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Evolving microbes for desirable phenotypes, including stress resistance or the production of specific compounds, is a powerful approach in biotechnology and precision fermentation. Genetic diversity is essential for evolving microorganisms as it provides the raw material for screening/selection of improved variants. Efficient evolutionary engineering often requires tools that increase genetic diversity through tuning of mutation rates and the genomic location of mutations. Novel synthetic biology tools enable a controlled increase of the genetic diversity of the host. These tools can be implemented either in vitro or in vivo and target different types of mutations and target windows. Evolutionary engineering helps to improve cellular processes and metabolic pathways by, for example, optimizing gene stoichiometry or improving enzyme catalysis. The natural process of evolutionary adaptation is often exploited as a powerful tool to obtain microbes with desirable traits. For industrial microbes, evolutionary engineering is often used to generate variants that show increased yields or resistance to stressful industrial environments, thus obtaining superior microbial cell factories. However, even in large populations, the natural supply of beneficial mutations is typically low, which implies that obtaining improved microbes is often time-consuming and inefficient. To overcome this limitation, different techniques have been developed that boost mutation rates. While some of these methods simply increase the overall mutation rate across a genome, others use recent developments in DNA synthesis, synthetic biology, and CRISPR-Cas techniques to control the type and location of mutations. This review summarizes the most important recent developments and methods in the field of evolutionary engineering in model microorganisms. It discusses how both in vitro and in vivo approaches can increase the genetic diversity of the host, with a special emphasis on in vivo techniques for the optimization of metabolic pathways for precision fermentation. [ABSTRACT FROM AUTHOR]

Penicillin G acylase (PGA) serves as a critical biocatalyst for the hydrolysis of penicillin G, yielding 6-aminopenicillanic acid, a vital precursor for β-lactam semi-synthetic antibiotics. The catalytic efficiency of PGA, however, remains suboptimal in native Escherichia coli strains. To improve this, E. coli BL21 was engineered as a microbial cell factory via heterologous expression and site-directed mutagenesis to enhance PGA activity. The heterologous pga gene from Providencia rettgeri was integrated into E. coli BL21 (DE3) for the biosynthesis of PGA, achieving a PGA activity of 253 ± 2 U/mL after 16 hours of fermentation. The N167 site underwent mutation, producing the sites N167A and N167I. Plasmids carrying these mutations were introduced into E. coli BL21(DE3), and the enzymatic activities were recorded as 293 ± 3 U/mL for the N167A mutant and 238 ± 2 U/mL for the N167I mutant. This study not only introduces a novel approach to enhancing PGA activity but also illustrates the potential for catalytic optimization through targeted modifications of the enzyme's active site. • Penicillin G acylase (PGA) from the strain BL21-pga exhibits high enzyme activity. • Validation of pga gene expression in E. coli BL21(DE3) from multiple levels. • Molecular simulations of PGA were docked to analyse sites of action of this enzyme. • Point mutation of the PGA active site to further enhance the PGA enzyme activity. • Enzyme activity changes in relation to enzyme active site and substrate affinity. [ABSTRACT FROM AUTHOR]

Highlights • GMO legal landscape in the EU may pose an obstacle to investments and development of new products. • Legal uncertainty of products developed using NBTs may lead to reluctance to invest in such methods. • Separate approval procedures on NBTs in EU do not seem likely in the near future. Abstract The comparatively low adoption rate of GMO products in the European Union (EU) market seems to be connected with the strictness of authorization regulations and inefficiency of the authorization process itself. These problems will apply to any product deemed to be a GMO that could potentially be marketable in the EU. Since modern methods of plant breeding involving oligonucleotide-directed mutagenesis (ODMs) or site-directed nucleases (SDNs), including Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), are becoming ever more popular, it is crucial to establish whether the products of such new breeding techniques (NBTs), in particular those which involve precise methods of mutagenesis, are exempted from the EU legislation on GMOs or not. Legal uncertainty as to their status may result in reluctance to invest in such methods and develop them further. Here, developments are presented in the legal classification of certain NBTs products in the context of recent decisions and jurisprudence. The socioeconomic aspects of GMO adoption in both global and European contexts are discussed. The legal and practical landscape of GMO regulation in the EU is presented and how it may pose an obstacle to investment and the development of new products. The latest jurisprudence (e.g., Case C-528/16) [ 1 ] on the interpretation of the legal concept of GMOs and the scope of the legislation are analyzed, with the conclusion that the strict regulations will probably also apply to products of the NBTs involving precise methods of mutagenesis. This in turn will probably result in the restriction of their application in the development of new plant varieties in the EU. [ABSTRACT FROM AUTHOR]

