publication . Article . 2018

Tools for engineering coordinated system behaviour in synthetic microbial consortia.

Nicolas Kylilis; Zoltan A. Tuza; Guy-Bart Stan; Karen M. Polizzi;
Open Access
  • Published: 01 Jul 2018
  • Country: United Kingdom
Abstract
Advancing synthetic biology to the multicellular level requires the development of multiple cell-to-cell communication channels that propagate information with minimal signal interference. The development of quorum-sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on cognate acyl-homoserine lactone (AHL)/transcription factor pairs, while the use of non-cognate pairs as a design feature has received limited attention. Here, we demonstrate a large library of AHL-receiver devices, with all cognate and non-cognate chemical signal interactions quantified, and we develop a software too...
Persistent Identifiers
Subjects
free text keywords: Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, RHAMNOLIPID BIOSURFACTANT SYNTHESIS, CELL-CELL COMMUNICATION, PSEUDOMONAS-AERUGINOSA, BACTERIAL CONSORTIA, GENE-EXPRESSION, LOGIC GATES, QUORUM, IDENTIFICATION, EVOLUTION, CIRCUIT, Acyl-Butyrolactones, Algorithms, Bacterial Proteins, Computational Biology, Ecosystem, Genetic Engineering, Microbial Consortia, Quorum Sensing, Software, Synthetic Biology, Transcription Factors, Article, Science, Q, lcsh:Science, lcsh:Q, Computer science, Software tool, Chemical signal, Bioprocess, In silico, Distributed computing, Software, business.industry, business, Communication channel, Synthetic biology, Signal interference
Related Organizations
Funded by
UKRI| Frontier Manufacturing: Scaling up synthetic biology
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: EP/K038648/1
  • Funding stream: EPSRC
,
UKRI| A novel, fast and efficient resource recycling system for improving the performance of engineered bacteria
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: EP/P009352/1
  • Funding stream: EPSRC
,
EC| COSY-BIO
Project
COSY-BIO
Control Engineering of Biological Systems for Reliable Synthetic Biology Applications
  • Funder: European Commission (EC)
  • Project Code: 766840
  • Funding stream: H2020 | RIA
Validated by funder
,
UKRI| Engineering Fellowships for Growth: Systems and control engineering framework for robust and efficient synthetic biology
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: EP/M002187/1
  • Funding stream: EPSRC
Communities
FET H2020FET OPEN: FET-Open research and innovation actions
FET H2020FET OPEN: Control Engineering of Biological Systems for Reliable Synthetic Biology Applications
47 references, page 1 of 4

Nielsen, AA. Genetic circuit design automation. Science. 2016; 352: aac7341 [OpenAIRE] [PubMed] [DOI]

Florea, M. Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain. Proc. Natl Acad. Sci. USA. 2016; 113: E3431-E3440 [OpenAIRE] [PubMed] [DOI]

Ro, DK. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature. 2006; 440: 940-943 [OpenAIRE] [PubMed] [DOI]

Pardee, K. Rapid, low-cost detection of zika virus using programmable biomolecular components. Cell. 2016; 165: 1255-1266 [OpenAIRE] [PubMed] [DOI]

Webb, AJ. A protease-based biosensor for the detection of schistosome cercariae. Sci. Rep.. 2016; 6: 24725 [OpenAIRE] [PubMed] [DOI]

Stanton, BC. Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat. Chem. Biol.. 2014; 10: 99-105 [OpenAIRE] [PubMed] [DOI]

Ceroni, F, Algar, R, Stan, GB, Ellis, T. Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat. Methods. 2015; 12: 415-418 [OpenAIRE] [PubMed] [DOI]

Tamsir, A, Tabor, JJ, Voigt, CA. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature. 2011; 469: 212-215 [OpenAIRE] [PubMed] [DOI]

Chen, AH, Silver, PA. Designing biological compartmentalization. Trends Cell Biol.. 2012; 22: 662-670 [OpenAIRE] [PubMed] [DOI]

Tsai, SL, Goyal, G, Chen, W. Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production. Appl. Environ. Microbiol. 2010; 76: 7514-7520 [OpenAIRE] [PubMed] [DOI]

Perry, N, Nelson, EM, Timp, G. Wiring together synthetic bacterial consortia to create a biological integrated circuit. ACS Synth. Biol.. 2016; 5: 1421-1432 [OpenAIRE] [PubMed] [DOI]

Bernstein, HC, Paulson, SD, Carlson, RP. Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. J. Biotechnol.. 2012; 157: 159-166 [OpenAIRE] [PubMed] [DOI]

Grant, PK. Orthogonal intercellular signaling for programmed spatial behavior. Mol. Syst. Biol.. 2016; 12: 849 [OpenAIRE] [PubMed] [DOI]

Shong, J, Jimenez Diaz, MR, Collins, CH. Towards synthetic microbial consortia for bioprocessing. Curr. Opin. Biotechnol.. 2012; 23: 798-802 [OpenAIRE] [PubMed] [DOI]

Waters, CM, Bassler, BL. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev. Cell Dev. Biol.. 2005; 21: 319-346 [OpenAIRE] [PubMed] [DOI]

