression levels were drastically reduced in young leaves of mutant background plants (treated by 10 and 100 Gy), whereas there were scant visible differences in the fluorescence of the nonmutant background plants. These early results indicate that transgenic plants could serve in a relevant sensor system to report radiation dose and the biological effects to organisms in response to radionuclide contamination.
Biswapriya Biswavas Misra's insight:

Transgenic plants can be designed to be ‘phytosensors’ for detection of environmental contaminants and pathogens. In this study, we describe the design and testing of a radiation phytosensor in the form of green fluorescence protein (GFP)-transgenic Arabidopsis plant utilizing a DNA repair deficiency mutant background as a host. Mutant lines of Arabidopsis AtATM (At3g48190), which are hypersensitive to gamma irradiation, were used to generate stable GFP transgenic plants in which a gfp gene was under the control of a strong constitutive CaMV 35S promoter. Mutant and nonmutant genetic background transgenic plants were treated with 0, 1, 5, 10 and 100 Gy radiation doses, respectively, using a Co-60 source. After 1 week, the GFP expression levels were drastically reduced in young leaves of mutant background plants (treated by 10 and 100 Gy), whereas there were scant visible differences in the fluorescence of the nonmutant background plants. These early results indicate that transgenic plants could serve in a relevant sensor system to report radiation dose and the biological effects to organisms in response to radionuclide contamination.

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Inference of Transcriptional Networks in Arabidopsis through Conserved Noncoding Sequence Analysis.

Transcriptional regulation plays an important role in establishing gene expression profiles during development or in response to (a)biotic stimuli. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity, and the identification of individual TFBS in genome sequences is a major goal to inferring regulatory networks. We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences (CNSs) across 12 dicot plants. Whereas both alignment and non-alignment-based techniques were applied to identify functional motifs in a multispecies context, our method accounts for incomplete motif conservation as well as high sequence divergence between related species. We identified 69,361 footprints associated with 17,895 genes. Through the integration of known TFBS obtained from the literature and experimental studies, we used the CNSs to compile a gene regulatory network in Arabidopsis thaliana containing 40,758 interactions, of which two-thirds act through binding events located in DNase I hypersensitive sites. This network shows significant enrichment toward in vivo targets of known regulators, and its overall quality was confirmed using five different biological validation metrics. Finally, through the integration of detailed expression and function information, we demonstrate how static CNSs can be converted into condition-dependent regulatory networks, offering opportunities for regulatory gene annotation.
Biswapriya Biswavas Misra's insight:

Transcriptional regulation plays an important role in establishing gene expression profiles during development or in response to (a)biotic stimuli. Transcription factor binding sites (TFBSs) are the functional elements that determine transcriptional activity, and the identification of individual TFBS in genome sequences is a major goal to inferring regulatory networks. We have developed a phylogenetic footprinting approach for the identification of conserved noncoding sequences (CNSs) across 12 dicot plants. Whereas both alignment and non-alignment-based techniques were applied to identify functional motifs in a multispecies context, our method accounts for incomplete motif conservation as well as high sequence divergence between related species. We identified 69,361 footprints associated with 17,895 genes. Through the integration of known TFBS obtained from the literature and experimental studies, we used the CNSs to compile a gene regulatory network in Arabidopsis thaliana containing 40,758 interactions, of which two-thirds act through binding events located in DNase I hypersensitive sites. This network shows significant enrichment toward in vivo targets of known regulators, and its overall quality was confirmed using five different biological validation metrics. Finally, through the integration of detailed expression and function information, we demonstrate how static CNSs can be converted into condition-dependent regulatory networks, offering opportunities for regulatory gene annotation.

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Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest

Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

In this study we sequenced bacterial communities present on tree leaves in a neotropical forest in Panama, to quantify the poorly understood relationships between bacterial biodiversity on leaves (the phyllosphere) vs. host tree attributes. Bacterial community structure on leaves was highly correlated with host evolutionary relatedness and suites of plant functional traits related to host ecological strategies for resource uptake and growth/mortality tradeoffs. The abundance of several bacterial taxa was correlated with host growth, mortality, and function. Our study quantifies the drivers of variation in plant-associated microbial biodiversity; our results suggest that incorporating information on plant-associated microbes will improve our understanding of the functional biogeography of plants and plant–microbe interactions.