Prime editing, developed by Anzalone et al. , brings genome editing to a new level, because this approach allows introduction of all mutation types, including insertions, deletions, and all putative 12 types of base-to-base conversions. Previously tested in human cells, this technique has been adapted for use in plants by Lin et al. [ABSTRACT FROM AUTHOR]

Precise and efficient use of genome editing tools are hampered by the introduction of DNA double-strand breaks, donor DNA templates, or homology-directed repair. A recent study expands the genome editing toolbox with the introduction of prime editing, which overcomes previous challenges and introduces insertions, deletions, and all putative 12 types of base-to-base conversions in human cells. [ABSTRACT FROM AUTHOR]

Genome editing technology using artificial nucleases, including zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regulatory interspaced short palindromic repeats (CRISPR)-Cas9, can mutagenize the target sites of genes of interest. This technology has been successfully applied in several crops, including the Solanaceae plants, such as tomato, potato, tobacco, and petunia. Among the three nucleases, CRISPR-Cas9 is the best for breeding, crop improvement, and the functional analysis of genes of interest, because of its simplicity and high efficiency. Although the technology is useful for reverse genetics, its use in plants is limited due to a lack of regeneration protocols and sequence information. In this review, the present status of genome editing technology in Solanaceae plants is described, and techniques that may improve genome editing technologies are discussed. [ABSTRACT FROM AUTHOR]

Summary In vivo , replication forks proceed beyond replication-blocking lesions by way of downstream repriming, generating daughter strand gaps that are subsequently processed by post-replicative repair pathways such as homologous recombination and translesion synthesis (TLS). The way these gaps are filled during TLS is presently unknown. The structure of gap repair synthesis was assessed by sequencing large collections of single DNA molecules that underwent specific TLS events in vivo . The higher error frequency of specialized relative to replicative polymerases allowed us to visualize gap-filling events at high resolution. Unexpectedly, the data reveal that a specialized polymerase, Pol V, synthesizes stretches of DNA both upstream and downstream of a site-specific DNA lesion. Pol V-mediated untargeted mutations are thus spread over several hundred nucleotides, strongly eliciting genetic instability on either side of a given lesion. Consequently, post-replicative gap repair may be a source of untargeted mutations critical for gene diversification in adaptation and evolution. [ABSTRACT FROM AUTHOR]

The clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated (Cas9) system has enabled efficient genome engineering in diverse plant species. However, delivery of genome engineering reagents, such as the single guide RNA (sgRNA), into plant cells remains challenging. Here, we report the engineering of Tobacco rattle virus (TRV) and Pea early browning virus (PEBV) to deliver one or multiple sgRNAs into Nicotiana benthamiana and Arabidopsis thaliana (Col-0) plants that overexpress a nuclear localization signal containing Cas9 . Our data showed that TRV and PEBV can deliver sgRNAs into inoculated and systemic leaves, and this resulted in mutagenesis of the targeted genomic loci. Moreover, in N. benthamiana , PEBV-based sgRNA delivery resulted in more targeted mutations than TRV-based delivery. Our data indicate that TRV and PEBV can facilitate plant genome engineering and can be used to produce targeted mutations for functional analysis and other biotechnological applications across diverse plant species. Key message : Delivery of genome engineering reagents into plant cells is challenging and inefficient and this limit the applications of this technology in many plant species. RNA viruses such as TRV and PEBV provide an efficient tool to systemically deliver sgRNAs for targeted genome modification. [ABSTRACT FROM AUTHOR]

