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Bioengineering and physicochemical optimization of ergothioneine production by Aspergillus oryzae. 米曲霉生产麦角硫因的生物工程及理化优化。
IF 5.6 2区 生物学
New biotechnology Pub Date : 2026-09-04 DOI: 10.1016/j.nbt.2026.09.002
Waill A Elkhateeb, Ghoson M Daba, Keishi Inoue, Ryoichiro Fukuhara, Taisei Yamamoto, Takeshi Zendo, Yoshinori Katakura, Kaoru Takegawa, Yujiro Higuchi
{"title":"Bioengineering and physicochemical optimization of ergothioneine production by Aspergillus oryzae.","authors":"Waill A Elkhateeb, Ghoson M Daba, Keishi Inoue, Ryoichiro Fukuhara, Taisei Yamamoto, Takeshi Zendo, Yoshinori Katakura, Kaoru Takegawa, Yujiro Higuchi","doi":"10.1016/j.nbt.2026.09.002","DOIUrl":"https://doi.org/10.1016/j.nbt.2026.09.002","url":null,"abstract":"<p><p>Ergothioneine (EGT) is a bioactive, rare variant of histidine with many applications in the medical, pharmaceutical, and food fields. Therefore, we aimed to investigate in this study the impact of genomic and physicochemical factors on EGT production by the industrial filamentous fungus Aspergillus oryzae. Firstly, to facilitate efficient EGT production, we analyzed the subcellular localization of the three EGT biosynthetic enzymes present in A. oryzae. During screening for the most potent producer of EGT among bioengineered constructed transformants, the strain EgtACO overexpressing both AoegtA and AoegtC showed promising EGT production in DPY medium. Five days of incubation was the optimum period, and CZYP medium was the optimum medium for EGT production. Co-cultivation with the nisin Z-producing Lactococcus lactis JCM 7638 yielded EGT production equivalent to that of the EgtACO strain alone. Having broad-spectrum antimicrobial activity without suppressing growth of the EgtACO strain suggested that bacteriocin may help reduce the risk of contamination during long-term cultivation. Moreover, supplementing the production medium with L-methionine or zinc sulfate improved EGT production (1468.5 or 1565mg/L, respectively). Furthermore, repeated inoculation of the producer strain EgtACO and incubation in blue light were the optimum conditions for EGT production (1895 mg/L). Finally, we achieved cost-effective EGT production using A. oryzae strain EgtACO under the optimal culture conditions using agricultural wastes: potato peel and sweet potato peel (293 and 308mg/L, respectively).</p>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148892325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
LLM-guided prediction of riboswitch-ligand binding affinity under data-limited conditions. 在数据有限的条件下,llm引导的核糖体开关配体结合亲和力预测。
IF 5.6 2区 生物学
New biotechnology Pub Date : 2026-09-02 DOI: 10.1016/j.nbt.2026.08.008
Sunggi An, Sofia Mun, Yousung Jung, Hyun Uk Kim
{"title":"LLM-guided prediction of riboswitch-ligand binding affinity under data-limited conditions.","authors":"Sunggi An, Sofia Mun, Yousung Jung, Hyun Uk Kim","doi":"10.1016/j.nbt.2026.08.008","DOIUrl":"https://doi.org/10.1016/j.nbt.2026.08.008","url":null,"abstract":"<p><p>Riboswitches are RNA regulatory elements that sense small molecules and regulate gene expression through ligand-induced conformational changes in an aptamer domain. They enable synthetic biology applications such as biosensing and gene circuit design. Accurate prediction of riboswitch-ligand binding affinity, quantified by the dissociation constant (K<sub>d</sub>), is essential for rational riboswitch engineering. We present a neuro-symbolic framework in which LLM-derived embeddings encode riboswitch sequences, secondary structures, and ligand representations into a unified representation that captures riboswitch-ligand interaction context, while domain-informed rules encode explicit biochemical priors. Despite limited labeled data, this framework achieves strong predictive performance and improved data efficiency. It predicts min-max log-scaled pK<sub>d</sub> values and supports binary classification of binding strength, particularly by mitigating systematic overestimation of affinity. More broadly, the results suggest that LLM-based neuro-symbolic representations provide an effective route for modeling riboswitch-ligand interactions under data-limited conditions.</p>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148881201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Peptide barcoding: an alternative to the phenotype-genotype problem. 肽条形码:表型-基因型问题的另一种选择。
