skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP

Abstract

Bacteria colonize highly diverse and complex environments, from gastrointestinal tracts to soil and plant surfaces. This colonization process is controlled in part by the intracellular signal cyclic di-GMP, which regulates bacterial motility and biofilm formation. To interrogate cyclic di-GMP signaling networks, a variety of fluorescent biosensors for live cell imaging of cyclic di-GMP have been developed. However, the need for external illumination precludes the use of these tools for imaging bacteria in their natural environments, including in deep tissues of whole organisms and in samples that are highly autofluorescent or photosensitive. The need for genetic encoding also complicates the analysis of clinical isolates and environmental samples. Toward expanding the study of bacterial signaling to these systems, we have developed the first chemiluminescent biosensors for cyclic di-GMP. The biosensor design combines the complementation of split luciferase (CSL) and bioluminescence resonance energy transfer (BRET) approaches. Furthermore, we developed a lysate-based assay for biosensor activity that enabled reliable high-throughput screening of a phylogenetic library of 92 biosensor variants. The screen identified biosensors with very large signal changes (~40- and 90-fold) as well as biosensors with high affinities for cyclic di-GMP ($$K_D$$ < 50 nM). These chemiluminescent biosensors then were applied to measure cyclic di-GMP levels in $E. coli$. The cellular experiments revealed an unexpected challenge for chemiluminescent imaging in Gram negative bacteria but showed promising application in lysates. Taken together, this work establishes the first chemiluminescent biosensors for studying cyclic di-GMP signaling and provides a foundation for using these biosensors in more complex systems.

Authors:
 [1];  [1];  [2];  [2]; ORCiD logo [3]
  1. Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
  2. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  3. Univ. of California, Berkeley, CA (United States). Dept. of Chemistry, and Dept. of Molecular & Cell Biology
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1563956
Alternate Identifier(s):
OSTI ID: 1543712
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
ACS Chemical Biology
Additional Journal Information:
Journal Volume: 13; Journal Issue: 7; Journal ID: ISSN 1554-8929
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology

Citation Formats

Dippel, Andrew B., Anderson, Wyatt A., Evans, Robert S., Deutsch, Samuel, and Hammond, Ming C.. Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP. United States: N. p., 2018. Web. https://doi.org/10.1021/acschembio.7b01019.
Dippel, Andrew B., Anderson, Wyatt A., Evans, Robert S., Deutsch, Samuel, & Hammond, Ming C.. Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP. United States. https://doi.org/10.1021/acschembio.7b01019
Dippel, Andrew B., Anderson, Wyatt A., Evans, Robert S., Deutsch, Samuel, and Hammond, Ming C.. Wed . "Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP". United States. https://doi.org/10.1021/acschembio.7b01019. https://www.osti.gov/servlets/purl/1563956.
@article{osti_1563956,
title = {Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP},
author = {Dippel, Andrew B. and Anderson, Wyatt A. and Evans, Robert S. and Deutsch, Samuel and Hammond, Ming C.},
abstractNote = {Bacteria colonize highly diverse and complex environments, from gastrointestinal tracts to soil and plant surfaces. This colonization process is controlled in part by the intracellular signal cyclic di-GMP, which regulates bacterial motility and biofilm formation. To interrogate cyclic di-GMP signaling networks, a variety of fluorescent biosensors for live cell imaging of cyclic di-GMP have been developed. However, the need for external illumination precludes the use of these tools for imaging bacteria in their natural environments, including in deep tissues of whole organisms and in samples that are highly autofluorescent or photosensitive. The need for genetic encoding also complicates the analysis of clinical isolates and environmental samples. Toward expanding the study of bacterial signaling to these systems, we have developed the first chemiluminescent biosensors for cyclic di-GMP. The biosensor design combines the complementation of split luciferase (CSL) and bioluminescence resonance energy transfer (BRET) approaches. Furthermore, we developed a lysate-based assay for biosensor activity that enabled reliable high-throughput screening of a phylogenetic library of 92 biosensor variants. The screen identified biosensors with very large signal changes (~40- and 90-fold) as well as biosensors with high affinities for cyclic di-GMP ($K_D$ < 50 nM). These chemiluminescent biosensors then were applied to measure cyclic di-GMP levels in $E. coli$. The cellular experiments revealed an unexpected challenge for chemiluminescent imaging in Gram negative bacteria but showed promising application in lysates. Taken together, this work establishes the first chemiluminescent biosensors for studying cyclic di-GMP signaling and provides a foundation for using these biosensors in more complex systems.},
doi = {10.1021/acschembio.7b01019},
journal = {ACS Chemical Biology},
number = 7,
volume = 13,
place = {United States},
year = {2018},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 8 works
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: This is Figure 1 for the article titled "Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP".

