Sunday Evening News 370 - Week 13 / 14 - 2024
Weekly report on genetic engineering, genome editing, biotechnology and legal regulations.
March 2024-03-25 – April 2024-04-07
Das Unglück derer, die nichts begreifen, ist, dass sie sich selbst für klug halten, so dass sie wahre Weisheit sicher nicht begreifen.“
Lü Bu We (Lü Buwei) (300 - 235 v. Chr.)
The misfortune of those who do not understand anything is that they think they are clever, so they certainly do not understand true wisdom."
Lü Bu We (Lü Buwei) ( 300 - 235 v. Chr.)
Meetings – Conferences / Veranstaltungen - Konferenzen
Podiumsdiskussion "Grüne Gentechnik – klimafreundlich, nachhaltig, zukunftsfähig?"
Zeit: 29. April 2024, 18.30-20.00 Uhr
Ort: Angewandte Interdisciplinary Lab (AIL), Otto-Wagner Postsparkasse / Georg-Coch-Platz 2, 1010 Wien und online
Die Genschere in Wien, 24. – 26.5.24
https://www.crispr-whisper.de/2024/03/22/die-genschere-in-wien-24-26-5-24/
ÖAW: Lange Nacht der Forschung
24.05.2024; 17:00 Uhr
https://www.oeaw.ac.at/detail/veranstaltung/lange-nacht-der-forschung-12
Press Releases -Media / Presse- und Medienberichte
POINT NEWSLETTER NR. 261 – MÄRZ 2024 - Aktuelle Biotechnologie
https://www.scienceindustries.ch/_file/35705/point-2024-03-261-d.pdf
European Coordination Via Campesina: Open letter – Patents, ANSES reports and detection/identification : the European
Parliament must not consolidate its position on GMOs/NGTs before these key issues are resolved
WGG: Sitzung des Agrarrats (AGRIFISH) am 26.03.2024
https://www.biotech-gm-food.com/
BMEL: Tagung des Rates (Landwirtschaft und Fischerei) am 26. März 2024 in Brüssel Ergebnisbericht
Bauernstimme: Keine Einigung und Beschlussfassung zu NGT im EU-Agrarrat
https://www.bauernstimme.de/news/details/keine-beschlussfassung-zu-ngt-im-eu-agrarrat
Arboleas M.S., Manzanaro S.S.: EU muss Einführung von Gentechnik in der Landwirtschaft verschieben
EU unable to approve new gene-editing plans in current mandate
Manzanaro S.S.: Belgiens Gesundheitsbehörde befürwortet neue Gentechnik-Vorschriften
Belgium’s health authority endorses new gene-editing rules, clashing with French opinion
The report: Superior Health Council: Proposal of European Regulation on plants produced by certain New Genomic Techniques (NGTs). Brussels: SHC; 2024. Report 9801.
Habermann C.: Neue Gentechnik: Alte Interessen und neue wissenschaftliche Erkenntnisse
Wager R., Miller H.I. The EU Continues Its Unscientific, Anti-Innovation Policymaking
Only some selected press releases or media reports are listed here. The daily up-date of the press releases and
media reports are ►here: March week 13-2024 and April week 14-2024
Publications – Publikationen
Larsen A.E., Noack F., Claire Powers L.C. (2024): Spillover effects of organic agriculture on pesticide use on nearby fields.
Science 383, Issue 6689 | DOI: 10.1126/science.adf2572
INTRODUCTION: Reducing the environmental footprint of agriculture while maintaining or improving yields is a major challenge of the coming decades. Organic agriculture is often suggested as a means to improve agricultural sustainability through more natural production methods, particularly in regards to pesticides and pest control. However, the environmental impacts of organic production practices are only partially understood and it remains unknown whether such production practices have spillover impacts, beneficial or not, for surrounding producers.