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Plant Metabolic Flux Analysis: Methods and Protocols

Plant Metabolic Flux Analysis: Methods and Protocols | PlantBioInnovation | Scoop.it
In Plant Metabolic Flux Analysis, expert researchers in the field provide detailed experimental procedures for each step of the flux quantification workflow. Steady state and dynamic modelin
Biswapriya Biswavas Misra's insight:
In Plant Metabolic Flux Analysis, expert researchers in the field provide detailed experimental procedures for each step of the flux quantification workflow. Steady state and dynamic modeling are considered, as well as recent developments for the reconstruction of metabolic networks and for a predictive modeling. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls.   Authoritative and practical Plant Metabolic Flux Analysis,  seeks to aid scientists in the further study of cutting-edge protocols and methodologies that are crucial to getting ahead in MFA.
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Talking through walls: mechanisms of lateral root emergence in Arabidopsis thaliana

Talking through walls: mechanisms of lateral root emergence in Arabidopsis thaliana | PlantBioInnovation | Scoop.it
Lateral roots are formed postembryonically and determine the final shape of the root system, a determinant of the plants ability to uptake nutrients and water. The lateral root primordia are initiated deep into the main root and to protrude out the primary root they have to grow through three cell layers. Recent findings have revealed that these layers are not merely a passive physical obstacle to the emergence of the lateral root but have an active role in its formation. Here, we review examples of communication between the lateral root primordium and the surrounding tissues, highlighting the importance of auxin-mediated growth coordination as well as cell and tissue mechanics for the morphogenesis of lateral roots.
Biswapriya Biswavas Misra's insight:

Lateral roots are formed postembryonically and determine the final shape of the root system, a determinant of the plants ability to uptake nutrients and water. The lateral root primordia are initiated deep into the main root and to protrude out the primary root they have to grow through three cell layers. Recent findings have revealed that these layers are not merely a passive physical obstacle to the emergence of the lateral root but have an active role in its formation. Here, we review examples of communication between the lateral root primordium and the surrounding tissues, highlighting the importance of auxin-mediated growth coordination as well as cell and tissue mechanics for the morphogenesis of lateral roots.

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Auxin – a novel regulator of stomata differentiation

Auxin – a novel regulator of stomata differentiation | PlantBioInnovation | Scoop.it
Three recent publications identify the phytohormone auxin as a novel regulator of stomata development and distribution. We discuss how auxin signaling and polar auxin transport blend in with the established signaling network that controls cell division and differentiation within the stomatal cell lineage.
Biswapriya Biswavas Misra's insight:

Three recent publications identify the phytohormone auxin as a novel regulator of stomata development and distribution. We discuss how auxin signaling and polar auxin transport blend in with the established signaling network that controls cell division and differentiation within the stomatal cell lineage.

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Rescooped by Biswapriya Biswavas Misra from microbial pathogenesis and plant immunity
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Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis

Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis | PlantBioInnovation | Scoop.it

Peptide fragments of Nep1-like proteins (NLPs), occurring in diverse microorganisms of three different kingdoms of life, were found to trigger immunity in the model plant Arabidopsis, indicating that they act as a microbe-associated molecular pattern (MAMP). A synthetic peptide of 24 aa from the central part of the downy mildew HaNLP3 protein was found to activate the plant immune system and trigger resistance to this pathogen. Strikingly, not only peptides of oomycete NLPs, but also those of bacteria and fungi were shown to act as a MAMP. This unprecedented broad taxonomic distribution demonstrates that the occurrence of a MAMP is not necessarily restricted to a class of microorganisms but can occur in a wide range of species from the tree of life.


Via Jim Alfano
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Jim Alfano's curator insight, November 3, 2014 4:27 PM

Interesting new PAMP - one that is present in bacteria, fungi, and oomycetes.

