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Clustered regularly interspaced short palindromic repeats (CRISPR) has revolutionized the field of genome editing. To circumvent the permanent modifications made by traditional CRISPR techniques and facilitate the study of both essential and nonessential genes, CRISPR interference (CRISPRi) was developed. This gene-silencing technique employs a deactivated Cas effector protein and a guide RNA to block transcription initiation or elongation. Continuous improvements and a better understanding of the mechanism of CRISPRi have expanded its scope, facilitating genome-wide high-throughput screens to investigate the genetic basis of phenotypes. Additionally, emerging CRISPR-based alternatives have further expanded the possibilities for genetic screening. This review delves into the mechanism of CRISPRi, compares it with other high-throughput gene-perturbation techniques, and highlights its superior capacities for studying complex microbial traits. We also explore the evolution of CRISPRi, emphasizing enhancements that have increased its capabilities, including multiplexing, inducibility, titratability, predictable knockdown efficacy, and adaptability to nonmodel microorganisms. Beyond CRISPRi, we discuss CRISPR activation, RNA-targeting CRISPR systems, and single-nucleotide resolution perturbation techniques for their potential in genome-wide high-throughput screens in microorganisms. Collectively, this review gives a comprehensive overview of the general workflow of a genome-wide CRISPRi screen, with an extensive discussion of strengths and weaknesses, future directions, and potential alternatives., (© The Author(s) 2024. Published by Oxford University Press on behalf of FEMS.)

Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis . Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.

Self-organization of inorganic matter enables bottom-up construction of materials with target shapes suited to their function. Positioning the building blocks in the growth process involves a well-balanced interplay of the reaction and diffusion. Whereas (supra)molecular structures have been used to template such growth processes, we reasoned that molecular assemblies can be employed to actively create concentration gradients that guide the deposition of solid, wire-like structures. The core of our approach comprises the interaction between myelin assemblies that deliver copper(II) ions to the tips of copper dendrites, which in turn grow along the Cu 2+ gradient upon electrodeposition. First, we successfully include Cu 2+ ions among amphiphile bilayers in myelin filaments, which grow from tri(ethylene glycol) monododecyl ether (C 12 E 3 ) source droplets over air-water interfaces. Second, we characterize the growth of dendritic copper structures upon electrodeposition from a negative electrode at the sub-mM Cu 2+ concentrations that are anticipated upon release from copper(II)-loaded myelins. Third, we assess the intricate growth of copper dendrites upon electrodeposition, when combined with copper(II)-loaded myelins. The myelins deliver Cu 2+ at a negative electrode, feeding copper dendrite growth upon electrodeposition. Intriguingly, the copper dendrites follow the Cu 2+ gradient toward the myelins and grow along them toward the source droplet. We demonstrate the growth of dynamic connections among electrodes and surfactant droplets in reconfigurable setups─featuring a unique interplay between molecular assemblies and inorganic, solid structures.

Bacterial persisters constitute a small fraction of cells that transiently display multidrug tolerance, allowing them to survive antibiotic treatment and to establish a new population upon recovery from the persistent state. Here, we present a protocol to quantify post-antibiotic persister recovery kinetics and physiological states at the single-cell level. We describe steps for sample preparation, technical setup, and data acquisition using spectrophotometry. Our assay allows for the elucidation of genes and mechanisms involved in persister survival. For complete details on the use and execution of this protocol, please refer to Wilmaerts et al. 1 ., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Organisms rely on mutations to fuel adaptive evolution. However, many mutations impose a negative effect on fitness. Cells may have therefore evolved mechanisms that affect the phenotypic effects of mutations, thus conferring mutational robustness. Specifically, so-called buffer genes are hypothesized to interact directly or indirectly with genetic variation and reduce its effect on fitness. Environmental or genetic perturbations can change the interaction between buffer genes and genetic variation, thereby unmasking the genetic variation's phenotypic effects and thus providing a source of variation for natural selection to act on. This review provides an overview of our understanding of mutational robustness and buffer genes, with the chaperone gene HSP90 as a key example. It discusses whether buffer genes merely affect standing variation or also interact with de novo mutations, how mutational robustness could influence evolution, and whether mutational robustness might be an evolved trait or rather a mere side-effect of complex genetic interactions., (© 2024. The Author(s).)

