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Cotton MON 88701 was developed through Agrobacterium tumefaciens‐mediated transformation to express the dicamba mono‐oxygenase (DMO) protein, conferring tolerance to dicamba, and the phosphinothricin N‐acetyltransferase PAT protein, conferring tolerance to glufosinate ammonium‐based herbicides. The molecular characterisation data and bioinformatics analyses did not identify issues requiring further assessment for food/feed safety. The agronomic and phenotypic characteristics tested revealed no relevant differences between cotton MON 88701 and its conventional counterpart. Since complete compositional results were reported for only three sites, the EFSA Panel on Genetically Modified Organisms (GMO Panel) is not in the position to complete the assessment of the compositional analysis. Moreover, as no 28‐day toxicity study in rodents on the MON 88701 DMO protein was provided, the GMO Panel is not in the position to complete the safety assessment of this protein in cotton MON 88701. Consequently, the GMO Panel cannot complete the toxicological, allergenicity and nutritional assessment of food/feed derived from cotton MON 88701. The safety assessment identified no concerns regarding the potential toxicity and allergenicity of the PAT protein newly expressed in cotton MON 88701. Considering the routes of exposure and limited exposure levels, the GMO Panel concludes that cotton MON 88701 would not give rise to safety concerns in the event of accidental release of viable seeds into the environment. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of cotton MON 88701. In conclusion, in the absence of an appropriate comparative assessment and an appropriate assessment of the MON 88701 DMO protein, the GMO Panel is not in a position to complete its food/feed risk assessment of cotton MON 88701. The GMO Panel concludes that the cotton MON 88701 is unlikely to have any adverse effect on the environment in the context of the scope of the application.

The GMO Panel has previously assessed genetically modified (GM) soybean BPS‐CV127‐9. This soybean was found to be as safe and nutritious as its conventional counterpart and commercial soybean varieties with respect to potential effects on human and animal health and the environment in the context of its intended uses. On 16 February 2018, European Commission requested EFSA to analyse new nucleic acid sequencing data and updated bioinformatics data for GM soybean BPS‐CV127‐9 and to indicate whether the previous conclusions of the GMO Panel on safety of GM soybean BPS‐CV127‐9 remain valid. The new sequencing data indicated a two nucleotide difference in the unannotated Arabidopsis genomic DNA sequence downstream of the 3′ untranslated region of the ahasl (also referred to as csr1‐2) gene as compared to the sequencing data originally provided. One of these nucleotide differences reported in the new nucleic acid sequencing data from GM soybean event BPS‐CV127‐9 was shown to be already present in the original plant material used for the risk assessment. However, for the other nucleotide difference reported, no evidence could be provided to differentiate between a sequencing error and point‐mutation. With the exception of bioinformatics analyses, the studies performed for the risk assessment of the single event soybean BPS‐CV127‐9 remain valid. The new sequencing data and the bioinformatics analyses performed on the new sequence did not give rise to safety issues. Therefore, EFSA concludes that the original risk assessment of soybean BPS‐CV127‐9 remains valid.

In the EU novel proteins used in food or feed are assessed for their potential toxic effects in humans and livestock animals. The discovery of clear molecular features linked to the toxicity of a protein may be an important step towards the use of predictive protein toxicity in risk assessment.

The metabolic intermediate trehalose-6-P (T6P) has emerged as a key regulator of plant growth and development, but the underlying mechanisms remain largely elusive. A recent publication reported a new chemical intervention strategy, providing a powerful tool to dissect T6P-mediated metabolic signaling.

The GMO Panel has previously assessed genetically modified (GM) carnation FLO‐40685‐2 and concluded that there is no scientific reason to consider that the import, distribution and retailing in the EU of carnation FLO‐40685‐2 cut flowers for ornamental use will cause any adverse effects on human health or the environment. On 7 November 2017, European Commission requested EFSA to analyse new nucleic acid sequencing data and updated bioinformatics data for carnation FLO‐40685‐2 and to indicate whether the conclusions of the GMO Panel on the previously assessed GM carnation FLO‐40685‐2 remain valid. The new sequencing data indicated an additional three base pairs compared to the sequencing data originally provided: one base pair addition to the polyA tail of each of the two inserted flavonoid 3',5'–hydroxylase elements and one base pair addition to the sequence of one of the two D8 promoters in locus 1. These sequence differences are located outside the coding sequence for the newly expressed proteins and the base pairs described as differences in the new nucleic acid sequencing data for carnation FLO‐40685‐2 were reported to have been already present in the original plant material used for the risk assessment. Thus, with the exception of bioinformatics analyses, the studies performed for the risk assessment of GM carnation FLO‐40685‐2 remain valid. The new sequencing data and the bioinformatics analyses performed on the new sequence did not give rise to safety issues. Therefore, EFSA concludes that the original risk assessment of carnation FLO‐40685‐2 remains valid.

