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Biofortification of plants with altered antioxidant content and composition: genetic engineering strategies - Zhu - 2012 - Plant Biotechnology Journal - Wiley Online Library

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SummaryAntioxidants are protective molecules that neutralize reactive oxygen species and preventoxidative damage to cellular components such as membranes, proteins and nucleic acids,therefore reducing the rate of cell death and hence the effects of ageing and ageing-relateddiseases. The fortification of food with antioxidants represents an overlap between two diverseenvironments, namely fortification of staple foods with essential nutrients that happen to haveantioxidant properties (e.g. vitamins C and E) and the fortification of luxury foods with health-promoting but non-essential antioxidants such as flavonoids as part of the nutraceuticals/functional foods industry. Although processed foods can be artificially fortified with vitamins,minerals and nutraceuticals, a more sustainable approach is to introduce the traits for suchhealth-promoting compounds at source, an approach known as biofortification. Regardless ofthe target compound, the same challenges arise when considering the biofortification of plantswith antioxidants, that is the need to modulate endogenous metabolic pathways to increase theproduction of specific antioxidants without affecting plant growth and development andwithout collateral effects on other metabolic pathways. These challenges become even moreintricate as we move from the engineering of individual pathways to several pathwayssimultaneously. In this review, we consider the state of the art in antioxidant biofortification anddiscuss the challenges that remain to be overcome in the development of nutritionally complete

and health-promoting functional foods.

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Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea | PlantBioInnovation | Scoop.it
We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabuli chromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement.
Biswapriya Biswavas Misra's insight:

We discovered 26785 and 16573 high-quality SNPs differentiating two parental genotypes of a RIL mapping population using reference desi and kabuli genome-based GBS assay. Of these, 3625 and 2177 SNPs have been integrated into eight desi and kabulichromosomes, respectively in order to construct ultra-high density (0.20–0.37 cM) intra-specific chickpea genetic linkage maps. One of these constructed high-resolution genetic map has potential to identify 33 major genomic regions harbouring 35 robust QTLs (PVE: 17.9–39.7%) associated with three agronomic traits, which were mapped within <1 cM mean marker intervals on desi chromosomes. The extended LD (linkage disequilibrium) decay (~15 cM) in chromosomes of genetic maps have encouraged us to use a rapid integrated approach (comparative QTL mapping, QTL-region specific haplotype/LD-based trait association analysis, expression profiling and gene haplotype-based association mapping) rather than a traditional QTL map-based cloning method to narrow-down one major seed weight (SW) robust QTL region. It delineated favourable natural allelic variants and superior haplotype-containing one seed-specific candidate embryo defective gene regulating SW in chickpea. The ultra-high-resolution genetic maps, QTLs/genes and alleles/haplotypes-related genomic information generated and integrated strategy for rapid QTL/gene identification developed have potential to expedite genomics-assisted breeding applications in crop plants, including chickpea for their genetic enhancement.

  
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Negative regulatory roles of DE-ETIOLATED1 in flowering time in Arabidopsis

Negative regulatory roles of DE-ETIOLATED1 in flowering time in Arabidopsis | PlantBioInnovation | Scoop.it
Arabidopsis flowers early under long days (LD) and late under short days (SD). The repressor of photomorphogenesis DE-ETIOLATED1 (DET1) delays flowering; det1-1 mutants flower early, especially under SD, but the molecular mechanism of DET1 regulation remains unknown. Here we examine the regulatory function of DET1 in repression of flowering. Under SD, the det1-1 mutation causes daytime expression of FKF1 and CO; however, their altered expression has only a small effect on early flowering in det1-1 mutants. Notably, DET1 interacts with GI and binding of GI to the FT promoter increases in det1-1 mutants, suggesting that DET1 mainly restricts GI function, directly promoting FT expression independent of CO expression. Moreover, DET1 interacts with MSI4/FVE, which epigenetically inhibits FLC expression, indicating that the lack of FLC expression in det1-1 mutants likely involves altered histone modifications at the FLC locus. These data demonstrate that DET1 acts in both photoperiod and autonomous pathways to inhibit expression of FT and SOC1. Consistent with this, the early flowering of det1-1 mutants disappears completely in the ft-1 soc1-2 double mutant background. Thus, we propose that DET1 is a strong repressor of flowering and has a pivotal role in maintaining photoperiod sensitivity in the regulation of flowering time.
Biswapriya Biswavas Misra's insight:

Arabidopsis flowers early under long days (LD) and late under short days (SD). The repressor of photomorphogenesis DE-ETIOLATED1 (DET1) delays flowering; det1-1mutants flower early, especially under SD, but the molecular mechanism of DET1 regulation remains unknown. Here we examine the regulatory function of DET1 in repression of flowering. Under SD, the det1-1 mutation causes daytime expression ofFKF1 and CO; however, their altered expression has only a small effect on early flowering in det1-1 mutants. Notably, DET1 interacts with GI and binding of GI to the FT promoter increases in det1-1 mutants, suggesting that DET1 mainly restricts GI function, directly promoting FT expression independent of CO expression. Moreover, DET1 interacts with MSI4/FVE, which epigenetically inhibits FLC expression, indicating that the lack of FLCexpression in det1-1 mutants likely involves altered histone modifications at the FLClocus. These data demonstrate that DET1 acts in both photoperiod and autonomous pathways to inhibit expression of FT and SOC1. Consistent with this, the early flowering ofdet1-1 mutants disappears completely in the ft-1 soc1-2 double mutant background. Thus, we propose that DET1 is a strong repressor of flowering and has a pivotal role in maintaining photoperiod sensitivity in the regulation of flowering time.