IF 5.6 2区 生物学
New biotechnology Pub Date : 2026-08-23 DOI: 10.1016/j.nbt.2026.08.007
Oliver Hong, Thibault Mayor, Jaya Joshi
{"title":"Peptide barcoding: an alternative to the phenotype-genotype problem.","authors":"Oliver Hong, Thibault Mayor, Jaya Joshi","doi":"10.1016/j.nbt.2026.08.007","DOIUrl":"10.1016/j.nbt.2026.08.007","url":null,"abstract":"<p><p>Barcoding methods are powerful tools for screening large libraries and have successfully been employed using DNA-centric approaches for over two decades. Yet despite the central role of proteins in most biological processes, protein-based barcoding methods have only recently emerged as a viable alternative. In this review we summarize recent advances in peptide barcoding and highlight its diverse applications, including screening of binding affinity, lipid nanoparticles, mRNA untranslated regions, and designed protein libraries. We discuss key challenges in barcode design, library construction, and mass spectrometry methods for accurate, scalable, and high-throughput screening. We propose that peptide barcoding represents a conceptual shift in genotype-phenotype mapping and will play an increasingly important role in AI-driven protein engineering, delivery technologies, and synthetic biology.</p>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":" ","pages":"17-22"},"PeriodicalIF":5.6,"publicationDate":"2026-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148808989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterization of an aromatic O-prenyltransferase from the edible mushroom Sparassis crispa 食用菌Sparassis crispa芳香型o -戊烯基转移酶的研究。
IF 4.9 2区 生物学
New biotechnology Pub Date : 2026-07-25 Epub Date: 2026-02-02 DOI: 10.1016/j.nbt.2026.01.015
Pimvisuth Chunkrua, Martijn Hazendonk, Peicheng Sun, Janniek H. Ritsema, Lucia Corrà, Jean-Paul Vincken, Willem J.H. van Berkel, Mirjam A. Kabel, Wouter J.C. de Bruijn
{"title":"Characterization of an aromatic O-prenyltransferase from the edible mushroom Sparassis crispa","authors":"Pimvisuth Chunkrua,&nbsp;Martijn Hazendonk,&nbsp;Peicheng Sun,&nbsp;Janniek H. Ritsema,&nbsp;Lucia Corrà,&nbsp;Jean-Paul Vincken,&nbsp;Willem J.H. van Berkel,&nbsp;Mirjam A. Kabel,&nbsp;Wouter J.C. de Bruijn","doi":"10.1016/j.nbt.2026.01.015","DOIUrl":"10.1016/j.nbt.2026.01.015","url":null,"abstract":"<div><div>Prenylated plant phenolics are a large group of secondary metabolites known for their bioactivity that is beneficial for plant and human alike, for example as antimicrobial agents against pathogenic microbes. However, the limited availability of prenylated phenolics, especially <em>O</em>-prenylated phenolics, and the complexity of the plant metabolite mixtures hinder bioactivity studies and further application. To explore approaches for more efficient production of prenylated phenolics, we produced and characterized a novel prenyltransferase (ScPT<sub>MY</sub>) from the edible mushroom <em>Sparassis crispa</em>. ScPT<sub>MY</sub> belongs to the dimethylallyl tryptophan synthase (DMATS) family and was found to primarily catalyze <em>O</em>-prenylation of structurally diverse phenolics. The best substrates included <span>l</span>-tryptophan, <span>l</span>-tyrosine, stilbenes, and isoflavonoids. The ScPT<sub>MY</sub> reactions predominantly yielded a single mono-<em>O</em>-prenylated product with an exception of the isoflavonoids, for which more products were obtained, including di-prenylated ones. Notably, we demonstrated the potential of this <em>O</em>-prenylating DMATS to enhance bioactivity by showing that enzymatic <em>O</em>4′-prenylation conferred antimicrobial activity to resveratrol, a compound with otherwise very poor antimicrobial activity. Finally, our phylogenetic analysis suggested the possibility of combining evolutionary relationships with structural insights to predict substrate scope and regioselectivity, while also revealing seven largely unexplored fungal DMATS clades that may harbor novel functions for biotechnological applications.