RoboMoClo: A Robotics-Assisted Modular Cloning Framework for Multiple Gene Assembly in Biofoundry

The knowledge driven DBTL cycle provides mechanistic insights while optimising dopamine production in Escherichia coli

BACKGROUND

Dopamine is a promising organic compound with several key applications in emergency medicine, diagnosis and treatment of cancer, production of lithium anodes, and wastewater treatment. Since studies on in vivo dopamine production are limited, this study demonstrates the development and optimisation of a dopamine production strain by the help of the knowledge driven design-build-test-learn (DBTL) cycle for rational strain engineering.

RESULTS

The knowledge driven DBTL cycle, involving upstream in vitro investigation, is an automated workflow that enables both mechanistic understanding and efficient DBTL cycling. Following the in vitro cell lysate studies, the results were translated to the in vivo environment through high-throughput ribosome binding site (RBS) engineering. As a result, we developed a dopamine production strain capable of producing dopamine at concentrations of 69.03 ± 1.2 mg/L which equals 34.34 ± 0.59 mg/gbiomass. Compared to state-of-the-art in vivo dopamine production, our approach improved performance by 2.6 and 6.6-fold, respectively.

CONCLUSION

In essence, a highly efficient dopamine production strain was developed by implementing the knowledge driven DBTL cycle involving upstream in vitro investigation. The fine-tuning of the dopamine pathway by high-throughput RBS engineering clearly demonstrated the impact of GC content in the Shine-Dalgarno sequence on the RBS strength.

Bacterial biosynthesis of abietane-type diterpene ferruginol from glucose

BACKGROUND

Microbial supply of plant extracts is a promising biomanufacturing strategy that requires engineering of metabolic pathways and enzymes. This study presents the engineering of Corynebacterium glutamicum for heterologous production of diterpenes miltiradiene and ferruginol.

RESULTS

Through targeted metabolic pathway modifications, including inactivation of pyruvate carboxylase and phytoene synthase, the HL01 strain was optimized to enhance pyruvate and geranylgeranyl pyrophosphate (GGPP) pools. Overexpression of key MEP pathway enzymes (Dxs and Idi) and implementation of three GGPP synthase modules further boosted diterpene synthesis. Then, combining those modules with diterpene synthase (DiTPS) and intact P450 reductase modules (CYP76AH1 and CPR1) enabled production of miltiradiene (ferruginol equivalent) at 237.46 ± 34.8 mg/L and ferruginol at 107.34 ± 1.2 mg/L under constant glucose feeding, respectively.

CONCLUSIONS

Modular gene expression for heterologous metabolic pathway can be optimized for bacterial biosynthesis. This is the first demonstration of ferruginol production in bacteria. These findings pave the way for further optimization of diterpene biosynthesis through pathway engineering and module integration in bacterial systems.

A novel MoClo-mediated intron insertion system facilitates enhanced transgene expression in Chlamydomonas reinhardtii

The Chlamydomonas Modular Cloning (MoClo) toolkit allows for straightforward and flexible construction of genetic modules for gene expression in the microalgal model species, fostering developments in algal biotechnology. Efficiently expressing transgenes from the nuclear genome of C. reinhardtii requires the proper insertion of introns throughout the respective gene, as it can substantially enhance the gene expression. To facilitate synthetic biology approaches in this microalga, we developed a novel strategy for intron insertion into synthetic DNA fragments. Our method aligns with current MoClo standards, and its feasibility is demonstrated by assembling genes of various lengths and successfully expressing them in C. reinhardtii. Examples include enhanced NanoLuc expression with increased intron numbers, a fungal luciferase enabling bioluminescence in C. reinhardtii, and a fungal tryptophan decarboxylase.

Golden Gate Cloning in Actinobacteria: Opportunities and Challenges

As we exploit biological machineries and circuits to redesign nature, it is just important to use efficient cloning strategies and methods to heterologously express the resulting DNA constructs. Golden Gate cloning allows the assembly of multiple fragments in a single reaction, making the process efficient and seamless. Although Golden Gate strategies have already been employed for different organisms, it is still not well-established for Actinobacteria. Here, we describe methods for Golden Gate cloning and how it can be utilized for Actinobacteria.

