Expanding the toolbox of probiotic Escherichia coli Nissle 1917 for synthetic biology

Design of a Continuous GAA-Producing Probiotic as a Potential Mitigator of the Effects of Sleep Deprivation

Creatine is a popular athletic supplement that has also been shown to improve cognitive performance upon sleep deprivation. However, it is rapidly cleared from the gastrointestinal tract a few hours after consumption. Toward providing a persistent creatine dose, we engineered the human probiotic Escherichia coli Nissle (EcN) to produce guanidinoacetic acid (GAA), which is converted to creatine in the liver. We find GAA-producing enzymes present in the human microbiome and compare their activities to known enzymes. Three copies of arginine:glycine amidinotransferase (AGAT) from Actinokineospora terrae are expressed from the genome, and native gcvP, argR, and argA are edited or deleted to improve substrate availability without negatively impacting cell viability. A standard EcN dose (1012 cells) produces 41 ± 7 mg GAA per hour under laboratory conditions. This work demonstrates that a probiotic bacterium can be engineered to produce sustained GAA titers known to impact cognitive performance.

Integrase enables synthetic intercellular logic via bacterial conjugation

Integrases have been widely used in synthetic biology for genome engineering and genetic circuit design. They mediate DNA recombination to alter the genotypes of single cell lines in vivo, with these changes being permanently recorded and inherited via vertical gene transfer. However, integrase-based intercellular DNA messaging and its regulation via horizontal gene transfer remain underexplored. Here, we introduce a versatile strategy to design, build, and test integrase-based intercellular DNA messaging through bacterial conjugation. First, we screened conjugative plasmids and recipient cells for efficient conjugation. Then, we established a layered framework to describe the interactions among hierarchical E. coli strains and implemented dual-layer Boolean logic gates to demonstrate intercellular DNA messaging and management. Finally, we expanded the design to include four-layer single-processing pathways and dual-layer multi-processing systems. This strategy advances intercellular DNA messaging, hierarchical signal processing, and the application of integrase in systems and synthetic biology.

Multi-gene precision editing tool using CRISPR-Cas12a/Cpf1 system in Ogataea polymorpha

BACKGROUND

Ogataea polymorpha, a non-conventional methylotrophic yeast, has demonstrated significant potential for heterologous protein expression and the production of high-value chemicals and biopharmaceuticals. However, the lack of precise and efficient genome editing tools severely hinders the construction of cell factories. Although the CARISP-Cas9 system has been established in Ogataea polymorpha, the gene editing efficiency, especially for multiple genes edition, needs to be further improved.

RESULTS

In this study, we developed an efficient CRISPR-Cpf1-mediated genome editing system in O. polymorpha that exhibited high editing efficiency for single gene (98.1 ± 1.7%), duplex genes (93.9 ± 2.4%), and triplex genes (94.0 ± 6.0%). Additionally, by knocking out non-homologous end joining (NHEJ) related genes, homologous recombination (HR) efficiency was increased from less than 30% to 90 ~ 100%, significantly enhancing precise genome editing capabilities. The increased HR rates enabled over 90% integration efficiency of triplex genes, as well as over 90% deletion rates of large DNA fragments up to 20 kb. Furthermore, using this developed CRISPR-Cpf1 system, triple genes were precisely integrated into the genome by one-step, enabling lycopene production in O. polymorpha.

CONCLUSIONS

This novel multiplexed genome-editing tool mediated by CRISPR-Cpf1 can realize the deletion and integration of multiple genes, which holds great promise for accelerating engineering efforts on this non-conventional methylotrophic yeast for metabolic engineering and genomic evolution towards its application as an industrial cell factory.

Blue-Purple evaluation: Chromoproteins facilitate the identification of BioBrick compatibility

Synthetic BioBricks introduce novel capabilities to manipulate genetic information, direct transcription-translation processes, and program cellular behaviors in living organisms. To maintain the stability and functionality of synthetic BioBricks, assembled DNA fragments should be mutually compatible without inducing negative effects such as metabolic burden or cellular toxicity in host cells. However, a simple, rapid, and reliable method to evaluate BioBrick compatibility remains to be developed. In this study, we report BP (Blue/Purple, Ban/Pick) evaluation, a method utilizing chromoproteins to facilitate the identification of BioBrick compatibility in one-pot reactions. By visualizing and quantifying the ratio of blue to purple Escherichia coli (E. coli) colonies on LB-agar plates, we can easily validate the compatibility of desired BioBrick constructions. To demonstrate our design, we characterized BioBrick assemblies with antitoxin-toxin pair ccdA-ccdB, lysis protein E, or heterologous protein sfGFP. Among these, we successfully identified several compatible assemblies. We anticipate that BP evaluation will enhance biotechnological assessments of BioBrick compatibility in vivo and expand the application of chromoproteins in synthetic biology.

