Synthetic memory circuits for stable cell reprogramming in plants

Lloyd, James P. B.; Ly, Florence; Gong, Patrick; Swain, Tessa; Pflueger, Jahnvi; Fourie, Elliott; Khan, Muhammad Adil; Kidd, Brendan N.; Lister, Ryan

doi:10.1038/s41587-022-01383-2

Cited by 57 publications

(38 citation statements)

References 68 publications

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“…The development of circuits with memory is essential step towards biological computation and decision-making systems. Long term memories can be obtained by DNA reorganization using recombinases (47)(48)(49), however biological memories where information can be stored and deleted or modified are essential for computation. Here, we implemented a memory module to improve remarkably the digital behavior of the circuits.…”

Section: Discussionmentioning

confidence: 99%

Implementing re-configurable biological computation with distributed multicellular consortia

Canadell

Ortiz-Vaquerizas

Mogas-Diez

et al. 2022

Nucleic Acids Research

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The use of synthetic biological circuits to deal with numerous biological challenges has been proposed in several studies, but its implementation is still remote. A major problem encountered is the complexity of the cellular engineering needed to achieve complex biological circuits and the lack of general-purpose biological systems. The generation of re-programmable circuits can increase circuit flexibility and the scalability of complex cell-based computing devices. Here we present a new architecture to produce reprogrammable biological circuits that allow the development of a variety of different functions with minimal cell engineering. We demonstrate the feasibility of creating several circuits using only a small set of engineered cells, which can be externally reprogrammed to implement simple logics in response to specific inputs. In this regard, depending on the computation needs, a device composed of a number of defined cells can generate a variety of circuits without the need of further cell engineering or rearrangements. In addition, the inclusion of a memory module in the circuits strongly improved the digital response of the devices. The reprogrammability of biological circuits is an intrinsic capacity that is not provided in electronics and it may be used as a tool to solve complex biological problems.

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Section: Discussionmentioning

confidence: 99%

Implementing re-configurable biological computation with distributed multicellular consortia

Canadell

Ortiz-Vaquerizas

Mogas-Diez

et al. 2022

Nucleic Acids Research

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“…One study in N. benthamiana used a recombination directionality factor (RDF), which when combined with the integrase, allowed reversing of the integrase reaction 24 . In addition, tyrosine integrases were recently used to implement logic circuits in Arabidopsis 18 . Here, we developed a toolbox of well-characterized parts to build synthetic circuits in Arabidopsis using PhiC31 and Bxb1 integrases.…”

Section: Introductionmentioning

confidence: 99%

“…Gene-regulatory parts, such as promoters or terminators, can be placed between integrase sites to mediate a specific gene expression pattern dependent on integrase expressions. Complex genetic circuits have been developed using integrases, implementing Boolean logic (in bacteria 15, 16 , mammalian cells 17 , and plant protoplasts 18 ), history-dependent logic (in bacteria 19, 20 ), and cell-lineage tracing (in animals 14 ). Serine integrases can also be used to induce expression of toxic genes at a specific time, to mediate site-specific DNA integration 21 , and has been also used for multi-part in vitro cloning 22 .…”

Section: Introductionmentioning

confidence: 99%

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An integrase toolbox to record gene-expression during plant development

Guiziou

Maranas

Chu

et al. 2022

Preprint

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There are many open questions about the mechanisms that coordinate the dynamic, multicellular behaviors required for organogenesis. Synthetic circuits that can record in vivo signaling networks have been critical in elucidating animal development. Here, we report on the transfer of this technology to plants using orthogonal serine integrases to mediate site-specific and irreversible DNA recombination visualized by switching between fluorescent reporters. When combined with promoters expressed during lateral root initiation, integrases amplified reporter signal and permanently marked all descendants. In addition, we have developed a suite of methods to tune the threshold for integrase switching, including: RNA/protein degradation tags, a nuclear localization signal, and a split-intein system. These tools improved the robustness of integrase-mediated switching with different promoters and the stability of switching behavior over multiple generations. This integrase toolbox can be used to build history-dependent circuits to decode the order of expression during organogenesis in many contexts.

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“…However, forward engineering plants with these capabilities remain a substantial technical hurdle. Ongoing efforts have sought to fill knowledge gaps by uncovering design rules and building genetic part catalogs for plant-based circuits [10][11][12][13].…”

Section: Introductionmentioning

confidence: 99%

Genetic Circuit Design in Rhizobacteria

Dundas

Dinneny

2022

BioDesign Res

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Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.

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Synthetic memory circuits for stable cell reprogramming in plants

Cited by 57 publications

References 68 publications

Implementing re-configurable biological computation with distributed multicellular consortia

Implementing re-configurable biological computation with distributed multicellular consortia

An integrase toolbox to record gene-expression during plant development

Genetic Circuit Design in Rhizobacteria

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