Biofoundry-Assisted Golden Gate Cloning with AssemblyTron

Golden Gate assembly is a requisite method in synthetic biology that facilitates critical conventions such as genetic part abstraction and rapid prototyping. However, compared to robotic implementation, manual Golden Gate implementation is cumbersome, error-prone, and inconsistent for complex assembly designs. AssemblyTron is an open-source python package that provides an affordable automation solution using open-source OpenTrons OT-2 lab robots. Automating Golden Gate assembly with AssemblyTron can reduce failure-rate, resource consumption, and training requirements for building complex DNA constructs, as well as indexed and combinatorial libraries. Here, we dissect a panel of upgrades to AssemblyTron's Golden Gate assembly capabilities, which include Golden Gate assembly into modular cloning part vectors, error-prone polymerase chain reaction (PCR) combinatorial mutant library assembly, and modular cloning indexed plasmid library assembly. These upgrades enable a broad pool of users with varying levels of experience to readily implement advanced Golden Gate applications using low-cost, open-source lab robotics.

An Optimized Version of the Small Synthetic Genome (Mini-Synplastome) for Plastid Metabolic Engineering in Solanum tuberosum (Potato)

Plastids represent promising targets in plant genetic engineering for many biotech applications, ranging from their use as bioreactors for the overproduction of valuable molecules to the installation of transgenes for improving plant traits. For over 30 years, routine methods of plastid transformation have relied on homologous recombination integrating vectors. However, nonintegrating episomal plasmids have recently received more attention as an innovative tool for the plastid genetic engineering of plant cells. One of these novel technologies is the mini-synplastome, an episomal plasmid with a chloroplast-specific origin of replication (ori) used to express transgenes in plastids. In order to improve episome sequence stability overtime by reducing the frequency of spurious recombination events, an optimized version of mini-synplastome (Gen3) was designed. The innovation in the Gen3 design was to substantially reduce the size of the plastomic sequence containing oris to include only domains involved in replication and to reduce the sequence homology of the whole episome with the endogenous plastome. In this work, we have demonstrated that Gen3 can be used to install a multigene pathway in Solanum tuberosum (potato) chloroplasts, and the episome is stable in a full-length circular form at high copy number throughout all plant developmental stages to anthesis in plants with normal phenotypic parameters. It is anticipated that in the next decade the mini-synplastome will be a valuable tool for installing complex genetic circuits in plastids.

Metabolic engineering of Corynebacterium glutamicum: Unlocking its potential as a key cell factory platform for organic acid production

Corynebacterium glutamicum, a well-studied industrial model microorganism, has garnered widespread attention due to its ability for producing amino acids with a long history. In recent years, research efforts have been increasingly focused on exploring its potential for producing various organic acids beyond amino acids. Organic acids, which are characterized by their acidic functional groups, have diverse applications across industries such as food, agriculture, pharmaceuticals, and biobased materials. Leveraging advancements in metabolic engineering and synthetic biology, the metabolic pathways of C. glutamicum have been broadened to facilitate the production of numerous high-value organic acids. This review summarizes the recent progress in metabolic engineering for the production of both amino acids and other organic acids by C. glutamicum. Notably, these acids include, amino acids (lysine, isoleucine, and phenylalanine), TCA cycle-derived organic acids (succinic acid, α-ketoglutaric acid), aromatic organic acids (protocatechuate, 4-amino-3-hydroxybenzoic acid, anthranilate, and para-coumaric acid), and other organic acids (itaconic acid and cis, cis-muconic acid).