  
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Limited Sexual Reproduction and Quick Turnover in the Population Genetic Structure of Phytophthora infestans in Fujian, China

Limited Sexual Reproduction and Quick Turnover in the Population Genetic Structure of Phytophthora infestans in Fujian, China | PlantBioInnovation | Scoop.it
The mating system plays an important role in the spatiotemporal dynamics of pathogen populations through both its direct and indirect impact on the generation and distribution of genetic variation. Here, we used a combination of microsatellite and phenotypic markers to investigate the spatiotemporal distribution of genetic variation in Phytophthora infestans isolates collected from Fujian, China and to determine the role of sexual reproduction in the dynamics. Although the pathogen populations in this region were dominated by self-fertile genotypes, sexual reproduction only occurred occasionally and its contributions to the population genetic structure of P. infestans and epidemics of late blight in the region were limited. Only 49 genotypes were detected among the 534 isolates assayed and the pathogen populations displayed significant heterozygosity excess. Hierarchical analysis revealed that 21.42% of genetic variation was attributed to the difference among sampling years while only 4.45% was attributed to the difference among locations, suggesting temporal factors play a more important role in the population genetic dynamics of P. infestans than spatial factors in this region. We propose that clonal reproduction, combined with founder effects and long distance dispersal of sporangia, is responsible for the observed pattern of spatiotemporal dynamics in P. infestans.
Biswapriya Biswavas Misra's insight:

The mating system plays an important role in the spatiotemporal dynamics of pathogen populations through both its direct and indirect impact on the generation and distribution of genetic variation. Here, we used a combination of microsatellite and phenotypic markers to investigate the spatiotemporal distribution of genetic variation in Phytophthora infestans isolates collected from Fujian, China and to determine the role of sexual reproduction in the dynamics. Although the pathogen populations in this region were dominated by self-fertile genotypes, sexual reproduction only occurred occasionally and its contributions to the population genetic structure of P. infestansand epidemics of late blight in the region were limited. Only 49 genotypes were detected among the 534 isolates assayed and the pathogen populations displayed significant heterozygosity excess. Hierarchical analysis revealed that 21.42% of genetic variation was attributed to the difference among sampling years while only 4.45% was attributed to the difference among locations, suggesting temporal factors play a more important role in the population genetic dynamics of P. infestans than spatial factors in this region. We propose that clonal reproduction, combined with founder effects and long distance dispersal of sporangia, is responsible for the observed pattern of spatiotemporal dynamics in P. infestans.

  
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Arabidopsis seed mucilage secretory cells: regulation and dynamics

Arabidopsis seed mucilage secretory cells: regulation and dynamics | PlantBioInnovation | Scoop.it
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Seeds from various angiosperm species produce polysaccharide mucilage facilitating germination and, therefore, conferring major evolutionary advantages. The seed epidermal mucilage secretory cells (MSCs) undergo numerous tightly controlled changes of their extracellular matrixes (ECMs) throughout seed development. Recently, major progress based on the model species Arabidopsis thaliana was published, including the identification of 54 genes necessary for mucilage synthesis and release. Here, we review these genes that constitute the so-called ‘MSC toolbox’, within which transcription factors and proteins related to polysaccharide production, secretion, modification, and stabilization are the most abundant and belong to complex regulatory networks. We also discuss how seed coat ‘omics data-mining, comparative genomics, and operon-like gene cluster studies will provide means to identify new members of the MSC toolbox.

  
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Current understanding of grapevine defense mechanisms against the biotrophic fungus (Erysiphe necator), the causal agent of powdery mildew disease

Current understanding of grapevine defense mechanisms against the biotrophic fungus (Erysiphe necator), the causal agent of powdery mildew disease | PlantBioInnovation | Scoop.it
Horticulture Research, Published online: 20 May 2015; | doi:10.1038/hortres.2015.20
Biswapriya Biswavas Misra's insight:

The most economically important disease of cultivated grapevines worldwide is powdery mildew (PM) caused by the ascomycete fungus Erysiphe necator. The majority of grapevine cultivars used for wine, table grape, and dried fruit production are derived from the Eurasian grape species Vitis vinifera because of its superior aroma and flavor characteristics. However, this species has little genetic resistance against E. necator meaning that grape production is highly dependent on the frequent use of fungicides. The integration of effective genetic resistance into cultivated grapevines would lead to significant financial and environmental benefits and represents a major challenge for viticultural industries and researchers worldwide. This review will outline the strategies being used to increase our understanding of the molecular basis of V. viniferasusceptibility to this fungal pathogen. It will summarize our current knowledge of different resistance loci/genes that have evolved in wild grapevine species to restrict PM infection and assess the potential application of these defense genes in the generation of PM-resistant grapevine germplasm. Finally, it addresses future research priorities which will be important in the rapid identification, evaluation, and deployment of new PM resistance genes which are capable of conferring effective and durable resistance in the vineyard.

 
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Pathogen-secreted proteases activate a novel plant immune pathway

Pathogen-secreted proteases activate a novel plant immune pathway | PlantBioInnovation | Scoop.it
Mitogen-activated protein kinase (MAPK) cascades play central roles in innate immune signalling networks in plants and animals. In plants, however, the molecular mechanisms of how signal perception is transduced to MAPK activation remain elusive. Here we report that pathogen-secreted proteases activate a previously unknown signalling pathway in Arabidopsis thaliana involving the G[agr], G[bgr], and G[ggr] subunits of heterotrimeric G-protein complexes, which function upstream of an MAPK cascade. In this pathway, receptor for activated C kinase 1 (RACK1) functions as a novel scaffold that binds to the G[bgr] subunit as well as to all three tiers of the MAPK cascade, thereby linking upstream G-protein signalling to downstream activation of an MAPK cascade. The protease-G-protein-RACK1-MAPK cascade modules identified in these studies are distinct from previously described plant immune signalling pathways such as that elicited by bacterial flagellin, in which G proteins function downstream of or in parallel to an MAPK cascade without the involvement of the RACK1 scaffolding protein. The discovery of the new protease-mediated immune signalling pathway described here was facilitated by the use of the broad host range, opportunistic bacterial pathogen Pseudomonas aeruginosa. The ability of P. aeruginosa to infect both plants and animals makes it an excellent model to identify novel immunoregulatory strategies that account for its niche adaptation to diverse host tissues and immune systems.
Biswapriya Biswavas Misra's insight:

