Noor Ul Huda, Noor Hassan, Hazrat Ali, Yingqian Kang
{"title":"Regulation and molecular biology of prodigiosin by <i>Serratia marcescens</i>.","authors":"Noor Ul Huda, Noor Hassan, Hazrat Ali, Yingqian Kang","doi":"10.1080/07388551.2025.2529588","DOIUrl":"https://doi.org/10.1080/07388551.2025.2529588","url":null,"abstract":"<p><p>Prodigiosin is an alkaloid, cell-associated, red pigment extensively produced as a secondary metabolite by Gram negative bacterium, <i>Serratia marcescens</i>. The red pigment holds immense recognition for multifunctional tri-pyrrole structure and as a promising candidate for wide array of industrial applications. The biosynthesis and regulation of prodigiosin in <i>S. marcescens</i> is a complex process, manifesting biological information at multiple cellular levels as genomics, transcriptomics and proteomics. The current review delves into molecular biology of <i>S. marcescens</i> highlighting it as a prolific producer of prodigiosin. This review also highlights crucial aspects of regulatory mechanisms for prodigiosin production in <i>S. marcescens</i>, along with recent advancements in strain improvement and heterologous production of pigment in industrially compliant host. In addition, this review integrates current knowledge on molecular biology and regulation of prodigiosin, addressing the approaches employed for high level of prodigiosin production, potential applications, challenges and future perspective for harnessing industrial potential of prodigiosin in future.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-20"},"PeriodicalIF":8.1,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144674062","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}
William R Newson, Eva Johansson, Konstantinos Papoutsis
{"title":"Holistic approach in the valorization of fruit and vegetable by-products generated through processing and postharvest storage.","authors":"William R Newson, Eva Johansson, Konstantinos Papoutsis","doi":"10.1080/07388551.2025.2529590","DOIUrl":"https://doi.org/10.1080/07388551.2025.2529590","url":null,"abstract":"<p><p>A large amount of fruit and vegetable waste is generated after harvest, during processing from the food industry and along the supply chain due to fresh produce quality deterioration. Fruit and vegetable waste may impact various sectors, such as the environment, economy, and society. In the last two decades, several studies have tried to mitigate the impact of fruit and vegetable waste by developing and optimizing extraction methods, targeting specific compounds without considering the value and further utilization of the remaining wet residue. Recently, biorefinery systems have been explored and developed for the holistic valorization of fruit and vegetable waste. The current research aims to summarize recent studies examining the valorization of different fruit and vegetable by-products using a holistic biorefinery approach. The various steps in a biorefinery process are presented and discussed. Biorefinery systems should be chosen and developed considering the presence or absence of fat-soluble compounds (i.e., oils) in fruit and vegetable waste. In the current study, different biorefinery systems are proposed based on fruit and vegetable waste composition. In conclusion, the phytochemicals and products produced during the biorefinery process can benefit various industries, such as: the food, pharmaceutical, cosmetics, transportation, chemical, heating, agricultural, and horticultural industries. Future multidisciplinary studies are encouraged to investigate the techno-economic and environmental impacts of the biorefinery processes.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-18"},"PeriodicalIF":8.1,"publicationDate":"2025-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144674061","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":"Comprehensive insights into microbial-derived antimicrobial peptides (AMPs): classification, mechanisms, applications, and purification strategies.","authors":"Hairun Pei, Kaiyue Bao, Tian Han, Xueli Cao","doi":"10.1080/07388551.2025.2518308","DOIUrl":"https://doi.org/10.1080/07388551.2025.2518308","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) play a crucial defensive role in living organisms, capable of rapidly responding to and eliminating invading microorganisms. Their mechanisms of action are diverse, primarily involving the disruption of microbial cell membranes. The interest in AMPs stems from their potential to address antibiotic resistance and improve human health. AMPs exhibit: broad-spectrum antimicrobial activity, low toxicity, thermal stability, and high specificity, making them promising candidates for new antimicrobial drugs with applications in medicine, food preservation, and agriculture. This review provides a comprehensive summary of the historical development and classification of AMPs. It details their: classification, mechanisms of action, application fields, and processes involved in the isolation, purification, and structural identification of microbial-derived AMPs. Additionally, it introduces a novel green extraction method using deep eutectic solvents (DESs) for peptide extraction.