Rescooped by Biswapriya Biswavas Misra from microbial pathogenesis and plant immunity
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Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis

Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis | PlantBioInnovation | Scoop.it

Peptide fragments of Nep1-like proteins (NLPs), occurring in diverse microorganisms of three different kingdoms of life, were found to trigger immunity in the model plant Arabidopsis, indicating that they act as a microbe-associated molecular pattern (MAMP). A synthetic peptide of 24 aa from the central part of the downy mildew HaNLP3 protein was found to activate the plant immune system and trigger resistance to this pathogen. Strikingly, not only peptides of oomycete NLPs, but also those of bacteria and fungi were shown to act as a MAMP. This unprecedented broad taxonomic distribution demonstrates that the occurrence of a MAMP is not necessarily restricted to a class of microorganisms but can occur in a wide range of species from the tree of life.


Via Jim Alfano
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Jim Alfano's curator insight, November 3, 2014 4:27 PM

Interesting new PAMP - one that is present in bacteria, fungi, and oomycetes.

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Phenotypic and genomic responses to titanium dioxide and cerium oxide nanoparticles in Arabidopsis germinants

Phenotypic and genomic responses to titanium dioxide and cerium oxide nanoparticles in Arabidopsis germinants | PlantBioInnovation | Scoop.it
The effects of exposure to nanoparticles of titanium dioxide (nano-titanium) and cerium oxide (nano-cerium) on gene expression and growth in Arabidopsis thaliana germinants were studied by using microarrays and quantitative real-time polymerase chain reaction (qPCR), and by evaluating germinant phenotypic plasticity. Exposure to 12 d of either nano-titania or nano-ceria altered the regulation of 204 and 142 genes, respectively. Genes induced by the nanoparticles mainly include ontology groups annotated as stimuli responsive, including both abiotic (oxidative stress, salt stress, water transport) and biotic (respiratory burst as a defense against pathogens) stimuli. Further analysis of the differentially expressed genes indicates that both nanoparticles affected a range of metabolic processes (deoxyribonucleic acid [DNA] metabolism, hormone metabolism, tetrapyrrole synthesis, and photosynthesis). Individual exposures to the nanoparticles increased percentages of seeds with emergent radicals, early development of hypocotyls and cotyledons, and those with fully grown leaves. Although there were distinct differences between the nanoparticles in their affect on molecular mechanisms attributable to enhancing germinant growth, both particles altered similar suites of genes related to various pathways and processes related to enhanced growth. Environ Toxicol Chem 2014;9999:XX–XX. Published 2014 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
Biswapriya Biswavas Misra's insight:

The effects of exposure to nanoparticles of titanium dioxide (nano-titanium) and cerium oxide (nano-cerium) on gene expression and growth in Arabidopsis thaliana germinants were studied by using microarrays and quantitative real-time polymerase chain reaction (qPCR), and by evaluating germinant phenotypic plasticity. Exposure to 12 d of either nano-titania or nano-ceria altered the regulation of 204 and 142 genes, respectively. Genes induced by the nanoparticles mainly include ontology groups annotated as stimuli responsive, including both abiotic (oxidative stress, salt stress, water transport) and biotic (respiratory burst as a defense against pathogens) stimuli. Further analysis of the differentially expressed genes indicates that both nanoparticles affected a range of metabolic processes (deoxyribonucleic acid [DNA] metabolism, hormone metabolism, tetrapyrrole synthesis, and photosynthesis). Individual exposures to the nanoparticles increased percentages of seeds with emergent radicals, early development of hypocotyls and cotyledons, and those with fully grown leaves. Although there were distinct differences between the nanoparticles in their affect on molecular mechanisms attributable to enhancing germinant growth, both particles altered similar suites of genes related to various pathways and processes related to enhanced growth. Environ Toxicol Chem 2014;9999:XX–XX. Published 2014 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.

