Sunday Evening News 402 - Week 47 - 2024
Weekly report on genetic engineering, genome editing, biotechnology and legal regulation.
November 2024-11-18 - 2024-11-24
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without additives
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without genetic engineering
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Das besondere Menu - Man kocht ganz ohne Chemie / Dann guten Appetit
The special menu - cooking without chemicals / Bon appetite then
https://edlguetl.de/gut-essen
Meetings-Veranstaltungen
BUND: Onlineveranstaltung: Neue Gentechnik – Ein Risiko für die Biodiversität?
Donnerstag, 28.11.2024, 19:00-21:00, Online über Zoom
Anmeldung und Program: https://aktion.bund.net/veranstaltung-neue-gentechnik-ein-risiko-fuer-die-biodiversitaet?
Press Releases - Media / Presse- und Medienberichte
Tagesspiegel Background: Ungarn greift NGT-Streit noch einmal kurz auf
Die Franzosen plädieren darin für ein umfassendes Überwachungssystem für NGT und kritisieren die angestrebte Deregulierung von NGT-Pflanzen der Kategorie 1.
Gentechnik: Kroatien kritisiert Pläne der EU-Kommission
In den Reihen der EU-Agrarminister stoßen die Pläne der EU-Kommission zur Liberalisierung des EU-Gentechnikrechts auf Kritik. In den Reihen der EU-Agrarminister stoßen die Pläne der EU-Kommission zur Liberalisierung des EU-Gentechnikrechts auf Kritik. Das zeigte ein Treffen des Rates am Montag in Brüssel. In einer schriftlichen Stellungnahme äußerte Kroatien Zweifel daran, eine Koexistenz von NGT-1-Pflanzen und Ökolandbau ermöglichen zu können.
https://table.media/europe/news/gentechnik-kroatien-kritisiert-plaene-der-eu-kommission/
GeN: Sinkende Aktienkurse von Gentechnik-Unternehmen
Miller H. I.:
A Call for Scientific Leadership
https://henrymillermd.org/28185/a-call-for-scientific-leadership
GM Watch: CRISPR gene editing causes large-scale genetic damage while correcting mutant genes
https://gmwatch.org/en/106-news/latest-news/20479
BASF: Genome Editing: The Next Step in Plant Breeding Innovation
Only some selected press releases or media reports are listed here. The daily up-date of the press releases and
media reports are ►here: November week 47
Publications – Publikationen
Meldolesi, A. (2024): Italy tests first gene-edited vines for winemaking. Nat Biotechnol 42, 1630 |
https://doi.org/10.1038/s41587-024-02478-8 | https://www.nature.com/articles/s41587-024-02478-8
Hernandez‑Soto A.,·Gatica‑Arias A. (2024):Genome editing in Latin America: research achievements and regulatory
evolution. Plant Cell Tissue and Organ Culture 159(3) DOI:10.1007/s11240-024-02904-4
Genome editing, mainly CRISPR/Cas9, has been revolutionizing agricultural biotechnology through precise modifications to plant and animal genomes. This review highlights advancements in research and regulatory development of genome editing across Latin America. The region has seen substantial progress in building a regulatory framework to adopt genome editing technologies that enhance crop yield, nutritional content, and resistance to pests and diseases, as well as address critical challenges such as food insecurity and climate change. The article discusses the evolution of regulatory frameworks in various Latin American countries and their trends toward using foreign genetic material to determine regulatory oversight. Argentina pioneered this approach, followed by Brazil, Colombia, Chile, Paraguay, Honduras, and Guatemala. Recent updates from Costa Rica, El Salvador, Ecuador, Uruguay, and Colombia reflect a similar rationale to balance innovation with safety and compliance with international standards. Regional examples of genome editing demonstrate the potential to improve crop quality and sustainability of coffee, rice, cacao,beans, and potatoes. Public perception and acceptance of genome editing are also explored, with surveys indicating strong support for regulatory measures in Costa Rica. The article further explores public perception and acceptance of genome editing indicating strong support for regulation in Costa Rica. The review underscores the importance of continued research, public engagement, and international cooperation that foster responsible development of genome-editing technologies in Latin America.
