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An innovative obligate mobile element guided activity (OMEGA)-R system integrates SpyCatcher-enIscB and PolI3M-TBD-SpyTag, offering superior performance in targeted random mutagenesis compared with existing technologies.OMEGA-R achieves a mutation rate of 1.4 × 10–5 base pairs per generation and an extended window length, crucial for continuous evolution processes.OMEGA-R has good adaptability with high-throughput screening technologies, including fluorescence-activated droplet sorting (FADS) and phage-assisted continuous evolution (PACE).High-performance GFP and autocyclizing ribozyme mutants valuable for developing advanced biotechnology tools are successfully obtained by OMEGA-R.OMEGA-R has broad application potential for identifying a range of mutants, particularly industrial enzymes with economic benefits, in gene-editing systems, pharmaceutical synthesis, food processing, biological carbon fixation, biofuel production, and in generating targeted mutant libraries for crop and microbial breeding. Targeted random mutagenesis is crucial for breeding, directed evolution, and gene function studies, yet efficient tools remain scarce. Here, we present obligate mobile element guided activity (OMEGA)-R, an innovative targeted random mutagenesis system that integrates SpyCatcher-enIscB and PolI3M-TBD-SpyTag, outperforming existing state-of-the-art technologies in key metrics, such as protein size, mutagenesis efficiency, window length, and continuity. OMEGA-R achieves a dramatic enhancement of on-target mutagenesis, reaching a rate of 1.4 × 10–5 base pairs (bp) per generation (bpg), with minimal off-target effects, in both Escherichia coli and Bacillus subtilis. The system also demonstrates exceptional compatibility with high-throughput screening (HTS) technologies, including fluorescence-activated droplet sorting (FADS) and phage-assisted continuous evolution (PACE). Utilizing OMEGA-R, we successfully identified a series of effective mutations within the T7 promoter (pT7), ribosome-binding site (RBS), superfolder GFP (sfGFP), and autocyclizing ribozyme (AR), which are invaluable for the development of high-performance biotechnology tools. These findings underscore the high efficiency and broad application potential of OMEGA-R. [Display omitted] The obligate mobile element guided activity (OMEGA)-R system presented in this study has achieved a Technology Readiness Level (TRL) of 4, signifying its successful laboratory validation using well-characterized Escherichia coli and Bacillus subtilis strains and two state-of-the-art high-throughput screening technologies. While OMEGA-R has demonstrated significant improvements in mutagenesis efficiency and window length, several challenges must be addressed before it can be fully implemented. These include improving mutagenesis efficiency and controllability, reducing its target adjacent motif (TAM) dependency, conducting more comprehensive application testing, and optimizing delivery methods for in vivo applications. Overcoming these challenges will require advances in directed evolution and enzyme-engineering techniques, such as the development of more effective and TAM-independent IscB mutants to broaden the application of OMEGA-R, as well as the refinement of delivery techniques, such as the development of more effective lipid nanoparticles or viral vectors. In addition, the implementation of OMEGA-R in clinical settings will depend on obtaining regulatory approval and developing comprehensive guidelines to ensure safety and efficacy. Upon fulfillment of these readiness criteria, the OMEGA-R system will be recognized as a potential method for mutagenesis breeding, directed evolution, and gene therapy, as well as a robust approach for expanding the toolkit available for genome editing applications. Obligate mobile element guided activity (OMEGA)-R represents a significant progress in targeted gene random mutagenesis, integrating SpyCatcher-enIscB and PolI3M-TBD-SpyTag to streamline the generation of mutant libraries for genes of interest. This system is designed to seamlessly combine with downstream high-throughput screening technologies, thereby significantly accelerating the processes involved in directed evolution.

A robust three-tier cocktail of random mutagenesis involving atmospheric and room temperature plasma, gamma-rays, and N -methyl- N’ -nitro- N -nitrosoguanidine exposures was applied to induce glycolipopeptide overproduction in Pseudomonas aeruginosa strain IKW1 (GenBank Accession No.: PV664482.1). Auxanographic investigations suggested unrepaired metabolic blocking of the threonine, and hence, isoleucine branches of the aspartate pathway in the overproducing mutant, Thr − Ile − PGN4. Glycolipopeptide overproduction significantly correlated with increases in urease activity, Ni 2+ uptake, cytosolic Ni 2+ localization and upregulation of histidine biosynthesis. Scalability by batch fermentation in modified optimized medium in 5-L bioreactor led to 1.24-fold higher volumetric oxygen transfer coefficient, k L a , with an oxygen uptake rate (OUR) of 18.6 mmol O 2 gDCW − 1 h − 1 , which resulted in 3.86-fold higher glycolipopeptide productivity. Periodic biochemical and thin layer chromatographic analysis revealed trophophasic synthesis of a functional surface-active rhamnolipid base with surface (SFT) and interfacial (IFT) tension reductions to 29.74 dynes cm − 1 and 2.22 dynes cm − 1 , respectively. A late idiophasic peptidation of the rhamnolipid base further reduced SFT and IFT to 24.41 and 0.87 dynes cm − 1 , respectively. Superior catalysis by catechol 1,2-dioxygenase favored glycolipopeptide-mediated crude oil degradation by Pseudomonas putida strain ATCC 49,182 compared to commercial biosurfactants giving rate constants of 0.115 d − 1 (glycolipopeptide), 0.087 d − 1 (di-rhamnolipid), 0.096 d − 1 (surfactin) and 0.065 d − 1 (without surfactant). The technology is recommended for sustainable glycolipopeptide production toward efficient crude oil-impacted ecosystems’ bioremediation.

