Developing a PAM-Flexible CRISPR-Mediated Dual-Deaminase Base Editor to Regulate Extracellular Electron Transport in Shewanella oneidensis

Unlocking the potential of Shewanella in metabolic engineering: Current status, challenges, and opportunities

Shewanella species are facultative anaerobes with distinctive electrochemical properties, making them valuable for applications in energy conversion and environmental bioremediation. Due to their well-characterized electron transfer mechanisms and ease of genetic manipulation, Shewanella spp. have emerged as a promising chassis for metabolic engineering. In this review, we provide a comprehensive overview of the advancements in Shewanella-based metabolic engineering. We begin by discussing the physiological characteristics of Shewanella, with a particular focus on its extracellular electron transfer (EET) capability. Next, we outline the use of Shewanella as a metabolic engineering chassis, presenting a general framework for strain construction based on the Design-Build-Test-Learn (DBTL) cycle and summarizing key advancements in the engineering of Shewanella's metabolic modules. Finally, we offer a perspective on the future development of Shewanella chassis, highlighting the need for deeper mechanistic insights, rational strain design, and interdisciplinary collaboration to drive further progress.

Shewanella oneidensis: Biotechnological Application of Metal-Reducing Bacteria

What is an unconventional organism in biotechnology? The γ-proteobacterium Shewanella oneidensis might fall into this category as it was initially established as a laboratory model organism for a process that was not seen as potentially interesting for biotechnology. The reduction of solid-state extracellular electron acceptors such as iron and manganese oxides is highly relevant for many biogeochemical cycles, although it turned out in recent years to be quite relevant for many potential biotechnological applications as well. Applications started with the production of nanoparticles and dramatically increased after understanding that electrodes in bioelectrochemical systems can also be used by these organisms. From the potential production of current and hydrogen in these systems and the development of biosensors, the field expanded to anode-assisted fermentations enabling fermentation reactions that were - so far - dependent on oxygen as an electron acceptor. Now the field expands further to cathode-dependent production routines. As a side product to all these application endeavors, S. oneidensis was understood more and more, and our understanding and genetic repertoire is at eye level to E. coli. Corresponding to this line of thought, this chapter will first summarize the available arsenal of tools in molecular biology that was established for working with the organism and thereafter describe so far established directions of application. Last but not least, we will highlight potential future directions of work with the unconventional model organism S. oneidensis.

Rewiring native post-transcriptional global regulators to achieve designer, multi-layered genetic circuits

As synthetic biology expands, creating "drag-and-drop" regulatory tools that can achieve diverse regulatory outcomes are paramount. Herein, we develop a approach for engineering complex post-transcriptional control by rewiring the Carbon Storage Regulatory (Csr) Network of Escherichia coli. We co-opt native interactions of the Csr Network to establish post-transcriptional logic gates and achieve complex bacterial regulation. First, we rationally engineer RNA-protein interactions to create a genetic toolbox of 12 BUFFER Gates that achieves a 15-fold range of expression. Subsequently, we develop a Csr-regulated NOT Gate by integrating a cognate 5' UTR that is natively Csr-activated into our platform. We then deploy the BUFFER and NOT gates to build a bi-directional regulator, two input Boolean Logic gates OR, NOR, AND and NAND and a pulse-generating circuit. Last, we port our Csr-regulated BUFFER Gate into three industrially relevant bacteria simply by leveraging the conserved Csr Network in each species.

Multiplex CRISPR-Cas Genome Editing: Next-Generation Microbial Strain Engineering

Genome editing is a crucial technology for obtaining desired phenotypes in a variety of species, ranging from microbes to plants, animals, and humans. With the advent of CRISPR-Cas technology, it has become possible to edit the intended sequence by modifying the target recognition sequence in guide RNA (gRNA). By expressing multiple gRNAs simultaneously, it is possible to edit multiple targets at the same time, allowing for the simultaneous introduction of various functions into the cell. This can significantly reduce the time and cost of obtaining engineered microbial strains for specific traits. In this review, we investigate the resolution of multiplex genome editing and its application in engineering microorganisms, including bacteria and yeast. Furthermore, we examine how recent advancements in artificial intelligence technology could assist in microbial genome editing and engineering. Based on these insights, we present our perspectives on the future evolution and potential impact of multiplex genome editing technologies in the agriculture and food industry.

Engineering extracellular electron transfer pathways of electroactive microorganisms by synthetic biology for energy and chemicals production

The excessive consumption of fossil fuels causes massive emission of CO2, leading to climate deterioration and environmental pollution. The development of substitutes and sustainable energy sources to replace fossil fuels has become a worldwide priority. Bio-electrochemical systems (BESs), employing redox reactions of electroactive microorganisms (EAMs) on electrodes to achieve a meritorious combination of biocatalysis and electrocatalysis, provide a green and sustainable alternative approach for bioremediation, CO2 fixation, and energy and chemicals production. EAMs, including exoelectrogens and electrotrophs, perform extracellular electron transfer (EET) (i.e., outward and inward EET), respectively, to exchange energy with the environment, whose rate determines the efficiency and performance of BESs. Therefore, we review the synthetic biology strategies developed in the last decade for engineering EAMs to enhance the EET rate in cell-electrode interfaces for facilitating the production of electricity energy and value-added chemicals, which include (1) progress in genetic manipulation and editing tools to achieve the efficient regulation of gene expression, knockout, and knockdown of EAMs; (2) synthetic biological engineering strategies to enhance the outward EET of exoelectrogens to anodes for electricity power production and anodic electro-fermentation (AEF) for chemicals production, including (i) broadening and strengthening substrate utilization, (ii) increasing the intracellular releasable reducing equivalents, (iii) optimizing c-type cytochrome (c-Cyts) expression and maturation, (iv) enhancing conductive nanowire biosynthesis and modification, (v) promoting electron shuttle biosynthesis, secretion, and immobilization, (vi) engineering global regulators to promote EET rate, (vii) facilitating biofilm formation, and (viii) constructing cell-material hybrids; (3) the mechanisms of inward EET, CO2 fixation pathway, and engineering strategies for improving the inward EET of electrotrophic cells for CO2 reduction and chemical production, including (i) programming metabolic pathways of electrotrophs, (ii) rewiring bioelectrical circuits for enhancing inward EET, and (iii) constructing microbial (photo)electrosynthesis by cell-material hybridization; (4) perspectives on future challenges and opportunities for engineering EET to develop highly efficient BESs for sustainable energy and chemical production. We expect that this review will provide a theoretical basis for the future development of BESs in energy harvesting, CO2 fixation, and chemical synthesis.