Control of synthetic microbial consortia in time, space, and composition

Grandel, Nicolas E.; Gamas, Kiara Reyes; Bennett, Matthew R.

doi:10.1016/j.tim.2021.04.001

Cited by 51 publications

(32 citation statements)

References 88 publications

(102 reference statements)

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“…P. putida is a nonpathogenic environmental bacterium that naturally thrives in soil and the plant rhizosphere, but has emerged also in recent years as a metabolic engineering platform for a suite of industrial and environmental applications. ,,, One promising stratagem to strengthen the biotechnological possibilities of such platforms is to combine the intrinsic catalytic abilities of the cells with their physical shapes and material properties in what has been called synthetic morphologies. Different approaches include altering cell shape, assembling synthetic consortia with a given architecture, , and promoting adhesion to solid surfaces for forming catalytic biofilms. − In the last case, the predominant strategy is the manipulation of the native cdGMP network of species/strain at stake for production of surface-gluing polymers that secure bacterial binding to any material at hand. , In this work we present a further step in this direction by either (i) combining the natural biofilm forming potential of P. putida with an artificial device to provide a site of early attachment to a target solidwhich facilitates later buildup of a standard biofilmsor (ii) replacing altogether the extracellular mediators of surface attachment by a synthetic one. In either case, the key instrument to this end is ectopic expression of a nanobody that recognizes a distinct, well-defined target, thereby acting as a synthetic adhesin .…”

Section: Discussionmentioning

confidence: 99%

Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies

et al. 2021

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Gram-negative bacteria are endowed with complex outer membrane (OM) structures that allow them to both interact with other organisms and attach to different physical structures. However, the design of reliable bacterial coatings of solid surfaces is still a considerable challenge. In this work, we report that ectopic expression of a fibrinogen-specific nanobody on the envelope of Pseudomonas putida cells enables controllable formation of a bacterial monolayer strongly bound to an antigen-coated support. To this end, either the wild type or a surface-naked derivative of P. putida was engineered to express a hybrid between the β-barrel of an intimin-type autotransporter inserted in the outer membrane and a nanobody (V HH ) moiety that targets fibrinogen as its cognate interaction partner. The functionality of the thereby presented V HH and the strength of the resulting cell attachment to a solid surface covered with the cognate antigen were tested and parametrized with Quartz Crystal Microbalance technology. The results not only demonstrated the value of using bacteria with reduced OM complexity for efficient display of artificial adhesins, but also the potential of this approach to engineer specific bacterial coverings of predetermined target surfaces.

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Section: Discussionmentioning

confidence: 99%

Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies

et al. 2021

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“…Stable cocultivation systems should prevent faster-growing species from wiping out slower-growing ones. While standard methods (e.g., agar plates and liquid cultures) are straightforward, they cannot control the time, space, strength, and direction of cell growth and molecule exchange and increase the chance for interferences due to cell growth competition in dependence relationships (see, e.g., the review [47]). Spatial-temporally distributed chips (e.g., the multilayer mVLSI devices proposed here) are microfluidic systems with varying microfluidic chambers (i.e., monolayer traps for bacteria) that allow monoclonal and coculturing communities to grow and stay alive for short periods (e.g., hours or days) [66] while maintaining the exchange of chemicals and metabolites and preventing the effect of cell growth compe-tition.…”

Section: Design Automation "Software" Workflow Formentioning

confidence: 99%

Hardware, Software, and Wetware Codesign Environment for Synthetic Biology

Oliveira

Densmore

2022

BioDesign Res

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Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of “biodesign automation,” where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a “hardware, software, wetware” codesign vision where software tools can be made to act as “genetic compilers” that transform high-level specifications into engineered “genetic circuits” (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems’ actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.

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“…33 While creating stable consortia poses some challenges, e.g., the development of orthogonal (noncross-interacting) genetic engineering tools and control of relative growth rates, ll very recent advances in synthetic and computational biology can provide solutions to these issues. 33,34 Peptide chains can also be connected by exploiting split-protein/peptide systems. These domains are usually very small in size and can be fused to proteins without interfering with expression.…”

Section: Challenge 1: Controlling Secretion and Assembly To Deliver Engineerable Protein-based Elmsmentioning

confidence: 99%

Bottom-up approaches to engineered living materials: Challenges and future directions

Molinari

Tesoriero

Ajo‐Franklin

2021

Matter

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Biomaterials made by living systems, while very diverse, generally share similar organization: different lineages of cells are precisely patterned within a matrix to create a hierarchically defined structure. This meticulous organization allows for their multifunctional properties, which often exceed those of traditional materials. For these reasons, there is growing interest in creating engineered living materials (ELMs) that will have capabilities similar to those of natural living materials yet with tailored functions. This review aims to highlight technologies still missing from the field of ELMs, which currently prevents more impactful applications. We briefly review the existing literature and identify challenges in designing novel protein-based and non-ribosomally synthesized matrix elements, producing and incorporating biominerals, and improving critical material properties such as lifespan, spatial patterning, and cell-cell communication. We also discuss the interplay between these challenges and the need for the development of new chassis and corresponding genetic toolboxes. By overcoming these obstacles, we come ever closer to unlocking the potential and versatility of biomaterials to create designer ELMs.Protein-based materials (PBMs) are ubiquitous in nature and have often been studied and explored for commercial applications-especially in the biomedical field.

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Control of synthetic microbial consortia in time, space, and composition

Cited by 51 publications

References 88 publications

Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies

Engineering Tropism of Pseudomonas putida toward Target Surfaces through Ectopic Display of Recombinant Nanobodies

Hardware, Software, and Wetware Codesign Environment for Synthetic Biology

Bottom-up approaches to engineered living materials: Challenges and future directions

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