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Expression Profiling during Arabidopsis/Downy Mildew Interaction Reveals a Highly-Expressed Effector That Attenuates Responses to Salicylic Acid

Expression Profiling during Arabidopsis/Downy Mildew Interaction Reveals a Highly-Expressed Effector That Attenuates Responses to Salicylic Acid | PlantBioInnovation | Scoop.it
From molecules to physiology
Biswapriya Biswavas Misra's insight:

Plants have evolved strong innate immunity mechanisms, but successful pathogens evade or suppress plant immunity via effectors delivered into the plant cell. Hyaloperonospora arabidopsidis (Hpa) causes downy mildew on Arabidopsis thaliana, and a genome sequence is available for isolate Emoy2. Here, we exploit the availability of genome sequences for Hpa and Arabidopsis to measure gene-expression changes in both Hpa and Arabidopsis simultaneously during infection. Using a high-throughput cDNA tag sequencing method, we reveal expression patterns of Hpa predicted effectors and Arabidopsis genes in compatible and incompatible interactions, and promoter elements associated with Hpa genes expressed during infection. By resequencing Hpa isolate Waco9, we found it evades Arabidopsis resistance gene RPP1 through deletion of the cognate recognized effector ATR1. Arabidopsis salicylic acid (SA)-responsive genes including PR1 were activated not only at early time points in the incompatible interaction but also at late time points in the compatible interaction. By histochemical analysis, we found that Hpa suppresses SA-inducible PR1 expression, specifically in the haustoriated cells into which host-translocated effectors are delivered, but not in non-haustoriated adjacent cells. Finally, we found a highly-expressed Hpa effector candidate that suppresses responsiveness to SA. As this approach can be easily applied to host-pathogen interactions for which both host and pathogen genome sequences are available, this work opens the door towards transcriptome studies in infection biology that should help unravel pathogen infection strategies and the mechanisms by which host defense responses are overcome.

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MicroRNAs Suppress NB Domain Genes in Tomato That Confer Resistance to Fusarium oxysporum

MicroRNAs Suppress NB Domain Genes in Tomato That Confer Resistance to Fusarium oxysporum | PlantBioInnovation | Scoop.it
MicroRNAs (miRNAs) suppress the transcriptional and post-transcriptional expression of genes in plants. Several miRNA families target genes encoding nucleotide-binding site–leucine-rich repeat (NB-LRR) plant innate immune receptors. The fungus Fusarium oxysporum f. sp. lycopersici causes vascular wilt disease in tomato. We explored a role for miRNAs in tomato defense against F. oxysporum using comparative miRNA profiling of susceptible (Moneymaker) and resistant (Motelle) tomato cultivars. slmiR482f and slmiR5300 were repressed during infection of Motelle with F. oxysporum. Two predicted mRNA targets each of slmiR482f and slmiR5300 exhibited increased expression in Motelle and the ability of these four targets to be regulated by the miRNAs was confirmed by co-expression in Nicotiana benthamiana. Silencing of the targets in the resistant Motelle cultivar revealed a role in fungal resistance for all four genes. All four targets encode proteins with full or partial nucleotide-binding (NB) domains. One slmiR5300 target corresponds to tm-2, a susceptible allele of the Tomato Mosaic Virus resistance gene, supporting functions in immunity to a fungal pathogen. The observation that none of the targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Taken together, our findings suggest that Moneymaker is highly susceptible because its potential resistance is insufficiently expressed due to the action of miRNAs.
Biswapriya Biswavas Misra's insight:

MicroRNAs (miRNAs) suppress the transcriptional and post-transcriptional expression of genes in plants. Several miRNA families target genes encoding nucleotide-binding site–leucine-rich repeat (NB-LRR) plant innate immune receptors. The fungus Fusarium oxysporum f. sp. lycopersici causes vascular wilt disease in tomato. We explored a role for miRNAs in tomato defense against F. oxysporum using comparative miRNA profiling of susceptible (Moneymaker) and resistant (Motelle) tomato cultivars. slmiR482f and slmiR5300 were repressed during infection of Motelle with F. oxysporum. Two predicted mRNA targets each of slmiR482f and slmiR5300 exhibited increased expression in Motelle and the ability of these four targets to be regulated by the miRNAs was confirmed by co-expression in Nicotiana benthamiana. Silencing of the targets in the resistant Motelle cultivar revealed a role in fungal resistance for all four genes. All four targets encode proteins with full or partial nucleotide-binding (NB) domains. One slmiR5300 target corresponds to tm-2, a susceptible allele of the Tomato Mosaic Virus resistance gene, supporting functions in immunity to a fungal pathogen. The observation that none of the targets correspond to I-2, the only known resistance (R) gene for F. oxysporum in tomato, supports roles for additional R genes in the immune response. Taken together, our findings suggest that Moneymaker is highly susceptible because its potential resistance is insufficiently expressed due to the action of miRNAs.