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"93 ","pages":"Pages 21-32"},"PeriodicalIF":4.9,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146119631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Combining metabolic engineering and fermentation optimization to achieve cost-effective oil production by Cutaneotrichosporon oleaginosus 结合代谢工程和发酵优化,实现油梨皮三磷酸霉的高性价比产油
IF 4.9 2区 生物学
New biotechnology Pub Date : 2026-07-25 Epub Date: 2026-02-05 DOI: 10.1016/j.nbt.2026.01.017
Zeynep Efsun Duman-Özdamar , Rudolf Marcel Veloo , Elena Tsepani , Mattijs K. Julsing , Vitor A.P. Martins dos Santos , Jeroen Hugenholtz , Maria Suarez-Diez
{"title":"Combining metabolic engineering and fermentation optimization to achieve cost-effective oil production by Cutaneotrichosporon oleaginosus","authors":"Zeynep Efsun Duman-Özdamar ,&nbsp;Rudolf Marcel Veloo ,&nbsp;Elena Tsepani ,&nbsp;Mattijs K. Julsing ,&nbsp;Vitor A.P. Martins dos Santos ,&nbsp;Jeroen Hugenholtz ,&nbsp;Maria Suarez-Diez","doi":"10.1016/j.nbt.2026.01.017","DOIUrl":"10.1016/j.nbt.2026.01.017","url":null,"abstract":"<div><div>Microbial oils, produced by oleaginous microorganisms, offer a sustainable alternative to plant-derived oils. Among these microorganisms, <em>Cutaneotrichosporon oleaginosus</em> is a promising microbial cell factory for sustainable oil production due to its capacity to accumulate lipids with a similar composition to palm oil. Although <em>C. oleaginosus</em> can reach higher lipid contents than other oleaginous yeasts, enhanced productivity is still necessary to have a feasible microbial oil production process via <em>C. oleaginosus</em>. In this study, we followed a combinatorial approach for strain design and bioprocess development to improve the lipid content and lipid yield. Initially, we deployed a full factorial design with genetic factors (ATP-citrate lyase (<em>ACL</em>), acetyl-CoA carboxylase (<em>ACC</em>), threonine synthase (<em>TS</em>) and carbon-to-nitrogen ratio (C/N) in the medium. The C/N ratio appeared to have the most impact on oil accumulation. Combined with genetic modifications, lipid content and lipid yield increased by 1.6-fold. In a two-stage fermentation approach at a 2 L scale, the triple transformant overexpressing <em>ACL</em>, <em>ACC</em>, and <em>TS</em> outperformed the wild-type by achieving a lipid content of 75.4 % (w/w) with lipid productivity of 0.40 g L<sup>−1</sup> h<sup>−1</sup> and around 0.30 g lipids/g glycerol. In all, we established a cultivation strategy and strain that reached almost the theoretical maximum yield, and highest lipid content reported for a medium containing glycerol as a carbon source. These results strengthen the basis of using <em>C. oleaginous</em> as a platform for microbial oil production, thereby facilitating the development of processes substituting palm oil with a sustainable alternative.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"93 ","pages":"Pages 1-8"},"PeriodicalIF":4.9,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146135690","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterising complex metabolic responses in an engineered, cross-feeding microbial co-culture using quantitative proteomics 利用定量蛋白质组学表征工程交叉饲养微生物共培养中的复杂代谢反应。
IF 4.9 2区 生物学
New biotechnology Pub Date : 2026-07-25 Epub Date: 2026-02-04 DOI: 10.1016/j.nbt.2026.02.001
Mengxun Shi , Josie McQuillan , Caroline Evans , Yanmeng Liu , Xiaoxia Nina Lin , Brett Barney , Jagroop Pandhal