RATIONALE: Organic crop production includes a suite of on-farm practices that differ from conventional management techniques. These practices include using different pest management approaches, which may result in the spillover of agricultural pests and/or their natural enemies to nearby agricultural fields resulting in higher or lower pest damage and pesticide use. Here we seek to identify the direct and spillover effects of surrounding organic cropland on pesticide use on both organic and conventional crop fields. To do so, we used field-level pesticide use and crop data for ~14,000 fields over seven years in Kern County, California, alongside US-wide data on organic agriculture and pesticide use.
RESULTS: We find that the presence of surrounding organic cropland generally leads to a decrease in pesticide use on organic fields, which appears mostly driven by a reduction in insecticides. By contrast, surrounding organic agriculture leads to a small but significant increase in pesticide use on conventional fields. Based on these results, we simulate how changing the proportion of organic cropland changes net insecticide use. While net insecticide use decreases at high levels of organic cropland, at commonly observed levels net insecticide use increases due to the positive (insecticide increasing) effects of surrounding organic cropland on conventional fields. This effect can be entirely mitigated by clustering organic cropland. A coarser, national-scale analysis further evidences the inverted U-shape relationship between organic cropland area and net insecticide use.
CONCLUSION: These results suggest that efforts to increase organic cropland could lead to a decrease in pesticide use, but that is more likely at higher levels of organic cropland in the landscape. At low levels of organic cropland, the opposite is expected. Spatially clustering organic fields and spatially separating organic and conventional fields could reduce the environmental footprint of both organic and conventional croplands.
https://www.science.org/doi/10.1126/science.adf2572
Rotundo, J.L., Marshall, R., McCormick, R. et al. (2024): European soybean to benefit people and the environment.
Sci Rep 14, 7612 | https://doi.org/10.1038/s41598-024-57522-z
Europe imports large amounts of soybean that are predominantly used for livestock feed, mainly sourced from Brazil, USA and Argentina. In addition, the demand for GM-free soybean for human consumption is project to increase. Soybean has higher protein quality and digestibility than other legumes, along with high concentrations of isoflavones, phytosterols and minerals that enhance the nutritional value as a human food ingredient. Here, we examine the potential to increase soybean production across Europe for livestock feed and direct human consumption, and review possible effects on the environment and human health. Simulations and field data indicate rainfed soybean yields of 3.1 ± 1.2 t ha−1 from southern UK through to southern Europe (compared to a 3.5 t ha−1 average from North America). Drought-prone southern regions and cooler northern regions require breeding to incorporate stress-tolerance traits. Literature synthesized in this work evidenced soybean properties important to human nutrition, health, and traits related to food processing compared to alternative protein sources. While acknowledging the uncertainties inherent in any modelling exercise, our findings suggest that further integrating soybean into European agriculture could reduce GHG emissions by 37–291 Mt CO2e year−1 and fertiliser N use by 0.6–1.2 Mt year−1, concurrently improving human health and nutrition
https://www.nature.com/articles/s41598-024-57522-z
Goodman R.E. (2024): Twenty-eight years of GM Food and feed without harm: why not accept them?
GM Crops & Food, 15:1, 40-50, DOI: 10.1080/21645698.2024.2305944
Since the first genetically engineered or modified crops or organisms (GMO) were approved for commercial production in 1995, no new GMO has been proven to be a hazard or cause harm to human consumers. These modifications have improved crop efficiency, reduced losses to insect pests, reduced losses to viral and microbial plant pathogens and improved drought tolerance. A few have focused on nutritional improvements producing beta carotene in Golden Rice. Regulators in the United States and countries signing the CODEX Alimentarius and Cartagena Biosafety agreements have evaluated human and animal food safety considering potential risks of allergenicity, toxicity, nutritional and anti-nutritional risks. They consider risks for non-target organisms and the environment. There are no cases where post-market surveillance has uncovered harm to consumers or the environment including potential transfer of DNA from the GMO to non-target organisms. In fact, many GMOs have helped improve production, yield and reduced risks from chemical insecticides or fungicides. Yet there are generic calls to label foods containing any genetic modification as a GMO and refusing to allow GM events to be labeled as organic. Many African countries have accepted the Cartagena Protocol as a tool to keep GM events out of their countries while facing food insecurity. The rationale for those restrictions are not rational. Other issues related to genetic diversity, seed production and environmental safety must be addressed. What can be done to increase acceptance of safe and nutritious foods as the population increases, land for cultivation is reduced and energy costs soar?