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-28"},"PeriodicalIF":8.1,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658632","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":"Modern approaches to engineering human reporter cell lines using CRISPR within Safe Harbor loci and endogenous genes.","authors":"A G Bykonya, D Y Guschin, N A Barlev","doi":"10.1080/07388551.2025.2515834","DOIUrl":"https://doi.org/10.1080/07388551.2025.2515834","url":null,"abstract":"<p><p>Reporter systems are gaining increasing popularity in modern molecular biology as they provide reliable and clear readouts for various types of assays, both <i>in cellulo</i> and <i>in vivo</i>. The generation of reporter cell lines is instrumental for screening activators and inhibitors of signaling pathways to develop new therapeutic approaches. Reporter cell lines are those with stably integrated reporter constructs containing signaling genes (often luciferase or fluorescent proteins), enabling the visualization and tracking of protein expression. Although seemingly harmless and straightforward, untargeted genomic integration of reporter genes may severely affect the expression of neighboring genes, causing unwanted and unpredictable effects. Unlike the untargeted approach, the CRISPR/Cas9 system provides a more precise method of reporter integration, especially when reporters are integrated into Safe Harbor loci. This ensures minimal influence on neighboring genomic regions. This review discusses recent advancements in creating reporter lines using the CRISPR/Cas9 system and experimental approaches for identifying suitable Safe Harbor loci.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-17"},"PeriodicalIF":8.1,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144658633","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}
Sadaf-Ilyas Kayani, Xinjuan Hu, Qian Shen, Bin Zou, Feifei Zhu, Zhen Yu, Muhammad Abdur Rehman Shah, Obaid Ur Rehman, Shuhao Huo
{"title":"Transcriptional control in microalgae: co-regulated fatty acid biosynthesis and carbon dioxide fixation.","authors":"Sadaf-Ilyas Kayani, Xinjuan Hu, Qian Shen, Bin Zou, Feifei Zhu, Zhen Yu, Muhammad Abdur Rehman Shah, Obaid Ur Rehman, Shuhao Huo","doi":"10.1080/07388551.2025.2503788","DOIUrl":"https://doi.org/10.1080/07388551.2025.2503788","url":null,"abstract":"<p><p>Microalgae are desirable candidates for performing about half of the World's organic carbon fixation and its conversion to essential metabolites of human metabolism, including polyunsaturated fatty acids (PUFAs). However, the yields of microalgal FAs produced naturally are typically insufficient to cover the expenses of their commercial utilization. To overcome this problem, gene engineering techniques have been used to change the activity of endogenous enzymes. This review aims to find knowledge about the mechanism of regulation of fatty acid (FA) biosynthesis and CO<sub>2</sub> fixation in microalgae. Firstly, this study discusses molecular strategies toward accelerating FA biosynthesis with a main emphasis on a critical review of transcriptional engineering. Some transcription factors (TFs) are known to increase FA content and related gene expression. However, a research gap is revealed toward understanding their regulatory mechanism and finding their role in regulating CO<sub>2</sub> fixation. Secondly, a critical review of studies on CO<sub>2</sub> fixation regulated by Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo) and RuBisCo activase (<i>RCA</i>) disclosed that no studies have yet been reported about their transcriptional control. Thirdly, prospects are given on the genetic basis of parallel transcriptional regulation of genes involved in FA biosynthesis and CO<sub>2</sub> fixation in microalgae. This study should potentially provide considerable knowledge on developing eco-friendly and sustainable microalgae genetic resources to maximize the yield of value-added FAs using TF engineering.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-22"},"PeriodicalIF":8.1,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144215178","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":"Harnessing <i>Bacillus</i> keratinases for sustainable keratin waste valorization: a current appraisal.","authors":"Pranshi Gupta, Isha Sharma, Naveen Kango","doi":"10.1080/07388551.2025.2495281","DOIUrl":"https://doi.org/10.1080/07388551.2025.2495281","url":null,"abstract":"<p><p>The global accumulation of keratin-rich waste, primarily from poultry and livestock industries, presents significant environmental and economic challenges. This review explores the potential of <i>Bacillus</i>-derived keratinases as a sustainable solution for keratin waste valorization and prospects of value-addition. Keratinases, the keratin hydrolyzing proteases produced predominantly by various <i>Bacillus</i> species, exhibit exceptional capability in degrading keratin, a highly stable and recalcitrant protein. This degradation process not only