{"title":"Characterising complex metabolic responses in an engineered, cross-feeding microbial co-culture using quantitative proteomics","authors":"Mengxun Shi ,&nbsp;Josie McQuillan ,&nbsp;Caroline Evans ,&nbsp;Yanmeng Liu ,&nbsp;Xiaoxia Nina Lin ,&nbsp;Brett Barney ,&nbsp;Jagroop Pandhal","doi":"10.1016/j.nbt.2026.02.001","DOIUrl":"10.1016/j.nbt.2026.02.001","url":null,"abstract":"<div><div>Microbial communities play a key role in biogeochemical transformations in a wide range of ecosystems, but they also hold significant potential to enhance the bioproduction of desired chemicals. Although designing synthetic microbial consortia has generated a lot of interest, a more in-depth understanding of the interactions between strains is required, particularly when strains are engineered to cross-feed, but are not isolated from related environments. Challenges include enhancing stability, productivity and controllability. Here, we used a synthetic microbial co-culture consisting of engineered strains of the photosynthetic cyanobacterium <em>Synechococcus elongatus</em> PCC 7942 cscB/SPS and nitrogen-fixing bacterium <em>Azotobacter vinelandii</em> AV3. Each relies on the other for conversion of atmospheric carbon (CO<sub>2</sub>) and nitrogen (N<sub>2</sub>) into organic forms, <em>i.e.</em> sucrose and ammonia, respectively, resources which can be shared. As both strains have such contrasting growth dynamics in co-culture compared to monoculture, we applied a label-free quantitative proteomics approach to characterise metabolism in both strains. The proteomes of both shifted when in co-culture to reflect adaptive restructuring of carbon and nitrogen metabolism, although <em>A. vinelandii</em> appeared to transition to a more stressed state, inducing proteins linked to polymer biosynthesis. An analysis of the co-culture over 16 days led to phenotypic changes, including cell structure alterations in <em>A. vinelandii</em> AV3 over time, with the proteome suggesting cell envelope remodelling and potentially encystment. These findings suggest that physiological control of parameters, such as oxygen and nutrient availability, may enable cultivation of more stable co-cultures.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"93 ","pages":"Pages 9-20"},"PeriodicalIF":4.9,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146132493","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Advances in microbial strain selection and carbon source valorization for Polyhydroxyalkanoates (PHA) production 聚羟基烷酸酯(PHA)生产微生物菌种选择和碳源评价研究进展。
IF 4.9 2区 生物学
New biotechnology Pub Date : 2026-07-25 Epub Date: 2026-02-04 DOI: 10.1016/j.nbt.2026.01.016
William Mawuko Siegu , Piotr Drożdżyński , Vignesh Kumaravel , Olga Marchut-Mikołajczyk
{"title":"Advances in microbial strain selection and carbon source valorization for Polyhydroxyalkanoates (PHA) production","authors":"William Mawuko Siegu ,&nbsp;Piotr Drożdżyński ,&nbsp;Vignesh Kumaravel ,&nbsp;Olga Marchut-Mikołajczyk","doi":"10.1016/j.nbt.2026.01.016","DOIUrl":"10.1016/j.nbt.2026.01.016","url":null,"abstract":"<div><div>Polyhydroxyalkanoates (PHAs) are biodegradable polymers produced by various microorganisms as intracellular carbon and energy reserves. Their potential to replace petroleum-based plastics has made them central to sustainable materials research. However, their large-scale commercialization is hindered by high production costs, prompting efforts to improve yield and identify low-cost, non-food carbon sources. This review examines PHA biosynthesis optimization via advances in microbial strain-substrate selection ensuring economic feasibility. Focus is placed on three key bacterial genera, <em>Cupriavidus</em>, <em>Pseudomonas</em>, and <em>Escherichia coli</em> analyzing their metabolic flexibility, suitable substrate range and PHA content (g product/ g substrate). <em>Escherichia coli</em> species and <em>Cupriavidus necator</em> demonstrate high polymer contents from largely simple sugars and fatty-acid substrates