Systems metabolic engineering as an enabling technology in accomplishing sustainable development goals

Supplementation with Amino Acid Sources Facilitates Fermentative Growth of Shewanella oneidensis MR-1 in Defined Media

Shewanella oneidensis MR-1 is a facultative anaerobe that grows by respiration using a variety of electron acceptors. This organism serves as a model to study how bacteria thrive in redox-stratified environments. A glucose-utilizing engineered derivative of MR-1 has been reported to be unable to grow in glucose minimal medium (GMM) in the absence of electron acceptors, despite this strain having a complete set of genes for reconstructing glucose to lactate fermentative pathways. To gain insights into why MR-1 is incapable of fermentative growth, this study examined a hypothesis that this strain is programmed to repress the expression of some carbon metabolic genes in the absence of electron acceptors. Comparative transcriptomic analyses of the MR-1 derivative were conducted in the presence and absence of fumarate as an electron acceptor, and these found that the expression of many genes involved in carbon metabolism required for cell growth, including several tricarboxylic acid (TCA) cycle genes, was significantly downregulated in the absence of fumarate. This finding suggests a possibility that MR-1 is unable to grow fermentatively on glucose in minimal media owing to the shortage of nutrients essential for cell growth, such as amino acids. This idea was demonstrated in subsequent experiments that showed that the MR-1 derivative fermentatively grows in GMM containing tryptone or a defined mixture of amino acids. We suggest that gene regulatory circuits in MR-1 are tuned to minimize energy consumption under electron acceptor-depleted conditions, and that this results in defective fermentative growth in minimal media. IMPORTANCE It is an enigma why S. oneidensis MR-1 is incapable of fermentative growth despite having complete sets of genes for reconstructing fermentative pathways. Understanding the molecular mechanisms behind this defect will facilitate the development of novel fermentation technologies for the production of value-added chemicals from biomass feedstocks, such as electro-fermentation. The information provided in this study will also improve our understanding of the ecological strategies of bacteria living in redox-stratified environments.

The Emergence of Genome Editing—Innovation Network Dynamics of Academic Publications, Patents, and Business Activities

Transformative societal change can both be triggered and influenced by both macro-level political means and the emergence of technologies. Key enabling technologies and therein biotechnology hold the power to drive those changes forward, evolving from breakthrough academic discoveries into business activities. Due to its increasing empirical relevance, we picked genome editing as an example for an emerging technology and extracted publication, patent, and company data from the years 2000 to 2020. By drawing upon social network analysis, we identify major networks and clusters that are dominating the respective time and layer. Based on these networks, we draw vertical connections between scientific knowledge, patented technologies, and business activities to visualize the interlevel relationships between actors through technological development. Thereby, we identify network dynamics of the emergence of genome editing, the most important actors and clusters evolving, and its spread into different areas.

Towards Application of Electro-Fermentation for the Production of Value-Added Chemicals From Biomass Feedstocks

According to recent social demands for sustainable developments, the value of biomass as feedstocks for chemical industry is increasing. With the aid of metabolic engineering and genome editing, microbial fermentation has been developed for producing value-added chemicals from biomass feedstocks, while further improvements are desired for producing more diverse chemicals and increasing the production efficiency. The major intrinsic limitation in conventional fermentation technologies is associated with the need for balancing the net redox equivalents between substrates and products, resulting in limited repertories of fermentation products. One solution for this limitation would be “electro-fermentation (EF)” that utilizes bioelectrochemical systems for modifying the intracellular redox state of electrochemically active bacteria, thereby overcoming the redox constraint of fermentation. Recent studies have attempted the production of chemicals based on the concept of EF, while its utility has not been sufficiently demonstrated in terms of low production efficiencies. Here we discuss EF in terms of its concept, current status and future directions, which help us develop its practical applications to sustainable chemical industries.

