TY - JOUR
T1 - The effect of metabolic stress on genome stability of a synthetic biology chassis Escherichia coli K12 strain
AU - Couto, Jillian M.
AU - McGarrity, Anne
AU - Russell, Julie
AU - Sloan, William T.
PY - 2018/1/22
Y1 - 2018/1/22
N2 - Background: Synthetic organism-based biotechnologies are increasingly being proposed for environmental applications, such as in situ sensing. Typically, the novel function of these organisms is delivered by compiling genetic fragments in the genome of a chassis organism. To behave predictably, these chassis are designed with reduced genomes that minimize biological complexity. However, in these proposed applications it is expected that even when contained within a device, organisms will be exposed to fluctuating, often stressful, conditions and it is not clear whether their genomes will retain stability. Results: Here we employed a chemostat design which enabled us to maintained two strains of E. coli K12 under sustained starvation stress: first the reduced genome synthetic biology chassis MDS42 and then, the control parent strain MG1655. We estimated mutation rates and utilised them as indicators of an increase in genome instability. We show that within 24h the spontaneous mutation rate had increased similarly in both strains, destabilizing the genomes. High rates were maintained for the duration of the experiment. Growth rates of a cohort of randomly sampled mutants from both strains were utilized as a proxy for emerging phenotypic, and by association genetic variation. Mutant growth rates were consistently less than rates in non-mutants, an indicator of reduced fitness and the presence of mildly deleterious mutations in both the strains. In addition, the effect of these mutations on the populations as a whole varied by strain. Conclusions: Overall, this study shows that genome reductions in the MDS42 did not stabilize the chassis under metabolic stress. Over time, this could compromise the effectiveness of synthetic organisms built on chassis in environmental applications.
AB - Background: Synthetic organism-based biotechnologies are increasingly being proposed for environmental applications, such as in situ sensing. Typically, the novel function of these organisms is delivered by compiling genetic fragments in the genome of a chassis organism. To behave predictably, these chassis are designed with reduced genomes that minimize biological complexity. However, in these proposed applications it is expected that even when contained within a device, organisms will be exposed to fluctuating, often stressful, conditions and it is not clear whether their genomes will retain stability. Results: Here we employed a chemostat design which enabled us to maintained two strains of E. coli K12 under sustained starvation stress: first the reduced genome synthetic biology chassis MDS42 and then, the control parent strain MG1655. We estimated mutation rates and utilised them as indicators of an increase in genome instability. We show that within 24h the spontaneous mutation rate had increased similarly in both strains, destabilizing the genomes. High rates were maintained for the duration of the experiment. Growth rates of a cohort of randomly sampled mutants from both strains were utilized as a proxy for emerging phenotypic, and by association genetic variation. Mutant growth rates were consistently less than rates in non-mutants, an indicator of reduced fitness and the presence of mildly deleterious mutations in both the strains. In addition, the effect of these mutations on the populations as a whole varied by strain. Conclusions: Overall, this study shows that genome reductions in the MDS42 did not stabilize the chassis under metabolic stress. Over time, this could compromise the effectiveness of synthetic organisms built on chassis in environmental applications.
KW - chassis
KW - chemostat
KW - environmental biotechnology
KW - escherichia coli
KW - genome reduction
KW - metabolic stress
KW - mutation rate
KW - synthetic biology
UR - http://www.scopus.com/inward/record.url?scp=85040864340&partnerID=8YFLogxK
U2 - 10.1186/s12934-018-0858-2
DO - 10.1186/s12934-018-0858-2
M3 - Article
C2 - 29357936
AN - SCOPUS:85040864340
SN - 1475-2859
VL - 17
JO - Microbial Cell Factories
JF - Microbial Cell Factories
M1 - 8
ER -