https://www.tandfonline.com/doi/full/10.1080/21645698.2024.2305944
Lukasiewicz, J.M., van de Wiel, C.C.M., Lotz, L.A.P. et al. (2024): Consumer transparency in the production chain for plant
varieties produced using new genomic techniques. aBIOTECH | https://doi.org/10.1007/s42994-024-00142-y
Plants edited with new genomic techniques (NGTs) currently fall under the Genetically Modified Organisms Directive (2001/18/EC) in the European Union. In the proposal of the European Commission, NGT plants are partially exempted from the regulations of this directive. The proposal makes a distinction between two categories of NGT plants: NGT-1 and NGT-2. NGT-1 category plants are considered equal to plants obtained through conventional breeding methods. These plants will not be labelled for the consumer, although they will be labelled as seeds. NGT-2 category plants may be labelled with additional information as a positive incentive. Labelling of seeds of varieties made with gene editing, but not the products, would mean that most steps in the production chain are transparent, but not the last step towards consumers. The “right to know” and increasing knowledge of gene-edited food is a common theme in food labelling towards consumers. Here, we describe current labelling regimes and registers and how these may be applied to provide transparency on gene-edited products to consumers. Furthermore, we also look into consumer studies, which indicate a greater acceptance of gene-edited food among consumers, especially when additional benefits such as sustainability are mentioned.
https://link.springer.com/article/10.1007/s42994-024-00142-y
Evanega, S. Brown, Z., Bubeck D., Falck-Zapeda, J. et al. (2024): Applications, benefits, and challenges of genome edited
crops. CAST Issue Paper 74. Ames, Iowa: Council for Agricultural Science and Technology (CAST).
National Academies of Sciences, Engineering, and Medicine. (2024): Charting a Future for Sequencing RNA and Its Modifications: A New Era for Biology and Medicine. Washington, DC: The National Academies Press.
https://doi.org/10.17226/27165.
Healey, A.L., Garsmeur, O., Lovell, J.T. et al. (2024): The complex polyploid genome architecture of sugarcane.
Nature https://doi.org/10.1038/s41586-024-07231-4
Sugarcane, the world’s most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype (‘monoploid’) representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.
https://www.nature.com/articles/s41586-024-07231-4
Puli M.R., Muchoki P., Yaaran A., +10 , and Yalovsky S. (2024): Null mutants of a tomato Rho of plants exhibit enhanced water
use efficiency without a penalty to yield. PNAS 121 (4) e2309006120 | https://doi.org/10.1073/pnas.2309006120
Improving water use efficiency in crops is a significant challenge as it involves balancing water transpiration and CO2 uptake through stomatal pores. This study investigates the role of SlROP9, a tomato Rho of Plants protein, in guard cells and its impact on plant transpiration. The results reveal that SlROP9 null mutants exhibit reduced stomatal conductance while photosynthetic CO2 assimilation remains largely unaffected. Notably, there is a notable decrease in whole-plant transpiration in the rop9 mutants compared to the wild type, especially during noon hours when the water pressure deficit is high. The elevated stomatal closure observed in rop9 mutants is linked to an increase in reactive oxygen species formation. This is very likely dependent on the respiratory burst oxidase homolog (RBOH) NADPH oxidase and is not influenced by abscisic acid (ABA). Consistently, activated ROP9 can interact with RBOHB in both yeast and plants. In diverse tomato accessions, drought stress represses ROP9 expression, and in Arabidopsis stomatal guard cells, ABA suppresses ROP signaling. Therefore, the phenotype of the rop9 mutants may arise from a disruption in ROP9-regulated RBOH activity. Remarkably, large-scale field experiments demonstrate that the rop9 mutants display improved water use efficiency without compromising fruit yield. These findings provide insights into the role of ROPs in guard cells and their potential as targets for enhancing water use efficiency in crops.