Mitogen-activated protein kinase (MAPK) cascades play central roles in innate immune signalling networks in plants and animals1, 2. In plants, however, the molecular mechanisms of how signal perception is transduced to MAPK activation remain elusive1. Here we report that pathogen-secreted proteases activate a previously unknown signalling pathway in Arabidopsis thaliana involving the Gα, Gβ, and Gγ subunits of heterotrimeric G-protein complexes, which function upstream of an MAPK cascade. In this pathway, receptor for activated C kinase 1 (RACK1) functions as a novel scaffold that binds to the Gβ subunit as well as to all three tiers of the MAPK cascade, thereby linking upstream G-protein signalling to downstream activation of an MAPK cascade. The protease–G-protein–RACK1–MAPK cascade modules identified in these studies are distinct from previously described plant immune signalling pathways such as that elicited by bacterial flagellin, in which G proteins function downstream of or in parallel to an MAPK cascade without the involvement of the RACK1 scaffolding protein. The discovery of the new protease-mediated immune signalling pathway described here was facilitated by the use of the broad host range, opportunistic bacterial pathogen Pseudomonas aeruginosa. The ability of P. aeruginosa to infect both plants and animals makes it an excellent model to identify novel immunoregulatory strategies that account for its niche adaptation to diverse host tissues and immune systems.

  
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ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data | PlantBioInnovation | Scoop.it
Author Summary Diploid organisms, such as human beings, have two “copies” of each chromosome, whereas polyploid organisms have multiple “copies” (we use quotes to stress that the “copies” are not identical). A key difference between diploid and polyploid organisms is that the “copies” tend to be less similar in polyploid organisms. This difference leads to important differences in the process of de novo genome assembly from short fragments of DNA. In particular, when assembling polyploid or
Biswapriya Biswavas Misra's insight:

As a result of improvements in genome assembly algorithms and the ever decreasing costs of high-throughput sequencing technologies, new high quality draft genome sequences are published at a striking pace. With well-established methodologies, larger and more complex genomes are being tackled, including polyploid plant genomes. Given the similarity between multiple copies of a basic genome in polyploid individuals, assembly of such data usually results in collapsed contigs that represent a variable number of homoeologous genomic regions. Unfortunately, such collapse is often not ideal, as keeping contigs separate can lead both to improved assembly and also insights about how haplotypes influence phenotype. Here, we describe a first step in avoiding inappropriate collapse during assembly. In particular, we describe ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, we report findings regarding errors in sequencing. The method can be used for whole genome shotgun (WGS) sequencing data. We also show applicability of the method for variant calling and allele dosage estimation. Results for simulated and real datasets are discussed and provide evidence that ConPADE performs well as long as enough sequencing coverage is available, or the true contig ploidy is low. We show that ConPADE may also be used for related applications, such as the identification of duplicated genes in fragmented assemblies, although refinements are needed.

 
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Fungal artificial chromosomes for mining of the fungal secondary metabolome

With thousands of fungal genomes being sequenced, each genome containing up to 70 secondary metabolite (SM) clusters 30–80 kb in size, breakthrough techniques are needed to characterize this SM wealth.
Biswapriya Biswavas Misra's insight:

AbstractBackground

With thousands of fungal genomes being sequenced, each genome containing up to 70 secondary metabolite (SM) clusters 30–80 kb in size, breakthrough techniques are needed to characterize this SM wealth.

Results

Here we describe a novel system-level methodology for unbiased cloning of intact large SM clusters from a single fungal genome for one-step transformation and expression in a model host. All 56 intact SM clusters from Aspergillus terreus were individually captured in self-replicating fungal artificial chromosomes (FACs) containing both the E. coli F replicon and an Aspergillusautonomously replicating sequence (AMA1). Candidate FACs were successfully shuttled between E. coli and the heterologous expression host A. nidulans. As proof-of-concept, an A. nidulans FAC strain was characterized in a novel liquid chromatography-high resolution mass spectrometry (LC-HRMS) and data analysis pipeline, leading to the discovery of the A. terreus astechrome biosynthetic machinery.

Conclusion

The method we present can be used to capture the entire set of intact SM gene clusters and/or pathways from fungal species for heterologous expression in A. nidulans and natural product discovery.

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Tomato (Solanum lycopersicum L.) SlIPT3 and SlIPT4 isopentenyltransferases mediate salt stress response in tomato

Tomato (Solanum lycopersicum L.) SlIPT3 and SlIPT4 isopentenyltransferases mediate salt stress response in tomato | PlantBioInnovation | Scoop.it
Background

Cytokinins (CKs) are involved in response to various environmental cues, including salinity. It has been previously reported that enhancing CK contents improved salt stress tolerance in tomato. However, the underlying mechanisms of CK metabolism and signaling under salt stress conditions remain to be deciphered.
Results

Two tomato isopentenyltransferases, SlIPT3 and SlIPT4, were characterized in tomato and Arabidopsis. Both proteins displayed isopentenyltransferase (IPT) activity in vitro, while their encoding genes exhibited different spatio-temporal expression patterns during tomato plant development. SlIPT3 and SlIPT4 were affected by the endogenous CK status, tightly connected with CKs feedback regulation, as revealed by hormonal treatements. In response to salt stress, SlIPT3 and SlIPT4 were strongly repressed in tomato roots, and differently affected in young and old leaves. SlIPT3 overexpression in tomato resulted in high accumulation of different CK metabolites, following modifications of CK biosynthesis-, signaling- and degradation-gene expression. In addition, 35S::SlIPT3 tomato plants displayed improved tolerance to salinity consecutive to photosynthetic pigments and K+/Na+ ratio retention. Involvement of SlIPT3 and SlIPT4 in salt stress response was also observed in Arabidopsis ipt3 knock-out complemented plants, through maintenance of CK homeostasis.
Conclusions

SlIPT3 and SlIPT4 are functional IPTs encoded by differently expressed genes, distinctively taking part in the salinity response. The substantial participation of SlIPT3 in CK metabolism during salt stress has been determined in 35S::SlIPT3 tomato transformants, where enhancement of CKs accumulation significantly improved plant tolerance to salinity, underlining the importance of this phytohormone in stress response.

