The phage T4 DNA ligase in vivo improves the survival-coupled bacterial mutagenesis

Genome-guided approaches and evaluation of the strategies to influence bioprocessing assisted morphological engineering of Streptomyces cell factories

Streptomyces genera serve as adaptable cell factories for secondary metabolites with various and distinctive chemical structures that are relevant to the pharmaceutical industry. Streptomyces' complex life cycle necessitated a variety of tactics to enhance metabolite production. Identification of metabolic pathways, secondary metabolite clusters, and their controls have all been accomplished using genomic methods. Besides this, bioprocess parameters were also optimized for the regulation of morphology. Kinase families were identified as key checkpoints in the metabolic manipulation (DivIVA, Scy, FilP, matAB, and AfsK) and morphology engineering of Streptomyces. This review illustrates the role of different physiological variables during fermentation in the bioeconomy coupled with genome-based molecular characterization of biomolecules responsible for secondary metabolite production at different developmental stages of the Streptomyces life cycle.

An Efficient High-Throughput Screening of High Gentamicin-Producing Mutants Based on Titer Determination Using an Integrated Computer-Aided Vision Technology and Machine Learning

The "design-build-test-learn" (DBTL) cycle has been adopted in rational high-throughput screening to obtain high-yield industrial strains. However, the mismatch between build and test slows the DBTL cycle due to the lack of high-throughput analytical technologies. In this study, a highly efficient, accurate, and noninvasive detection method of gentamicin (GM) was developed, which can provide timely feedback for the high-throughput screening of high-yield strains. First, a self-made tool was established to obtain data sets in 24-well plates based on the color of the cells. Subsequently, the random forest (RF) algorithm was found to have the highest prediction accuracy with an R² value of 0.98430 for the same batch. Finally, a stable genetically high-yield strain (998 U/mL) was successfully screened out from 3005 mutants, which was verified to improve the titer by 72.7% in a 5 L bioreactor. Moreover, the verified new data sets were updated on the model database in order to improve the learning ability of the DBTL cycle.

Phage Enzyme-Assisted Direct In Vivo DNA Assembly in Multiple Microorganisms

The assembly of DNA fragments is extremely important for molecular biology. Increasing numbers of studies have focused on streamlining the laborious and costly protocols via in vivo DNA assembly. However, the existing methods were mainly developed for Escherichia coli or Saccharomyces cerevisiae, whereas there are few direct in vivo DNA assembly methods for other microorganisms. The use of shuttle vectors and tedious plasmid extraction and transformation procedures make DNA cloning in other microorganisms laborious and inefficient, especially for DNA library construction. In this study, we developed a "phage enzyme-assisted in vivo DNA assembly" (PEDA) method via combinatorial expression of T5 exonuclease and T4 DNA ligase. PEDA facilitated the in vivo assembly of DNA fragments with homologous sequences as short as 5 bp, and it is applicable to multiple microorganisms, such as Ralstonia eutropha, Pseudomonas putida, Lactobacillus plantarum, and Yarrowia lipolytica. The cloning efficiency of optimized PEDA is much higher than that of the existing in vivo DNA assembly methods and comparable to that of in vitro DNA assembly, making it extremely suitable for DNA library cloning. Collectively, PEDA will boost the application of in vivo DNA assembly in various microorganisms.

Direct visualization of local activities of long DNA strands via image-time correlation

Bacteriophages with long DNA genomes are of interest due to their diverse mutations dependent on environmental factors. By lowering the ionic strength of a hydrophobic (PPh4Cl) antagonistic salt (at 1 mM), single long T4 DNA strand fluctuations were clearly observed, while condensed states of T4 DNA globules were formed above 5-10 mM salt. These long DNA strands were treated with fluorescently labeled probes, for which photo bleaching is often unavoidable over a short time of measurement. In addition, long (few tens of [Formula: see text]) length scales are required to have larger fields of view for better sampling, with shorter temporal resolutions. Thus, an optimization between length and time is crucial to obtain useful information. To facilitate the challenge of detecting large biomacromolecules, we here introduce an effective method of live image data analysis for direct visualization and quantification of local thermal fluctuations. The motions of various conformations for the motile long DNA strands were examined for the single- and multi-T4 DNA strands. We find that the unique correlation functions exhibit a relatively high-frequency oscillatory behavior superimposed on the overall slower decay of the correlation function with a splitting of amplitudes deriving from local activities of the long DNA strands. This work shows not only the usefulness of an image-time correlation for analyzing large biomacromolecules, but also provides insight into the effects of a hydrophobic antagonistic salt on active T4 bacteriophage long DNA strands, including thermal translocations in their electrostatic interactions.

Bi- and Multi-directional Gene Transfer in the Natural Populations of Polyvalent Bacteriophages, and Their Host Species Spectrum Representing Foodborne Versus Other Human and/or Animal Pathogens

Unraveling the trends of phage-host versus phage-phage coevolution is critical for avoiding possible undesirable outcomes from the use of phage preparations intended for therapeutic, food safety or environmental safety purposes. We aimed to investigate a phenomenon of intergeneric recombination and its trajectories across the natural populations of phages predominantly linked to foodborne pathogens. The results from the recombination analyses, using a large array of the recombination detection algorithms imbedded in SplitsTree, RDP4, and Simplot software packages, provided strong evidence (fit: 100; P  ≤ 0.014) for both bi- and multi-directional intergeneric recombination of the genetic loci involved collectively in phage morphogenesis, host specificity, virulence, replication, and persistence. Intergeneric recombination was determined to occur not only among conspecifics of the virulent versus temperate phages but also between the phages with these different lifestyles. The recombining polyvalent phages were suggested to interact with fairly large host species networks, including sometimes genetically very distinct species, such as e.g., Salmonella enterica and/or Escherichia coli versus Staphylococcus aureus or Yersinia pestis. Further studies are needed to understand whether phage-driven intergeneric recombination can lead to undesirable changes of intestinal and other microbiota in humans and animals.

CRISPR-based metabolic pathway engineering

A highly effective metabolic pathway is the key for an efficient cell factory. However, the engineered homologous or heterologous multi-gene pathway may be unbalanced, inefficient and causing the accumulation of potentially toxic intermediates. Therefore, pathways must be constructed optimally to minimize these negative effects and maximize catalytic efficiency. With the development of CRISPR technology, some of the problems of previous pathway engineering and genome editing techniques were resolved, providing higher efficiency, lower cost, and easily customizable targets. Moreover, CRISPR was demonstrated as robust and effective in various organisms including both prokaryotes and eukaryotes. In recent years, researchers in the field of metabolic engineering and synthetic biology have exploited various CRISPR-based pathway engineering approaches, which are both effective and convenient, as well as valuable from a theoretical standpoint. In this review, we systematically summarize novel pathway engineering techniques and strategies based on CRISPR nucleases system, CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa), including figures and descriptions for easy understanding, with the aim to facilitate their broader application among fellow researchers.