As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel, 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. The European Commission has mandated EFSA to develop a technical note to the applicants on, and checking of, the quality of the methodology, analysis and reporting covering complete sequencing of the insert and flanking regions, insertion site analysis of the GM event, and generational stability and integrity. This Technical Note puts together requirements and recommendations for when DNA sequencing is part of the molecular characterisation of GM plants, in particular for the characterisation of the inserted genetic material at each insertion site and flanking regions, the determination of the copy number of all detectable inserts, and the analysis of the genetic stability of the inserts, when addressed by Sanger sequencing or NGS. This document reflects the current knowledge in scientific‐technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. From 1 October 2018, this Technical Note will replace the JRC guideline of 2016 (updated April 2017) related to the verification and quality assessment of the sequencing of the insert(s) and flanking regions. It does not take into consideration the verification and validation of the detection method which remains under the remit of the JRC.

The GMO Panel has previously assessed genetically modified (GM) soybean 305423 as a single event and as part of a two‐event stack, 305423 × 40‐3‐2. These soybean events were found to be as safe as their conventional counterparts and other appropriate comparators with respect to potential effects on human and animal health and the environment. On 23 February 2017, European Commission requested EFSA to analyse new nucleic acid sequencing data and updated bioinformatics data for soybean event 305423 and to indicate whether the previous conclusions of the GMO Panel on the previously assessed GM soybeans remain valid. The new sequencing data indicated a four base pair (bp) difference compared to the sequencing data originally provided: one bp located in the genomic 3′ flanking region, two bp located in a gene silencing cassette and one bp in a partial promoter. These bp reported as differences in the new nucleic acid sequencing data on soybean event 305423 were already present in the original plant material used for the risk assessment. Thus, with the exception of bioinformatics analyses, including an off‐target search with the dsRNA expression cassette, the studies performed for the risk assessment of the single event soybean 305423 and the two‐event stack soybean 305423 × 40‐3‐2 remain valid. The new sequencing data and the bioinformatic analyses performed on the new sequence including the RNAi off‐target search, did not give rise to safety issues. Therefore, EFSA concludes that the original risk assessment of the single soybean event 305423 and the two‐event stack soybean 305423 × 40‐3‐2 remains valid., This publication is linked to the following EFSA Journal article: http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2017.4968/full

RNAi offers opportunities to generate new traits in genetically modified (GM) plants. Instead of expressing novel proteins, RNAi-based GM plants reduce target gene expression. Silencing of off-target genes may trigger unintended effects, and identifying these genes would facilitate risk assessment. However, using bioinformatics alone is not reliable, due to the lack of genomic data and insufficient knowledge of mechanisms governing mRNA–small (s)RNA interactions., F.N. was supported by the Agence National de la Recherche (program ANR-11-BTBR-0001-GENIUS).

The AMPK/SNF1/SnRK1 protein kinases are a family of ancient and highly conserved eukaryotic energy sensors that function as heterotrimeric complexes. These typically comprise catalytic α subunits and regulatory β and γ subunits, the latter function as the energy-sensing modules of animal AMPK through adenosine nucleotide binding. The ability to monitor accurately and adapt to changing environmental conditions and energy supply is essential for optimal plant growth and survival, but mechanistic insight in the plant SnRK1 function is still limited. In addition to a family of γ-like proteins, plants also encode a hybrid βγ protein that combines the Four-Cystathionine β-synthase (CBS)-domain (FCD) structure in γ subunits with a glycogen-binding domain (GBD), typically found in β subunits. We used integrated functional analyses by ectopic SnRK1 complex reconstitution, yeast mutant complementation, in-depth phylogenetic reconstruction, and a seedling starvation assay to show that only the hybrid KINβγ protein that recruited the GBD around the emergence of the green chloroplast-containing plants, acts as the canonical γ subunit required for heterotrimeric complex formation. Mutagenesis and truncation analysis further show that complex interaction in plant cells and γ subunit function in yeast depend on both a highly conserved FCD and a pre-CBS domain, but not the GBD. In addition to novel insight into canonical AMPK/SNF/SnRK1 γ subunit function, regulation and evolution, we provide a new classification of plant FCD genes as a convenient and reliable tool to predict regulatory partners for the SnRK1 energy sensor and novel FCD gene functions.