https://www.pnas.org/doi/10.1073/pnas.2309006120
Ali M., Shafiq M., Haider M.Z., Sami A., Alam P. et al. (2024): Genome-wide analysis of NPR1-like genes in citrus species and
expression analysis in response to citrus canker (Xanthomonas axonopodis pv. citri). Front. Plant Sci. 15:1333286. doi: 10.3389/fpls.2024.1333286
Citrus fruits, revered for their nutritional value, face significant threats from diseases like citrus canker, particularly impacting global citrus cultivation, notably in Pakistan. This study delves into the critical role of NPR1-like genes, the true receptors for salicylic acid (SA), in the defense mechanisms of citrus against Xanthomonas axonopodis pv. citri (Xcc). By conducting a comprehensive genome-wide analysis and phylogenetic study, the evolutionary dynamics of Citrus limon genes across diverse citrus cultivars are elucidated. Structural predictions unveil conserved domains, such as the BTB domain and ankyrin repeat domains, crucial for the defense mechanism. Motif analysis reveals essential conserved patterns, while cis-regulatory elements indicate their involvement in transcription, growth, response to phytohormones, and stress. The predominantly cytoplasmic and nuclear localization of NPR1-like genes underscores their pivotal role in conferring resistance to various citrus species. Analysis of the Ks/Ka ratio indicates a purifying selection of NPR1-like genes, emphasizing their importance in different species. Synteny and chromosomal mapping provide insights into duplication events and orthologous links among citrus species. Notably, Xac infection stimulates the expression of NPR1-like genes, revealing their responsiveness to pathogenic challenges. Interestingly, qRT-PCR profiling post-Xac infection reveals cultivar-specific alterations in expression within susceptible and resistant citrus varieties. Beyond genetic factors, physiological parameters like peroxidase, total soluble protein, and secondary metabolites respond to SA-dependent PR genes, influencing plant characteristics. Examining the impact of defense genes (NPR1) and plant characteristics on disease resistance in citrus, this study marks the inaugural investigation into the correlation between NPR1-associated genes and various plant traits in both susceptible and resistant citrus varieties to citrus bacterial canker.
https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1333286/full
Leite Dias et al. (2024): Biosynthesis of the allelopathic alkaloid gramine in barley by a cryptic oxidative rearrangement.
Science. | DOI: 10.1126/science.adk6112.
The defensive alkaloid gramine not only protects barley and other grasses from insects but also negatively affects their palatability to ruminants. The key gene for gramine formation has remained elusive, hampering breeding initiatives. In this work, we report that a gene encoding cytochrome P450 monooxygenase CYP76M57, which we name AMI synthase (AMIS), enables the production of gramine in Nicotiana benthamiana, Arabidopsis thaliana, and Saccharomyces cerevisiae. We reconstituted gramine production in the gramine-free barley (Hordeum vulgare) variety Golden Promise and eliminated it from cultivar Tafeno by Cas-mediated gene editing. In vitro experiments unraveled that an unexpected cryptic oxidative rearrangement underlies this noncanonical conversion of an amino acid to a chain-shortened biogenic amine. The discovery of the genetic basis of gramine formation now permits tailor-made optimization of gramine-linked traits in barley by plant breeding.
https://www.science.org/doi/10.1126/science.adk6112
Mallapaty S. & Kozlov M. (2024): First pig kidney transplant in a person: what it means for the future.