Via Christophe Jacquet
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Nitrogenase diversity and activity in the gastrointestinal tract of the wood-eating catfish Panaque nigrolineatus

The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
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The Amazonian catfish, Panaque nigrolineatus, consume large amounts of wood in their diets. The nitrogen-fixing community within the gastrointestinal (GI) tract of these catfish was found to include nifH phylotypes that are closely related to Clostridium sp., Alpha and Gammaproteobacteria, and sequences associated with GI tracts of lower termites. Fish fed a diet of sterilized palm wood were found to contain nifH messenger RNA within their GI tracts, displaying high sequence similarity to the nitrogen-fixing Bradyrhizobium group. Nitrogenase activity, measured by acetylene reduction assays, could be detected in freshly dissected GI tract material and also from anaerobic enrichment cultures propagated in nitrogen-free enrichment media; nifH sequences retrieved from these cultures were dominated by Klebsiella- and Clostridium-like sequences. Microscopic examination using catalyzed reporter deposition-enhanced immunofluorescence revealed high densities of nitrogenase-containing cells colonizing the woody digesta within the GI tract, as well as cells residing within the intestinal mucous layer. Our findings suggest that the P. nigrolineatus GI tract provides a suitable environment for nitrogen fixation that may facilitate production of reduced nitrogen by the resident microbial population under nitrogen limiting conditions. Whether this community is providing reduced nitrogen to the host in an active or passive manner and whether it is present in a permanent or transient relationship remains to be determined. The intake of a cellulose rich diet and the presence of a suitable environment for nitrogen fixation suggest that the GI tract microbial community may allow a unique trophic niche for P. nigrolineatus among fish.

 
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Regulation of the Arabidopsis CBF regulon by a complex low-temperature regulatory network

Regulation of the Arabidopsis CBF regulon by a complex low-temperature regulatory network | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Exposure of Arabidopsis thaliana plants to low non-freezing temperatures results in an increase in freezing tolerance that involves action of the C-repeat binding factor (CBF) regulatory pathway. CBF1, CBF2 and CBF3, which are rapidly induced in response to low temperature, encode closely related AP2/ERF DNA-binding proteins that recognize the C-repeat (CRT)/dehydration-responsive element (DRE) DNA regulatory element present in the promoters of CBF-regulated genes. The CBF transcription factors alter the expression of more than 100 genes, known as the CBF regulon, which contribute to an increase in freezing tolerance. In this study, we investigated the extent to which cold induction of the CBF regulon is regulated by transcription factors other than CBF1, CBF2 and CBF3, and whether freezing tolerance is dependent on a functional CBF–CRT/DRE regulatory module. To address these issues we generated transgenic lines that constitutively overexpressed a truncated version of CBF2 that had dominant negative effects on the function of the CBF–CRT/DRE regulatory module, and 11 transcription factors encoded by genes that were rapidly cold-induced in parallel with the ‘first-wave’ CBF genes, and determined the effects that overexpressing these proteins had on global gene expression and freezing tolerance. Our results indicate that cold regulation of the CBF regulon involves extensive co-regulation by other first-wave transcription factors; that the low-temperature regulatory network beyond the CBF pathway is complex and highly interconnected; and that the increase in freezing tolerance that occurs with cold acclimation is only partially dependent on the CBF–CRT/DRE regulatory module.

 
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Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection

Phytophthora effector targets a novel component of small RNA pathway in plants to promote infection | PlantBioInnovation | Scoop.it
Phytophthora is a major threat to agriculture. However, the molecular interaction of these severe pathogens with plant hosts is poorly understood. Here, we report that the Phytophthora Suppressor of RNA Silencing 1 (PSR1) effectively promotes infection in Arabidopsis thaliana by directly targeting an essential protein containing a aspartate–glutamate–alanine–histidine-box RNA helicase domain. This PSR1-Interacting Protein 1 (PINP1) is required for the accumulation of distinct classes of endogenous small RNAs and acts as a positive regulator of plant immunity. Silencing of PINP1 impaired the assembly of microRNA-processing complexes in the nucleus, leading to defects in development and immunity. This study revealed a conserved RNA helicase as a regulator of RNA silencing and provides mechanistic insight into Phytophthora pathogenesis.
Biswapriya Biswavas Misra's insight:

Phytophthora is a major threat to agriculture. However, the molecular interaction of these severe pathogens with plant hosts is poorly understood. Here, we report that the Phytophthora Suppressor of RNA Silencing 1 (PSR1) effectively promotes infection in Arabidopsis thaliana by directly targeting an essential protein containing a aspartate–glutamate–alanine–histidine-box RNA helicase domain. This PSR1-Interacting Protein 1 (PINP1) is required for the accumulation of distinct classes of endogenous small RNAs and acts as a positive regulator of plant immunity. Silencing of PINP1impaired the assembly of microRNA-processing complexes in the nucleus, leading to defects in development and immunity. This study revealed a conserved RNA helicase as a regulator of RNA silencing and provides mechanistic insight into Phytophthora pathogenesis.

 
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Antagonistic regulation of growth and immunity by the Arabidopsis basic helix-loop-helix transcription factor homolog of brassinosteroid enhanced e...

