Development of a genetically engineered Escherichia coli strain for plasmid transformation in Corynebacterium glutamicum

AutoBioTech─A Versatile Biofoundry for Automated Strain Engineering

The inevitable transition from petrochemical production processes to renewable alternatives has sparked the emergence of biofoundries in recent years. Manual engineering of microbes will not be sufficient to meet the ever-increasing demand for novel producer strains. Here we describe the AutoBioTech platform, a fully automated laboratory system with 14 devices to perform operations for strain construction without human interaction. Using modular workflows, this platform enables automated transformations of Escherichia coli with plasmids assembled via modular cloning. A CRISPR/Cas9 toolbox compatible with existing modular cloning frameworks allows automated and flexible genome editing of E. coli. In addition, novel workflows have been established for the fully automated transformation of the Gram-positive model organism Corynebacterium glutamicum by conjugation and electroporation, with the latter proving to be the more robust technique. Overall, the AutoBioTech platform excels at versatility due to the modularity of workflows and seamless transitions between modules. This will accelerate strain engineering of Gram-negative and Gram-positive bacteria.

Generation of tools for expression and purification of the phage-encoded Type I restriction enzyme inhibitor, Ocr

DNA manipulation is an essential tool in molecular microbiology research that is dependent on the ability of bacteria to take up and preserve foreign DNA by horizontal gene transfer. This process can be significantly impaired by the activity of bacterial restriction modification systems; bacterial operons comprising paired enzymatic activities that protectively methylate host DNA, while cleaving incoming unmodified foreign DNA. Ocr is a phage-encoded protein that inhibits Type I restriction modification systems, the addition of which significantly improves bacterial transformation efficiency. We recently established an improved and highly efficient transformation protocol for the important human pathogen group A Streptococcus using commercially available recombinant Ocr protein, manufacture of which has since been discontinued. In order to ensure the continued availability of Ocr protein within the research community, we have generated tools and methods for in-house Ocr production and validated the activity of the purified recombinant protein.

Construction of prophage-free and highly-transformable Limosilactobacillus reuteri strains and their use for production of 1,3-propanediol

The lactic acid bacterium Limosilactobacillus reuteri (formerly Lactobacillus reuteri) is a desirable host for the production of 1,3-propanediol (1,3-PDO) from glycerol when 1,3-PDO is used in the food or cosmetic industry. However, the production is hindered by strain instability, causing cell lysis, and difficult gene manipulation. This study reveals that the stability of L. reuteri DSM 20016 and its 1,3-PDO production, especially in the alcohol dehydrogenases (ADHs)-deletion mutants, are greatly enhanced after the deletion of two prophages (Φ3 and Φ4) present in the L. reuteri's chromosome. The resulting phage-free and ADHs-deletion mutant could produce >825 mM 1,3-PDO in 48 h without cell lysis at the theoretical maximum yield on glucose of ~2 mol/mol. Compared to the wild-type strain, the mutant exhibited a 45.2% increase in 1,3-PDO production titer and a 2.1-fold increase in yield. In addition, this study reports that the transformation efficiency of L. reuteri Δadh2Δadh6 mutant strains were greatly enhanced by >300-fold after the deletion of prophage Φ3, probably due to the removal of a restriction-modification (RM) system which resides in the phage genome. With improved stability and higher transformation efficiency, recombinant L. reuteri DSM 20016 Δadh2Δadh6ΔΦ3ΔΦ4 can be a more reliable and amenable host for industrial applications.

Nanoparticles drug delivery for 5-aminolevulinic acid (5-ALA) in photodynamic therapy (PDT) for multiple cancer treatment: a critical review on biosynthesis, detection, and therapeutic applications

Photodynamic therapy (PDT) is a promising cancer treatment that kills cancer cells selectively by stimulating reactive oxygen species generation with photosensitizers exposed to specific light wavelengths. 5-aminolevulinic acid (5-ALA) is a widely used photosensitizer. However, its limited tumour penetration and targeting reduce its therapeutic efficacy. Scholars have investigated nano-delivery techniques to improve 5-ALA administration and efficacy in PDT. This review summarises recent advances in biological host biosynthetic pathways and regulatory mechanisms for 5-ALA production. The review also highlights the potential therapeutic efficacy of various 5-ALA nano-delivery modalities, such as nanoparticles, liposomes, and gels, in treating various cancers. Although promising, 5-ALA nano-delivery methods face challenges that could impair targeting and efficacy. To determine their safety and biocompatibility, extensive preclinical and clinical studies are required. This study highlights the potential of 5-ALA-NDSs to improve PDT for cancer treatment, as well as the need for additional research to overcome barriers and improve medical outcomes.