mitigates the environmental impact of keratin waste, but also converts it into valuable by-products with potential industrial applications. We systematically review various aspects, including: the production, properties and the mechanism of keratin degradation by <i>Bacillus</i> keratinases, highlighting their enzymatic properties, substrate specificity, and efficiency in valorizing keratin into peptides and amino acids. Biomolecular aspects and catalytic behavior relevant to the activity and stability of <i>Bacillus</i> keratinases are visited <i>via in silico</i> modeling. The economic and environmental benefits of utilizing keratinases for waste valorization are assessed, including reductions in waste disposal costs, greenhouse gas emissions, and the potential for creating new economic opportunities through the utilization of keratin-derived products. The recent advancements in keratin waste enzyme treatment and their utilization in developing circular bioeconomy are highlighted in the present article.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-24"},"PeriodicalIF":8.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207881","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}
Farhan Goher, Faiza Shafique Khan, Shengren Sun, Qinnan Wang
{"title":"Calcium-dependent protein kinase (CDPK/CPK)-mediated salicylic acid cascade: the key arsenal of plants under pathogens attack.","authors":"Farhan Goher, Faiza Shafique Khan, Shengren Sun, Qinnan Wang","doi":"10.1080/07388551.2025.2498463","DOIUrl":"https://doi.org/10.1080/07388551.2025.2498463","url":null,"abstract":"<p><p>Upon pathogen attack, cytosolic Ca<sup>2+</sup> levels increase in plant cells. The first innate immune response is activated by detecting microbe/pathogen-associated molecular patterns (MAMPs/PAMPs) and is called PAMPs-triggered immunity (PTI). The second immune response is triggered by recognizing pathogens' effector proteins named effectors-triggered immunity (ETI). Calcium-dependent protein kinases (CDPKs or CPKs) are well-known calcium sensors that have a mediator role both in PTI and ETI. Calcium can bind to the elongation factor (EF)-hand domain at the C-terminus of CDPKs, which then phosphorylates substrates at the N-terminal catalytic kinase domain to transfer calcium signals directly. Improving the stress resilience of crops is a critical strategy in attaining global food security. In plants, when a stimulus is seen, there is an increase in Ca<sup>2+</sup> concentration, which activates CDPKs which are in charge of sending out the immunological signals needed for disease tolerance. During the immune response, CDPKs are subject to numerous levels of regulation, including Ca<sup>2+</sup> dependency to decipher various Ca<sup>2+</sup> signals. Furthermore, salicylic acid (SA) regulation by CDPKs provides a comprehensive overview of CDPKs-mediated SA signaling during immune response in plants under pathogen attack. The critical part of CDPKs in SA biosynthesis, from the regulation of SA biosynthesis to how NPR1 perceives SA upon biotic stress, is comprehensively reviewed in this paper with the latest advancements in research. However, more research about CDPKs-mediated SA signaling under pathogen attack is mandatory to further dissect their co-role in crop protection against various diseases to achieve sustainable production goals in the future.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-17"},"PeriodicalIF":8.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207880","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":"Upcoming generation nanoengineered antimicrobial delivery system for targeting multidrug-resistant microbes.","authors":"Aditya Upadhyay, Dharm Pal, Awanish Kumar","doi":"10.1080/07388551.2025.2506611","DOIUrl":"https://doi.org/10.1080/07388551.2025.2506611","url":null,"abstract":"<p><p>The rise of chronic and acute infections has increased reliance on antimicrobial agents. However, conventional antimicrobials often fail to deliver optimal therapeutic outcomes due to limitations such as low bioavailability, poor biocompatibility, nonspecific targeting, drug-induced toxicity, and the growing issue of antimicrobial resistance. Therefore, the concept of a resistance-proof antimicrobial agent (RPAA) and its smart delivery was introduced to overcome the existing problem and a targeted delivery due to the specific properties, such as: high bioavailability, biocompatibility, low drug-induced toxicity, biodegradability, high binding capacity with the pathogen, multiple targeting delivery, etc. This system generates a positive impact and could quash the multidrug resistance problem. In this review, we discuss: the rationale for developing a nanoengineering-based smart-delivery system for RPAA, the advantageous properties of such a system, the possible mechanism of delivery, and challenges in the development of a nano-drug delivery therapeutics tool for RPAA delivery as a solution to combat the global problem of drug resistance. We emphasize the urgent need for the development of such a next-generation drug delivery system and discuss the opportunities/hurdles as well as the questions that remain to be addressed. The article is important because it sheds light on the properties of nanoengineered drug delivery that could initiate new ways of thinking about the development of future-generation delivery systems. The article shares a promising idea that would be an essential foundation for opening a new window in the field of drug discovery and development of the smart delivery system for RPAA.