Use of RNA-guided endonucleases for targeted genome editing is one of the most important breakthrough discoveries of the 21st century. Recent studies have described modifications of this precise base editing technique that open up a new dimension to plant genome editing. [ABSTRACT FROM AUTHOR]

Targeted genome editing using artificial nucleases has the potential to accelerate basic research as well as plant breeding by providing the means to modify genomes rapidly in a precise and predictable manner. Here we describe the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system, a recently developed tool for the introduction of site-specific double-stranded DNA breaks. We highlight the strengths and weaknesses of this technology compared with two well-established genome editing platforms: zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). We summarize recent results obtained in plants using CRISPR/Cas9 technology, discuss possible applications in plant breeding and consider potential future developments. [ABSTRACT FROM AUTHOR]

Abstract: Klebsiella pneumoniae is an important and versatile bacterium that can be found in diverse environments and is also a frequent cause of human infections. Limited data exists on the mechanisms of interaction between K. pneumoniae and the human host and of adaptations to other environments. Coupled with the high genetic diversity of this species, these factors highlight the necessity for substantial further K. pneumoniae-focused molecular genetics studies. In this report we describe a simple and efficient experimental protocol for suicide vector-based allelic exchange in K. pneumoniae. The protocol has been validated by mutating multiple loci in four distinct K. pneumoniae strains, including highly capsulated and/or multi-antibiotic resistant clinical isolates. Three key enhancements are reported:(1) Use of pDS132-derived conjugative plasmids carrying improved cloning sites, (2) Performance of sacB counterselection at 25°C as opposed to higher temperatures, and (3) Exploitation of Flp-recombinase-mediated deletion of FRT (Flp recombinase target) flanked resistance cassettes to allow for reiterative manipulations with a single selectable marker. This study also highlights a problem that may be encountered when the aacC1 gentamicin resistance marker is used in K. pneumoniae and suggests alternative markers. The protocol developed in this study will help investigate the plethora of uncharacterized genes present in the K. pneumoniae pan-genome and shed further light upon clinically and industrially important phenotypes observed in this ubiquitous species. [Copyright &y& Elsevier]

Abstract: Ric-8 is a guanine nucleotide exchange factor for a subset of Gα proteins and it is required to maintain Gαq and the Gαs pathways in functional state. In adult mice Ric-8 is expressed in regions involved in the regulation of behavior (neocortex, cingulate cortex and hippocampus). As Ric-8 is shown to regulate neuronal transmitter release, the aim of present study was to perform behavioral analysis of ric-8 mutant. Homozygous (−/−) ric-8 mutant mice are not viable and die in early embryonic development, therefore for behavioral analysis heterozygous (+/−) ric-8 mutant mice were used. We found decreased anxiety of ric-8 heterozygous mice in light–dark compartment test where mutant mice significantly avoided the light compartment. In spatial learning paradigm (Morris water maze) the performance of ric-8 (+/−) mice was impaired. Namely, in the reversal test, ric-8 (+/−) mice exhibited significant delay to find the hidden platform compared to wild-type (wt) littermates. We did not find differences in the behavioral tests reflecting the motor abilities of mice (motor activity, rota-rod). Therefore, described alterations seem to be specific for anxiety and spatial learning. Based on these results we can conclude the importance of ric-8 in the regulation of memory and emotional behavior. [Copyright &y& Elsevier]

Abstract: As the use of gene knockout models in thermoregulation studies has gained popularity, the reported incidence of redundant or discrepant phenotypes between studies has also increased. Several gene knockout models mimic human processes and have provided valuable insight into the role of endogenous mediators in thermoregulatory processes. There are also many examples of mutant strains expressing virtually identical phenotypes as their wild-type controls, causing concern regarding the appropriateness of these models for the study of physiological processes. In some cases, discrepancies in results are being reported from different laboratories that are studying the same gene knockout model. While mutant strains provide a powerful tool for analysis of gene function in vivo, the breeding strategies used to generate the strain may have a profound impact on the expressed phenotype. This review examines the intricacies of working with a small rodent such as the mouse and discusses the advantages and disadvantages of using gene knockout models for thermoregulatory research. A number of experimental strategies that can be used to minimize the occurrence of redundant phenotypes are presented. The influence of background strain effects is also considered, since this may be one of the most important factors influencing a mutant phenotype. A future perspective is provided in which more advanced technologies using conditional gene inactivation and the production of rat knockout strains will improve current experimental design. [Copyright &y& Elsevier]

