Yingjie Song, Chunlin Long, Ying Wang, Yuxing An, Yinglin Lu
{"title":"Advancements in multi-omics for nutraceutical enhancement and traits improvement in buckwheat.","authors":"Yingjie Song, Chunlin Long, Ying Wang, Yuxing An, Yinglin Lu","doi":"10.1080/07388551.2024.2373282","DOIUrl":"10.1080/07388551.2024.2373282","url":null,"abstract":"<p><p>Buckwheat (<i>Fagopyrum</i> spp.) is a typical pseudocereal, valued for its extensive nutraceutical potential as well as its centuries-old cultivation. Tartary buckwheat and common buckwheat have been used globally and become well-known nutritious foods due to their high quantities of: proteins, flavonoids, and minerals. Moreover, its increasing demand makes it critical to improve nutraceutical, traits and yield. In this review, bioactive compounds accumulated in buckwheat were comprehensively evaluated according to their chemical structure, properties, and physiological function. Biosynthetic pathways of flavonoids, phenolic acids, and fagopyrin were methodically summarized, with the regulation of flavonoid biosynthesis. Although there are classic synthesis pathways presented in the previous research, the metabolic flow of how these certain compounds are being synthesized in buckwheat still remains uncovered. The functional genes involved in the biosynthesis of flavonols, stress response, and plant development were identified based on multi-omics research. Furthermore, it delves into the applications of multi-omics in improving buckwheat's agronomic traits, including: yield, nutritional content, stress resilience, and bioactive compounds biosynthesis. While pangenomics combined with other omics to mine elite genes, the regulatory network and mechanism of specific agronomic traits and biosynthetic of bioactive components, and developing a more efficient genetic transformation system for genetic engineering require further investigation for the execution of breeding designs aimed at enhancing desirable traits in buckwheat. This critical review will provide a comprehensive understanding of multi-omics for nutraceutical enhancement and traits improvement in buckwheat.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"530-555"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T P Tim Cushnie, Vijitra Luang-In, Darren W Sexton
{"title":"Necrophages and necrophiles: a review of their antibacterial defenses and biotechnological potential.","authors":"T P Tim Cushnie, Vijitra Luang-In, Darren W Sexton","doi":"10.1080/07388551.2024.2389175","DOIUrl":"10.1080/07388551.2024.2389175","url":null,"abstract":"<p><p>With antibiotic resistance on the rise, there is an urgent need for new antibacterial drugs and products to treat or prevent infection. Many such products in current use, for example human and veterinary antibiotics and antimicrobial food preservatives, were discovered and developed from nature. Natural selection acts on all living organisms and the presence of bacterial competitors or pathogens in an environment can favor the evolution of antibacterial adaptations. In this review, we ask if vultures, blow flies and other carrion users might be a good starting point for antibacterial discovery based on the selection pressure they are under from bacterial disease. Dietary details are catalogued for over 600 of these species, bacterial pathogens associated with the diets are described, and an overview of the antibacterial defenses contributing to disease protection is given. Biotechnological applications for these defenses are then discussed, together with challenges facing developers and possible solutions. Examples include use of (a) the antimicrobial peptide (AMP) gene <i>sarcotoxin IA</i> to improve crop resistance to bacterial disease, (b) peptide antibiotics such as serrawettin W2 as antibacterial drug leads, (c) lectins for targeted drug delivery, (d) bioconversion-generated chitin as an antibacterial biomaterial, (e) bacteriocins as antibacterial food preservatives and (f) mutualistic microbiota bacteria as alternatives to antibiotics in animal feed. We show that carrion users encounter a diverse range of bacterial pathogens through their diets and interactions, have evolved many antibacterial defenses, and are a promising source of genes, molecules, and microbes for medical, agricultural, and food industry product development.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"625-642"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142092502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Khin Myo Myo Tint, Xin Wei, Peng Wang, Guang-Lei Liu, Mei Zhang, Zhen-Ming Chi, Zhe Chi