Plants need to finely balance resources allocated to growth and immunity to achieve optimal fitness. A tradeoff between pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and brassinosteroid (BR)-mediated growth was recently reported, but more information about the underlying mechanisms is needed. Here, we identify the basic helix-loop-helix (bHLH) transcription factor homolog of brassinosteroid enhanced expression2 interacting with IBH1 (HBI1) as a negative regulator of PTI signaling in Arabidopsis (Arabidopsis thaliana). HBI1 expression is down-regulated in response to different PAMPs. HBI1 overexpression leads to reduced PAMP-triggered responses. This inhibition correlates with reduced steady-state expression of immune marker genes, leading to increased susceptibility to the bacterium Pseudomonas syringae. Overexpression of the HBI1-related bHLHs brassinosteroid enhanced expression2 (BEE2) and cryptochrome-interacting bHLH (CIB1) partially inhibits immunity, indicating that BEE2 and CIB1 may act redundantly with HBI1. In contrast to its expression pattern upon PAMP treatment, HBI1 expression is enhanced by BR treatment. Also, HBI1-overexpressing plants are hyperresponsive to BR and more resistant to the BR biosynthetic inhibitor brassinazole. HBI1 is nucleus localized, and a mutation in a conserved leucine residue within the first helix of the protein interaction domain impairs its function in BR signaling. Interestingly, HBI1 interacts with several inhibitory atypical bHLHs, which likely keep HBI1 under negative control. Hence, HBI1 is a positive regulator of BR-triggered responses, and the negative effect of PTI is likely due to the antagonism between BR and PTI signaling. This study identifies a novel component involved in the complex tradeoff between innate immunity and BR-regulated growth.
Biswapriya Biswavas Misra's insight:

Plants need to finely balance resources allocated to growth and immunity to achieve optimal fitness. A tradeoff between pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and brassinosteroid (BR)-mediated growth was recently reported, but more information about the underlying mechanisms is needed. Here, we identify the basic helix-loop-helix (bHLH) transcription factor homolog of brassinosteroid enhanced expression2 interacting with IBH1 (HBI1) as a negative regulator of PTI signaling in Arabidopsis (Arabidopsis thaliana). HBI1 expression is down-regulated in response to different PAMPs. HBI1 overexpression leads to reduced PAMP-triggered responses. This inhibition correlates with reduced steady-state expression of immune marker genes, leading to increased susceptibility to the bacterium Pseudomonas syringae. Overexpression of the HBI1-related bHLHs brassinosteroid enhanced expression2 (BEE2) and cryptochrome-interacting bHLH (CIB1) partially inhibits immunity, indicating that BEE2 and CIB1 may act redundantly with HBI1. In contrast to its expression pattern upon PAMP treatment, HBI1 expression is enhanced by BR treatment. Also, HBI1-overexpressing plants are hyperresponsive to BR and more resistant to the BR biosynthetic inhibitor brassinazole. HBI1 is nucleus localized, and a mutation in a conserved leucine residue within the first helix of the protein interaction domain impairs its function in BR signaling. Interestingly, HBI1 interacts with several inhibitory atypical bHLHs, which likely keep HBI1 under negative control. Hence, HBI1 is a positive regulator of BR-triggered responses, and the negative effect of PTI is likely due to the antagonism between BR and PTI signaling. This study identifies a novel component involved in the complex tradeoff between innate immunity and BR-regulated growth.

  
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A Tale of Two Hyper-diversities: Diversification dynamics of the two largest families of lichenized fungi

A Tale of Two Hyper-diversities: Diversification dynamics of the two largest families of lichenized fungi | PlantBioInnovation | Scoop.it
Renewed interests in macroevolutionary dynamics have led to the proliferation of studies on diversification processes in large taxonomic groups, such as angiosperms, mammals, and birds. However, such a study has yet to be conducted in lichenized fungi – an extremely successful and diverse group of fungi. Analysing the most comprehensive time-calibrated phylogenies with a new analytical method, we illustrated drastically different diversification dynamics between two hyper-diverse families of lichenized fungi, Graphidaceae and Parmeliaceae, which represent more than a fourth of the total species diversity of lichenized fungi. Despite adopting a similar nutrition mode and having a similar number of species, Graphidaceae exhibited a lower speciation rate, while Parmeliaceae showed a sharp increase in speciation rate that corresponded with the aridification during the Oligocene-Miocene transition, suggesting their adaptive radiation into a novel arid habitat.
Biswapriya Biswavas Misra's insight:

Renewed interests in macroevolutionary dynamics have led to the proliferation of studies on diversification processes in large taxonomic groups, such as angiosperms, mammals, and birds. However, such a study has yet to be conducted in lichenized fungi – an extremely successful and diverse group of fungi. Analysing the most comprehensive time-calibrated phylogenies with a new analytical method, we illustrated drastically different diversification dynamics between two hyper-diverse families of lichenized fungi, Graphidaceae and Parmeliaceae, which represent more than a fourth of the total species diversity of lichenized fungi. Despite adopting a similar nutrition mode and having a similar number of species, Graphidaceae exhibited a lower speciation rate, while Parmeliaceae showed a sharp increase in speciation rate that corresponded with the aridification during the Oligocene-Miocene transition, suggesting their adaptive radiation into a novel arid habitat.

  
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Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms | PlantBioInnovation | Scoop.it
The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
Biswapriya Biswavas Misra's insight:

Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams.