Nature | https://www.nature.com/articles/d41586-024-00879-y
The operation’s early success has made researchers hopeful that clinical trials for xenotransplanted organs will start soon
Hallerman, E., Bredlau, J., Camargo, L.S.A. et al. (2024): Enabling regulatory policy globally will promote realization of the
potential of animal biotechnology. CABI Agric Biosci 5, 25 | https://doi.org/10.1186/s43170-024-00221-6
Animal biotechnologies have the potential to improve the sustainability and security of our global food systems. Government regulatory authorities are responsible for ensuring the safety of food their citizens consume, whether it is produced via conventional breeding methods or biotechnologies. While some countries have implemented animal biotechnology oversight policies, many countries have yet to develop theirs. Historically, regulatory approvals were required before products of biotechnology could enter the marketplace, and the high cost of the approval process limited the number and types of animal and plant products that sought approval. Only one biotech animal in the world that was developed for food production has reached the market under a GMO or rDNA approval process. The advent of genome editing techniques has revolutionized the scientific approach to introducing changes into DNA sequences and how biotechnology can be used to enhance agricultural breeding. Regulatory dialogs about biotechnology also have changed as a result of these new technologies. Regulatory agencies have begun to respond to these scientific advances, and a growing number of countries are looking to modernize regulatory approaches for these products, based on risk (or lack thereof) and similarity to organisms that could be produced via conventional breeding methods. Advances in animal biotechnology, especially genome editing, can accelerate the incorporation of valued phenotypes in animals, including enhanced yield, disease resistance, resilience to changing climate, and improved animal welfare, as well as food qualities valued by consumers. For animals with these biotechnology-introduced traits to enter agricultural production and reach consumers, clear risk-proportionate regulatory approaches must be in place, and to facilitate international trade of animal products, regulatory processes need to be aligned and compatible. Effective scientific public communication is crucial to build public trust in precision animal biotechnology and risk-proportionate regulatory approaches. An international workshop on regulatory approaches for animal biotechnology was convened in 2022 with 27 countries represented. We synthesize here technical progress, development of regulatory policy, and strategies for engagement with diverse publics on animal biotechnology reported in the workshop. Our goal is to encourage development and implementation of risk-proportionate regulatory approaches and policies in a global context.
https://cabiagbio.biomedcentral.com/articles/10.1186/s43170-024-00221-6
Maini Rekdal, V., van der Luijt, C.R.B., Chen, Y. et al. (2024): Edible mycelium bioengineered for enhanced nutritional value
and sensory appeal using a modular synthetic biology toolkit. Nat Commun 15, 2099 (2024). https://doi.org/10.1038/s41467-024-46314-8
Filamentous fungi are critical in the transition to a more sustainable food system. While genetic modification of these organisms has promise for enhancing the nutritional value, sensory appeal, and scalability of fungal foods, genetic tools and demonstrated use cases for bioengineered food production by edible strains are lacking. Here, we develop a modular synthetic biology toolkit for Aspergillus oryzae, an edible fungus used in fermented foods, protein production, and meat alternatives. Our toolkit includes a CRISPR-Cas9 method for gene integration, neutral loci, and tunable promoters. We use these tools to elevate intracellular levels of the nutraceutical ergothioneine and the flavor-and color molecule heme in the edible biomass. The strain overproducing heme is red in color and is readily formulated into imitation meat patties with minimal processing. These findings highlight the promise of synthetic biology to enhance fungal foods and provide useful genetic tools for applications in food production and beyond.
https://www.nature.com/articles/s41467-024-46314-8#author-information
Qian, W., Wang, X., Kang, Y. et al. (2024): A general model for predicting enzyme functions based on enzymatic reactions.
J Cheminform 16, 38 | https://doi.org/10.1186/s13321-024-00827-y
Accurate prediction of the enzyme comission (EC) numbers for chemical reactions is essential for the understanding and manipulation of enzyme functions, biocatalytic processes and biosynthetic planning. A number of machine leanring (ML)-based models have been developed to classify enzymatic reactions, showing great advantages over costly and long-winded experimental verifications. However, the prediction accuracy for most available models trained on the records of chemical reactions without specifying the enzymatic catalysts is rather limited. In this study, we introduced BEC-Pred, a BERT-based multiclassification model, for predicting EC numbers associated with reactions. Leveraging transfer learning, our approach achieves precise forecasting across a wide variety of Enzyme Commission (EC) numbers solely through analysis of the SMILES sequences of substrates and products. BEC-Pred model outperformed other sequence and graph-based ML methods, attaining a higher accuracy of 91.6%, surpassing them by 5.5%, and exhibiting superior F1 scores with improvements of 6.6% and 6.0%, respectively. The enhanced performance highlights the potential of BEC-Pred to serve as a reliable foundational tool to accelerate the cutting-edge research in synthetic biology and drug metabolism. Moreover, we discussed a few examples on how BEC-Pred could accurately predict the enzymatic classification for the Novozym 435-induced hydrolysis and lipase efficient catalytic synthesis. We anticipate that BEC-Pred will have a positive impact on the progression of enzymatic research.