All life forms on earth require a continuous input and monitoring of carbon and energy supplies. The AMP-activated kinase (AMPK)/sucrose nonfermenting1 (SNF1)/Snf1-related kinase1 (SnRK1) protein kinases are evolutionarily conserved metabolic sensors found in all eukaryotic organisms from simple unicellular fungi (yeast SNF1) to animals (AMPK) and plants (SnRK1). Activated by starvation and energy-depleting stress conditions, they enable energy homeostasis and survival by up-regulating energy-conserving and energy-producing catabolic processes, and by limiting energy-consuming anabolic metabolism. In addition, they control normal growth and development as well as metabolic homeostasis at the organismal level. As such, the AMPK/SNF1/SnRK1 kinases act in concert with other central signaling components to control carbohydrate uptake and metabolism, fatty acid and lipid biosynthesis and the storage of carbon energy reserves. Moreover, they have a tremendous impact on developmental processes that are triggered by environmental changes such as nutrient depletion or stress. Although intensive research by many groups has partly unveiled the factors that regulate AMPK/SNF1/SnRK1 kinase activity as well as the pathways and substrates they control, several fundamental issues still await to be clarified. In this review, we will highlight these issues and focus on the structure, function and regulation of the AMPK/SNF1/SnRK1 kinases.

Summary RNA interference (RNAi) is an emerging technology that offers new opportunities for the generation of new traits in genetically modified (GM) plants. Potential risks associated with RNAi-based GM plants and issues specific to their risk assessment were discussed during an international scientific workshop (June 2014) organized by the European Food Safety Authority (EFSA). Selected key outcomes of the workshop are reported here.

Higher plants typically do not produce trehalose in large amounts, but their genome sequences reveal large families of putative trehalose metabolism enzymes. An important regulatory role in plant growth and development is also emerging for the metabolic intermediate trehalose-6-P (T6P). Here, we present an update on Arabidopsis trehalose metabolism and a resource for further detailed analyses. In addition, we provide evidence that Arabidopsis encodes a single trehalose-6-P synthase (TPS) next to a family of catalytically inactive TPS-like proteins that might fulfill specific regulatory functions in actively growing tissues.

Insertion of foreign DNA into plant genomes occurs randomly and with low frequency. Hence, a selectable marker is generally required to identify transgenic plants. Until now, all selection systems have been based on the use of non-plant genes, derived from microorganisms and usually conferring antibiotic or herbicide resistance. The use of microorganism-derived genes however has raised biosafety concerns.We have developed a novel selection system based on enhancing the expression of a plant-intrinsic gene and the use of a harmless selection agent. Selection takes advantage of the reduced glucose sensitivity of seedlings with enhanced expression of AtTPS1, a gene encoding trehalose-6-P synthase. As a result, transformants can be identified as developing green seedlings amongst the background of small, pale non-transformed plantlets on high glucose medium. In addition, vegetative regeneration of tobacco leaf explants is very sensitive to high external glucose. Overexpression of AtTPS1 in tobacco allows selecting glucose insensitive transgenic shoots. ispartof: Journal of Biotechnology vol:121 issue:3 pages:309-317 ispartof: location:Netherlands status: published

Plants, restricted by their environment, need to integrate a wide variety of stimuli with their metabolic activity, growth and development. Sugars, generated by photosynthetic carbon fixation, are central in coordinating metabolic fluxes in response to the changing environment and in providing cells and tissues with the necessary energy for continued growth and survival. A complex network of metabolic and hormone signaling pathways are intimately linked to diverse sugar responses. A combination of genetic, cellular and systems analyses have uncovered nuclear HXK1 (hexokinase1) as a pivotal and conserved glucose sensor, directly mediating transcription regulation, while the KIN10/11 energy sensor protein kinases function as master regulators of transcription networks under sugar and energy deprivation conditions. The involvement of disaccharide signals in the regulation of specific cellular processes and the potential role of cell surface receptors in mediating sugar signals add to the complexity. This chapter gives an overview of our current insight in the sugar sensing and signaling network and describes some of the molecular mechanisms involved.

All life forms on earth require a continuous input and monitoring of carbon and energy supplies. The AMP-activated kinase (AMPK)/sucrose non-fermenting1 (SNF1)/Snf1-related kinase1 (SnRK1) protein kinases are evolutionarily conserved metabolic sensors found in all eukaryotic organisms from simple unicellular fungi (yeast SNF1) to animals (AMPK) and plants (SnRK1). Activated by starvation and energy-depleting stress conditions, they enable energy homeostasis and survival by up-regulating energy-conserving and energy-producing catabolic processes, and by limiting energy-consuming anabolic metabolism. In addition, they control normal growth and development as well as metabolic homeostasis at the organismal level. As such, the AMPK/SNF1/SnRK1 kinases act in concert with other central signaling components to control carbohydrate uptake and metabolism, fatty acid and lipid biosynthesis and the storage of carbon energy reserves. Moreover, they have a tremendous impact on developmental processes that are triggered by environmental changes such as nutrient depletion or stress. Although intensive research by many groups has partly unveiled the factors that regulate AMPK/SNF1/SnRK1 kinase activity as well as the pathways and substrates they control, several fundamental issues still await to be clarified. In this review, we will highlight these issues and focus on the structure, function and regulation of the AMPK/SNF1/SnRK1 kinases.