respectively, while <em>Pseudomonas</em> species offer a broad substrate adaptability, particularly waste streams. The environmental impact assessment of some <em>Cupriavidus necator</em> and <em>Pseudomonas</em> strains highlight low carbon footprint from waste lipids compared to PHA production from glucose or bottle-grade PET, however these results are contingent to specific scenarios without a reproducible and quantifiable GWP values across these genera. Integrating microbial engineering of agro-industrial and organic wastes in adherence to regulatory frameworks around waste valorization and optimization, genus-specific LCA bioprocessing approach offers a path toward economically viable and environmentally sustainable PHA production.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"93 ","pages":"Pages 44-53"},"PeriodicalIF":4.9,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146132415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Beyond CAT, BSD, and URA: SUL, A novel selectable marker for Cyanidioschyzon merolae 继CAT、BSD和URA: SUL之后,一种新的菊苣可选标记。
IF 4.9 2区 生物学
New biotechnology Pub Date : 2026-07-25 Epub Date: 2026-02-03 DOI: 10.1016/j.nbt.2026.01.012
Yissell Borges-Rodríguez , Martha R. Stark , Elise Kerckhofs , Julie Mueller , Kyle J. Lauersen , Daniel Schubert , Stephen D. Rader
{"title":"Beyond CAT, BSD, and URA: SUL, A novel selectable marker for Cyanidioschyzon merolae","authors":"Yissell Borges-Rodríguez ,&nbsp;Martha R. Stark ,&nbsp;Elise Kerckhofs ,&nbsp;Julie Mueller ,&nbsp;Kyle J. Lauersen ,&nbsp;Daniel Schubert ,&nbsp;Stephen D. Rader","doi":"10.1016/j.nbt.2026.01.012","DOIUrl":"10.1016/j.nbt.2026.01.012","url":null,"abstract":"<div><div>The unicellular red alga <em>Cyanidioschyzon merolae</em> is a valuable model organism for studying pre-mRNA splicing, stress adaptation, and biotechnological applications. However, the limited availability of selectable markers has constrained its potential in genetic engineering. In this study, we evaluated the <em>sul1</em> gene, which encodes a sulfadiazine-resistant variant of dihydropteroate synthase, as a new selectable marker (SUL) for <em>C. merolae</em> transformation. SUL has previously been used for this purpose in plants and green algae. We analyzed the sensitivity of <em>C. merolae</em> to sulfadiazine and determined the concentration that effectively inhibited cell growth. To test the effectiveness of SUL as a selectable marker<strong>,</strong> we designed a transformation construct containing SUL directed to the algal mitochondria through a native targeting peptide, along with mVenus to visualize transformation. We integrated the construct into a neutral genomic locus via homologous recombination. Fluorescence microscopy confirmed stable mVenus expression, and sulfadiazine selection successfully enriched transformed cells. As a demonstration of the utility of this marker, we rescued the large-cell phenotype of a cell division cycle-like kinase 2 (CmClk2) mutant by replacing the CAT-marked kinase domain deletion with the SUL-marked native kinase domain, thereby restoring CmClk2 function and recycling the CAT marker. The deletion phenotype provides evidence for a conserved cell-cycle regulatory role for CmClk2 in <em>C. merolae</em>. Beyond establishing SUL as an effective selectable marker, this highlights how SUL facilitates functional genetic studies of essential cellular regulators.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"93 ","pages":"Pages 33-43"},"PeriodicalIF":4.9,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146125760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Semi-automated Ribosome Display for High-Throughput DARPin Binder Selection. 用于高通量DARPin粘结剂选择的半自动核糖体显示。
IF 5.6 2区 生物学
New biotechnology Pub Date : 2026-06-27 DOI: 10.1016/j.nbt.2026.06.007
Andri Häfliger, Sylvie Briand-Schumacher, Sven Furler, Birgit Dreier, Andreas Plückthun