 
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Hippocampal memory enhancing activity of pine needle extract against scopolamine-induced amnesia in a mouse model

Hippocampal memory enhancing activity of pine needle extract against scopolamine-induced amnesia in a mouse model | PlantBioInnovation | Scoop.it
We evaluated the neuropharmacological effects of 30% ethanolic pine needle extract (PNE) on memory impairment caused by scopolamine injection in mice hippocampus. Mice were orally pretreated with PNE (25, 50, and 100 mg/kg) or tacrine (10 mg/kg) for 7 days, and scopolamine (2 mg/kg) was injected intraperitoneally, 30 min before the Morris water maze task on first day. To evaluate memory function, the Morris water maze task was performed for 5 days consecutively. Scopolamine increased the escape latency and cumulative path-length but decreases the time spent in target quadrant, which were ameliorated by pretreatment with PNE. Oxidant-antioxidant balance, acetylcholinesterase activity, neurogenesis and their connecting pathway were abnormally altered by scopolamine in hippocampus and/or sera, while those alterations were recovered by pretreatment with PNE. As lipid peroxidation, 4HNE-positive stained cells were ameliorated in hippocampus pretreated with PNE. Pretreatment with PNE increased the proliferating cells and immature neurons against hippocampal neurogenesis suppressed by scopolamine, which was confirmed by ki67- and DCX-positive stained cells. The expression of brain-derived neurotrophic factor (BDNF) and phosphorylated cAMP response element-binding protein (pCREB) in both protein and gene were facilitated by PNE pretreatment. These findings suggest that PNE could be a potent neuropharmacological drug against amnesia, and its possible mechanism might be modulating cholinergic activity via CREB-BDNF pathway.
Biswapriya Biswavas Misra's insight:

We evaluated the neuropharmacological effects of 30% ethanolic pine needle extract (PNE) on memory impairment caused by scopolamine injection in mice hippocampus. Mice were orally pretreated with PNE (25, 50, and 100 mg/kg) or tacrine (10 mg/kg) for 7 days, and scopolamine (2 mg/kg) was injected intraperitoneally, 30 min before the Morris water maze task on first day. To evaluate memory function, the Morris water maze task was performed for 5 days consecutively. Scopolamine increased the escape latency and cumulative path-length but decreases the time spent in target quadrant, which were ameliorated by pretreatment with PNE. Oxidant-antioxidant balance, acetylcholinesterase activity, neurogenesis and their connecting pathway were abnormally altered by scopolamine in hippocampus and/or sera, while those alterations were recovered by pretreatment with PNE. As lipid peroxidation, 4HNE-positive stained cells were ameliorated in hippocampus pretreated with PNE. Pretreatment with PNE increased the proliferating cells and immature neurons against hippocampal neurogenesis suppressed by scopolamine, which was confirmed by ki67- and DCX-positive stained cells. The expression of brain-derived neurotrophic factor (BDNF) and phosphorylated cAMP response element-binding protein (pCREB) in both protein and gene were facilitated by PNE pretreatment. These findings suggest that PNE could be a potent neuropharmacological drug against amnesia, and its possible mechanism might be modulating cholinergic activity via CREB-BDNF pathway.

  
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A terpenoid phytoalexin plays a role in basal defense of Nicotiana benthamiana against Potato virus X

A terpenoid phytoalexin plays a role in basal defense of Nicotiana benthamiana against Potato virus X | PlantBioInnovation | Scoop.it
Terpenoid phytoalexins function as defense compound against a broad spectrum of pathogens and pests in the plant kingdom. However, the role of phytoalexin in antiviral defense is still elusive. In this study, we identified the biosynthesis pathway of a sesquiterpenoid phytoalexin, capsidiol 3-acetate as an antiviral response against RNA virus Potato Virus X (PVX) in Nicotiana benthamiana. NbTPS1 and NbEAH genes were found strongly induced by PVX-infection. Enzymatic activity and genetic evidence indicated that both genes were involved in the PVX-induced biosynthesis of capsidiol 3-acetate. NbTPS1- or NbEAH-silenced plant was more susceptible to PVX. The accumulation of capsidiol 3-acetate in PVX-infected plant was partially regulated by jasmonic acid signaling receptor COI1. These findings provide an insight into a novel mechanism of how plant uses the basal arsenal machinery to mount a fight against virus attack even in susceptible species.
Biswapriya Biswavas Misra's insight:

Terpenoid phytoalexins function as defense compound against a broad spectrum of pathogens and pests in the plant kingdom. However, the role of phytoalexin in antiviral defense is still elusive. In this study, we identified the biosynthesis pathway of a sesquiterpenoid phytoalexin, capsidiol 3-acetate as an antiviral response against RNA virus Potato Virus X (PVX) in Nicotiana benthamiana. NbTPS1 and NbEAH genes were found strongly induced by PVX-infection. Enzymatic activity and genetic evidence indicated that both genes were involved in the PVX-induced biosynthesis of capsidiol 3-acetate. NbTPS1- or NbEAH-silenced plant was more susceptible to PVX. The accumulation of capsidiol 3-acetate in PVX-infected plant was partially regulated by jasmonic acid signaling receptor COI1. These findings provide an insight into a novel mechanism of how plant uses the basal arsenal machinery to mount a fight against virus attack even in susceptible species.

  
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Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats

Transcriptome sequencing of three Ranunculus species (Ranunculaceae) reveals candidate genes in adaptation from terrestrial to aquatic habitats | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Adaptation to aquatic habitats is a formidable challenge for terrestrial angiosperms that has long intrigued scientists. As part of a suite of work to explore the molecular mechanism of adaptation to aquatic habitats, we here sequenced the transcriptome of the submerged aquatic plant Ranunculus bungei, and two terrestrial relatives R. cantoniensis and R. brotherusii, followed by comparative evolutionary analyses to determine candidate genes for adaption to aquatic habitats. We obtained 126,037, 140,218 and 114,753 contigs for R. bungei, R. cantoniensis and R. brotherusiirespectively. Bidirectional Best Hit method and OrthoMCL method identified 11,362 and 8,174 1:1:1 orthologous genes (one ortholog is represented in each of the three species) respectively. Non-synonymous/synonymous (dN/dS) analyses were performed with a maximum likelihood method and an approximate method for the three species-pairs. In total, 14 genes of R. bungeipotentially involved in the adaptive transition from terrestrial to aquatic habitats were identified. Some of the homologs to these genes in model plants are involved in vacuole protein formation, regulating ‘water transport process’ and ‘microtubule cytoskeleton organization’. Our study opens the door to understand the molecular mechanism of plant adaptation from terrestrial to aquatic habitats.