Save / Share:

Works referenced in this record:

Regulation of cellulose synthesis in Acetobacter xylinum by cyclic diguanylic acid
journal, January 1987

  • Ross, P.; Weinhouse, H.; Aloni, Y.
  • Nature, Vol. 325, Issue 6101
  • DOI: 10.1038/325279a0

Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger
journal, March 2013

  • Romling, U.; Galperin, M. Y.; Gomelsky, M.
  • Microbiology and Molecular Biology Reviews, Vol. 77, Issue 1
  • DOI: 10.1128/MMBR.00043-12

Principles of c-di-GMP signalling in bacteria
journal, April 2009


More than Enzymes That Make or Break Cyclic Di-GMP—Local Signaling in the Interactome of GGDEF/EAL Domain Proteins of Escherichia coli
journal, November 2017


Visualizing the Perturbation of Cellular Cyclic di-GMP Levels in Bacterial Cells
journal, December 2012

  • Ho, Chun Loong; Chong, Kavin Shi Jie; Oppong, Jamila Akosua
  • Journal of the American Chemical Society, Vol. 135, Issue 2
  • DOI: 10.1021/ja310497x

Asymmetrical Distribution of the Second Messenger c-di-GMP upon Bacterial Cell Division
journal, June 2010


A direct screen for c-di-GMP modulators reveals a Salmonella Typhimurium periplasmic ʟ-arginine–sensing pathway
journal, June 2015


Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP
journal, July 2016

  • Wang, Xin C.; Wilson, Stephen C.; Hammond, Ming C.
  • Nucleic Acids Research, Vol. 44, Issue 17
  • DOI: 10.1093/nar/gkw580

Guided by the light: visualizing biomolecular processes in living animals with bioluminescence
journal, February 2010

  • Prescher, Jennifer A.; Contag, Christopher H.
  • Current Opinion in Chemical Biology, Vol. 14, Issue 1
  • DOI: 10.1016/j.cbpa.2009.11.001

Recent progress in luminescent proteins development
journal, August 2015


Bioluminescent Indicators for Ca2+ Based on Split Renilla Luciferase Complementation in Living Cells
journal, January 2008

  • Kaihara, Asami; Umezawa, Yoshio; Furukawa, Tetsushi
  • Analytical Sciences, Vol. 24, Issue 11
  • DOI: 10.2116/analsci.24.1405

Novel Genetically Encoded Biosensors Using Firefly Luciferase
journal, June 2008

  • Fan, Frank; Binkowski, Brock F.; Butler, Braeden L.
  • ACS Chemical Biology, Vol. 3, Issue 6
  • DOI: 10.1021/cb8000414

Molecular imaging of Akt kinase activity
journal, August 2007

  • Zhang, Limin; Lee, Kuei C.; Bhojani, Mahaveer S.
  • Nature Medicine, Vol. 13, Issue 9
  • DOI: 10.1038/nm1608

Bioluminescent Indicator for Highly Sensitive Analysis of Estrogenic Activity in a Cell-Based Format
journal, October 2016


Sustained accurate recording of intracellular acidification in living tissues with a photo-controllable bioluminescent protein
journal, May 2013

  • Hattori, Mitsuru; Haga, Sanae; Takakura, Hideo
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 23
  • DOI: 10.1073/pnas.1304056110

Auto-Luminescent Genetically-Encoded Ratiometric Indicator for Real-Time Ca2+ Imaging at the Single Cell Level
journal, April 2010


Use of a cAMP BRET Sensor to Characterize a Novel Regulation of cAMP by the Sphingosine 1-Phosphate/G13 Pathway
journal, April 2007

  • Jiang, Lily I.; Collins, Julie; Davis, Richard
  • Journal of Biological Chemistry, Vol. 282, Issue 14
  • DOI: 10.1074/jbc.M609695200

The GAF Domain of the cGMP-Binding, cGMP-Specific Phosphodiesterase (PDE5) Is a Sensor and a Sink for cGMP
journal, February 2008