{"title":"Biotechnological application of <i>Aureobasidium</i> spp. as a promising chassis for biosynthesis of ornithine-urea cycle-derived bioproducts.","authors":"Khin Myo Myo Tint, Xin Wei, Peng Wang, Guang-Lei Liu, Mei Zhang, Zhen-Ming Chi, Zhe Chi","doi":"10.1080/07388551.2024.2382954","DOIUrl":"10.1080/07388551.2024.2382954","url":null,"abstract":"<p><p>The ornithine-urea cycle (OUC) in fungal cells has biotechnological importance and many physiological functions and is closely related to the acetyl glutamate cycle (AGC). Fumarate can be released from argininosuccinate under the catalysis of argininosuccinate lyase in OUC which is regulated by the Ca<sup>2+</sup> signaling pathway and over 93.9 ± 0.8 g/L fumarate can be yielded by the engineered strain of <i>Aureobasidium pullulans</i> var. <i>aubasidan</i>i in the presence of CaCO<sub>3</sub>. Furthermore, 2.1 ± 0.02 mg of L-ornithine (L-Orn)/mg of the protein also can be synthesized <i>via</i> OUC by the engineered strains of <i>Aureobasidum melanogenum</i>. Fumarate can be transformed into many drugs and amino acids and L-Orn can be converted into siderophores (1.7 g/L), putrescine (33.4 g/L) and L-piperazic acid (L-Piz) (3.0 g/L), by different recombinant strains of <i>A. melanogenum</i>. All the fumarate, L-Orn, siderophore, putrescine and L-Piz have many applications. As the yeast-like fungi and the promising chassis, <i>Aureobasidium</i> spp, have many advantages over any other fungal strains. Further genetic manipulation and bioengineering will enhance the biosynthesis of fumarate and L-Orn and their derivates.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"591-605"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142003803","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chinmaya Panda, Sachin Kumar, Sharad Gupta, Lalit M Pandey
{"title":"Insulin fibrillation under physicochemical parameters of bioprocessing and intervention by peptides and surface-active agents.","authors":"Chinmaya Panda, Sachin Kumar, Sharad Gupta, Lalit M Pandey","doi":"10.1080/07388551.2024.2387167","DOIUrl":"10.1080/07388551.2024.2387167","url":null,"abstract":"<p><p>Even after the centenary celebration of insulin discovery, there prevail challenges concerning insulin aggregation, not only after repeated administration but also during industrial production, storage, transport, and delivery, significantly impacting protein quality, efficacy, and effectiveness. The aggregation reduces insulin bioavailability, increasing the risk of heightened immunogenicity, posing a threat to patient health, and creating a dent in the golden success story of insulin therapy. Insulin experiences various physicochemical and mechanical stresses due to modulations in pH, temperature, ionic strength, agitation, shear, and surface chemistry, during the upstream and downstream bioprocessing, resulting in insulin unfolding and subsequent fibrillation. This has fueled research in the pharmaceutical industry and academia to unveil the mechanistic insights of insulin aggregation in an attempt to devise rational strategies to regulate this unwanted phenomenon. The present review briefly describes the impacts of environmental factors of bioprocessing on the stability of insulin and correlates with various intermolecular interactions, particularly hydrophobic and electrostatic forces. The aggregation-prone regions of insulin are identified and interrelated with biophysical changes during stress conditions. The quest for novel additives, surface-active agents, and bioderived peptides in decelerating insulin aggregation, which results in overall structural stability, is described. We hope this review will help tackle the real-world challenges of insulin aggregation encountered during bioprocessing, ensuring safer, stable, and globally accessible insulin for efficient management of diabetes.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"643-664"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141981916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Precise metabolic modeling in post-omics era: accomplishments and perspectives.","authors":"Yawen Kong, Haiqin Chen, Xinlei Huang, Lulu Chang, Bo Yang, Wei Chen","doi":"10.1080/07388551.2024.2390089","DOIUrl":"10.1080/07388551.2024.2390089","url":null,"abstract":"<p><p>Microbes have been extensively utilized for their sustainable and scalable properties in synthesizing desired bio-products. However, insufficient knowledge about intracellular metabolism has impeded further microbial applications. The genome-scale metabolic models (GEMs) play a pivotal role in facilitating a global understanding of cellular metabolic mechanisms. These models enable rational modification by exploring metabolic pathways and predicting potential targets in microorganisms, enabling precise cell regulation without experimental costs. Nonetheless, simplified GEM only considers genome information and network stoichiometry while neglecting other important bio-information, such as enzyme functions, thermodynamic properties, and kinetic parameters. Consequently, uncertainties persist particularly when predicting microbial behaviors in complex and fluctuant systems. The advent of the omics era with its massive quantification of genes, proteins, and metabolites under various conditions has led to the flourishing of multi-constrained models and updated algorithms with improved predicting power and broadened dimension. Meanwhile, machine learning (ML) has demonstrated exceptional analytical and predictive capacities when applied to training sets of biological big data. Incorporating the discriminant strength of ML with GEM facilitates mechanistic modeling efficiency and improves predictive accuracy. This paper provides an overview of research innovations in the GEM, including multi-constrained modeling, analytical approaches, and the latest applications of ML, which may contribute comprehensive knowledge toward genetic refinement, strain development, and yield enhancement for a broad range of biomolecules.