Challenges and opportunities in bioremediation of micro-nano plastics: A review

Rising level of micro-nano plastics (MNPs) in the natural ecosystem adversely impact the health of the environment and living organisms globally. MNPs enter in to the agro-ecosystem, flora and fauna, and human body via trophic transfer, ingestion and inhalation, resulting impediment in blood vessel, infertility, and abnormal behaviors. Therefore, it becomes indispensable to apply a novel approach to remediate MNPs from natural environment. Amongst the several prevailing technologies of MNPs remediation, microbial remediation is considered as greener technology. Microbial degradation of plastics is typically influenced by several biotic as well as abiotic factors, such as enzymatic mechanisms, substrates and co-substrates concentration, temperature, pH, oxidative stress, etc. Therefore, it is pivotal to recognize the key pathways adopted by microbes to utilize plastic fragments as a sole carbon source for the growth and development. In this context, this review critically discussed the role of various microbes and their enzymatic mechanisms involved in biodegradation of MNPs in wastewater (WW) stream, municipal sludge, municipal solid waste (MSW), and composting starting with biological and toxicological impacts of MNPs. Moreover, this review comprehensively discussed the deployment of various MNPs remediation technologies, such as enzymatic, advanced molecular, and bio-membrane technologies in fostering the bioremediation of MNPs from various environmental compartments along with their pros and cons and prospects for future research.

Applications of artificial intelligence to enzyme and pathway design for metabolic engineering

Metabolic engineering for developing industrial strains capable of overproducing bioproducts requires good understanding of cellular metabolism, including metabolic reactions and enzymes. However, metabolic pathways and enzymes involved are still unknown for many products of interest, which presents a key challenge in their biological production. This challenge can be partly overcome by constructing novel biosynthetic pathways through enzyme and pathway design approaches. With the increase in bio-big data, data-driven approaches using artificial intelligence (AI) techniques are allowing more advanced protein and pathway design. In this paper, we review recent studies on AI-aided protein engineering and design, focusing on directed evolution that uses AI approaches to efficiently construct mutant libraries. Also, recent works of AI-aided pathway design strategies, including template-based and template-free approaches, are discussed.

Escherichia coli as a platform microbial host for systems metabolic engineering

Bio-based production of industrially important chemicals and materials from non-edible and renewable biomass has become increasingly important to resolve the urgent worldwide issues including climate change. Also, bio-based production, instead of chemical synthesis, of food ingredients and natural products has gained ever increasing interest for health benefits. Systems metabolic engineering allows more efficient development of microbial cell factories capable of sustainable, green, and human-friendly production of diverse chemicals and materials. Escherichia coli is unarguably the most widely employed host strain for the bio-based production of chemicals and materials. In the present paper, we review the tools and strategies employed for systems metabolic engineering of E. coli. Next, representative examples and strategies for the production of chemicals including biofuels, bulk and specialty chemicals, and natural products are discussed, followed by discussion on materials including polyhydroxyalkanoates (PHAs), proteins, and nanomaterials. Lastly, future perspectives and challenges remaining for systems metabolic engineering of E. coli are discussed.

Automated engineering of synthetic metabolic pathways for efficient biomanufacturing

Metabolic engineering involves the engineering and optimization of processes from single-cell to fermentation in order to increase production of valuable chemicals for health, food, energy, materials and others. A systems approach to metabolic engineering has gained traction in recent years thanks to advances in strain engineering, leading to an accelerated scaling from rapid prototyping to industrial production. Metabolic engineering is nowadays on track towards a truly manufacturing technology, with reduced times from conception to production enabled by automated protocols for DNA assembly of metabolic pathways in engineered producer strains. In this review, we discuss how the success of the metabolic engineering pipeline often relies on retrobiosynthetic protocols able to identify promising production routes and dynamic regulation strategies through automated biodesign algorithms, which are subsequently assembled as embedded integrated genetic circuits in the host strain. Those approaches are orchestrated by an experimental design strategy that provides optimal scheduling planning of the DNA assembly, rapid prototyping and, ultimately, brings forward an accelerated Design-Build-Test-Learn cycle and the overall optimization of the biomanufacturing process. Achieving such a vision will address the increasingly compelling demand in our society for delivering valuable biomolecules in an affordable, inclusive and sustainable bioeconomy.

