Synthetic gene regulation for independent external induction of the Saccharomyces cerevisiae pseudohyphal growth phenotype

Pothoulakis, Georgios; Ellis, Tom

doi:10.1038/s42003-017-0008-0

Cited by 13 publications

(14 citation statements)

References 47 publications

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“…Since b-estradiol is not a yeast metabolite or signaling molecule, cellular metabolism is not perturbed (McIsaac et al, 2013b). ZEVs have been widely used for basic and applied research, including studies of gene regulatory networks (Hackett et al, 2020;Kang et al, 2020;Ma & Brent, 2020), individual gene function (Elfving et al, 2014;Lyon et al, 2016;Weir et al, 2017;Tran et al, 2018;Kim et al, 2019;Smith et al, 2020;Wang et al, 2020;Kira et al, 2021), gene regulation (Carey, 2015;Hendrickson et al, 2018a;Schikora-Tamarit et al, 2018;Lutz et al, 2019;Brion et al, 2020;preprint: Leydon et al, 2021), metabolic engineering (Liu et al, 2020), synthetic biology (Schikora-Tamarit et al, 2016;Aranda-D ıaz et al, 2017;Gander et al, 2017;Pothoulakis & Ellis, 2018;Bashor et al, 2019;Kotopka & Smolke, 2020;Shaw et al, 2019;Yang et al, 2019), biocontainment (Agmon et al, 2017), living materials (Gilbert et al, 2021), highthroughput screening (Younger et al, 2017;Staller et al, 2018), and they have also been adapted to fission yeast (Ohira et al, 2017;G omez-Gil et al, 2020;Nuckolls et al, 2020) and Pichia pastoris (Perez-Pinera et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

A genome‐scale yeast library with inducible expression of individual genes

Arita

Kim

et al. 2021

Molecular Systems Biology

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The ability to switch a gene from off to on and monitor dynamic changes provides a powerful approach for probing gene function and elucidating causal regulatory relationships. Here, we developed and characterized YETI (Yeast Estradiol strains with Titratable Induction), a collection in which > 5,600 yeast genes are engineered for transcriptional inducibility with single‐gene precision at their native loci and without plasmids. Each strain contains SGA screening markers and a unique barcode, enabling high‐throughput genetics. We characterized YETI using growth phenotyping and BAR‐seq screens, and we used a YETI allele to identify the regulon of Rof1, showing that it acts to repress transcription. We observed that strains with inducible essential genes that have low native expression can often grow without inducer. Analysis of data from eukaryotic and prokaryotic systems shows that native expression is a variable that can bias promoter‐perturbing screens, including CRISPRi. We engineered a second expression system, Z 3 EB42, that gives lower expression than Z 3 EV, a feature enabling conditional activation and repression of lowly expressed essential genes that grow without inducer in the YETI library.

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Section: Introductionmentioning

confidence: 99%

A genome‐scale yeast library with inducible expression of individual genes

Arita

Kim

et al. 2021

Molecular Systems Biology

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“…The budding yeast Saccharomyces cerevisiae can differentiate from unicellular to pseudohyphal filamentous form in response to stress under the regulation of cyclic AMP-protein kinase A (cAMP/PKA) and the filamentation mitogen-activated protein kinase (fMAPK), rat sarcoma/protein kinase A (RAS/PKA), sucrose nonfermentable (SNF), and target of rapamycin (TOR) signaling pathways ( Kim and Rose, 2015 ). Notably, GPCRs such as Gα subunit Gpa2 of the RAS pathway were recognized during cell differentiation to the filamentous form ( Cullen and Sprague, 2012 ; Pothoulakis and Ellis, 2018 ). Furthermore, S .…”

Section: Discussionmentioning

confidence: 99%

GPCR Genes as Activators of Surface Colonization Pathways in a Model Marine Diatom

Chaiboonchoe

Dohai

et al. 2020

iScience

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Summary Surface colonization allows diatoms, a dominant group of phytoplankton in oceans, to adapt to harsh marine environments while mediating biofoulings to human-made underwater facilities. The regulatory pathways underlying diatom surface colonization, which involves morphotype switching in some species, remain mostly unknown. Here, we describe the identification of 61 signaling genes, including G-protein-coupled receptors (GPCRs) and protein kinases, which are differentially regulated during surface colonization in the model diatom species, Phaeodactylum tricornutum . We show that the transformation of P . tricornutum with constructs expressing individual GPCR genes induces cells to adopt the surface colonization morphology. P . tricornutum cells transformed to express GPCR1A display 30% more resistance to UV light exposure than their non-biofouling wild-type counterparts, consistent with increased silicification of cell walls associated with the oval biofouling morphotype. Our results provide a mechanistic definition of morphological shifts during surface colonization and identify candidate target proteins for the screening of eco-friendly, anti-biofouling molecules.

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“…Specifically, we used an S. cerevisiae strain (yGPH093) expressing the BED-activated synthetic transcription factor Z3EV and a GFP reporter under control of the Z3EV-responsive promoter (Fig. 5b) 56 . Pellicles grown from K. rhaeticus with yGPH093 yeast produced a strong GFP signal when exposed to exogenous BED (Fig.…”

Section: Engineering Living Bc Materials To Sense-and-respondmentioning

confidence: 99%

Living materials with programmable functionalities grown from engineered microbial co-cultures

et al. 2021

Self Cite

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Biological systems assemble tissues and structures with advanced properties in ways that cannot be achieved by man-made materials. Living materials self-assemble under mild conditions, are autonomously patterned, can self-repair and sense and respond to their environment. Inspired by this, the field of engineered living materials (ELMs) aims to use genetically-engineered organisms to generate novel materials. Bacterial cellulose (BC) is a biological material with impressive physical properties and low cost of production that is an attractive substrate for ELMs. Inspired by how plants build materials from tissues with specialist cells we here developed a system for making novel BCbased ELMs by addition of engineered yeast programmed to add functional traits to a cellulose matrix. This is achieved via a synthetic 'symbiotic culture of bacteria and yeast' (Syn-SCOBY) approach that uses a stable co-culture of Saccharomyces cerevisiae with BC-producing Komagataeibacter rhaeticus bacetria. Our Syn-SCOBY approach allows inoculation of engineered cells into simple growth media, and under mild conditions materials self-assemble with genetically-programmable functional properties in days. We show that co-cultured yeast can be engineered to secrete enzymes into BC, generating autonomously grown catalytic materials and enabling DNA-encoded modification of BC bulk material properties. We further developed a method for incorporating S. cerevisiae within the growing cellulose matrix, creating living materials that can sense chemical and optical inputs. This enabled growth of living sensor materials that can detect and respond to environmental pollutants, as well as living films that grow images based on projected patterns. This novel and robust Syn-SCOBY system empowers the sustainable production of BC-based ELMs..

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Synthetic gene regulation for independent external induction of the Saccharomyces cerevisiae pseudohyphal growth phenotype

Cited by 13 publications

References 47 publications

A genome‐scale yeast library with inducible expression of individual genes

A genome‐scale yeast library with inducible expression of individual genes

GPCR Genes as Activators of Surface Colonization Pathways in a Model Marine Diatom

Living materials with programmable functionalities grown from engineered microbial co-cultures

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