Functional regions that regulate biological phenomena are interspersed throughout eukaryotic genomes. The most definitive approach for identifying such regions is to confirm the phenotype of cells or organisms in which specific regions have been mutated or removed from the genome. This approach is invaluable for the functional analysis of genes with a defined functional element, the protein-coding sequence. By contrast, no functional analysis platforms have been established for the study of cis-elements or microRNA cluster regions consisting of multiple microRNAs with functional overlap. Whole-genome mutagenesis approaches, such as via N-ethyl-N-nitrosourea and gene trapping, have greatly contributed to elucidating the function of coding genes. These methods almost never induce deletions of genomic regions or multiple mutations within a narrow region. In other words, cis-elements and microRNA clusters cannot be effectively targeted in such a manner. Herein, we established a novel region-specific random mutagenesis method named CRISPR- and transposase-based regional mutagenesis (CTRL-mutagenesis). We demonstrate that CTRL-mutagenesis randomly induces diverse mutations within target regions in murine embryonic stem cells. Comparative analysis of mutants harbouring subtly different mutations within the same region would facilitate the further study of cis-element and microRNA clusters.

Streptomyces 5.1 is a bacterium isolated from rice soils in the south of the Tolima department (Colombia). This microorganism is characterized by its antagonistic activity against rubber tree phytopathogens like Colletotrichum gloeosporioides, the causal agent of leaf anthracnose. The antifungal activity of this Streptomyces isolate has been associated with secondary metabolites production. However, the identity of those metabolites is unknown because its purification and identification have not been possible through classic chemical studies. Therefore, aiming to contribute in the study of the secondary metabolites produced by 5.1 from a molecular approach, this research seeks to identify -preliminarily- the genomic fingerprint changes associated with the production of antifungal secondary metabolites produced by Streptomyces 5.1 through the evaluation of a mutant library of 5.1 obtained by random mutagenesis using controlled ultraviolet light exposure. The antifungal activity of obtained mutants was evaluated using Colletotrichum gloeosporioides (C1) fungus as a biosensor, isolated by the Biotechnology Institute of Universidad Nacional de Colombia. In this way, the library of mutants of 5.1, initially formed by 300 isolations, was classified into two phenotypic groups of interest: enhanced mutants (1 isolate) and null mutants (11 isolates) of secondary metabolites. The genomic changes in both groups were analyzed by obtaining the genomic profile of the isolates using Repetitive Extragenic Palindromic (Rep-PCR). The obtained profiles evidenced the presence of one additional band in the enhanced mutant, and the absence of a specific band in the non-producing mutants, both in comparison with the original strain. These bands are proposed for a future sequencing study which will define their role in the production process of metabolites with antifungal activity in Streptomyces 5.1.

The marine microalga Nannochloropsis oculata is a bioproducer of eicosapentaenoic acid (EPA), a fatty acid. EPA is incorporated into monogalactosyldiacylglycerol within N. oculata thylakoid membranes, and there is a biotechnological need to remodel EPA synthesis to maximize production and simplify downstream processing. In this study, random mutagenesis and chemical inhibitor-based selection method were devised to increase EPA production and accessibility for improved extraction. Ethyl methanesulfonate was used as the mutagen with selective pressure achieved by using two enzyme inhibitors of lipid metabolism: cerulenin and galvestine-1. Fatty acid methyl ester analysis of a selected fast-growing mutant strain had a higher percentage of EPA (37.5% of total fatty acids) than the wild-type strain (22.2% total fatty acids), with the highest EPA quantity recorded at 68.5 mg/g dry cell weight, while wild-type cells had 48.6 mg/g dry cell weight. Label-free quantitative proteomics for differential protein expression analysis revealed that the wild-type and mutant strains might have alternative channeling pathways for EPA synthesis. The mutant strain showed potentially improved photosynthetic efficiency, thus synthesizing a higher quantity of membrane lipids and EPA. The EPA synthesis pathways could also have deviated in the mutant, where fatty acid desaturase type 2 (13.7-fold upregulated) and lipid droplet surface protein (LDSP) (34.8-fold upregulated) were expressed significantly higher than in the wild-type strain. This study increases the understanding of EPA trafficking in N. oculata , leading to further strategies that can be implemented to enhance EPA synthesis in marine microalgae.

Adeno-associated virus (AAV) capsids can deliver transformative gene therapies, but our understanding of AAV biology remains incomplete. We generated the complete first-order AAV2 capsid fitness landscape, characterizing all single-codon substitutions, insertions, and deletions across multiple functions relevant for in vivo delivery. We discovered a frameshifted gene in the VP1 region that expresses a membrane-associated accessory protein that limits AAV production through competitive exclusion. Mutant biodistribution revealed the importance of both surface-exposed and buried residues, with a few phenotypic profiles characterizing most variants. Finally, we algorithmically designed and experimentally verified a diverse in vivo targeted capsid library with viability far exceeding random mutagenesis approaches. These results demonstrate the power of systematic mutagenesis for deciphering complex genomes and the potential of empirical machine-guided protein engineering.