47 references, page 1 of 4
Abstract
Advancing synthetic biology to the multicellular level requires the development of multiple cell-to-cell communication channels that propagate information with minimal signal interference. The development of quorum-sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on cognate acyl-homoserine lactone (AHL)/transcription factor pairs, while the use of non-cognate pairs as a design feature has received limited attention. Here, we demonstrate a large library of AHL-receiver devices, with all cognate and non-cognate chemical signal interactions quantified, and we develop a software too...
Persistent Identifiers
Subjects
free text keywords: Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, RHAMNOLIPID BIOSURFACTANT SYNTHESIS, CELL-CELL COMMUNICATION, PSEUDOMONAS-AERUGINOSA, BACTERIAL CONSORTIA, GENE-EXPRESSION, LOGIC GATES, QUORUM, IDENTIFICATION, EVOLUTION, CIRCUIT, Acyl-Butyrolactones, Algorithms, Bacterial Proteins, Computational Biology, Ecosystem, Genetic Engineering, Microbial Consortia, Quorum Sensing, Software, Synthetic Biology, Transcription Factors, Article, Science, Q, lcsh:Science, lcsh:Q, Computer science, Software tool, Chemical signal, Bioprocess, In silico, Distributed computing, Software, business.industry, business, Communication channel, Synthetic biology, Signal interference
Related Organizations
Funded by
UKRI| Frontier Manufacturing: Scaling up synthetic biology
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: EP/K038648/1
  • Funding stream: EPSRC
,
UKRI| A novel, fast and efficient resource recycling system for improving the performance of engineered bacteria
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: EP/P009352/1
  • Funding stream: EPSRC
,
EC| COSY-BIO
Project
COSY-BIO
Control Engineering of Biological Systems for Reliable Synthetic Biology Applications
  • Funder: European Commission (EC)
  • Project Code: 766840
  • Funding stream: H2020 | RIA
Validated by funder
,
UKRI| Engineering Fellowships for Growth: Systems and control engineering framework for robust and efficient synthetic biology
Project
  • Funder: UK Research and Innovation (UKRI)
  • Project Code: EP/M002187/1
  • Funding stream: EPSRC
Communities
FET H2020FET OPEN: FET-Open research and innovation actions
FET H2020FET OPEN: Control Engineering of Biological Systems for Reliable Synthetic Biology Applications
47 references, page 1 of 4

Nielsen, AA. Genetic circuit design automation. Science. 2016; 352: aac7341 [OpenAIRE] [PubMed] [DOI]

Florea, M. Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain. Proc. Natl Acad. Sci. USA. 2016; 113: E3431-E3440 [OpenAIRE] [PubMed] [DOI]

Ro, DK. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature. 2006; 440: 940-943 [OpenAIRE] [PubMed] [DOI]

Pardee, K. Rapid, low-cost detection of zika virus using programmable biomolecular components. Cell. 2016; 165: 1255-1266 [OpenAIRE] [PubMed] [DOI]

Webb, AJ. A protease-based biosensor for the detection of schistosome cercariae. Sci. Rep.. 2016; 6: 24725 [OpenAIRE] [PubMed] [DOI]

Stanton, BC. Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat. Chem. Biol.. 2014; 10: 99-105 [OpenAIRE] [PubMed] [DOI]

Ceroni, F, Algar, R, Stan, GB, Ellis, T. Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat. Methods. 2015; 12: 415-418 [OpenAIRE] [PubMed] [DOI]

Tamsir, A, Tabor, JJ, Voigt, CA. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature. 2011; 469: 212-215 [OpenAIRE] [PubMed] [DOI]

Chen, AH, Silver, PA. Designing biological compartmentalization. Trends Cell Biol.. 2012; 22: 662-670 [OpenAIRE] [PubMed] [DOI]

Tsai, SL, Goyal, G, Chen, W. Surface display of a functional minicellulosome by intracellular complementation using a synthetic yeast consortium and its application to cellulose hydrolysis and ethanol production. Appl. Environ. Microbiol. 2010; 76: 7514-7520 [OpenAIRE] [PubMed] [DOI]

Perry, N, Nelson, EM, Timp, G. Wiring together synthetic bacterial consortia to create a biological integrated circuit. ACS Synth. Biol.. 2016; 5: 1421-1432 [OpenAIRE] [PubMed] [DOI]

Bernstein, HC, Paulson, SD, Carlson, RP. Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. J. Biotechnol.. 2012; 157: 159-166 [OpenAIRE] [PubMed] [DOI]

Grant, PK. Orthogonal intercellular signaling for programmed spatial behavior. Mol. Syst. Biol.. 2016; 12: 849 [OpenAIRE] [PubMed] [DOI]

Shong, J, Jimenez Diaz, MR, Collins, CH. Towards synthetic microbial consortia for bioprocessing. Curr. Opin. Biotechnol.. 2012; 23: 798-802 [OpenAIRE] [PubMed] [DOI]

Waters, CM, Bassler, BL. Quorum sensing: cell-to-cell communication in bacteria. Annu Rev. Cell Dev. Biol.. 2005; 21: 319-346 [OpenAIRE] [PubMed] [DOI]

47 references, page 1 of 4
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