A SNP associated with alternative splicing of RPT5b causes unequal redundancy between RPT5a and RPT5b among Arabidopsis thaliana natural variation

<p>Abstract</p> <p>Background</p> <p>The proteasome subunit RPT5, which is essential for gametophyte development, is encoded by two genes in <it>Arabidopsis thaliana</it>; <it>RPT5a </it>and <it>RPT5b</it>. We showed previously that <it>RPT5a </it>and <it>RPT5b </it>are fully redundant in the Columbia (Col-0) accession, whereas in the Wassilewskia accession (Ws-4), <it>RPT5b </it>does not complement the effect of a strong <it>rpt5a </it>mutation in the male gametophyte, and only partially complements <it>rpt5a </it>mutation in the sporophyte. <it>RPT5b^Col-0</it>and <it>RPT5b^Ws-4</it>differ by only two SNPs, one located in the promoter and the other in the seventh intron of the gene.</p> <p>Results</p> <p>By exploiting natural variation at <it>RPT5b </it>we determined that the SNP located in <it>RPT5b </it>intron seven, rather than the promoter SNP, is the sole basis of this lack of redundancy. In Ws-4 this SNP is predicted to create a new splicing branchpoint sequence that induces a partial mis-splicing of the pre-mRNA, leading to the introduction of a Premature Termination Codon. We characterized 5 accessions carrying this A-to-T substitution in intron seven and observed a complete correlation between this SNP and both a 10 to 20% level of the <it>RPT5b </it>pre-mRNA mis-splicing and the lack of ability to complement an <it>rpt5a </it>mutant phenotype.</p> <p>Conclusion</p> <p>The accession-dependent unequal redundancy between <it>RPT5a </it>and <it>RPT5b </it>genes illustrates an example of evolutionary drifting between duplicated genes through alternative splicing.</p

Risk assessment of new sequencing data on GM maize event MIR604

In 2009 and 2010, the EFSA GMO Panel concluded the assessment of genetically modified (GM) maizes MIR604, MIR604 × GA21, MIR604 × Bt11 and MIR604 × GA21 × Bt11. These maizes 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 July 2015, the European Commission (EC) received from Syngenta new nucleic acid sequencing data on maize event MIR604 and updated bioinformatic analyses using the new sequencing data. EC tasked EFSA to analyse these data and to indicate whether the previous conclusions of the EFSA GMO Panel on the above-listed GM maizes remain valid. The EFSA GMO Panel used the appropriate principles described in its guidelines for the risk assessment of GM plants to analyse the received data. The new sequencing data indicated a single base pair difference compared to the sequencing data originally provided, located in a non-coding region of the insert. which had already been 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 remain valid. The new sequencing data and the bioinformatic analyses performed on the new sequence did not give rise to safety issues. Therefore, the GMO Panel concludes that the original risk assessment of event MIR604 as a single and as a part of stacked events remains valid

Applicability of the EFSA Opinion on site-directed nucleases type 3 for the safety assessment of plants developed using site-directed nucleases type 1 and 2 and oligonucleotide directed mutagenesis

© 2020 European Food Safety Authority.The European Commission requested the EFSA Panel on Genetically Modified Organisms (GMO) to assess whether section 4 (hazard identification) and the conclusions of EFSA's Scientific opinion on the risk assessment of plants developed using zinc finger nuclease type 3 technique (ZFN‐3) and other site‐directed nucleases (SDN) with similar function are valid for plants developed via SDN‐1, SDN‐2 and oligonucleotide‐directed mutagenesis (ODM). In delivering this Opinion, the GMO Panel compared the hazards associated with plants produced via SDN‐1, SDN‐2 and ODM with those associated with plants obtained via both SDN‐3 and conventional breeding. Unlike for SDN‐3 methods, the application of SDN‐1, SDN‐2 and ODM approaches aims to modify genomic sequences in a way which can result in plants not containing any transgene, intragene or cisgene. Consequently, the GMO Panel concludes that those considerations which are specifically related to the presence of a transgene, intragene or cisgene included in section 4 and the conclusions of the Opinion on SDN‐3 are not relevant to plants obtained via SDN‐1, SDN‐2 or ODM as defined in this Opinion. Overall, the GMO Panel did not identify new hazards specifically linked to the genomic modification produced via SDN‐1, SDN‐2 or ODM as compared with both SDN‐3 and conventional breeding. Furthermore, the GMO Panel considers that the existing Guidance for risk assessment of food and feed from genetically modified plants and the Guidance on the environmental risk assessment of genetically modified plants are sufficient but are only partially applicable to plants generated via SDN‐1, SDN‐2 or ODM. Indeed, those guidance documents’ requirements that are linked to the presence of exogenous DNA are not relevant for the risk assessment of plants developed via SDN‐1, SDN‐2 or ODM approaches if the genome of the final product does not contain exogenous DNA

Scientific Opinion on application EFSA‐GMO‐BE‐2013‐117 for authorisation of genetically modified maize MON 87427 × MON 89034 × NK603 and subcombinations independently of their origin, for food and feed uses, import and processing submitted under Regulation (EC) No 1829/2003 by Monsanto Company