Getting the Right Clones in an Automated Manner: An Alternative to Sophisticated Colony-Picking Robotics

In recent years, the design-build-test-learn (DBTL) cycle has become a key concept in strain engineering. Modern biofoundries enable automated DBTL cycling using robotic devices. However, both highly automated facilities and semi-automated facilities encounter bottlenecks in clone selection and screening. While fully automated biofoundries can take advantage of expensive commercially available colony pickers, semi-automated facilities have to fall back on affordable alternatives. Therefore, our clone selection method is particularly well-suited for academic settings, requiring only the basic infrastructure of a biofoundry. The automated liquid clone selection (ALCS) method represents a straightforward approach for clone selection. Similar to sophisticated colony-picking robots, the ALCS approach aims to achieve high selectivity. Investigating the time analogue of five generations, the model-based set-up reached a selectivity of 98 ± 0.2% for correctly transformed cells. Moreover, the method is robust to variations in cell numbers at the start of ALCS. Beside Escherichia coli, promising chassis organisms, such as Pseudomonas putida and Corynebacterium glutamicum, were successfully applied. In all cases, ALCS enables the immediate use of the selected strains in follow-up applications. In essence, our ALCS approach provides a 'low-tech' method to be implemented in biofoundry settings without requiring additional devices.

Measuring the economic efficiency of laboratory automation in biotechnology

Laboratory automation with robot-assisted processes enhances synthetic biology, but its economic impact on projects is uncertain. We have proposed an experiment price index (EPI) for a quantitative comparison of factors in time, cost, and sample numbers, helping measure the efficiency of laboratory automation in synthetic biology and biomolecular engineering.

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.

Automated in vivo enzyme engineering accelerates biocatalyst optimization

Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. Their realization through in vitro enzyme characterization and engineering is mostly low throughput and labor-intensive. Therefore, strategies for increasing throughput while diminishing manual labor are gaining momentum, such as in vivo screening and evolution campaigns. Computational tools like machine learning further support enzyme engineering efforts by widening the explorable design space. Here, we propose an integrated solution to enzyme engineering challenges whereby ML-guided, automated workflows (including library generation, implementation of hypermutation systems, adapted laboratory evolution, and in vivo growth-coupled selection) could be realized to accelerate pipelines towards superior biocatalysts.

CRISPR-dCas13a system for programmable small RNAs and polycistronic mRNA repression in bacteria

Bacterial small RNAs (sRNAs) function in post-transcriptional regulatory responses to environmental changes. However, the lack of eukaryotic RNA interference-like machinery in bacteria has limited the systematic engineering of RNA repression. Here, we report the development of clustered regularly interspaced short palindromic repeats (CRISPR)-guided dead CRIPSR-associated protein 13a (dCas13a) ribonucleoprotein that utilizes programmable CRISPR RNAs (crRNAs) to repress trans-acting and cis-acting sRNA as the target, altering regulatory mechanisms and stress-related phenotypes. In addition, we implemented a modular loop engineering of the crRNA to promote modular repression of the target gene with 92% knockdown efficiency and a single base-pair mismatch specificity. With the engineered crRNAs, we achieved targetable single-gene repression in the polycistronic operon. For metabolic application, 102 crRNAs were constructed in the biofoundry and used for screening novel knockdown sRNA targets to improve lycopene (colored antioxidant) production in Escherichia coli. The CRISPR-dCas13a system will assist as a valuable systematic tool for the discovery of novel sRNAs and the fine-tuning of bacterial RNA repression in both scientific and industrial applications.

Automated Platform for the Plasmid Construction Process

There is a growing need for applications capable of handling large synthesis biology experiments. At the core of synthetic biology is the process of cloning and manipulating DNA as plasmids. Here, we report the development of an application named DNAda capable of writing automation instructions for any given DNA construct design generated by the J5 DNA assembly program. We also describe the automation pipeline and several useful features. The pipeline is particularly useful for the construction of combinatorial DNA assemblies. Furthermore, we demonstrate the platform by constructing a library of polyketide synthase parts, which includes 120 plasmids ranging in size from 7 to 14 kb from 4 to 7 DNA fragments.

