Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns

Norred, Sarah Elizabeth; Caveney, Patrick M.; Chauhan, Gaurav; Collier, Lauren K.; Collier, C. Patrick; Abel, Steven M.; Simpson, Michael L.

doi:10.1021/acssynbio.8b00139

Title: Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns

Journal Article · Tue Apr 24 00:00:00 EDT 2018 · ACS Synthetic Biology

DOI:https://doi.org/10.1021/acssynbio.8b00139· OSTI ID:1439942

^[1]; Caveney, Patrick M. ^[1]; Chauhan, Gaurav ^[2]; Collier, Lauren K. ^[3];

^[3]; Abel, Steven M. ^[2];

^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
Univ. of Tennessee, Knoxville, TN (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Recent superresolution microscopy studies in E. coli demonstrate that the cytoplasm has highly variable local concentrations where macromolecular crowding plays a central role in establishing membrane-less compartmentalization. This spatial inhomogeneity significantly influences molecular transport and association processes central to gene expression. Yet, little is known about how macromolecular crowding influences gene expression bursting—the episodic process where mRNA and proteins are produced in bursts. Here, we simultaneously measured mRNA and protein reporters in cell-free systems, showing that macromolecular crowding decoupled the well-known relationship between fluctuations in the protein population (noise) and mRNA population statistics. Crowded environments led to a 10-fold increase in protein noise even though there were only modest changes in the mRNA population and fluctuations. Instead, cell-like macromolecular crowding created an inhomogeneous spatial distribution of mRNA (“spatial noise”) that led to large variability in the protein production burst size. As a result, the mRNA spatial noise created large temporal fluctuations in the protein population. Furthermore, these results highlight the interplay between macromolecular crowding, spatial inhomogeneities, and the resulting dynamics of gene expression, and provide insights into using these organizational principles in both cell-based and cell-free synthetic biology.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1439942

Journal Information:: ACS Synthetic Biology, Vol. 7, Issue 5; ISSN 2161-5063

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 22 works

Citation information provided by
Web of Science

References (49)