Characterization and Engineering of a Clostridium Glycine Riboswitch and Its Use To Control a Novel Metabolic Pathway for 5-Aminolevulinic Acid Production in Escherichia coli

A riboswitch, a regulatory RNA that controls gene expression by specifically binding a ligand, is an attractive genetic element for the control of conditional gene expression and metabolic pathways. In this study, we identified a glycine riboswitch located in the 5'-untranslated regions of a glycine:proton symporter gene in Clostridium pasteurianum. The glycine riboswitch is shown to contain two tandem aptamers and to function as an activator of expression of genes fused to its expression platform. Results of singlet aptamer experiments indicated that aptamer-2 has a much higher impact on regulating gene expression than aptamer-1. Further, we successfully obtained synthetic glycine-OFF riboswitches using a dual selection approach, and one of them repressed gene expression up to 10.2-fold with an improved dynamic range. The specific glycine-OFF riboswitch can function as an independent repressor in the presence of glycine, and its repression mechanism is inferred from predicted secondary structure. The selected glycine-OFF riboswitch was used to dynamically control the biosynthesis of 5-aminolevulinic acid (5-ALA) in Escherichia coli with an unnatural 5-ALA synthetic pathway, in which glycine plays a key role. It is demonstrated that the use of a synthetic Clostridium glycine-OFF riboswitch can lead to a significant increase (11%) of 5-ALA in E. coli harboring an unnatural biosynthetic pathway.

Metabolomics for industrial fermentation

Metabolomics is essential to understand the metabolism and identify engineering targets to improve the performances of strains and bioprocesses. Although numerous metabolomics techniques have been developed and applied to various organisms, the metabolome of Saccharopolyspora erythraea, a native producer of erythromycin, had never been studied. The 2017 best paper of Bioprocess and Biosystems Engineering reports examination of three methods for quenching and extraction to analyze the intracellular metabolome of S. erythraea, and identified the most reliable methods for studying different groups of the metabolites. Subsequent studies on the dynamics of the intracellular metabolome of S. erythraea during the fed-batch fermentation identified a positive correlation between the specific erythromycin production rate and the pool size of intracellular propionyl-CoA and other precursors of erythromycin. A series of follow-up studies, such as demonstrating the applicability of the quenching/extraction methods in other related antibiotic producers, demonstrating the generality of the best matches between the quenching/extraction methods and the metabolite groups, and combining metabolomics approaches with the fluxomics and systems metabolic engineering approaches, will facilitate the metabolomics studies on important antibiotic producers, enable standardization of the quenching/extraction protocols, and improve the performance of the antibiotic production with deeper insight into their metabolism.

Enabling the valorization of guaiacol-based lignin: Integrated chemical and biochemical production of cis,cis-muconic acid using metabolically engineered Amycolatopsis sp ATCC 39116

Lignin is nature's second most abundant polymer and displays a largely unexploited renewable resource for value-added bio-production. None of the lignin-based fermentation processes so far managed to use guaiacol (2-methoxy phenol), the predominant aromatic monomer in depolymerized lignin. In this work, we describe metabolic engineering of Amycolatopsis sp. ATCC 39116 to produce cis,cis-muconic acid (MA), a precursor of recognized industrial value for commercial plastics, from guaiacol. The microbe utilized a very broad spectrum of lignin-based aromatics, such as catechol, guaiacol, phenol, toluene, p-coumarate, and benzoate, tolerated them in elevated amounts and even preferred them over sugars. As a next step, we developed a novel approach for genomic engineering of this challenging, GC-rich actinomycete. The successful introduction of conjugation and blue-white screening, using β-glucuronidase, enabled tailored genomic modifications within ten days. Successive deletion of two putative muconate cycloisomerases from the genome provided the mutant Amycolatopsis sp. ATCC 39116 MA-2, which accumulated 3.1gL^-1 MA from guaiacol within 24h, achieving a yield of 96%. The mutant was found also capable to produce MA from a guaiacol-rich true lignin hydrolysate, obtained from pine through hydrothermal conversion. This provides an important proof-of-concept to successfully coupling chemical and biochemical process steps into a value chain from the lignin polymer to an industrial chemical. In addition, Amycolatopsis sp. ATCC 39116 MA-2 was able to produce 2-methyl MA from o-cresol (2-methyl phenol), which opens possibilities towards polymers with novel architecture and properties.

Systems metabolic engineering as an enabling technology in accomplishing sustainable development goals

With pressing issues arising in recent years, the United Nations proposed 17 Sustainable Development Goals (SDGs) as an agenda urging international cooperations for sustainable development. In this perspective, we examine the roles of systems metabolic engineering (SysME) and its contribution to improving the quality of life and protecting our environment, presenting how this field of study offers resolutions to the SDGs with relevant examples. We conclude with offering our opinion on the current state of SysME and the direction it should move forward in the generations to come, explicitly focusing on addressing the SDGs.