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"1-20"},"PeriodicalIF":8.1,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144207882","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":"Amplification-free nucleic acids detection with next-generation CRISPR/dx systems.","authors":"Cia-Hin Lau, Siping Huang, Haibao Zhu","doi":"10.1080/07388551.2024.2399560","DOIUrl":"10.1080/07388551.2024.2399560","url":null,"abstract":"<p><p>CRISPR-based diagnostics (CRISPR/Dx) have revolutionized the field of molecular diagnostics. It enables home self-test, field-deployable, and point-of-care testing (POCT). Despite the great potential of CRISPR/Dx in diagnoses of biologically complex diseases, preamplification of the template often is required for the sensitive detection of low-abundance nucleic acids. Various amplification-free CRISPR/Dx systems were recently developed to enhance signal detection at sufficient sensitivity. Broadly, these amplification-free CRISPR/Dx systems are classified into five groups depending on the signal enhancement strategies employed: CRISPR/Cas12a and/or CRISPR/Cas13a are integrated with: (1) other catalytic enzymes (Cas14a, Csm6, Argonaute, duplex-specific nuclease, nanozyme, or T7 exonuclease), (2) rational-designed oligonucleotides (multivalent aptamer, tetrahedral DNA framework, RNA G-quadruplexes, DNA roller machine, switchable-caged guide RNA, hybrid locked RNA/DNA probe, hybridized cascade probe, or \"U\" rich stem-loop RNA), (3) nanomaterials (nanophotonic structure, gold nanoparticle, micromotor, or microbeads), (4) electrochemical and piezoelectric plate biosensors (SERS nanoprobes, graphene field-effect transistor, redox probe, or primer exchange reaction), or (5) cutting-edge detection technology platforms (digital bioanalysis, droplet microfluidic, smartphone camera, or single nanoparticle counting). Herein, we critically discuss the advances, pitfalls and future perspectives for these amplification-free CRISPR/Dx systems in nucleic acids detection. The continued refinement of these CRISPR/Dx systems will pave the road for rapid, cost-effective, ultrasensitive, and ultraspecific on-site detection without resorting to target amplification, with the ultimate goal of establishing CRISPR/Dx as the paragon of diagnostics.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"859-886"},"PeriodicalIF":8.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142281514","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":"Pilot scale polyhydroxyalkanoates biopolymer production using pure cultures: current status and future opportunities.","authors":"Phavit Wongsirichot","doi":"10.1080/07388551.2024.2409112","DOIUrl":"10.1080/07388551.2024.2409112","url":null,"abstract":"<p><p>The development and commercialization of bio-based and biodegradable polyhydroxyalkanoates (PHAs) biopolymers could be crucial for the transition toward a sustainable circular economy. However, despite potential traditional and novel applications in the packaging, textiles, agriculture, automotive, electronics, and biomedical industries, the commercialization of PHAs is limited by their current market competitiveness. This review provides the first critical assessment of the current pure culture pilot-scale PHA literature, which could be crucial in translating promising laboratory-scale developments into industrial-scale commercial PHA production. It will also complement reviews of mixed microbial cultures currently dominating pilot-scale PHA literature. Pure culture fermentations could provide advantages, such as ease of characterizing microbial producers' behavior, higher PHA productivities, and better alignment with existing PHA commercialization and industrial biotechnology approaches. Key aspects, including producer organisms, fermentation volumes and schemes, control schemes, optimization, and properties of the polymers produced, are discussed in-depth, to elucidate important trends, achievements, and knowledge gaps. Furthermore, specific ways for future pilot-scale studies to help address current PHA commercialization challenges are also identified. The insights, and recommendations provided will be extremely beneficial for the future development of PHA production, at both pilot and commercial scales, whilst also being beneficial to the production of other microbial polymers and industrial biotechnology as a whole.</p>","PeriodicalId":10752,"journal":{"name":"Critical Reviews in Biotechnology","volume":" ","pages":"887-903"},"PeriodicalIF":8.1,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142459844","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}