Macromolecular crowding: obvious but underappreciated Ellis, R. John Trends in Biochemical Sciences, Vol. 26, Issue 10 https://doi.org/10.1016/S0968-0004(01)01938-7	journal	October 2001
Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences Zhou, Huan-Xiang; Rivas, Germán; Minton, Allen P. Annual Review of Biophysics, Vol. 37, Issue 1, p. 375-397 https://doi.org/10.1146/annurev.biophys.37.032807.125817	journal	June 2008
Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli Zimmerman, Steven B.; Trach, Stefan O. Journal of Molecular Biology, Vol. 222, Issue 3 https://doi.org/10.1016/0022-2836(91)90499-V	journal	December 1991
Cell-Free Protein Expression under Macromolecular Crowding Conditions Ge, Xumeng; Luo, Dan; Xu, Jianfeng PLoS ONE, Vol. 6, Issue 12 https://doi.org/10.1371/journal.pone.0028707	journal	December 2011
Molecular crowding shapes gene expression in synthetic cellular nanosystems Tan, Cheemeng; Saurabh, Saumya; Bruchez, Marcel P. Nature Nanotechnology, Vol. 8, Issue 8 https://doi.org/10.1038/nnano.2013.132	journal	July 2013
General properties of transcriptional time series in Escherichia coli So, Lok-hang; Ghosh, Anandamohan; Zong, Chenghang Nature Genetics, Vol. 43, Issue 6 https://doi.org/10.1038/ng.821	journal	May 2011
Real-Time Kinetics of Gene Activity in Individual Bacteria Golding, Ido; Paulsson, Johan; Zawilski, Scott M. Cell, Vol. 123, Issue 6 https://doi.org/10.1016/j.cell.2005.09.031	journal	December 2005
Frequency domain chemical Langevin analysis of stochasticity in gene transcriptional regulation Simpson, Michael L.; Cox, Chris D.; Sayler, Gary S. Journal of Theoretical Biology, Vol. 229, Issue 3 https://doi.org/10.1016/j.jtbi.2004.04.017	journal	August 2004
Gene Circuit Performance Characterization and Resource Usage in a Cell-Free “Breadboard” Siegal-Gaskins, Dan; Tuza, Zoltan A.; Kim, Jongmin ACS Synthetic Biology, Vol. 3, Issue 6 https://doi.org/10.1021/sb400203p	journal	April 2014
Translational Cross Talk in Gene Networks Mather, William H.; Hasty, Jeff; Tsimring, Lev S. Biophysical Journal, Vol. 104, Issue 11 https://doi.org/10.1016/j.bpj.2013.04.049	journal	June 2013
Stochasticity in Transcriptional Regulation: Origins, Consequences, and Mathematical Representations Kepler, Thomas B.; Elston, Timothy C. Biophysical Journal, Vol. 81, Issue 6 https://doi.org/10.1016/S0006-3495(01)75949-8	journal	December 2001
Mechanism of Transcriptional Bursting in Bacteria Chong, Shasha; Chen, Chongyi; Ge, Hao Cell, Vol. 158, Issue 2 https://doi.org/10.1016/j.cell.2014.05.038	journal	July 2014
Noise in eukaryotic gene expression Blake, William J.; KÆrn, Mads; Cantor, Charles R. Nature, Vol. 422, Issue 6932 https://doi.org/10.1038/nature01546	journal	April 2003
Control of Stochasticity in Eukaryotic Gene Expression Raser, J. M. Science, Vol. 304, Issue 5678 https://doi.org/10.1126/science.1098641	journal	June 2004
Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms Padovan-Merhar, Olivia; Nair, Gautham P.; Biaesch, Andrew G. Molecular Cell, Vol. 58, Issue 2 https://doi.org/10.1016/j.molcel.2015.03.005	journal	April 2015
Screening for noise in gene expression identifies drug synergies Dar, R. D.; Hosmane, N. N.; Arkin, M. R. Science, Vol. 344, Issue 6190 https://doi.org/10.1126/science.1250220	journal	June 2014
Quantitative assessment of the relative contributions of steric repulsion and chemical interactions to macromolecular crowding Minton, Allen P. Biopolymers, Vol. 99, Issue 4 https://doi.org/10.1002/bip.22163	journal	January 2013
Macromolecular Crowding In Vitro , In Vivo , and In Between Rivas, Germán; Minton, Allen P. Trends in Biochemical Sciences, Vol. 41, Issue 11 https://doi.org/10.1016/j.tibs.2016.08.013	journal	November 2016
Resource Sharing Controls Gene Expression Bursting Caveney, Patrick M.; Norred, S. Elizabeth; Chin, Charles W. ACS Synthetic Biology, Vol. 6, Issue 2 https://doi.org/10.1021/acssynbio.6b00189	journal	September 2016
Superresolution imaging of ribosomes and RNA polymerase in live Escherichia coli cells: Superresolution imaging of ribosome and RNAP Bakshi, Somenath; Siryaporn, Albert; Goulian, Mark Molecular Microbiology, Vol. 85, Issue 1 https://doi.org/10.1111/j.1365-2958.2012.08081.x	journal	May 2012
Phase transitions in the assembly of multivalent signalling proteins Li, Pilong; Banjade, Sudeep; Cheng, Hui-Chun Nature, Vol. 483, Issue 7389 https://doi.org/10.1038/nature10879	journal	March 2012
Cell-Free Translation Is More Variable than Transcription Chizzolini, Fabio; Forlin, Michele; Yeh Martín, Noël ACS Synthetic Biology, Vol. 6, Issue 4 https://doi.org/10.1021/acssynbio.6b00250	journal	February 2017
The Low Noise Limit in Gene Expression Dar, Roy D.; Razooky, Brandon S.; Weinberger, Leor S. PLOS ONE, Vol. 10, Issue 10 https://doi.org/10.1371/journal.pone.0140969	journal	October 2015
Cellular Decision Making and Biological Noise: From Microbes to Mammals Balázsi, Gábor; van Oudenaarden, Alexander; Collins, James J. Cell, Vol. 144, Issue 6 https://doi.org/10.1016/j.cell.2011.01.030	journal	March 2011
Stress‐response balance drives the evolution of a network module and its host genome González, Caleb; Ray, Joe Christian J.; Manhart, Michael Molecular Systems Biology, Vol. 11, Issue 8 https://doi.org/10.15252/msb.20156185	journal	August 2015
