Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

Whitford, Christopher M.; Dymek, Saskia; Kerkhoff, Denise; März, Camilla; Schmidt, Olga; Edich, Maximilian; Droste, Julian; Pucker, Boas; Rückert, Christian; Kalinowski, Jörn

doi:10.1186/s13036-018-0105-8

Journal of Biological Engineering

Table 1 Biosafety parts in the iGEM competition

From: Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

Team	Mechanism	Organism	Characteristics	BioBrick	Status ^a	References
NTU Taida 2012	Type I TA-system	E. coli	SrnB-SrnC TA-system, used for plasmid maintenance	BBa_K817015	Available	[90]
University of Maryland 2015	Type I TA-system	E. coli	Hok-Sok TA-system, antibiotic free plasmid maintenance	BBa_K1783001	Not available	[91]
Paris Bettencourt 2012	Type II TA-system	E. coli	Col E2 TA-system, located on two separate plasmids	BBa_K914001, Ba_K914002	Available, complicated	[104]
Wageningen UR 2014	Type II TA-system	E. coli	Combination of the Kis-Kid and the Epsilon-Zeta TA-system to prevent horizontal gene transfer, located on two separate plasmids	BBa_K1493601, BBa_K1493603	Available, complicated	[105]
UC Berkeley 2008	Type II TA-system	E. coli	Holin-antiholin TA-system, coupled expression of lysozyme	BBa_K112808	Complicated	[106]
LMU Munich 2012	Sporulation induced killswitch	B. subtilis	mazF under control of P_ydfG, which is activated in germinating cells	BBa_K823044	Available	[113]
TU Eindhoven 2014	Timer-coupled killswitch	E. coli	Oscillating concentration of Spo0A^P induces expression of a toxin		Conceptional	[114]
UC Berkley 2007	RNase	E. coli	CDS of Barnase, without start codon	BBa_I716211	Available	[124]
Bielefeld Germany 2013	RNase	E. coli	CDS of Barnase	BBa_K1172904	Available	[77]
UC London 2012	Sequence specific self-destruction system	E. coli	threefold active biological containment system containing EcoRI/EcoRI methyltransferase, Holin/Anti-Holin Endolysin and Colicin-E3/Colicin Immunity E3	BBa_K729009, BBa_K729010	Not available	[133]
TU Munich 2013	Sequence unspecific self-destruction system	Physcomitrella patens	Mature Nuclease NucA from Staphylococcus aureus (Thermonuclease) in RFC [25]	BBa_K1159105	Available	[138]
HKU Hongkong 2015	Sequence specific and unspecific self-destruction system	E. coli	CRISPR/Cas9 containment device repressed by arabinose and tryptophan	BBa_K1774000	Not available	[160]
Harvard 2010	Genetic fence	E. coli	Barnase: gene for the genetic fence, Barstar: Inhibitor of barnase	−/−	Conceptional	[374]
Virginia 2016	Dependency on a modified amino acid	E. coli	N-carbobenzyloxy (CBZ)-cleavage enzyme to detach the protecting group frim amino acids	BBa_K1879000	Not available	[375]
Virginia 2016	Dependency on a modified amino acid	E. coli	Mutatnt Leucyl-tRNA synthetase	−/−	Conceptional	[375]
Bielefeld-CeBiTec 2015	Cell free protein synthesis	E. coli extract	Mixture of amino acids, co factors, cell extract, NTPs, energy source, DNA template, Mg- and K-glutamate solutions, nuclease free water for cell free protein synthesis in microcentrifuge tubes or a multi-well plate	−/−	−/−	[280]
Freiburg 2015	DiaMIX	E. coli extract	Cell-free expression mix for reaction in a microfluidic chamber	−/−	−/−	[284]
Paris Saclay 2015	Microencapsulation		Silica beads			[302]
Paris Bettencourt 2012	Microencapsulation		Alginate beads			[104]
Paris Saclay 2015	RNA-Thermometer	E. coli	Thermosensitive cI repressor (cI857) is placed under the control of the RNA thermometer ROSE	BBa_K1707013	Not available	[302]
TU Delft 2008	RNA-Thermometer	BradirhizobiumJaponicum, E. coli	ROSE-RNA Thermometer	BBa_K115001	Available	[346]
TU Delft 2008	RNA-Thermometer		ForU RNA-Thermometer	BBa_K115002	Available	[346]
NCTU Taiwan 2011	RNA-Thermometer	E. coli	Promoter (LacI regulated) + RNA thermometer+vioD with RNA thermometer+tetR+double terminator	BBa_K539461	Available	[347]
NCTU Taiwan 2011	RNA-Thermometer	E. coli	Promoter (LacI regulated) + alss+ilvC+ilvD (each preceded by own RBS) and RNA thermometer+terminator	BBa_K539691	Available	[347]
NCTU Taiwan 2011	RNA-Thermometer	E. coli	a RBS (B0030) + ilvC with a RBS (B0030) + ilvD	BBa_K539642	Available	[347]
NCTU Taiwan 2011	RNA-Thermometer	E. coli	a RBS (B0030) + ilvD with RNA thermometer+tetR+terminator	BBa_K539653	Available	[347]
NCTU Taiwan 2011	RNA-Thermometer	E. coli	a RBS (B0030) + ilvC+a RBS (B0030) + ilvD with RNA thermometer+tetR+terminator	BBa_K539674	Available	[347]
METU Ankara 2011	RNA-Thermometer	E. coli	Cell destruction via lysis casette		Conceptional	[376]
Cornell 2011	Light-sensor (green)	E. coli	CCaS and CCar are integral proteins involved in the green light-induced gene expression	BBa_K597105	Not available	[368]
NYMU Taipei 2014	Light sensor (blue)	E. coli	FixK2 blue light sensitive promoter for ccdB expression		Conceptional	[377]
Minnesota 2014	Light sensor (blue)		Blue light induced promotor with kill-switch gene be Endolysin and Holin		Conceptional	[378]
HNU China 2014	Light sensor (blue)		Blue light induced casp3 expression		Conceptional	[379]
Braunschweig 2014	Light sensor blue		Blue light leads to the dimerization of the VVD Domains inhibiting the transcription initiation		Conceptional	[380]

This table summarizes biosafety systems designed by iGEM teams. Not all systems make use of BioBricks, some are based on auxotrophic strains or cell-free formulation of a system. Since only BioBricks can be submitted to the iGEM Registry of Standard Biological Parts, no entry could be cited for such systems. The status of all BioBricks was adopted from the database. Ambiguous sequencing results might lead to the classification of functional parts as ‘complicated’. Teams are listed in order of mentions in text
^aStatus as stated in the iGEM Registry of Standard Biological Parts. Ambiguous sequencing results might lead to the classification of functional parts as ‘complicated’

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ISSN: 1754-1611

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