Targeted saturation mutagenesis of crop genes could be applied to produce genetic variants with improved agronomic performance. However, tools for directed evolution of plant genes, such as error-prone PCR or DNA shuffling, are limited 1 . We engineered five saturated targeted endogenous mutagenesis editors (STEMEs) that can generate de novo mutations and facilitate directed evolution of plant genes. In rice protoplasts, STEME-1 edited cytosine and adenine at the same target site with C > T efficiency up to 61.61% and simultaneous C > T and A > G efficiency up to 15.10%. STEME-NG, which incorporates the nickase Cas9-NG protospacer-adjacent motif variant, was used with 20 individual single guide RNAs in rice protoplasts to produce near-saturated mutagenesis (73.21%) for a 56-amino-acid portion of the rice acetyl-coenzyme A carboxylase (OsACC). We also applied STEME-1 and STEME-NG for directed evolution of the OsACC gene in rice and obtained herbicide resistance mutations. This set of two STEMEs will accelerate trait development and should work in any plants amenable to CRISPR-based editing. Saturation mutagenesis using dual base editors improves the herbicide resistance of rice.

With the rapid increase in the global population and the impact of climate change on agriculture, there is a need for crops with higher yields and greater tolerance to abiotic stress. However, traditional crop improvement via genetic recombination or random mutagenesis is a laborious process and cannot keep pace with increasing crop demand. Genome editing technologies such as clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) allow targeted modification of almost any crop genome sequence to generate novel variation and accelerate breeding efforts. We expect a gradual shift in crop improvement away from traditional breeding towards cycles of targeted genome editing. Crop improvement using genome editing is not constrained by limited existing variation or the requirement to select alleles over multiple breeding generations. However, current applications of crop genome editing are limited by the lack of complete reference genomes, the sparse knowledge of potential modification targets, and the unclear legal status of edited crops. We argue that overcoming technical and social barriers to the application of genome editing will allow this technology to produce a new generation of high-yielding, climate ready crops.

Yellow seed is a desirable trait with great potential for improving seed quality in Brassica crops. Unfortunately, no natural or induced yellow seed germplasms have been found in Brassica napus, an important oil crop, which likely reflects its genome complexity and the difficulty of the simultaneous random mutagenesis of multiple gene copies with functional redundancy. Here, we demonstrate the first application of CRISPR/Cas9 for creating yellow‐seeded mutants in rapeseed. The targeted mutations of the BnTT8 gene were stably transmitted to successive generations, and a range of homozygous mutants with loss‐of‐function alleles of the target genes were obtained for phenotyping. The yellow‐seeded phenotype could be recovered only in targeted mutants of both BnTT8 functional copies, indicating that the redundant roles of BnA09.TT8 and BnC09.TT8b are vital for seed colour. The BnTT8 double mutants produced seeds with elevated seed oil and protein content and altered fatty acid (FA) composition without any serious defects in the yield‐related traits, making it a valuable resource for rapeseed breeding programmes. Chemical staining and histological analysis showed that the targeted mutations of BnTT8 completely blocked the proanthocyanidin (PA)‐specific deposition in the seed coat. Further, transcriptomic profiling revealed that the targeted mutations of BnTT8 resulted in the broad suppression of phenylpropanoid/flavonoid biosynthesis genes, which indicated a much more complex molecular mechanism underlying seed colour formation in rapeseed than in Arabidopsis and other Brassica species. In addition, gene expression analysis revealed the possible mechanism through which BnTT8 altered the oil content and fatty acid composition in seeds.

Ferroptosis, marked by iron-dependent lipid peroxidation, may present an Achilles heel for the treatment of cancers. Ferroptosis suppressor protein-1 (FSP1), as the second ferroptosis mainstay, efficiently prevents lipid peroxidation via NAD(P)H-dependent reduction of quinones. Because its molecular mechanisms have remained obscure, we studied numerous FSP1 mutations present in cancer or identified by untargeted random mutagenesis. This mutational analysis elucidates the FAD/NAD(P)H-binding site and proton-transfer function of FSP1, which emerged to be evolutionarily conserved among different NADH quinone reductases. Using random mutagenesis screens, we uncover the mechanism of action of next-generation FSP1 inhibitors. Our studies identify the binding pocket of the first FSP1 inhibitor, iFSP1, and introduce the first species-independent FSP1 inhibitor, targeting the NAD(P)H-binding pocket. Conclusively, our study provides new insights into the molecular functions of FSP1 and enables the rational design of FSP1 inhibitors targeting cancer cells. Extensive mutational analyses of ferroptosis suppressor protein-1 (FSP1) reveal its molecular mechanism in ferroptosis prevention and uncover the mechanism of action of the FSP1 inhibitor iFSP1 and a new species-independent FSP1 inhibitor, viFSP1.