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Susan S. Golden


Circadian Rhythms of Gene Expression in Cyanobacteria

Diverse eukaryotes, and at least one group of prokaryotes—cyanobacteria—use a circadian (24 h) clock to control physiological events and gene expression. S. elongatus shows a circadian rhythm of bioluminescence when it is transformed with a reporter gene that encodes the luciferase of a bioluminescent marine bacterium or firefly. We are using this reporter system to identify components of circadian system. A group of interacting proteins, KaiA, KaiB, and KaiC are at the heart of the cyanobacterial clock, and kinases help to set the clock and transmit temporal information from it to the genes it regulates. Our goal is to understand the basic mechanism of timekeeping and how the clock becomes synchronized with the environment and controls cellular processes.

Functional Genomics in S. elongatus

We are identifying all of the genes in the S. elongatus genome that contribute to circadian rhythms by creating a mutation in each gene and assaying each mutant for circadian phenotypes. This project uses transposon insertions into cosmids and plasmids that contain pieces of S. elongatus DNA; each clone that carries a transposon insertion can be used for recombination into the S. elongatus genome to produce a gene "knockout."

Metabolic Engineering of Cyanobacteria for the production of Biofuels and other Molecules of Interest

Because cyanobacteria grow photosynthetically using water and CO2 and are easy to manipulate genetically, they are attractive organisms for the production of molecules that have industrial applications. One such application is the production of biofuels as a supplementation of or eventual replacement of petroleum fuels. We are using the powerful genetic tools that have been developed for S. elongatus to explore the production of biofuels in cyanobacteria.