A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat–containing RNA Strack, Rita L.; Disney, Matthew D.; Jaffrey, Samie R. Nature Methods, Vol. 10, Issue 12 https://doi.org/10.1038/nmeth.2701	journal	October 2013
Join the crowd Ellis, R. John; Minton, Allen P. Nature, Vol. 425, Issue 6953 https://doi.org/10.1038/425027a	journal	September 2003
Transcriptional burst frequency and burst size are equally modulated across the human genome Dar, R. D.; Razooky, B. S.; Singh, A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 43 https://doi.org/10.1073/pnas.1213530109	journal	October 2012
Probing Cell-Free Gene Expression Noise in Femtoliter Volumes Karig, David K.; Jung, Seung-Yong; Srijanto, Bernadeta ACS Synthetic Biology, Vol. 2, Issue 9 https://doi.org/10.1021/sb400028c	journal	May 2013
Transient-mediated fate determination in a transcriptional circuit of HIV Weinberger, Leor S.; Dar, Roy D.; Simpson, Michael L. Nature Genetics, Vol. 40, Issue 4 https://doi.org/10.1038/ng.116	journal	March 2008
Transcriptional Bursting from the HIV-1 Promoter Is a Significant Source of Stochastic Noise in HIV-1 Gene Expression Singh, Abhyudai; Razooky, Brandon; Cox, Chris D. Biophysical Journal, Vol. 98, Issue 8 https://doi.org/10.1016/j.bpj.2010.03.001	journal	April 2010
Regulation of noise in the expression of a single gene Ozbudak, Ertugrul M.; Thattai, Mukund; Kurtser, Iren Nature Genetics, Vol. 31, Issue 1 https://doi.org/10.1038/ng869	journal	April 2002
Translating the noise Hasty, Jeff; Collins, James J. Nature Genetics, Vol. 31, Issue 1 https://doi.org/10.1038/ng0502-13	journal	May 2002
Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells Taniguchi, Y.; Choi, P. J.; Li, G. -W. Science, Vol. 329, Issue 5991 https://doi.org/10.1126/science.1188308	journal	July 2010
Transcriptional Bursting Explains the Noise–Versus–Mean Relationship in mRNA and Protein Levels Dar, Roy D.; Shaffer, Sydney M.; Singh, Abhyudai PLOS ONE, Vol. 11, Issue 7 https://doi.org/10.1371/journal.pone.0158298	journal	July 2016
Effect of Macromolecular Crowding on Reaction Rates: A Computational and Theoretical Study Kim, Jun Soo; Yethiraj, Arun Biophysical Journal, Vol. 96, Issue 4 https://doi.org/10.1016/j.bpj.2008.11.030	journal	February 2009
Macromolecular crowding creates heterogeneous environments of gene expression in picolitre droplets Hansen, Maike M. K.; Meijer, Lenny H. H.; Spruijt, Evan Nature Nanotechnology, Vol. 11, Issue 2 https://doi.org/10.1038/nnano.2015.243	journal	October 2015
Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation Proshkin, S.; Rahmouni, A. R.; Mironov, A. Science, Vol. 328, Issue 5977 https://doi.org/10.1126/science.1184939	journal	April 2010
Molecular crowding reduces to a similar extent the diffusion of small solutes and macromolecules: measurement by fluorescence correlation spectroscopy Dauty, Emmanuel; Verkman, A. S. Journal of Molecular Recognition, Vol. 17, Issue 5 https://doi.org/10.1002/jmr.709	journal	September 2004
Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid Stracy, Mathew; Lesterlin, Christian; Garza de Leon, Federico Proceedings of the National Academy of Sciences, Vol. 112, Issue 32 https://doi.org/10.1073/pnas.1507592112	journal	July 2015
Nano‐enabled synthetic biology Doktycz, Mitchel J.; Simpson, Michael L. Molecular Systems Biology, Vol. 3, Issue 1 https://doi.org/10.1038/msb4100165	journal	January 2007
Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy Erickson, Harold P. Biological Procedures Online, Vol. 11, Issue 1 https://doi.org/10.1007/s12575-009-9008-x	journal	May 2009
Distribution and regulation of stochasticity and plasticity in Saccharomyces cerevisiae Dar, R. D.; Karig, D. K.; Cooke, J. F. Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol. 20, Issue 3 https://doi.org/10.1063/1.3486800	journal	September 2010
Synthetic biology: applications come of age Khalil, Ahmad S.; Collins, James J. Nature Reviews Genetics, Vol. 11, Issue 5 https://doi.org/10.1038/nrg2775	journal	May 2010
Chromosome position effects on gene expression in Escherichia coli K-12 Bryant, Jack A.; Sellars, Laura E.; Busby, Stephen J. W. Nucleic Acids Research, Vol. 42, Issue 18 https://doi.org/10.1093/nar/gku828	journal	September 2014
Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology Sun, Zachary Z.; Hayes, Clarmyra A.; Shin, Jonghyeon Journal of Visualized Experiments, Issue 79 https://doi.org/10.3791/50762	journal	January 2013
Stochasticity in Gene Expression in a Cell-Sized Compartment Nishimura, Kazuya; Tsuru, Saburo; Suzuki, Hiroaki ACS Synthetic Biology, Vol. 4, Issue 5 https://doi.org/10.1021/sb500249g	journal	September 2014
Unbiased Tracking of the Progression of mRNA and Protein Synthesis in Bulk and in Liposome-Confined Reactions van Nies, Pauline; Nourian, Zohreh; Kok, Maurits ChemBioChem, Vol. 14, Issue 15 https://doi.org/10.1002/cbic.201300449	journal	September 2013
High Variation of Fluorescence Protein Maturation Times in Closely Related Escherichia coli Strains Hebisch, Elke; Knebel, Johannes; Landsberg, Janek PLoS ONE, Vol. 8, Issue 10 https://doi.org/10.1371/journal.pone.0075991	journal	October 2013