Zaman Q.U., Raza A., Lozano-Juste G., Chao L., Jones M.G.K., Wang H.-F, Varshney R.K. (2024): Engineering plants using diverse
CRISPR-associated proteins and deregulation of genome-edited crops. Trends in Biotechnology, Volume 42, Issue 5, 560 - 574
The CRISPR/Cas system comprises RNA-guided nucleases, the target specificity of which is directed by Watson–Crick base pairing of target loci with single guide (sg)RNA to induce the desired edits. CRISPR-associated proteins and other engineered nucleases are opening new avenues of research in crops to induce heritable mutations. Here, we review the diversity of CRISPR-associated proteins and strategies to deregulate genome-edited (GEd) crops by considering them to be close to natural processes. This technology ensures yield without penalties, advances plant breeding, and guarantees manipulation of the genome for desirable traits. DNA-free and off-target-free GEd crops with defined characteristics can help to achieve sustainable global food security under a changingclimate, but need alignment of international regulations to operate in existing supply chains.
https://www.cell.com/action/showPdf?pii=S0167-7799%2823%2900298-6
Mešić, A., Jurić, M., Donsì, F. et al. (2024): Advancing climate resilience: technological innovations in plant-based,
alternative and sustainable food production systems. Discov Sustain 5, 423 | https://doi.org/10.1007/s43621-024-00581-z
Sustainable food production is becoming essential, and a shift from traditional practices to more responsible alternatives aiming to generate nutritious, safe, and accessible food while minimizing environmental impacts is crucial. This review article discusses the importance of sustainable food production technologies in meeting global food demand while addressing problems regarding climate change. Some of the key technologies include precision agriculture, hydroponics, aquaponics and vertical farming. Precision agriculture uses technology to enhance farming efficiency by gathering data on soil and water variations and optimizing practices like planting, fertilization, and irrigation. Hydroponics and aquaponics are other alternatives for growing plants using as much as 90% less water and producing more food compared to conventional methods, while vertical farming can increase crop yield per land area, particularly in urban settings, due to its potential to reduce the strain on conventional agricultural land suitable for urban regions. Additionally, genetic modification can help create desirable traits of some plants making them plausible to integrate in vertical farming systems, but this requires careful management. Furthermore, nanotechnology is emerging as another method poised to transform agriculture by providing sustainable and efficient solutions for nutrient regulation, plant growth, and disease resistance whereas Agriculture 5.0 combines traditional agriculture with modern technologies to improve sustainable food production. Finally, alternative protein sources, such as plant-based, insects, cultured meat, mycoprotein and microalgae have emerged as a sustainable solution to traditional meat production. Integrating the abovementioned technologies into agricultural practices is crucial for achieving multiple Sustainable Development Goals.
https://link.springer.com/article/10.1007/s43621-024-00581-z
COP29: New FAO analysis maps Nationally Determined Contributions, identifies opportunities, gaps and risks related
to agrifood climate solutions
Food insecurity and biodiversity loss are the top reported climate-related risks, featuring in 88% of national climate action plans
Kanbar A., Weinert C.H., Kottutz D., La Thinh et al. (2024): Cold tolerance of woodland strawberry (Fragaria vesca) is linked
to Cold Box Factor 4 and the dehydrin Xero2. Journal of Experimental Botany, 75, Issue 18, 5857–5879, https://doi.org/10.1093/jxb/erae263| DOI: 10.1093/jxb/erae263.
Domesticated strawberry is susceptible to sudden frost episodes, limiting the productivity of this cash crop in regions where they are grown during early spring. In contrast, the ancestral woodland strawberry (Fragaria vesca) has successfully colonized many habitats of the Northern Hemisphere. Thus, this species seems to harbour genetic factors promoting cold tolerance. Screening a germplasm established in the frame of the German Gene Bank for Crop Wild Relatives, we identified, among 70 wild accessions, a pair with contrasting cold tolerance. By following the physiological, biochemical, molecular, and metabolic responses of this contrasting pair, we identified the transcription factor Cold Box Factor 4 and the dehydrin Xero2 as molecular markers associated with superior tolerance to cold stress. Overexpression of green fluorescent protein fusions with Xero2 in tobacco BY-2 cells conferred cold tolerance to these recipient cells. A detailed analysis of the metabolome for the two contrasting genotypes allows the definition of metabolic signatures correlated with cold tolerance versus cold stress. This work provides a proof-of-concept for the value of crop wild relatives as genetic resources to identify genetic factors suitable to increase the stress resilience of crop plants.