Genetic toolkits for engineering Rhodococcus species with versatile applications

Rhodococcus spp. are a group of non-model gram-positive bacteria with diverse catabolic activities and strong adaptive capabilities, which enable their wide application in whole-cell biocatalysis, environmental bioremediation, and lignocellulosic biomass conversion. Compared with model microorganisms, the engineering of Rhodococcus is challenging because of the lack of universal molecular tools, high genome GC content (61% ~ 71%), and low transformation and recombination efficiencies. Nevertheless, because of the high interest in Rhodococcus species for bioproduction, various genetic elements and engineering tools have been recently developed for Rhodococcus spp., including R. opacus, R. jostii, R. ruber, and R. erythropolis, leading to the expansion of the genetic toolkits for Rhodococcus engineering. In this article, we provide a comprehensive review of the important developed genetic elements for Rhodococcus, including shuttle vectors, promoters, antibiotic markers, ribosome binding sites, and reporter genes. In addition, we also summarize gene transfer techniques and strategies to improve transformation efficiency, as well as random and precise genome editing tools available for Rhodococcus, including transposition, homologous recombination, recombineering, and CRISPR/Cas9. We conclude by discussing future trends in Rhodococcus engineering. We expect that more synthetic and systems biology tools (such as multiplex genome editing, dynamic regulation, and genome-scale metabolic models) will be adapted and optimized for Rhodococcus.

The optimization system for preparation of TG1 competent cells and electrotransformation

An efficient electrotransformation system that includes electrocompetent cells is a critical component for the success of large‐scale gene transduction and replication. The conditions of TG1 competent cell preparation and optimal electrotransformation were evaluated by investigating different parameters. Certain parameters for preparation of TG1 competent cells (≥8 × 10¹⁰ colony forming units (cfu)/μg DNA) include optimum culture time of monoclonal bacteria (8–10 hr), amplification growth concentration (approximately OD₆₀₀ = 0.45), and culture volume (400 ml in 2 L conical flask). With increased storage of competent cells at −80°C, electrotransformation efficiency gradually decreased, but it remains greater than ≥ 10¹⁰ cfu/μg DNA 3 months later. Moreover, the recovery time of electrotransformation also influenced electrotransformation efficiency (1.5–2 hr for optimization). The optimized transformation efficiency of TG1 (≥8 × 10¹⁰ cfu/μg DNA) was observed under suitable electric voltage (2.5 kV), electric intensity (15 kV/cm), and electric time (3.5 ms) of electricity for plasmid transformation. Optimized DNA amount (0.01–100 ng) dissolved in water led to the high efficiency of plasmid transformation (≥8 × 10¹⁰ cfu/μg DNA), but had low efficiency when dissolved in T4 ligation buffer (≤3 × 10¹⁰ cfu/μg DNA). These results indicated that an optimized TG1 transformation system is useful for high electrotransformation efficiency under general laboratory conditions. The optimized TG1 transformation system might facilitate large‐scale gene transduction for phage display library construction.