  • Rubin, B.E., K.M. Wetmore, M.N. Price, S. Diamond, R.K. Shultzaberger, L.C. Lowe, G. Curtin G, A.P. Arkin, A. Deutschbauer, and S.S. Golden. 2015. Proc. Natl. Acad. Sci. U S A. 2015 Oct 27. pii: 201519220. [Epub ahead of print] PMID: 26508635
  • Luke, C.S., J. Selimkhanov, L. Baumgart, S.E. Cohen, S.S. Golden, N.A. Cookson, and J. Hasty. 2015. A microfluidic platform for long term monitoring of algae in a dynamic environment. ACS Synth Biol. 2015 Sep 15. PMID: 26332284
  • Chang, Y.-G., S.E. Cohen, C. Phong, W.K. Myers, Y.-I. Kim, R. Tseng, J. Lin, L. Zhang, J.S. Boyd, Y. Lee, S. Kang, D. Lee, S. Li, R.D. Britt, M.J. Rust, S.S. Golden, and A. LiWang. 2015. Protein Fold Switch Joins the Circadian Oscillator to Clock Output in Cyanobacteria. Science 349(6245):324-8. doi: 10.1126/science.1260031. Epub 2015 Jun 25. PMID: 26113641
  • Diamond S, D. Jun, B.E. Rubin, and S.S. Golden. 2015. The circadian oscillator in Synechococcus elongatus controls metabolite partitioning during diurnal growth. Proc Natl Acad Sci U S A. 2015 2015 Apr 14;112(15):E1916-25. doi: 10.1073/pnas.1504576112. Epub 2015 Mar 30. PMID: 25825710
  • Espinosa, J., J.S. Boyd, R. Cantos, P. Salinas, S.S. Golden, and A. Contreras. 2015. Cross-talk and regulatory interactions between the essential response regulator RpaB and cyanobacterial circadian clock output. Proc. Natl. Acad. Sci. U S A. pii: 201424632. [Epub ahead of print] PMID: 25653337
  • Shultzaberger, R.K., J.S. Boyd, T. Katsuk, S.S. Golden, and R.J. Greenspan. 2014. Single mutations in sasA enable a simpler ΔcikA gene network architecture with equivalent circadian properties. 2014. Proc. Natl. Acad. Sci. U S A, 111:E5069-75. doi: 10.1073/pnas.1419902111 PMID: 25385627
  • Cohen, SE., M.L. Erb, J. Selimkhanov, G. Dong, J. Hasty, J. Pogliano, and S.S. Golden. 2014. Dynamic Localization of the Cyanobacterial Circadian Clock Proteins. 2014. Current Biology, 24:1836-44. PMID: 25385627
  • Taton A., F. Unglaub, N.E. Wright, W.Y. Zeng, J. Paz-Yepez, B. Brahamsha, B. Palenik, T.C. Peterson, F. Haerizadeh, S.S. Golden, and J.W. Golden JW. 2014. Broad-host-range vector system for synthetic biology and biotechnology in cyanobacteria. Nucleic Acids Res. 2014 Jul 29. pii: gku673. [Epub ahead of print] (open access)
  • Paddock, M.L., J.S. Boyd, D.M. Adin, and S.S. Golden. 2013. The active output state of the Synechococcus Kai circadian oscillator. Proc. Natl. Acad. Sci. U S A. 110(40):E3849-E3857. Epub 2013 Sep 16. PMID: 24043774
  • Boyd, J.S., J.R. Bordowitz, A.C. Bree, and S.S. Golden. 2013. An allele of the crm gene blocks cyanobacterial circadian rhythms. Proc. Natl. Acad. Sci. U S A. 110:13950-5. doi: 10.1073/pnas.1312793110. Epub 2013 Aug 5. PMID: 23918383
  • Vinyard D.J., J. Gimpel, G.M. Ananyev, M.A. Cornejo, S.S. Golden, S.P. Mayfield, and G.C. Dismukes. 2012. Natural variants of Photosystem II subunit D1 tune photochemical fitness to solar intensity. J. Biol. Chem. 288(8):5451-62. doi: 10.1074/jbc.M112.394668 Dec 27. [Epub ahead of print] PMID: 23271739
  • Kim, Y-I, D.J. Vinyard, G.M. Ananyev, G.C. Dismukes, and S.S. Golden. 2012. Oxidized quinones signal onset of darkness directly to the cyanobacterial circadian oscillator. Proc. Natl. Acad. Sci. USA 109:17765-9. doi: 10.1073/pnas.1216401109. Epub 2012 Oct 15. PMID: 23071342.
  • Simkovsky, R., E.F. Daniels, K. Tang, S. Huynh, S.S. Golden, and B. Brahamsha. 2012. Impairment of O-antigen production confers resistance to grazing in a model amoeba-cyanobacterium predator-prey system. Proc. Natl. Acad. Sci. USA, 109:16678-83. doi: 10.1073/pnas.1214904109. Epub 2012 Sep 24. PMID: 23012457
  • Rust, M.J, S.S. Golden, and Erin K. O’Shea. 2011. Light-driven changes in energy metabolism directly entrain the cyanobacterial circadian oscillator. Science 331:220-223.
  • Yang,Q., B.F. Pando, G. Dong, S.S. Golden, and A. van Oudenaarden. 2010. Circadian gating of the cell cycle revealed in single cyanobacterial cells. Science, 327:1522-1526.
  • Wood, T.L.*, J. Bridwell-Rabb*, Y.-I. Kim*, T. Gao, Y.-G. Chang, A. LiWang, D.P. Barondeau, and S.S. Golden. 2010. The KaiA protein of the cyanobacterial circadian oscillator is modulated by a redox-active cofactor. Proc. Natl. Acad. Sci. USA 107:5804-5809. PMCID: PMC2851934 * These authors contributed equally
  • Dong, G., Q. Yang, Q. Wang, Y.-I. Kim, T. Wood, K.W. Osteryoung, A. van Oudenaarden, and S.S. Golden. 2010. Elevated ATPase activity of KaiC applies a circadian checkpoint on cell division in Synechococcus elongatus. Cell 140:529-539. NIHMS168190
  • Chen,Y., Kim, Y-I, Mackey, S.R., Holtman,C.K., LiWang, A, and S.S. Golden. 2009. A novel allele of kaiA shortens circadian period and strengthens interaction of oscillator components in the cyanobacterium Synechococcus elongatus PCC 7942. J. Bacteriol. 191:4392-4400. PMCID: PMC2698500
  • Kim,Y-I, G. Dong, C. Carruthers, S.S. Golden, and A. LiWang. 2008. The day/night switch in KaiC, a central oscillator component of the circadian clock of cyanobacteria. Proc. Natl. Acad. Sci. USA 105:12825-30. PMCID: PMC2529086
  • Mackey, S.R., J-S. Choi, Y. Kitayama, H. Iwasaki, G. Dong, and S.S. Golden. 2008. Proteins found in a CikA-interaction assay link the circadian clock, metabolism, and cell division in Synechococcus elongatus. J. Bacteriol. 190: 3738–3746. PMCID: PMC2395015


Susan Golden received a B.A. (1978) in Biology from Mississippi University for Women and a Ph.D. (1983) in Genetics from the University of Missouri. After postdoctoral research at the University of Chicago, she joined the faculty of Biology at Texas A&M University (1986), where she was promoted to Distinguished Professor in 2003. She joined the Division of Biological Sciences at UCSD in 2008.

During her graduate work she developed genetic tools for the cyanobacterium Synechococcus elongatus (PCC 7942), the first cyanobacterium shown to be subject to genetic transformation. This led to work on regulation of light-responsive photosynthesis gene expression in this organism during her postdoctoral research and at Texas A&M. In the early 1990s she began a collaborative project with C.H. Johnson (Vanderbilt University) and T. Kondo (Nagoya University) that demonstrated circadian rhythms of gene expression in S. elongatus, which is currently the only model organism for a prokaryotic circadian clock. The molecular basis of timekeeping in S. elongatus is now a major focus of her lab. Susan is a member of the Faculty of 1000 Biology, a Fellow of the American Academy of Microbiology, and a Member of the National Academy of Sciences.