  • Biswas, Kabir Hassan; Sopory, Shailaja; Visweswariah, Sandhya S.
  • Biochemistry, Vol. 47, Issue 11
  • DOI: 10.1021/bi702025w

Coupling optogenetic stimulation with NanoLuc-based luminescence (BRET) Ca++ sensing
journal, October 2016

  • Yang, Jie; Cumberbatch, Derrick; Centanni, Samuel
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13268

Luminescent proteins for high-speed single-cell and whole-body imaging
journal, January 2012

  • Saito, Kenta; Chang, Y-F; Horikawa, Kazuki
  • Nature Communications, Vol. 3, Issue 1
  • DOI: 10.1038/ncomms2248

Expanded palette of Nano-lanterns for real-time multicolor luminescence imaging
journal, March 2015

  • Takai, Akira; Nakano, Masahiro; Saito, Kenta
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 14
  • DOI: 10.1073/pnas.1418468112

Five colour variants of bright luminescent protein for real-time multicolour bioimaging
journal, December 2016

  • Suzuki, Kazushi; Kimura, Taichi; Shinoda, Hajime
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms13718

The response threshold of Salmonella PilZ domain proteins is determined by their binding affinities for c-di-GMP : c-di-GMP binding affinities of PilZ domain proteins
journal, November 2012

  • Pultz, Ingrid Swanson; Christen, Matthias; Kulasekara, Hemantha Don
  • Molecular Microbiology, Vol. 86, Issue 6
  • DOI: 10.1111/mmi.12066

The PilZ Domain Is a Receptor for the Second Messenger c-di-GMP
journal, August 2006

  • Ryjenkov, Dmitri A.; Simm, Roger; Römling, Ute
  • Journal of Biological Chemistry, Vol. 281, Issue 41
  • DOI: 10.1074/jbc.C600179200

Structure of PP4397 Reveals the Molecular Basis for Different c-di-GMP Binding Modes by Pilz Domain Proteins
journal, April 2010


Optimized ratiometric calcium sensors for functional in vivo imaging of neurons and T lymphocytes
journal, January 2014

  • Thestrup, Thomas; Litzlbauer, Julia; Bartholomäus, Ingo
  • Nature Methods, Vol. 11, Issue 2
  • DOI: 10.1038/nmeth.2773

In Vitro and In Vivo Enzyme Activity Screening via RNA-Based Fluorescent Biosensors for S -Adenosyl- l -homocysteine (SAH)
journal, May 2016

  • Su, Yichi; Hickey, Scott F.; Keyser, Samantha G. L.
  • Journal of the American Chemical Society, Vol. 138, Issue 22
  • DOI: 10.1021/jacs.6b01621

The structural basis of cyclic diguanylate signal transduction by PilZ domains
journal, November 2007


The c-di-GMP Binding Protein YcgR Controls Flagellar Motor Direction and Speed to Affect Chemotaxis by a “Backstop Brake” Mechanism
journal, April 2010


Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein
journal, November 2004

  • Shaner, Nathan C.; Campbell, Robert E.; Steinbach, Paul A.
  • Nature Biotechnology, Vol. 22, Issue 12
  • DOI: 10.1038/nbt1037

A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications
journal, January 2002

  • Nagai, Takeharu; Ibata, Keiji; Park, Eun Sun
  • Nature Biotechnology, Vol. 20, Issue 1
  • DOI: 10.1038/nbt0102-87

Versatile modes of cellular regulation via cyclic dinucleotides
journal, March 2017

  • Krasteva, Petya Violinova; Sondermann, Holger
  • Nature Chemical Biology, Vol. 13, Issue 4
  • DOI: 10.1038/nchembio.2337

Cyclic Dinucleotides and the Innate Immune Response
journal, August 2013


Monitoring bacterial chemotaxis by using bioluminescence resonance energy transfer: Absence of feedback from the flagellar motors
journal, February 2006

  • Shimizu, Thomas S.; Delalez, Nicolas; Pichler, Klemens
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 7
  • DOI: 10.1073/pnas.0510958103

Protein production by auto-induction in high-density shaking cultures
journal, May 2005


    Works referencing / citing this record:

    Ratiometric BRET Measurements of ATP with a Genetically-Encoded Luminescent Sensor
    journal, August 2019

    • Min, Se-Hong; French, Alexander R.; Trull, Keelan J.
    • Sensors, Vol. 19, Issue 16
    • DOI: 10.3390/s19163502

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.