Cited By (5)

Transport of probe particles in a polymer network: effects of probe size, network rigidity and probe–polymer interaction Kumar, Praveen; Theeyancheri, Ligesh; Chaki, Subhasish Soft Matter, Vol. 15, Issue 44 https://doi.org/10.1039/c9sm01822k	journal	January 2019
Quantitative imaging of gene-expressing liposomes reveals rare favorable phenotypes Blanken, Duco; van Nies, Pauline; Danelon, Christophe Physical Biology, Vol. 16, Issue 4 https://doi.org/10.1088/1478-3975/ab0c62	journal	April 2019
Self-Organization Controls Expression More than Abundance of Molecular Components of Transcription and Translation in Confined Cell-Free Gene Expression Caveney, Patrick M.; Dabbs, Rosemary M.; Chauhan, Gaurav SSRN Electronic Journal https://doi.org/10.2139/ssrn.3259136	journal	January 2018
Cell-free microcompartmentalised transcription–translation for the prototyping of synthetic communication networks Dubuc, Emilien; Pieters, Pascal A.; van der Linden, Ardjan J. Current Opinion in Biotechnology, Vol. 58 https://doi.org/10.1016/j.copbio.2018.10.006	journal	August 2019
Bottom-up construction of complex biomolecular systems with cell-free synthetic biology Laohakunakorn, Nadanai; Grasemann, Laura; Lavickova, Barbora Zenodo https://doi.org/10.5281/zenodo.3591963	text	January 2020

Similar Records

Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion

Journal Article · Mon Nov 28 00:00:00 EST 2016 · PLoS Computational Biology (Online) · OSTI ID:1439942

Golkaram, Mahdi; Hellander, Stefan; Drawert, Brian; +1 more

Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles

Journal Article · Wed Oct 19 00:00:00 EDT 2022 · ACS Synthetic Biology · OSTI ID:1439942

Chauhan, Gaurav; Norred, S. Elizabeth; Dabbs, Rosemary M.; +5 more

Macromolecular crowding can account for RNase-sensitive constraint of bacterial nucleoid structure

Journal Article · Fri Apr 23 00:00:00 EDT 2010 · Biochemical and Biophysical Research Communications · OSTI ID:1439942

Foley, Patricia L.; Wilson, David B.

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
cell-free
gene expression bursting
gene expression noise
GUV
liposomes
macromolecular crowding

Title: Macromolecular Crowding Induces Spatial Correlations That Control Gene Expression Bursting Patterns

Citation Formats

References (49)

Cited By (5)

Similar Records

Related Subjects