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Proteomic investigation of response to FORL infection in tomato roots.

Fusarium oxysporum f. sp. radicis-lycopersici (FORL) leading to fusarium crown and root rot is considered one of the most destructive tomato soilborne diseases occurring in greenhouse and field crops. In this study, response to FORL infection in tomato roots was investigated by differential proteomics in susceptible (Monalbo) and resistant (Momor) isogenic tomato lines, thus leading to identify 33 proteins whose amount changed depending on the pathogen infection, and/or on the two genotypes. FORL infection induced accumulation of pathogen-related proteins (PR proteins) displaying glucanase and endochitinases activity or involved in redox processes in the Monalbo genotype. Interestingly, the level of the above mentioned PR proteins was not influenced by FORL infection in the resistant tomato line, while other proteins involved in general response mechanisms to biotic and/or abiotic stresses showed significant quantitative differences. In particular, the increased level of proteins participating to arginine metabolism and glutathione S-transferase (GST; EC 2.5.1.18) as well as that of protein LOC544002 and phosphoprotein ECPP44-like, suggested their key role in pathogen defence.
Biswapriya Biswavas Misra's insight:

Fusarium oxysporum f. sp. radicis-lycopersici (FORL) leading to fusarium crown and root rot is considered one of the most destructive tomato soilborne diseases occurring in greenhouse and field crops. In this study, response to FORL infection in tomato roots was investigated by differential proteomics in susceptible (Monalbo) and resistant (Momor) isogenic tomato lines, thus leading to identify 33 proteins whose amount changed depending on the pathogen infection, and/or on the two genotypes. FORL infection induced accumulation of pathogen-related proteins (PR proteins) displaying glucanase and endochitinases activity or involved in redox processes in the Monalbo genotype. Interestingly, the level of the above mentioned PR proteins was not influenced by FORL infection in the resistant tomato line, while other proteins involved in general response mechanisms to biotic and/or abiotic stresses showed significant quantitative differences. In particular, the increased level of proteins participating to arginine metabolism and glutathione S-transferase (GST; EC 2.5.1.18) as well as that of protein LOC544002 and phosphoprotein ECPP44-like, suggested their key role in pathogen defence.

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First Proteomic Study of S-Glutathionylation in Cyanobacteria

First Proteomic Study of S-Glutathionylation in Cyanobacteria | PlantBioInnovation | Scoop.it
Glutathionylation, the reversible post-translational formation of a mixed disulfide between a cysteine residue and glutathione (GSH), is a crucial mechanism for signal transduction and regulation of protein function. Until now this reversible redox modification was studied mainly in eukaryotic cells. Here we report a large-scale proteomic analysis of glutathionylation in a photosynthetic prokaryote, the model cyanobacterium Synechocystis sp. PCC6803. Treatment of acellular extracts with N,N-biotinyl glutathione disulfide (BioGSSG) induced glutathionylation of numerous proteins, which were subsequently isolated by affinity chromatography on streptavidin columns and identified by nano LC–MS/MS analysis. Potential sites of glutathionylation were also determined for 125 proteins following tryptic cleavage, streptavidin-affinity purification, and mass spectrometry analysis. Taken together the two approaches allowed the identification of 383 glutathionylatable proteins that participate in a wide range of cellular processes and metabolic pathways such as carbon and nitrogen metabolisms, cell division, stress responses, and H2 production. In addition, the glutathionylation of two putative targets, namely, peroxiredoxin (Sll1621) involved in oxidative stress tolerance and 3-phosphoglycerate dehydrogenase (Sll1908) acting on amino acids metabolism, was confirmed by biochemical studies on the purified recombinant proteins. These results suggest that glutathionylation constitutes a major mechanism of global regulation of the cyanobacterial metabolism under oxidative stress conditions.
Biswapriya Biswavas Misra's insight:

Glutathionylation, the reversible post-translational formation of a mixed disulfide between a cysteine residue and glutathione (GSH), is a crucial mechanism for signal transduction and regulation of protein function. Until now this reversible redox modification was studied mainly in eukaryotic cells. Here we report a large-scale proteomic analysis of glutathionylation in a photosynthetic prokaryote, the model cyanobacterium Synechocystis sp. PCC6803. Treatment of acellular extracts with N,N-biotinyl glutathione disulfide (BioGSSG) induced glutathionylation of numerous proteins, which were subsequently isolated by affinity chromatography on streptavidin columns and identified by nano LC–MS/MS analysis. Potential sites of glutathionylation were also determined for 125 proteins following tryptic cleavage, streptavidin-affinity purification, and mass spectrometry analysis. Taken together the two approaches allowed the identification of 383 glutathionylatable proteins that participate in a wide range of cellular processes and metabolic pathways such as carbon and nitrogen metabolisms, cell division, stress responses, and H2 production. In addition, the glutathionylation of two putative targets, namely, peroxiredoxin (Sll1621) involved in oxidative stress tolerance and 3-phosphoglycerate dehydrogenase (Sll1908) acting on amino acids metabolism, was confirmed by biochemical studies on the purified recombinant proteins. These results suggest that glutathionylation constitutes a major mechanism of global regulation of the cyanobacterial metabolism under oxidative stress conditions.

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Silencing of a metaphase I-specific gene results in a phenotype similar to that of the Pairing homeologous 1 (Ph1) gene mutations

Silencing of a metaphase I-specific gene results in a phenotype similar to that of the Pairing homeologous 1 (Ph1) gene mutations | PlantBioInnovation | Scoop.it
Maintaining diploid-like pairing behavior is essential for a polyploid to establish as a new species. The Pairing homeologous 1 (Ph1) gene, regulating such behavior in polyploid wheat, was identified in 1958, but its molecular function remained elusive. The present communication reports identification of the candidate Ph1 (C-Ph1) gene that is expressed exclusively during meiotic metaphase I, whose silencing resulted in formation of multivalents like the Ph1 gene mutations. Although the C-Ph1 gene has three homoeologous copies, the 5B copy has diverged in sequence from the other two copies. Heterologous gene silencing of the Arabidopsis homologue of the C-Ph1 gene also confirmed its function. Molecular characterization of this gene will make it possible to develop precise alien introgression strategies.
Biswapriya Biswavas Misra's insight:

Maintaining diploid-like pairing behavior is essential for a polyploid to establish as a new species. The Pairing homeologous 1 (Ph1) gene, regulating such behavior in polyploid wheat, was identified in 1958, but its molecular function remained elusive. The present communication reports identification of the candidate Ph1 (C-Ph1) gene that is expressed exclusively during meiotic metaphase I, whose silencing resulted in formation of multivalents like the Ph1 gene mutations. Although the C-Ph1 gene has three homoeologous copies, the 5B copy has diverged in sequence from the other two copies. Heterologous gene silencing of the Arabidopsis homologue of the C-Ph1 gene also confirmed its function. Molecular characterization of this gene will make it possible to develop precise alien introgression strategies.

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Species-specific defence responses facilitate conspecifics and inhibit heterospecifics in above–belowground herbivore interaction

Species-specific defence responses facilitate conspecifics and inhibit heterospecifics in above–belowground herbivore interaction | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Conspecific and heterospecific aboveground and belowground herbivores often occur together in nature and their interactions may determine community structure. Here we show how aboveground adults and belowground larvae of the tallow tree specialist beetle Bikasha collaris and multiple heterospecific aboveground species interact to determine herbivore performance. Conspecific aboveground adults facilitate belowground larvae, but other aboveground damage inhibits larvae or has no effect. Belowground larvae increase conspecific adult feeding, but decrease heterospecific aboveground insect feeding and abundance. Chemical analyses and experiments with plant populations varying in phenolics show that all these positive and negative effects on insects are closely related to root and shoot tannin concentrations. Our results show that specific plant herbivore responses allow herbivore facilitation and inhibition to co-occur, likely shaping diverse aboveground and belowground communities. Considering species-specific responses of plants is critical for teasing apart inter- and intraspecific interactions in aboveground and belowground compartments.

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