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"683-701"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142092503","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Strategic approaches for designing yeast strains as protein secretion and display platforms.","authors":"Luping Xu, Xingjian Bai, Eun Joong Oh","doi":"10.1080/07388551.2024.2385996","DOIUrl":"10.1080/07388551.2024.2385996","url":null,"abstract":"<p><p>Yeast has been established as a versatile platform for expressing functional molecules, owing to its well-characterized biology and extensive genetic modification tools. Compared to prokaryotic systems, yeast possesses advanced cellular mechanisms that ensure accurate protein folding and post-translational modifications. These capabilities are particularly advantageous for the expression of human-derived functional proteins. However, designing yeast strains as an expression platform for proteins requires the integration of molecular and cellular functions. By delving into the complexities of yeast-based expression systems, this review aims to empower researchers with the knowledge to fully exploit yeast as a functional platform to produce a diverse range of proteins. This review includes an exploration of the host strains, gene cassette structures, as well as considerations for maximizing the efficiency of the expression system. Through this in-depth analysis, the review anticipates stimulating further innovation in the field of yeast biotechnology and protein engineering.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"491-508"},"PeriodicalIF":8.1,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141975325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biomaterials for eco-friendly packaging in dairy products: towards a cleaner, greener, and sustainable future.","authors":"Vandana Chaudhary, Priyanka Kajla, Parveen Kumari, Ankur Luthra, Seema Ramniwas, Sarvesh Rustagi, R Pandiselvam","doi":"10.1080/07388551.2025.2482951","DOIUrl":"https://doi.org/10.1080/07388551.2025.2482951","url":null,"abstract":"<p><p>Milk and milk products are very susceptible to spoilage and therefore, suitable innovative packaging strategies are indispensable to enhance shelf life along with maintaining quality and safety. Transformation in the utilization of packaging materials and technologies in the dairy sector is trending to match and meet the changing demands of consumers aware of this. Smart, intelligent, and active packagings are a few innovative packaging strategies that aim at protracting the shelf stability of milk and milk products while enhancing safety and sensory qualities. Other packaging innovations also include the use of different packaging systems which are not only safe, compatible with food, and stable over a wide range of storage conditions but are more eco-friendly and thus posing the least possible burden on the environment. In this review, the authors attempt to compile innovative green packaging technologies for different dairy products. The properties and applications of biomaterials used for smart, active, and intelligent packaging of milk and milk products, such as: pasteurized milk, evaporated milk, sweetened milk, condensed milk, milk powder, along with: ice cream, butter, coagulated dairy products, and heat-desiccated milk products are briefly discussed. Environmental impact, safety regulations as well as challenges in the implementation of different innovative packaging technologies in the dairy sector are also covered. The use of eco-friendly packaging innovative approaches in terms of improved biodegradability and lesser environmental hazards aims to achieve environmental sustainability goals for a clean and green future.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-28"},"PeriodicalIF":8.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rubab Shabbir, Talha Javed, Wang Wenzhi, Chang Yating, Yang Benpeng, Shen Linbo, Sun Tingting, Zhang Shuzhen, Pinghua Chen