Scientific opinionRequestor: Competent Authority of BelgiumQuestion number: EFSA-Q-2013-00765In this opinion, the EFSA Panel on Genetically Modified Organisms (GMO Panel) assessed the three-event stack maize MON 87427 9 MON 89034 9 NK603 and its three subcombinations, independently of their origin. The GMO Panel has previously assessed the three single events combined to produce this three-event stack maize and did not identify safety concerns. No new data on the single events, leading to modification of the original conclusions on their safety, were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single maize events and of the newly expressed proteins in the three-event stack maize did not give rise to issues regarding food and feed safety or nutrition. In the case of accidental release of viable grains of maize MON 87427 9 MON 89034 9 NK603 into the environment, the three-event stack maize would not raise environmental safety concerns. The GMO Panel concludes that the threeevent stack maize is as safe and as nutritious as the non-GM comparator and the tested non-GM reference varieties in the context of its scope. The GMO Panel considered that its previous conclusions on the two-event stack maize MON 89034 9 NK603 remain valid. For the two maize subcombinations for which no experimental data were provided the GMO Panel assessed the likelihood of interactions among the single events, and concluded that their combination would not raise safety concerns. These two subcombinations are therefore expected to be as safe as the single events, the previously assessed maize MON 89034 9 NK603 and maize MON 87427 9 MON 89034 9 NK603. Since the post-market environmental monitoring plan for the three-event stack maize does not include any provisions for the two subcombinations not previously assessed, the GMO Panel recommended the applicant to revise the plan accordingly

Assessment of genetically modified oilseed rape GT73 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐RX‐002)

Following the submission of application EFSA-GMO-RX-002 under Regulation (EC) No 1829/2003 from Monsanto Company, the Panel on Genetically Modified Organisms of EFSA (GMO) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the herbicide-tolerant genetically modified oilseed rape GT73. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in oilseed rape GT73 considered for renewal of authorisation is identical to the sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-002 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on oilseed rape GT73

Statement on in vitro protein digestibility tests in allergenicity and protein safety assessment of genetically modified plants

This statement supplements and updates the GMO Panel guidance document on allergenicity of genetically modified (GM) plants published in 2017. In that guidance document, the GMO Panel considered that additional investigations on in vitro protein digestibility were needed before providing any additional recommendations in the form of guidance to applicants. Thus, an interim phase was proposed to assess the utility of an enhanced in vitro digestion test, as compared to the classical pepsin resistance test. Historically, resistance to degradation by pepsin using the classical pepsin resistance test has been considered as additional information, in a weight-of-evidence approach, for the assessment of allergenicity and toxicity of newly expressed proteins in GM plants. However, more recent evidence does not support this test as a good predictor of allergenic potential for hazard. Furthermore, there is a need for more reliable systems to predict the fate of the proteins in the gastrointestinal tract and how they interact with the relevant human cells. Nevertheless, the classical pepsin resistance test can still provide some information on the physicochemical properties of novel proteins relating to their stability under acidic conditions. But other methods can be used to obtain data on protein's structural and/or functional integrity. It is acknowledged that the classical pepsin resistance test is embedded into international guidelines, e.g. Codex Alimentarius and Regulation (EU) No 503/2013. For future development, a deeper understanding of protein digestion in the gastrointestinal tract could enable the framing of more robust strategies for the safety assessment of proteins. Given the high complexity of the digestion and absorption process of dietary proteins, it is needed to clarify and identify the aspects that could be relevant to assess potential risks of allergenicity and toxicity of proteins. To this end, a series of research questions to be addressed are also formulated in this statement

Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants

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

Assessment of genetically modified soybean MON 87701 × MON 89788 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐RX‐022)

Following the submission of application EFSA-GMO-RX-022 under Regulation (EC) No 1829/2003 from Bayer CropScience LP, the Panel on Genetically Modified Organisms of the European Food Safety Authority was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect-resistant and herbicide-tolerant genetically modified soybean MON 87701 × MON 89788, for food and feed uses, excluding cultivation within the European Union. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequences of the events in soybean MON 87701 × MON 89788 considered for renewal are identical to the sequences of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-022 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on soybean MON 87701 × MON 89788

Assessment of genetically modified soybean MON 87701 for renewal authorisation under Regulation (EC) No 1829/2003 (application EFSA‐GMO‐RX‐021)

Following the submission of application EFSA-GMO-RX-021 under Regulation (EC) No 1829/2003 from Bayer CropScience LP, the Panel on Genetically Modified Organisms of the European Food Safety Authority was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect-resistant genetically modified soybean MON 87701, for food and feed uses, excluding cultivation within the European Union. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequences of the event in soybean MON 87701 considered for renewal is identical to the sequences of the originally assessed event, the GMO Panel concludes that there is no evidence in renewal application EFSA-GMO-RX-021 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on soybean MON 87701

Guidance on allergenicity assessment of genetically modified plants

This document provides supplementary guidance on specific topics for the allergenicity risk assessment of genetically modified plants. In particular, it supplements general recommendations outlined in previous EFSA GMO Panel guidelines and Implementing Regulation (EU) No 503/2013. The topics addressed are non-IgE-mediated adverse immune reactions to foods, in vitro protein digestibility tests and endogenous allergenicity. New scientific and regulatory developments regarding these three topics are described in this document. Considerations on the practical implementation of those developments in the risk assessment of genetically modified plants are discussed and recommended, where appropriate. (C) 2017 European Food Safety Authority. EFSA Journal published by John Wiley and Sons Ltd on behalf of European Food Safety Authority