Programmed hierarchical patterning of bacterial populations

Nature Communications
Christian R BoehmJim Haseloff

Abstract

Modern genetic tools allow the dissection and emulation of fundamental mechanisms shaping morphogenesis in multicellular organisms. Several synthetic genetic circuits for control of multicellular patterning have been reported to date. However, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its importance in biological self-organization. Here we report a synthetic genetic system implementing population-based AND-logic for programmed autonomous induction of bacterial gene expression domains. We develop a ratiometric assay for bacteriophage T7 RNA polymerase activity and use it to systematically characterize different intact and split enzyme variants. We then utilize the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. We validate the AND gate-like behavior of this system both in cell suspension and in surface culture. Finally, we use the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations.

References

Nov 1, 1977·Journal of Bacteriology·S N Cohen, A C Chang
Jan 1, 1992·Journal of Bacteriology·I IostM Dreyfus
Jul 26, 1988·Biochemistry·D K MullerJ E Coleman
May 5, 1986·Journal of Molecular Biology·F W Studier, B A Moffatt
Oct 1, 1969·Journal of Theoretical Biology·L Wolpert
Jun 5, 1983·Journal of Molecular Biology·J J Dunn, F W Studier
Dec 19, 1995·Proceedings of the National Academy of Sciences of the United States of America·O V MakarovaM Dreyfus
Jan 1, 1997·Journal of Bacteriology·A M Stevens, E P Greenberg
Jan 22, 2004·The Journal of Biological Chemistry·Lian-Hui WangLian-Hui Zhang
Oct 27, 2004·Proceedings of the National Academy of Sciences of the United States of America·M SchusterE P Greenberg
Feb 9, 2005·Physical Review Letters·T BollenbachF Jülicher
Apr 19, 2006·Nature Reviews. Genetics·David Kimelman
Oct 26, 2007·Proceedings of the National Academy of Sciences of the United States of America·Katie BrennerFrances H Arnold
Apr 17, 2008·Molecular Systems Biology·Frederick K BalagaddéLingchong You
Apr 14, 2009·Nature Methods·Daniel G GibsonHamilton O Smith
Jul 1, 2009·Cell·Jeffrey J TaborAndrew D Ellington
Jul 10, 2009·Journal of Biological Engineering·Takayuki SohkaMarc Ostermeier
Aug 19, 2009·Annual Review of Genetics·Wai-Leung Ng, Bonnie L Bassler
Jan 13, 2010·Cold Spring Harbor Perspectives in Biology·Naama Barkai, Ben-Zion Shilo
Apr 15, 2010·Journal of the American Chemical Society·Aaron W ReinkeAmy E Keating
Aug 10, 2010·Nucleic Acids Research·David Greber, Martin Fussenegger
May 24, 2011·Methods in Enzymology·Howard M Salis
Mar 22, 2012·Nature Communications·Joachim GoedhartAntoine Royant
Jun 30, 2012·Nucleic Acids Research·Karsten TemmeChristopher A Voigt
Jun 30, 2012·Nature Methods·Johannes SchindelinAlbert Cardona
Oct 9, 2012·Nature·Tae Seok MoonChristopher A Voigt
Mar 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·David L Shis, Matthew R Bennett
Oct 10, 2013·Molecular Systems Biology·Stephen PayneLingchong You
Mar 19, 2014·ACS Synthetic Biology·Boyan YordanovAndrew Phillips
Aug 1, 2014·Molecular Systems Biology·Thomas H Segall-ShapiroChristopher A Voigt
Sep 24, 2014·Nature Communications·Yolanda SchaerliMark Isalan
Sep 30, 2014·Nucleic Acids Research·Yolanda SchaerliMark Isalan
Jan 1, 2015·Journal of the Royal Society, Interface·Wing-Cheong LoQing Nie
Oct 6, 2015·ACS Synthetic Biology·Timothy James RudgeJim Haseloff

❮ Previous
Next ❯

Citations

Sep 20, 2018·BioTechniques·Bill Jia, Arin Wongprommoon
Jun 9, 2020·Biochemical Society Transactions·Jamie A Davies, Fokion Glykofrydis
Jun 13, 2020·Molecular Systems Biology·Içvara BarbierYolanda Schaerli
Apr 1, 2019·Advanced Biosystems·Javier Santos-Moreno, Yolanda Schaerli
Nov 22, 2018·Microbial Biotechnology·Kenneth T WalkerTom Ellis
Oct 16, 2020·Bulletin of Mathematical Biology·Andrew L KrauseEamonn A Gaffney
Nov 4, 2020·Nature Communications·Paul K GrantAndrew Phillips
Nov 18, 2020·Current Opinion in Biotechnology·Kent M RappMichael J Betenbaugh
Mar 20, 2021·Bulletin of Mathematical Biology·Thomas E WoolleyEamonn A Gaffney
May 11, 2021·Trends in Microbiology·Nicolas E GrandelMatthew R Bennett
Nov 30, 2021·Microbial Biotechnology·Martina Oliver HuidobroMark Isalan

❮ Previous
Next ❯

Datasets Mentioned

BETA
KY643824
KX986152
KX986173

Software Mentioned

ImageJ
Ribosome Binding Site Calculator
Genetic Engineering of Cells ( GEC ) and

Related Concepts

Related Feeds

Biomaterial Engineering

Advances in biomaterial engineering have permitted the development of sophisticated drug-releasing materials with a biomimetic 3D support that allow a better control of the microenvironment of transplanted cells. Here is the latest research.

Related Papers

Pacific Symposium on Biocomputing
Eric A DavidsonAndrew D Ellington
Molekuliarnaia biologiia
E E RusakovaS N Kochetkov
© 2022 Meta ULC. All rights reserved