{"title":"Insights into recent advances in secondary metabolites (SMs)-mediated defense responses in plants.","authors":"Rubab Shabbir, Talha Javed, Wang Wenzhi, Chang Yating, Yang Benpeng, Shen Linbo, Sun Tingting, Zhang Shuzhen, Pinghua Chen","doi":"10.1080/07388551.2025.2484598","DOIUrl":"https://doi.org/10.1080/07388551.2025.2484598","url":null,"abstract":"<p><p>Climate change induces various environmental stressors that restrict plant processes, thereby limiting overall crop productivity. Plant secondary metabolites (SMs) enable plants to quickly detect a broad array of environmental stressors and respond in accordance to rapidly changing environmental scenarios. Notably, SMs regulate defense signaling cascades and provide defensive functions to safeguard plants against various biotic and abiotic stressors. In this review, we provide an overview of insights into recent advances in types and biosynthetic pathways of SMs. We emphasize the mechanisms of different biotic and abiotic elicitors-induced SMs synthesis and accumulation to regulate defense responses. In addition, SMs-mediated regulation of plant processes act through phytohormones signaling cascades is discussed. Finally, we show that transcriptional factors regulating SMs biosynthesis and associated regulatory networks could be used for creating resilient plants. Overall, this comprehensive review gives insight into recent advances regarding crucial roles of SMs in enhanced resistance and provides new ideas for the development of stress-resistant varieties under current climate change scenarios.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-15"},"PeriodicalIF":8.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143984092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"<i>AREB/ABF/ABI5</i> transcription factors in plant defense: regulatory cascades and functional diversity.","authors":"Atif Ayub, Talha Javed, Airish Nayab, Yunyou Nan, Yuyu Xie, Sadam Hussain, Yousuf Shafiq, Hui Tian, Jing Hui, Yajun Gao","doi":"10.1080/07388551.2025.2475127","DOIUrl":"10.1080/07388551.2025.2475127","url":null,"abstract":"<p><p>Basic leucine zipper transcription factors (TFs), also known as ABRE-BINDING PROTEINs/ABRE BINDING FACTORs (<i>AREBs/ABFs</i>), and ABA INSENSITIVE 5 (<i>ABI5</i>), show a great potential for the regulation of gene expressions in different crops under unfavorable conditions. These factors are involved in phytohormone signaling pathways, developmental metabolism, and growth regulation under environmental stresses. <i>ABI5</i> functions alongside <i>ABREs</i> to regulate gene expression, with their promoter regions composed of the receptors <i>PYR/PYL/RCAR</i>, kinases (sucrose non-fermenting-1-related protein kinase 2) and phosphatases (PROTEIN PHOSPHATASE 2 C). These TFs participate in signaling pathways that regulate key genes and control numerous morphological, physiological, biochemical, and molecular processes under stressful environments. In this review, we studied <i>ABFs/AREBs/ABI5s</i> TFs, the phytohormone signaling pathways and their crosstalk, which play critical roles in regulating responses to abiotic stresses. The key TFs discussed in this work regulate various metabolic pathways and are promising candidates for the development of stress-resilient crops <i>via</i> CRISPR/CRISPR-associated protein technology to address threats to food security and sustainability in agriculture.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-21"},"PeriodicalIF":8.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143967284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lin Fan, Ting Shi, Xuemei Chen, Yunjie Li, Pingping Han, Peter Ruhdal Jensen, Yi-Heng P Job Zhang
{"title":"Biosynthesis of a healthy natural sugar D-tagatose: advances and opportunities.","authors":"Lin Fan, Ting Shi, Xuemei Chen, Yunjie Li, Pingping Han, Peter Ruhdal Jensen, Yi-Heng P Job Zhang","doi":"10.1080/07388551.2025.2489424","DOIUrl":"https://doi.org/10.1080/07388551.2025.2489424","url":null,"abstract":"<p><p>D-tagatose is a natural low-calorie rare sugar with nearly the same sweet taste as sucrose. It has nutritional and functional properties of great interest for health, such as anti-diabetes, anti-caries, anti-atherosclerosis, anti-hyperlipidemia, anti-aging, improvement of intestinal microflora, etc. The production of D-tagatose from D-galactose catalyzed by an alkali suffers from limited supplies of costly feedstock (i.e., lactose) and high manufacturing costs due to harsh reaction conditions, costly separation, as well as severe degradation and pollution. In this review, we briefly present the properties of D-tagatose and its physiological effects, review the recent advances in the biosynthesis of D-tagatose from inexpensive and abundant glucans (e.g., starch) and their derivatives (e.g., D-glucose and D-fructose) and from lactose, including both academic literature and industrial patents, as well as discuss its future challenges and opportunities. The biosynthesis of D-tagatose can be catalyzed by four types of biocatalysts: enzymes, whole-cells, microbial fermentation, and <i>in vitro</i> multi-enzyme molecular machines. The biomanufacturing of starchy D-tagatose catalyzed by multi-enzyme molecular machines could be the most promising approach because it not only makes D-tagatose from ample starch but also surpasses the equilibria of monosaccharide isomerization reactions (e.g., D-fructose-to-D-tagatose, D-galactose-to-D-tagatose). D-tagatose as a filler for a variety of food and drinks or a key component mixed with other sweeteners would become a predominant starch-derived sweetener and partially replace high-fructose corn sirup in the future.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-16"},"PeriodicalIF":8.1,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143987172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}