Heat stress (HS) is a critical challenge in broilers due to the high metabolic rate and lack of sweat glands. Results from this study show that implementing a cyclic chronic HS (34 °C for 7 h/d) to finisher broilers decreased the diversity of cecal microbiota and impaired intestinal barrier, resulting in gut leak and decreased body weight (both P < 0.05). These alterations might be related to inflammatory outbursts and the retarded proliferation of intestinal epithelial cells (IECs) according to the transcriptome analysis. Considering the potential beneficial properties of Lactobacillus on intestinal development and function, the protective effects of Lactobacillus rhamnosus (L. rhamnosus) on the intestine were investigated under HS conditions in this study. Orally supplemented L. rhamnosus improved the composition of cecal microbiota and upregulated the transcription of tight junction proteins in both duodenum and jejunum, with a consequent suppression in intestinal gene expressions of pro-inflammatory cytokines and facilitation in digestive capability. Meanwhile, the jejunal villus height of the birds that received L. rhamnosus was significantly higher compared with those treated with the broth (P < 0.05). The expression abundances of genes related to IECs proliferation and differentiation were increased by L. rhamnosus, along with upregulated mRNA levels of Wnt3a and β-catenin in jejunum. In addition, L. rhamnosus attenuated enterocyte apoptosis as indicated by decreased caspase-3 and caspase-9 gene expressions. The results indicated that oral administration with L. rhamnosus mitigated HS-induced dysfunction by promoting intestinal development and epithelial maturation in broilers and that the effects of L. rhamnosus might be dependent of Wnt/β-catenin signaling., Competing Interests: Declaration of competing interest No potential conflict of interest was reported by the authors., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Effective treatment of bacterial infections proves increasingly challenging due to the emergence of bacterial variants that endure antibiotic exposure. Antibiotic resistance and persistence have been identified as two major bacterial survival mechanisms, and several studies have shown a rapid and strong selection of resistance or persistence mutants under repeated drug treatment. Yet, little is known about the impact of the environmental conditions on resistance and persistence evolution and the potential interplay between both phenotypes. Based on the distinct growth and survival characteristics of resistance and persistence mutants, we hypothesized that the antibiotic dose and availability of nutrients during treatment might play a key role in the evolutionary adaptation to antibiotic stress. To test this hypothesis, we combined high-throughput experimental evolution with a mathematical model of bacterial evolution under intermittent antibiotic exposure. We show that high nutrient levels during antibiotic treatment promote selection of high-level resistance, but that resistance mainly emerges independently of persistence when the antibiotic concentration is sufficiently low. At higher doses, resistance evolution is facilitated by the preceding or concurrent selection of persistence mutants, which ensures survival of populations in harsh conditions. Collectively, our experimental data and mathematical model elucidate the evolutionary routes toward increased bacterial survival under different antibiotic treatment schedules, which is key to designing effective antibiotic therapies., (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)

Heat stress (HS) in poultry has deleterious effects on intestinal development and barrier function, along with inflammatory outbursts. In the present study, chronic HS reduced body weight of broilers and activated mucosa-associated lymphoid tissue lymphoma translocation protein 1 (Malt1) /nuclear factor kappa B (NF-κB) signaling pathways to elicit the inflammatory cytokine response in jejunum. Subsequently, this study investigated the protective effects of the Malt1 inhibitor on the intestine of broilers under HS conditions. The 21-day-old male broilers were allocated to 8 pens housed in HS room (34°C for 7 h/d) until 28 d of age. During this period, 4 birds were selected from each heat-stressed pen and received intraperitoneal injection of 20 mg/kg body weight Mepazine (a Malt1 inhibitor) or the equivalent volume of phosphate buffer saline (PBS) every other day. When compared to PBS broilers, birds received Mepazine injection exhibited increased relative weight and higher villus height in jejunum (both P < 0.05). Mepazine treatment also increased (P < 0.05) the mRNA of zonula occludens-1 (ZO-1), claudin-1, and cadherin 1 of jejunum, which was companied by the reduced caspase-3 transcription under HS condition. Meanwhile, the gene expression levels of toll-like receptor 4 (TLR4), Malt1, NF-κB, interleukin-6 (IL-6), and tumor necrosis factor alpha (TNF-α) in the jejunum were significantly downregulated by Mepazine administration (P < 0.05). Although there were no significant differences in the relative weight of the thymus and bursa, the transcription levels of T helper 1 (Th1)- and Th17-related cytokines were lower in thymus of birds injected with Mepazine. The cytokines of Treg cytokine transforming growth factor beta (TGF-β) and forkhead box protein P3 (Foxp3) in both the thymus and bursa were not influenced. These results suggest that inhibition of Malt1 protease activity can protect intestinal integrity by promoting the production of tight junction proteins and attenuating NF-κB-mediated intestinal inflammation response under HS conditions., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)