  
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Genomic features separating ten strains of Neorhizobium galegae with different symbiotic phenotypes

The symbiotic phenotype of Neorhizobium galegae, with strains specifically fixing nitrogen with either Galega orientalis or G. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. The genomic differences between representative strains of the two symbiovars are, however, relatively small. This introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of the species. In this study, we produced draft genomes of eight strains of N. galegae having different symbiotic phenotypes, both with regard to host specificity and nitrogen fixation efficiency. These genomes were analysed together with the previously published complete genomes of N. galegae strains HAMBI 540T and HAMBI 1141.
Biswapriya Biswavas Misra's insight:
AbstractBackground

The symbiotic phenotype of Neorhizobium galegae, with strains specifically fixing nitrogen with either Galega orientalis or G. officinalis, has made it a target in research on determinants of host specificity in nitrogen fixation. The genomic differences between representative strains of the two symbiovars are, however, relatively small. This introduced a need for a dataset representing a larger bacterial population in order to make better conclusions on characteristics typical for a subset of the species. In this study, we produced draft genomes of eight strains of N. galegaehaving different symbiotic phenotypes, both with regard to host specificity and nitrogen fixation efficiency. These genomes were analysed together with the previously published complete genomes of N. galegae strains HAMBI 540T and HAMBI 1141.

Results

The results showed that the presence of an additional rpoN sigma factor gene in the symbiosis gene region is a characteristic specific to symbiovar orientalis, required for nitrogen fixation. Also the nifQ gene was shown to be crucial for functional symbiosis in both symbiovars. Genome-wide analyses identified additional genes characteristic of strains of the same symbiovar and of strains having similar plant growth promoting properties on Galega orientalis. Many of these genes are involved in transcriptional regulation or in metabolic functions.

Conclusions

The results of this study confirm that the only symbiosis-related gene that is present in one symbiovar of N. galegae but not in the other is an rpoN gene. The specific function of this gene remains to be determined, however. New genes that were identified as specific for strains of one symbiovar may be involved in determining host specificity, while others are defined as potential determinant genes for differences in efficiency of nitrogen fixation

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The plasticity of cyanobacterial metabolism supports direct CO2 conversion to ethylene

The cyanobacterial tricarboxylic acid (TCA) cycle functions in both in biosynthesis and energy generation. However, it has until recently been generally considered to be incomplete1,2 with limited flux3,4, and few attempts have been made to draw carbon from the cycle for biotechnological purposes. We demonstrated that ethylene can be sustainably and efficiently produced from the TCA cycle of the recombinant cyanobacterium Synechocystis 6803 expressing the Pseudomonas ethylene-forming enzyme (Efe)5. A new strain with a modified ribosome binding site upstream of the efe gene diverts 10% of fixed carbon to ethylene and shows increased photosynthetic activities. The highest specific ethylene production rate reached 718 ± 19 μl l–1 h–1per A730 nm. Experimental and computational analyses based on kinetic 13C-isotope tracer and liquid chromatography coupled with mass spectrometry (LC–MS) demonstrated that the TCA metabolism is activated by the ethylene forming reaction, resulting in a predominantly cyclic architecture. The outcome significantly enhanced flux through the remodelled TCA cycle (37% of total fixed carbon) compared with a complete, but bifurcated and low-flux (13% of total fixed carbon) TCA cycle in the wild type. Global carbon flux is redirected towards the engineered ethylene pathway. The remarkable metabolic network plasticity of this cyanobacterium is manifested by the enhancement of photosynthetic activity and redistribution of carbon flux, enabling efficient ethylene production from the TCA cycle.

  Nature Plants, Published online: 27 April 2015; | doi:10.1038/nplants.2015.53
Biswapriya Biswavas Misra's insight:

The cyanobacterial tricarboxylic acid (TCA) cycle functions in both in biosynthesis and energy generation. However, it has until recently been generally considered to be incomplete1,2 with limited flux3,4, and few attempts have been made to draw carbon from the cycle for biotechnological purposes. We demonstrated that ethylene can be sustainably and efficiently produced from the TCA cycle of the recombinant cyanobacterium Synechocystis 6803 expressing the Pseudomonas ethylene-forming enzyme (Efe)5. A new strain with a modified ribosome binding site upstream of the efe gene diverts 10% of fixed carbon to ethylene and shows increased photosynthetic activities. The highest specific ethylene production rate reached 718 ± 19 μl l–1 h–1per A730 nm. Experimental and computational analyses based on kinetic 13C-isotope tracer and liquid chromatography coupled with mass spectrometry (LC–MS) demonstrated that the TCA metabolism is activated by the ethylene forming reaction, resulting in a predominantly cyclic architecture. The outcome significantly enhanced flux through the remodelled TCA cycle (37% of total fixed carbon) compared with a complete, but bifurcated and low-flux (13% of total fixed carbon) TCA cycle in the wild type. Global carbon flux is redirected towards the engineered ethylene pathway. The remarkable metabolic network plasticity of this cyanobacterium is manifested by the enhancement of photosynthetic activity and redistribution of carbon flux, enabling efficient ethylene production from the TCA cycle.