Trehalose metabolism has profound effects on plant growth and metabolism, but the mechanisms involved are unclear. In Arabidopsis, 21 putative trehalose biosynthesis genes are classified in three subfamilies based on their similarity with yeast TPS1 (encoding a trehalose-6-phosphate synthase, TPS) or TPS2 (encoding a trehalose-6-phosphate phosphatase, TPP). Although TPS1 (Class I) and TPPA and TPPB (Class III) proteins have established TPS and TPP activity, respectively, the function of the Class II proteins (AtTPS5-AtTPS11) remains elusive. A complete set of promoter-beta-glucurinidase/green fluorescent protein reporters demonstrates their remarkably differential tissue-specific expression and responsiveness to carbon availability and hormones. Heterologous expression in yeast furthermore suggests that none of the encoded enzymes displays significant TPS or TPP activity, consistent with a regulatory rather than metabolic function for this remarkable class of proteins.

Trehalose metabolism, a short side-branch of primary carbon metabolism that is controlled by a surprisingly large gene family, is emerging as an important new regulatory pathway in plants. Two recent studies by Namiko Satoh-Nagasawa et al. and Leonardo Gomez et al. have highlighted its novel and possibly pivotal role in coordinating carbon supply with plant growth and development.

The disaccharide trehalose has dramatic effects on plant metabolism, growth and development. Arabidopsis seedlings grown on trehalose-containing medium without sucrose display increased expression of the starch synthesis gene ApL3, hyper-accumulation of starch in the cotyledons and inhibition of root growth. Here we show that the ABI4 transcription factor mediates the effects of trehalose on starch metabolism and growth, independently of abscisic acid (ABA) synthesis and hexokinase (HXK1) signaling. Surprisingly, although the abi4 mutation partially rescued trehalose inhibition of root elongation, ApL3 expression levels were still enhanced. Gene expression analysis suggests that trehalose affects both starch synthesis and starch breakdown. The expression of genes involved in starch breakdown, such as SEX1 and the beta-amylase gene BMY8/BAM3, was strongly down-regulated in WT plants grown on trehalose but not in abi4 mutants. Addition of trehalose to liquid-grown WT seedlings also significantly reduced SEX1 expression after 6 h. Bypassing the need for starch breakdown by growth in continuous light or addition of sucrose rescued root growth on trehalose medium similar to the abi4 mutation. These results suggest that inhibition of starch mobilization rather than increased synthesis is involved in growth inhibition by exogenous trehalose. Trehalose also significantly enhanced ABI4 expression but reduced its sucrose induction, providing a possible molecular mechanism for the trehalose effect on plant gene expression and growth.

A number of systems to insert foreign DNA into a plant genome have been developed so far. However, only a small percentage of transgenic plants are obtained using any of these methods. Stable transgenic plants are selected by co-introduction of a selectable marker gene, which in most cases are genes that confer resistance against antibiotics or herbicides. In this chapter we describe a new method for selection of transgenic plants after transformation. The selection agent used is the nontoxic and common sugar glucose. Wild-type Arabidopsis thaliana plantlets that have been germinated on glucose have small white cotyledons and remain petite because the external sugar switches off the photosynthetic mechanism. The selectable marker gene encodes the essential trehalose-6-phophate synthase, AtTPS1, that catalyzes the first reaction of the two-step trehalose synthesis. Upon ectopic expression of AtTPS1 driven by the 35S promoter, transformed Arabidopsis thaliana plants became insensitive to glucose in comparison to wild-type plants. After transformation using AtTPS1 as a selection marker and 6% glucose as selection agent it is possible to single out the green and normal sized transgenic plants amid the nontransformed plantlets.

A number of systems to insert foreign DNA into a plant genome have been developed so far. However, only a small percentage of transgenic plants are obtained using any of these methods. Stable transgenic plants are selected by co-introduction of a selectable marker gene, which in most cases are genes that confer resistance against antibiotics or herbicides. In this chapter we describe a new method for selection of transgenic plants after transformation. The selection agent used is the nontoxic and common sugar glucose. Wild-type Arabidopsis thaliana plantlets that have been germinated on glucose have small white cotyledons and remain petite because the external sugar switches off the photosynthetic mechanism. The selectable marker gene encodes the essential trehalose-6-phophate synthase, AtTPS1, that catalyzes the first reaction of the two-step trehalose synthesis. Upon ectopic expression of AtTPS1 driven by the 35S promoter, transformed Arabidopsis thaliana plants became insensitive to glucose in comparison to wild-type plants. After transformation using AtTPS1 as a selection marker and 6% glucose as selection agent it is possible to single out the green and normal sized transgenic plants amid the nontransformed plantlets.