Engineering genetically-encoded tools for optogenetic control of protein activity

Liu, Qi; Tucker, Chandra L.

doi:10.1016/j.cbpa.2017.05.001

Cited by 52 publications

(42 citation statements)

References 55 publications

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“…The conformation-based control can be powerful to reduce the background activity, but its broad applicability has been a challenge. A strategy to control protein activity is splitting the protein and then reassembling the split halves by ligand or light-induced dimerizers 1 , 3 , 5 , 6 , but these methods have been prone to significant spontaneous assembly 7 , 8 . Moreover, the approach suffers from the difficulty of identifying effective protein split sites.…”

Section: Introductionmentioning

confidence: 99%

Computational design of chemogenetic and optogenetic split proteins

et al. 2018

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Controlling protein activity with chemogenetics and optogenetics has proven to be powerful for testing hypotheses regarding protein function in rapid biological processes. Controlling proteins by splitting them and then rescuing their activity through inducible reassembly offers great potential to control diverse protein activities. Building split proteins has been difficult due to spontaneous assembly, difficulty in identifying appropriate split sites, and inefficient induction of effective reassembly. Here we present an automated approach to design effective split proteins regulated by a ligand or by light (SPELL). We develop a scoring function together with an engineered domain to enable reassembly of protein halves with high efficiency and with reduced spontaneous assembly. We demonstrate SPELL by applying it to proteins of various shapes and sizes in living cells. The SPELL server (spell.dokhlab.org) offers an automated prediction of split sites.

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Section: Introductionmentioning

confidence: 99%

Computational design of chemogenetic and optogenetic split proteins

et al. 2018

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“…To overcome the disadvantages of the above‐mentioned inducible systems that tend to form massive intermembrane ‘patches’ rather than discrete contact ‘sites’, optogenetic tools have been developed for selective manipulation of MCS assembly, particularly at the ER–plasma membrane contact sites. Compared with other methods, the optogenetic approach excels in its reversibility, genetic encodability, high spatiotemporal precision and non‐invasiveness (Liu & Tucker, ).…”

Section: Introductionmentioning

confidence: 99%

A molecular toolbox for interrogation of membrane contact sites

Ji¹,

Liu

Huang

et al. 2019

The Journal of Physiology

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Membrane contact sites (MCSs) are specialized subcellular compartments formed by closely apposed membranes from two organelles. The intermembrane gap is separated by a distance ranging from 10 to 35 nm. MCSs are typically maintained through dynamic protein-protein and protein-lipid interactions. These intermembrane contact sites constitute important intracellular signalling hotspots to mediate a plethora of cellular processes, including calcium homeostasis, lipid metabolism, membrane biogenesis and organelle remodelling. In recent years, a series of genetically encoded probes and chemogenetic or optogenetic actuators have been invented to aid the visualization and interrogation of MCSs in both fixed and living cells. These molecular tools have greatly accelerated the pace of mechanistic dissection of membrane contact sites at the molecular level. In this review, we present an overview on the latest progress in this endeavour, and provide a general guide to the selection of methods and molecular tools for probing interorganellar membrane contact sites.Abstract figure legend Schematic diagram showing the interorganellar membrane contact sites (MCSs), which are intimately involved in the regulation of lipid and ion exchange, organelle biogenesis and subcellular positioning. Innovative methods and genetically encoded molecular tools have been developed to aid the visualization of MCSs and non-invasive manipulation of interorganellar communication with high spatiotemporal precision.

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“…In addition to transcriptional control, biological circuits can also be tuned by offering direct control over protein activities (Table 1 ). Optical control of protein activities has been established in eukaryotic cells in part due to the access to a wide range of sensors (Brechun et al, 2017 ; Liu and Tucker, 2017 ). These sensors belong to one-component systems which undergo conformational changes or shifts in their dimerization or oligomerization states upon light illumination.…”

Section: Light In Tuning Synthetic Circuitsmentioning

confidence: 99%

Programming Bacteria With Light—Sensors and Applications in Synthetic Biology

et al. 2018

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Photo-receptors are widely present in both prokaryotic and eukaryotic cells, which serves as the foundation of tuning cell behaviors with light. While practices in eukaryotic cells have been relatively established, trials in bacterial cells have only been emerging in the past few years. A number of light sensors have been engineered in bacteria cells and most of them fall into the categories of two-component and one-component systems. Such a sensor toolbox has enabled practices in controlling synthetic circuits at the level of transcription and protein activity which is a major topic in synthetic biology, according to the central dogma. Additionally, engineered light sensors and practices of tuning synthetic circuits have served as a foundation for achieving light based real-time feedback control. Here, we review programming bacteria cells with light, introducing engineered light sensors in bacteria and their applications, including tuning synthetic circuits and achieving feedback controls over microbial cell culture.

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Engineering genetically-encoded tools for optogenetic control of protein activity

Cited by 52 publications

References 55 publications

Computational design of chemogenetic and optogenetic split proteins

Computational design of chemogenetic and optogenetic split proteins

A molecular toolbox for interrogation of membrane contact sites

Programming Bacteria With Light—Sensors and Applications in Synthetic Biology

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