https://academic.oup.com/jxb/article/75/18/5857/7716397?login=true
Andrew W. Legan, Carson W. Allan, Zoe N. Jensen, +8 , and Bruce E. Tabashnik (2024): Mismatch between lab-generated and
field-evolved resistance to transgenic Bt crops in Helicoverpa zea, PNAS V 121 (47) e2416091121 | https://doi.org/10.1073/pnas.2416091121
Transgenic crops producing crystalline (Cry) proteins from the bacterium Bacillus thuringiensis (Bt) have been used extensively to control some major crop pests. However, many populations of the noctuid moth Helicoverpa zea, one of the most important crop pests in the United States, have evolved practical resistance to several Cry proteins including Cry1Ac. Although mutations in single genes that confer resistance to Cry proteins have been identified in lab-selected and gene-edited strains of H. zea and other lepidopteran pests, the genetic basis of field-evolved resistance to Cry proteins in H. zea has remained elusive. We used a genomic approach to analyze the genetic basis of field-evolved resistance to Cry1Ac in 937 H. zea derived from 17 sites in seven states of the southern United States. We found evidence for extensive gene flow among all populations studied. Field-evolved resistance was not associated with mutations in 20 single candidate genes previously implicated in resistance or susceptibility to Cry proteins in H. zea or other lepidopterans. Instead, resistance in field samples was associated with increased copy number of a cluster of nine trypsin genes. However, trypsin gene amplification occurred in a susceptible sample and not in all resistant samples, implying that this amplification does not always confer resistance and mutations in other genes also contribute to field-evolved resistance to Cry1Ac in H. zea. The mismatch between lab-generated and field-evolved resistance in H. zea is unlike other cases of Bt resistance and reflects challenges for managing this pest.
https://www.pnas.org/doi/10.1073/pnas.2416091121
Zou J., Meng X., Hong Z., Li J., Yu H., Wang C. (2024): Cas9-PE: a robust multiplex gene editing tool for simultaneous precise
editing and site-specific random mutation in rice, Trends in Biotechnology (2024). DOI: 10.1016/j.tibtech.2024.10.012
In molecular design breeding, the simultaneous introduction of desired functional genes through specific nucleotide modifications and the elimination of genes regulating undesired phenotypic traits or agronomic components require advanced gene editing tools. Due to limited editing efficiency, even with the use of highly precise editing tools, such as prime editing (PE), simultaneous editing of multiple mutation types poses a challenge. Here, we replaced Cas9 nickase (nCas9) with Cas9 to construct a Cas9-mediated PE (Cas9-PE) system in rice. This system not only enables precise editing, but also allows for site-specific random mutation. Moreover, leveraging the precision of Cas9-PE, we established a transgene-free multiplex gene editing system using a co-editing strategy. This strategy involved the Agrobacterium-mediated transient expression of the precise editing rice endogenous acetolactate synthase gene ALSS627I to confer herbicide bispyribac-sodium (BS) resistance as a selection marker. This study provides a versatile and efficient multiplex gene editing tool for molecular design breeding.
Szarzanowicz, M.J., Waldburger, L.M., Busche, M. et al. (2024): Binary vector copy number engineering improves
Agrobacterium-mediated transformation. Nat Biotechnol | https://doi.org/10.1038/s41587-024-02462-2
The copy number of a plasmid is linked to its functionality, yet there have been few attempts to optimize higher-copy-number mutants for use across diverse origins of replication in different hosts. We use a high-throughput growth-coupled selection assay and a directed evolution approach to rapidly identify origin of replication mutations that influence copy number and screen for mutants that improve Agrobacterium-mediated transformation (AMT) efficiency. By introducing these mutations into binary vectors within the plasmid backbone used for AMT, we observe improved transient transformation of Nicotiana benthamiana in four diverse tested origins (pVS1, RK2, pSa and BBR1). For the best-performing origin, pVS1, we isolate higher-copy-number variants that increase stable transformation efficiencies by 60–100% in Arabidopsis thaliana and 390% in the oleaginous yeast Rhodosporidium toruloides. Our work provides an easily deployable framework to generate plasmid copy number variants that will enable greater precision in prokaryotic genetic engineering, in addition to improving AMT efficiency.
https://www.nature.com/articles/s41587-024-02462-2
Čepaitė R., Klein N., Mikšys A., Camara-Wilpert S. et al. (2024): Structural variation of types IV-A1- and IV-A3-mediated
CRISPR interference. Nature Communications 15, Article number: 9306 ) DOI: 10.1038/s41467-024-53778-1
CRISPR-Cas mediated DNA-interference typically relies on sequence-specific binding and nucleolytic degradation of foreign genetic material. Type IV-A CRISPR-Cas systems diverge from this general mechanism, using a nuclease-independent interference pathway to suppress gene expression for gene regulation and plasmid competition. To understand how the type IV-A system associated effector complex achieves this interference, we determine cryo-EM structures of two evolutionarily distinct type IV-A complexes (types IV-A1 and IV-A3) bound to cognate DNA-targets in the presence and absence of the type IV-A signature DinG effector helicase. The structures reveal how the effector complexes recognize the protospacer adjacent motif and target-strand DNA to form an R-loop structure. Additionally, we reveal differences between types IV-A1 and IV-A3 in DNA interactions and structural motifs that allow for in trans recruitment of DinG. Our study provides a detailed view of type IV-A mediated DNA-interference and presents a structural foundation for engineering type IV-A-based genome editing tools.