Genetically engineered bacteria as inflammatory bowel disease therapeutics

Inflammatory bowel disease (IBD) is a chronic and recurrent disease caused by immune response disorders that disrupt the intestinal lumen symbiotic ecosystem and dysregulate mucosal immune functions. Current therapies available for IBD primarily focus on symptom management, making early diagnosis and prompt intervention challenging. The development of genetically engineered bacteria using synthetic biology presents a new strategy for addressing these challenges. In this review, we present recent breakthroughs in the field of engineered bacteria for the treatment and detection of IBD and describe how bacteria can be genetically modified to produce therapeutic molecules or execute diagnostic functions. In particular, we discuss the challenges faced in translating live bacterial therapeutics from bacterial design to delivery strategies for further clinical applications.

Engineering a Novel Probiotic Toolkit in Escherichia coli Nissle 1917 for Sensing and Mitigating Gut Inflammatory Diseases

Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation with no cure and limited treatment options that often have systemic side effects. In this study, we developed a target-specific system to potentially treat IBD by engineering the probiotic bacterium Escherichia coli Nissle 1917 (EcN). Our modular system comprises three components: a transcription factor-based sensor (NorR) capable of detecting the inflammation biomarker nitric oxide (NO), a type 1 hemolysin secretion system, and a therapeutic cargo consisting of a library of humanized anti-TNFα nanobodies. Despite a reduction in sensitivity, our system demonstrated a concentration-dependent response to NO, successfully secreting functional nanobodies with binding affinities comparable to the commonly used drug Adalimumab, as confirmed by enzyme-linked immunosorbent assay and in vitro assays. This newly validated nanobody library expands EcN therapeutic capabilities. The adopted secretion system, also characterized for the first time in EcN, can be further adapted as a platform for screening and purifying proteins of interest. Additionally, we provided a mathematical framework to assess critical parameters in engineering probiotic systems, including the production and diffusion of relevant molecules, bacterial colonization rates, and particle interactions. This integrated approach expands the synthetic biology toolbox for EcN-based therapies, providing novel parts, circuits, and a model for tunable responses at inflammatory hotspots.

TIR predictor and optimizer: Web-tools for accurate prediction of translation initiation rate and precision gene design in Saccharomyces cerevisiae

Translation initiation is the primary determinant of the rate of protein production. The variation in the rate with which this step occurs can cause up to three orders of magnitude differences in cellular protein levels. Several mRNA features, including mRNA stability in proximity to the start codon, coding sequence length, and presence of specific motifs in the mRNA molecule, have been shown to influence the translation initiation rate. These molecular factors acting at different strengths allow precise control of in vivo translation initiation rate and thus the rate of protein synthesis. However, despite the paramount importance of translation initiation rate in protein synthesis, accurate prediction of the absolute values of initiation rate remains a challenge. In fact, as of now, there is no available model for predicting the initiation rate in Saccharomyces cerevisiae. To address this, we train a machine learning model for predicting the in vivo initiation rate in S. cerevisiae transcripts. The model is trained using a diverse set of mRNA transcripts, enabling the comparison of initiation rates across different transcripts. Our model exhibited excellent accuracy in predicting the translation initiation rate and demonstrated its effectiveness with both endogenous and exogenous transcripts. Then, by combining the machine learning model with the Monte-Carlo search algorithm, we have also devised a method to optimize the nucleotide sequence of any gene to achieve a specific target initiation rate. The machine learning model we've developed for predicting translation initiation rates, along with the gene optimization method, are deployed as a web server. Both web servers are accessible for free at the following link: ajeetsharmalab.com/TIRPredictor. Thus, this research advances our fundamental understanding of translation initiation processes, with direct applications in biotechnology.

Rainbow screening: Chromoproteins enable visualized molecular cloning

Molecular cloning facilitates the assembly of heterologous DNA fragments with vectors, resulting in the generation of plasmids that can steadily replicate in host cells. To efficiently and accurately screen out the expected plasmid candidates, various methods, such as blue-white screening, have been developed for visualization. However, these methods typically require additional genetic manipulations and costs. To simplify the process of visualized molecular cloning, here we report Rainbow Screening, a method that combines Gibson Assembly with chromoproteins to distinguish Escherichia coli (E. coli) colonies by naked eyes, eliminating the need for additional genetic manipulations or costs. To illustrate the design, we select both E. coli 16s rRNA and sfGFP expression module as two inserted fragments. Using Rainbow Screening, false positive colonies can be easily distinguished on LB-agar plates. Moreover, both the assembly efficiency and the construct accuracy can exceed 80%. We anticipate that Rainbow Screening will enrich the molecular cloning methodology and expand the application of chromoproteins in biotechnology and synthetic biology.