{"title":"Semi-automated Ribosome Display for High-Throughput DARPin Binder Selection.","authors":"Andri Häfliger, Sylvie Briand-Schumacher, Sven Furler, Birgit Dreier, Andreas Plückthun","doi":"10.1016/j.nbt.2026.06.007","DOIUrl":"https://doi.org/10.1016/j.nbt.2026.06.007","url":null,"abstract":"<p><p>The combination of the Designed Ankyrin Repeat Protein (DARPin) scaffold with the selection and evolution technology of Ribosome Display has generated a wide range of specific binders to hundreds of target proteins. The binders have been used in a very diverse set of applications, from research through diagnostics to therapy. In this article, we focus on the high-throughput (HT) methods that we have developed for this purpose, which have been applied in many selections for research applications, but have never been explained in detail. We describe here the HT methods used to select for many targets in parallel, permitting the use of even different buffers and components, as well as some of the downstream characterization. To illustrate the workflow, we summarize the properties of some of the binders so obtained and their applications as well as the structures of the DARPin/target complexes. Together, these HT methods establish a robust framework for the rapid discovery and characterization of DARPins across a broad spectrum of targets.</p>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":" ","pages":""},"PeriodicalIF":5.6,"publicationDate":"2026-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148339467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The GigaAssay: A combined high throughput and highly accurate platform for variant classification GigaAssay:结合了高通量和高度准确的变异分类平台。
IF 4.9 2区 生物学
New biotechnology Pub Date : 2026-05-25 Epub Date: 2025-12-23 DOI: 10.1016/j.nbt.2025.12.001
Christopher J. Giacoletto , Liz J. Valente , Lancer Brown , Sara Patterson , Rewatee Gokhale , Susan M. Mockus , Wayne W. Grody , Hong-Wen Deng , Jerome I. Rotter , Martin R. Schiller
{"title":"The GigaAssay: A combined high throughput and highly accurate platform for variant classification","authors":"Christopher J. Giacoletto ,&nbsp;Liz J. Valente ,&nbsp;Lancer Brown ,&nbsp;Sara Patterson ,&nbsp;Rewatee Gokhale ,&nbsp;Susan M. Mockus ,&nbsp;Wayne W. Grody ,&nbsp;Hong-Wen Deng ,&nbsp;Jerome I. Rotter ,&nbsp;Martin R. Schiller","doi":"10.1016/j.nbt.2025.12.001","DOIUrl":"10.1016/j.nbt.2025.12.001","url":null,"abstract":"<div><div><em>ERBB2</em> (HER2) is a critical oncogene, yet the comprehensive and standardized assessment of its variant effects, particularly concerning receptor tyrosine kinase function, remains a major challenge. To compare the oncogenic potential of benchmark variants, we utilized the GigaAssay, a modular high-throughput one-pot assay system capable of simultaneously measuring their molecular function. We designed the GigaAssay to evaluate the relative oncogenic potential of HER2 variants by measuring HER2 phosphorylation at Y1248 (pHER2) in a ligand-free system. Using a benchmark dataset, the HER2 GigaAssay demonstrated robust performance, achieving 100 % accuracy, sensitivity, and F1 score in classifying gain-of-function (GOF) variants linked to hyperphosphorylation and wild type (WT) variants. Furthermore, the normalization of GOF HER2 variants revealed a gradient of elevated phosphorylation activity. Three previously reported oncogenic mutants (Q679L, L726F, and H878Y) were identified as non-pY1248 GOF mutations, aligning with literature and independent flow cytometry measurements, and highlighting the complexity of HER2 signaling. This study establishes the GigaAssay as a highly accurate and standardized platform for the precision classification of HER2 variant function.</div></div>","PeriodicalId":19190,"journal":{"name":"New biotechnology","volume":"92 ","pages":"Pages 79-88"},"PeriodicalIF":4.9,"publicationDate":"2026-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145834328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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