https://www.nature.com/articles/s41467-024-53778-1
Cirincione, A., Simpson, D., Yan, W. et al. (2024): A benchmarked, high-efficiency prime editing platform for multiplexed
dropout screening. Nat Methods https://doi.org/10.1038/s41592-024-02502-4
Prime editing installs precise edits into the genome with minimal unwanted byproducts, but low and variable editing efficiencies have complicated application of the approach to high-throughput functional genomics. Here we assembled a prime editing platform capable of high-efficiency substitution editing suitable for functional interrogation of small genetic variants. We benchmarked this platform for pooled, loss-of-function screening using a library of ~240,000 engineered prime editing guide RNAs (epegRNAs) targeting ~17,000 codons with 1–3 bp substitutions. Comparing the abundance of these epegRNAs across screen samples identified negative selection phenotypes for 7,996 nonsense mutations targeted to 1,149 essential genes and for synonymous mutations that disrupted splice site motifs at 3′ exon boundaries. Rigorous evaluation of codon-matched controls demonstrated that these phenotypes were highly specific to the intended edit. Altogether, we established a prime editing approach for multiplexed, functional characterization of genetic variants with simple readouts.
https://www.nature.com/articles/s41592-024-02502-4
Raimondi, F., Siow, K.M., Wrona, D. et al. (2024): Gene editing of NCF1 loci is associated with homologous recombination
and chromosomal rearrangements. Commun Biol 7, 1291 | https://doi.org/10.1038/s42003-024-06959-z
CRISPR-based genome editing of pseudogene-associated disorders, such as p47phox-deficient chronic granulomatous disease (p47 CGD), is challenged by chromosomal rearrangements due to presence of multiple targets. We report that interactions between highly homologous sequences that are localized on the same chromosome contribute substantially to post-editing chromosomal rearrangements. We successfully employed editing approaches at the NCF1 gene and its pseudogenes, NCF1B and NCF1C, in a human cell line model of p47 CGD and in patient-derived human hematopoietic stem and progenitor cells. Upon genetic engineering, a droplet digital PCR-based method identified cells with altered copy numbers, spanning megabases from the edited loci. We attributed the high aberration frequency to the interaction between repetitive sequences and their predisposition to recombination events. Our findings emphasize the need for careful evaluation of the target-specific genomic context, such as the presence of homologous regions, whose instability can constitute a risk factor for chromosomal rearrangements upon genome editing.
https://www.nature.com/articles/s42003-024-06959-z
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Xu N., Gao H., Wang Y., Liu C,. Hu L., He A., Jiang W., Xin F. (2024): Recent advances in bio-based production of organic acids
by genetically engineered yeasts. Biochemical Engineering Journal; 109587 | https://doi.org/10.1016/j.bej.2024.109587
In order to achieve the sustainable development of society and reduce environmental footprint of chemical industry, some cleaner and greener production methods are still needed. Microbial fermentation has shown great potentials for sustainable production of chemicals, which can convert renewable resources into different products under mild conditions. Particularly, organic acids production has become a highly competitive and rapidly developed field, as they show broad applications in food, cosmetic and medical areas. Especially, yeasts have shown many advantages in organic acids production especially at high osmotic pressure or low pH. Accordingly, this review will discuss the latest progress of engineered yeasts as cell factories for organic acids production. Different strategies for improvement of organic acids production will be introduced, and future perspectives will also be proposed.
https://www.sciencedirect.com/science/article/pii/S1369703X24003747
EFSA:
Martinez, J.M., Gutiérrez, M., Moreno, B., Calvo, M., Fondevila, M., Belanche, A., Raso, J., Moreno, J., Álvarez, I., and Cebrián, G.
(2024): Investigating technological processing supporting the assessment of novel proteins in food and feed risk assessment scientific report. EFSA supporting publication 21 (11): EN-9113. 126 pp. | doi:10.2903/sp.efsa.2024.EN-9113
https://efsa.onlinelibrary.wiley.com/doi/epdf/10.2903/sp.efsa.2024.EN-9113