  
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The dominant negative ARM domain uncovers multiple functions of PUB13 in Arabidopsis immunity, flowering, and senescence

The dominant negative ARM domain uncovers multiple functions of PUB13 in Arabidopsis immunity, flowering, and senescence | PlantBioInnovation | Scoop.it
Regulating the intensity and duration of immune responses is crucial to combat infections without deleterious side effects. Arabidopsis FLS2, the receptor for bacterial flagellin, activates immune signalling by association with its partner BAK1. Upon flagellin (flg22) perception, the plant U-box E3 ubiquitin ligases PUB12 and PUB13 complex with FLS2 in a BAK1-dependent manner, and ubiquitinate FLS2 for protein degradation, thereby down-regulating flagellin signalling. Domain deletion analysis indicates that the ARM domain of PUB13 interacts with the FLS2–BAK1 complex and is phosphorylated by BAK1. Overexpression of the PUB13 ARM domain alone inhibits flg22-induced FLS2–PUB13 association and PUB12/13-mediated FLS2 ubiquitination and degradation in Arabidopsis, suggesting that ectopic expression of the ARM domain in planta generates a dominant negative effect via blocking the ubiquitination activity. Similar to the pub12pub13 double mutant, transgenic plants expressing the PUB13 ARM domain display enhanced immune responses compared with wild-type plants. Moreover, PUB13ARM transgenic plants and the pub12pub13 mutant are more sensitive to stress-induced leaf senescence accompanied by elevated expression of stress-induced senescence marker genes. The resemblance between PUB13ARM transgenic plants and the pub12pub13 mutant provides genetic evidence that ectopic expression of the PUB ARM domain serves as an alternative approach to dissect the overlapping functions of closely related PUB genes.

Via Christophe Jacquet
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DNA damage and genetic methylation changes caused by CD in Arabidopsis thaliana seedlings

DNA damage and genetic methylation changes caused by CD in Arabidopsis thaliana seedlings | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

Amplified Fragment Length Polymorphism (AFLP) and Methylation Sensitive Amplification Polymorphism (MASP) techniques are sensitive to DNA damage and genetic methylation respectively. In present experiment, Arabidopsis thaliana which cultured by 0 (CK), 0.5, 1.5, 5.0 mg/L Cd2+ for 16d was chosen to analyze the DNA damage and methylation changes caused by cadmium (Cd) using these two methods. The DNA was amplified by 14 AFLP primer-pairs and 13 MSAP primer combinations. In AFLP experiment, 62 polymorphic sites were found in the patterns of 11 primer combinations and a total of 1116 fragments were gotten in these patterns. There were no polymorphic bands in the remaining three pairs. The proportion of polymorphic sites in 0.5 mg/L Cd2+ and 5.0 mg/L Cd2+ treatments were significantly different. Seven polymorphic fragments were then separated and sequenced successfully, which included 6 nucleobases substitution and 1 nucleobase deletion. Similarly, in MSAP experiment, MSAP% and the number of Demethylated type bands were unchanged after Cd treated, but the number of Methylated type bands was increased significantly in 5.0 mg/L Cd2+ treatment, which may be associated with the AFLP results. The polymorphic bands were also sequenced and found the functions of their homologous genes. The DNA damage and methylation changes may be the primary cause of some pathology changes in plants caused by Cd. This article is protected by copyright. All rights reserved

 
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Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
Biswapriya Biswavas Misra's insight:

We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant–microbe interactions/rhizosphere microbiota/selection.

 
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PKS5/CIPK11, a SnRK3-Type Protein Kinase, is Important for ABA Responses in Arabidopsis through Phosphorylation of ABI5.

PKS5/CIPK11, a SnRK3-Type Protein Kinase, is Important for ABA Responses in Arabidopsis through Phosphorylation of ABI5. | PlantBioInnovation | Scoop.it
Plant Physiol. 2015 Apr 9. pii: pp.114.255455. [Epub ahead of print]
Biswapriya Biswavas Misra's insight:

ABA (abscisic acid) plays an essential role in seed germination. In this study, we demonstrate that one SnRK3 (SNF1-Related Protein Kinase subgroup 3)-type protein kinase, PKS5 (SOS2-like protein kinase 5, also known as CIPK11 or SnRK3.22), is involved in ABA signal transduction via phosphorylation of an interacting protein, ABI5 (ABA-INSENSITIVE 5). We found that pks5-3 and pks5-4, two previously identified PKS5 super-active kinase mutants with point mutations in the PKS5 FISL/NAF motif and the kinase domain, respectively, are hypersensitive to ABA during seed germination. PKS5 was found to interact with ABI5 in yeast, and this interaction was further confirmed in planta using bimolecular fluorescence complementation. Genetic studies revealed that ABI5 is epistatic to PKS5. PKS5 phosphorylates a Ser residue at position 42 in ABI5 and regulates ABA-responsive gene expression. This phosphorylation was induced by ABA in vivo and transactivated ABI5. Expression of ABI5 in which Se42 was mutated to Ala, could not fully rescue the ABA-insensitive phenotypes of the abi5-8 and pks5-4abi5-8 mutants. In contrast, mutating Ser42 to Asp rescued the ABA insensitivity of these mutants. These data demonstrate that PKS5-mediated phosphorylation of ABI5 at Ser42 is critical for ABA regulation of seed germination and gene expression in Arabidopsis.

 
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A World Beyond Arabidopsis: Updates on Small RNAs in Plant Development

A World Beyond Arabidopsis: Updates on Small RNAs in Plant Development | PlantBioInnovation | Scoop.it
Biswapriya Biswavas Misra's insight:

A wide range of developmental processes and stress responses involve negative regulation of coding genes by small RNAs, which are present in all plant transcriptomes (reviewed inChen, 2009). Several types of small RNAs are distinguishable based on their modes of biogenesis and functions (reviewed in Axtell, 2013). All arise by the action of Dicer-like endonucleases on double-stranded regions of RNA; microRNAs (miRNAs) are generated from a single-stranded mRNA that has formed a hairpin structure, whereas short interfering RNAs (siRNAs) are formed from duplexes of two strands of RNA, usually formed by the activity of an RNA-dependent RNA polymerase. Work in Arabidopsis thaliana has greatly advanced our understanding of small RNAs in plants. However, many small RNA regulatory target pairs are not conserved between species, and it is becoming clear that there can be large differences between species in terms of the types and functions of small RNAs. New reports from Thompson et al. (2014) and Arikit et al. (2014) herald exciting times for research on small RNAs in species beyond Arabidopsis.

 
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