Mutations in Peptidoglycan Synthesis Gene ponA Improve Electrotransformation Efficiency of Corynebacterium glutamicum ATCC 13869

Corynebacterium glutamicum is frequently engineered to serve as a versatile platform and model microorganism. However, due to its complex cell wall structure, transformation of C. glutamicum with exogenous DNA is inefficient. Although efforts have been devoted to improve the transformation efficiency by using cell wall-weakening agents, direct genetic engineering of cell wall synthesis for enhancing cell competency has not been explored thus far. Herein, we reported that engineering of peptidoglycan synthesis could significantly increase the transformation efficiency of C. glutamicum Comparative analysis of C. glutamicum wild-type strain ATCC 13869 and a mutant with high electrotransformation efficiency revealed nine mutations in eight cell wall synthesis-related genes. Among them, the Y489C mutation in bifunctional peptidoglycan glycosyltransferase/peptidoglycan dd-transpeptidase PonA dramatically increased the electrotransformation of strain ATCC 13869 by 19.25-fold in the absence of cell wall-weakening agents, with no inhibition on growth. The Y489C mutation had no effect on the membrane localization of PonA but affected the peptidoglycan structure. Deletion of the ponA gene led to more dramatic changes to the peptidoglycan structure but only increased the electrotransformation by 4.89-fold, suggesting that appropriate inhibition of cell wall synthesis benefited electrotransformation more. Finally, we demonstrated that the PonA^Y489C mutation did not cause constitutive or enhanced glutamate excretion, making its permanent existence in C. glutamicum ATCC 13869 acceptable. This study demonstrates that genetic engineering of genes involved in cell wall synthesis, especially peptidoglycan synthesis, is a promising strategy to improve the electrotransformation efficiency of C. glutamicum IMPORTANCE Metabolic engineering and synthetic biology are now the key enabling technologies for manipulating microorganisms to suit the practical outcomes desired by humankind. The introduction of exogenous DNA into cells is an indispensable step for this purpose. However, some microorganisms, including the important industrial workhorse Corynebacterium glutamicum, possess a complex cell wall structure to shield cells against exogenous DNA. Although genes responsible for cell wall synthesis in C. glutamicum are known, engineering of related genes to improve cell competency has not been explored yet. In this study, we demonstrate that mutations in cell wall synthesis genes can significantly improve the electrotransformation efficiency of C. glutamicum Notably, the Y489C mutation in bifunctional peptidoglycan glycosyltransferase/peptidoglycan dd-transpeptidase PonA increased electrotransformation efficiency by 19.25-fold by affecting peptidoglycan synthesis.

Bone morphogenetic protein-2 exhibits therapeutic benefits for osteonecrosis of the femoral head through induction of cartilage and bone cells

Osteonecrosis of the femoral head is an orthopedic disease caused by femoral head damage or insufficient blood supply, which leads to the death of bone cells and bone marrow. Osteonecrosis of the femoral head leads to changes in the structure of the femoral head, femoral head collapse and joint dysfunction. Bone morphogenetic protein-2 (BMP-2) exhibits beneficial effects on bone formation, repair and angiogenesis at the femoral head. In the present study, the therapeutic effects of recombinant human BMP-2 containing an Fc fragment (rBMP-2/Fc) were investigated on a steroid induced mouse model of osteonecrosis of the femoral head. Bone cell viability was used to determine the in vitro effects of rBMP-2/Fc. The therapeutic efficacies of rBMP-2/Fc on mice with osteonecrosis of the femoral head were evaluated using clinical arthritis scores. The expression levels of inflammatory factors in the mice were analyzed by reverse transcription-quantitative polymerase chain reaction. Histological analysis was used to evaluate the effects of rBMP-2/Fc on the femoral head. The results revealed that rBMP-2/Fc treatment significantly increased the IL-6, IL-10, vascular endothelial growth factor and macrophage colony-stimulating factor expression levels in synovial cells compared with the control group (P<0.01). Furthermore, it was observed that rBMP-2/Fc significantly improved the viability and growth of synovial cells (P<0.01) through the nuclear factor (NF)-κB signaling pathway. Treatment with rBMP-2/Fc significantly decreased receptor activator of NF-κB ligand expression levels. Furthermore, in vivo experiments demonstrated that rBMP-2/Fc treatment markedly relieved the arthralgia and damage caused by osteonecrosis of the femoral head. In conclusion, rBMP-2/Fc treatment may be beneficial for articular cartilage repair by the upregulation of angiogenesis factors through the down regulation of the NF-κB signaling pathway in mice with osteonecrosis of the femoral head. This preclinical data suggests that rBMP-2/Fc may be a promising novel agent for treatment of osteonecrosis of the femoral head.