Neuropeptide cholecystokinin (CCK) regulates the adaptation of rodents in the novel environment. In the present study we analysed the behavioural changes induced by the individual housing in mice, lacking CCK2 receptors. The wild-type (+/+) and homozygous (-/-) CCK2 receptor deficient mice of both gender were used throughout the study. The weight gain during the 21-day isolation period and changes in the locomotor activity following the social separation were measured. The elevated plus-maze and resident/intruder tests were also performed to test alterations in the emotional behaviour. Social isolation induced locomotor hyperactivity, reduced weight gain and increased aggressiveness in the wild-type (+/+) and homozygous (-/-) male mice. In the wild-type (+/+) female mice the significant reduction of exploratory activity in the plus-maze was evident. By contrast, in female mice, lacking CCK2 receptors, the exploration of the plus-maze was not significantly affected by the individual housing. This finding demonstrates that the social isolation does not cause anxiety-like state in the CCK2 receptor deficient mice. Moreover, the targeted invalidation of CCK2 receptors increased in male mice the affinity of dopamine D2 receptors in the sub-cortical structures, whereas in female mice the increased affinity of 5-hydroxytryptamine2 (5-HT2) receptors in the frontal cortex was established. The increased affinity of 5-HT2 receptors is probably the compensatory change to the lack of CCK2 receptors in female mice and probably reflects the reduced sensitivity of these animals to the anxiogenic manipulations. In conclusion, targeted mutation of CCK2 receptors selectively antagonised the behavioural changes induced by the individual housing in females, but not in male mice. [Copyright &y& Elsevier]

The effects of morphine, μ-opioid receptor agonist, and naloxone, a non-selective opioid receptor antagonist, in the locomotor activity and place conditioning tests were studied in the CCK2 receptor-deficient male mice. The exposure of mice to the motility boxes for 3 consecutive days induced a significant inhibition of locomotor activity in the wild-type (+/+) mice compared to homozygous (−/−) animals. The administration of naloxone (10 mg/kg i.p.) to animals, adapted to the motility boxes, induced a significant reduction of locomotor activity in the homozygous (−/−), but not in the wild-type (+/+) mice. Treatment of habituated mice with morphine (10 mg/kg i.p.) caused a stronger increase of locomotor activity in the wild-type (+/+) mice compared to the homozygous (−/−) littermates. In the place preference test the pairing of the preferred side with naloxone (1 and 10 mg/kg i.p.) induced a dose-dependent place aversion in the wild-type (+/+) mice. The treatment with naloxone was less effective in the homozygous (−/−) mice, because the high dose of naloxone (10 mg/kg) tended to shift the preference. The pairing of morphine (3 mg/kg i.p.) injections with the non-preferred side induced a significant place preference both in the wild-type (+/+) and homozygous (−/−) mice. The increased density of opioid receptors was established in the striatum of homozygous (−/−) mice, but not in the other forebrain structures. In conclusion, the targeted invalidation of CCK2 receptors induces a dissociation of behavioural effects of morphine and naloxone. Morphine-induced place preference remained unchanged, whereas hyper-locomotion was less pronounced in the mutant mice compared to the wild-type (+/+) littermates. By contrast, naloxone-induced place aversion was weaker, but naloxone caused a stronger inhibition of locomotor activity in the homozygous (−/−) mice than in the wild-type (+/+) animals. These behavioural alterations can be explained in the light of data that the targeted mutation of CCK2 receptors induces distinct changes in the properties of opioid receptors in various brain structures. [Copyright &y& Elsevier]