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-024-00827-y
Liu Y., Wang S., Wang L., Lu H., Zang T., Zamg W. (2024): Characterization of Genomic, Physiological, and Probiotic Features
of Lactiplantibacillus plantarum JS21 Strain Isolated from Traditional Fermented Jiangshui. Foods 13(7), 1082; https://doi.org/10.3390/foods13071082
This study aimed to understand the genetic and metabolic traits of a Lactiplantibacillus plantarum JS21 strain and its probiotic abilities through laboratory tests and computer analysis. L. plantarum JS21 was isolated from a traditional fermented food known as “Jiangshui” in Hanzhong city. In this research, the complete genetic makeup of JS21 was determined using Illumina and PacBio technologies. The JS21 genome consisted of a 3.423 Mb circular chromosome and five plasmids. It was found to contain 3023 protein-coding genes, 16 tRNA genes, 64 rRNA operons, 40 non-coding RNA genes, 264 pseudogenes, and six CRISPR array regions. The GC content of the genome was 44.53%. Additionally, the genome harbored three complete prophages. The evolutionary relationship and the genome collinearity of JS21 were compared with other L. plantarum strains. The resistance genes identified in JS21 were inherent. Enzyme genes involved in the Embden–Meyerhof–Parnas (EMP) and phosphoketolase (PK) pathways were detected, indicating potential for facultative heterofermentative pathways. JS21 possessed bacteriocins plnE/plnF genes and genes for polyketide and terpenoid assembly, possibly contributing to its antibacterial properties against Escherichia coli (ATCC 25922), Escherichia coli (K88), Staphylococcus aureus (CMCC 26003), and Listeria monocytogenes (CICC 21635). Furthermore, JS21 carried genes for Na+/H+ antiporters, F0F1 ATPase, and other stress resistance genes, which may account for its ability to withstand simulated conditions of the human gastrointestinal tract in vitro. The high hydrophobicity of its cell surface suggested the potential for intestinal colonization. Overall, L. plantarum JS21 exhibited probiotic traits as evidenced by laboratory experiments and computational analysis, suggesting its suitability as a dietary supplement.
https://www.mdpi.com/2304-8158/13/7/1082
EFSA
CEP Panel (2024): Safety evaluation of the food enzyme subtilisin from the genetically modified Bacillus licheniformis strain NZYM-CB.
EFSA Journal 22(4), e8723. https://doi.org/10.2903/j.efsa.2024.8723
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2024.8723
CEP Panel (2024). Safety evaluation of an extension of use of the food enzyme 4-α-glucanotransferase from the non-genetically
modified Aeribacillus pallidus strain AE-SAS. EFSA Journal 22(4), e8698. https://doi.org/10.2903/j.efsa.2024.8698
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2024.8698
CEP Panel (2024): Safety evaluation of an extension of use of the food enzyme endo-polygalacturonase from the genetically modified
Aspergillus oryzae strain AR-183. EFSA Journal 22(4), e8701. https://doi.org/10.2903/j.efsa.2024.8701
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2024.8701
CEP Panel (2024): Safety evaluation of an extension of use of the food enzyme pectinesterase from the genetically modified
Aspergillus oryzae strain AR-962. EFSA Journal 22(4), e8700. https://doi.org/10.2903/j.efsa.2024.8700
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/j.efsa.2024.8700