Physical Laboratory Automation in Synthetic Biology

Synthetic Biology has overcome many of the early challenges facing the field and is entering a systems era characterized by adoption of Design-Build-Test-Learn (DBTL) approaches. The need for automation and standardization to enable reproducible, scalable, and translatable research has become increasingly accepted in recent years, and many of the hardware and software tools needed to address these challenges are now in place or under development. However, the lack of connectivity between DBTL modules and barriers to access and adoption remain significant challenges to realizing the full potential of lab automation. In this review, we characterize and classify the state of automation in synthetic biology with a focus on the physical automation of experimental workflows. Though fully autonomous scientific discovery is likely a long way off, impressive progress has been made toward automating critical elements of experimentation by combining intelligent hardware and software tools. It is worth questioning whether total automation that removes humans entirely from the loop should be the ultimate goal, and considerations for appropriate automation versus total automation are discussed in this light while emphasizing areas where further development is needed in both contexts.

Plastid engineering using episomal DNA

KEY MESSAGE

Novel episomal systems have the potential to accelerate plastid genetic engineering for application in plant synthetic biology. Plastids represent valuable subcellular compartments for genetic engineering of plants with intrinsic advantages to engineering the nucleus. The ability to perform site-specific transgene integration by homologous recombination (HR), coordination of transgene expression in operons, and high production of heterologous proteins, all make plastids an attractive target for synthetic biology. Typically, plastid engineering is performed by homologous recombination; however, episomal-replicating vectors have the potential to accelerate the design/build/test cycles for plastid engineering. By accelerating the timeline from design to validation, it will be possible to generate translational breakthroughs in fields ranging from agriculture to biopharmaceuticals. Episomal-based plastid engineering will allow precise single step metabolic engineering in plants enabling the installation of complex synthetic circuits with the ambitious goal of reaching similar efficiency and flexibility of to the state-of-the-art genetic engineering of prokaryotic systems. The prospect to design novel episomal systems for production of transplastomic marker-free plants will also improve biosafety for eventual release in agriculture.

Research progress of engineering microbial cell factories for pigment production

Pigments are widely used in people's daily life, such as food additives, cosmetics, pharmaceuticals, textiles, etc. In recent years, the natural pigments produced by microorganisms have attracted increased attention because these processes cannot be affected by seasons like the plant extraction methods, and can also avoid the environmental pollution problems caused by chemical synthesis. Synthetic biology and metabolic engineering have been used to construct and optimize metabolic pathways for production of natural pigments in cellular factories. Building microbial cell factories for synthesis of natural pigments has many advantages, including well-defined genetic background of the strains, high-density and rapid culture of cells, etc. Until now, the technical means about engineering microbial cell factories for pigment production and metabolic regulation processes have not been systematically analyzed and summarized. Therefore, the studies about construction, modification and regulation of synthetic pathways for microbial synthesis of pigments in recent years have been reviewed, aiming to provide an up-to-date summary of engineering strategies for microbial synthesis of natural pigments including carotenoids, melanins, riboflavins, azomycetes and quinones. This review should provide new ideas for further improving microbial production of natural pigments in the future.

Biofoundry Palette: Planning-Assistant Software for Liquid Handler-Based Experimentation and Operation in the Biofoundry Workflow

Lab automation has facilitated synthetic biology applications in an automated workflow, and biofoundry facilities have enabled automated high-throughput experiments of gene cloning and genome engineering to be conducted following a precise experimental design and protocol. However, before-experiment procedures in biofoundry applications have been underdetermined. We aimed to develop a Python-based planning-assistant software, namely Biofoundry Palette, for liquid handler-based experimentation and operation in the biofoundry workflow. Depending on the synthetic biology project, variable information and content information may vary; the Biofoundry Palette provides precise information for the before-experiment units for each process module in the biofoundry workflow. As a demonstration, more than 200 unique information sets, generated by Biofoundry Palette, were used in automated gene cloning or pathway construction. The information on planning and management can potentially help the operator faithfully execute the biofoundry workflow after securing the before-experiment unit, thereby lowering the risk of human errors and performing successful biofoundry operations for synthetic biology applications.