Larvae of many lepidopteran species produce a mixture of secretory proteins, known as silk, for building protective shelters and cocoons. Silk consists of a water-insoluble silk filament core produced in the posterior silk gland (PSG) and a sticky hydrophilic coating produced by the middle silk gland (MSG). In Bombyx mori , the fiber core comprises three proteins: heavy chain fibroin (Fib-H), light chain fibroin (Fib-L) and fibrohexamerin (Fhx, previously referred to as P25). To learn more about the role of Fhx, we used transcription activator-like effector nuclease (TALEN) mutagenesis and prepared a homozygous line with a null mutation in the Fhx gene. Our characterization of cocoon morphology and silk quality showed that the mutation had very little effect. However, a detailed inspection of the secretory cells in the posterior silk gland (PSG) of mid-last-instar mutant larvae revealed temporary changes in the morphology of the endoplasmic reticulum. We also observed a morphological difference in fibroin secretory globules stored in the PSG lumen of Fhx mutants, which suggests that their fibroin complexes have a slightly lower solubility. Finally, we performed an LC-MS-based quantitative proteomic analysis comparing mutant and wild-type (wt) cocoon proteins and found a high abundance of a 16 kDa secretory protein likely involved in fibroin solubility. Overall, our study shows that whilst Fhx is dispensable for silk formation, it contributes to the stability of fibroin complexes during intracellular transport and affects the morphology of fibroin secretory globules in the PSG lumen. [Display omitted] • A knockout silkworm line lacking fibrohexamerin (Fhx) has been generated. • Fhx deletion has no obvious effects on silkworm viability or cocoon morphology. • Posterior silk gland cells lacking Fhx display altered endoplasmic reticulum. • Secretory silk globules in Fhx mutants appear abnormally compact. • Mutant cocoons contain increased levels of a protein likely involved in fibroin solubility. [ABSTRACT FROM AUTHOR]

Abstract: Zinc finger nucleases can be engineered to create highly efficient and precise changes to the genetic information within living cells. We report the investigation of an important parameter that defines the type of target site the nuclease can cleave. The active nuclease is a dimer, requiring that the DNA target site contain two zinc finger binding sites separated by a short spacer. Using a plasmid-based recombination assay in HEK 293T cells, we show that a 6 amino acid linker between the zinc finger DNA-binding domain and the FokI cleavage domain restricts nuclease activity to sites containing a 6bp spacer. These observations concur with other recent studies, suggesting this information will be useful in the design of new potent and accurate zinc finger nucleases. [Copyright &y& Elsevier]

Inconsistent activity limits the use of CRISPR-Cas9 in zebrafish. We show supernumerary guanine nucleotides at the 5′ ends of single guide RNAs (sgRNAs) account for diminished CRISPR-Cas9 activity in zebrafish embryos. Genomic sequences can be targeted consistently with extremely high efficiency using Cas9 ribonucleoproteins (RNPs) containing either a sgRNA molecule or a synthetic crRNA:tracrRNA duplex that perfectly matches the protospacer target site. Following injection of zebrafish eggs with such RNPs, virtually every copy of a targeted locus harbors an induced indel mutation. Loss of gene function is often complete, as F0 embryos closely resemble true null mutants without detectable non-specific effects. Mosaicism is sufficiently low in F0 embryos that cell non-autonomous gene functions can be probed effectively and redundant activities of genes can be uncovered when two genes are targeted simultaneously. Finally, heritable deletion mutations of at least 50 kbp can be readily induced using pairs of duplex guide RNPs targeted to a single chromosome. • Cas9 RNPs with synthetic crRNA:tracrRNAs are highly mutagenic in zebrafish embryos • Mutagenized F0 embryos mimic null mutants and lack confounding non-specific traits • Redundant gene activity can be uncovered, and heritable deletions can be induced • 5′ guanines of gRNAs that do not complement the protospacer diminish Cas9 RNP activity Cas9 RNP complexes consisting of synthetic crRNA:tracrRNA duplex guide RNAs consistently induce mutations in virtually all copies of a targeted gene in zebrafish embryos. Hoshijima et al. show these tools allow effective screening of individual or combinations of gene function in F0 embryos and the facile induction of deletion mutations. [ABSTRACT FROM AUTHOR]