Towards using bacterial microcompartments as a platform for spatial metabolic engineering in the industrially important and metabolically versatile Zymomonas mobilis
Abstract
Advances in synthetic biology have enabled the incorporation of novel biochemical pathways for the production of high-value products into industrially important bacterial hosts. However, attempts to redirect metabolic fluxes towards desired products often lead to the buildup of toxic or undesirable intermediates or, more generally, unwanted metabolic cross-talk. The use of shells derived from self-assembling protein-based prokaryotic organelles, referred to as bacterial microcompartments (BMCs), as a scaffold for metabolic enzymes represents a sophisticated approach that can both insulate and integrate the incorporation of challenging metabolic pathways into industrially important bacterial hosts. Here we took a synthetic biology approach and introduced the model shell system derived from the myxobacterium Haliangium ochraceum (HO shell) into the industrially relevant organism Zymomonas mobilis with the aim of constructing a BMC-based spatial scaffolding platform. SDS-PAGE, transmission electron microscopy, and dynamic light scattering analyses collectively demonstrated the ability to express and purify empty capped and uncapped HO shells from Z. mobilis . As a proof of concept to internally load or externally decorate the shell surface with enzyme cargo, we have successfully targeted fluorophores to the surfaces of the BMC shells. Overall, our results provide the foundation for incorporating enzymes and constructing BMCs with synthetic biochemicalmore »
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 2282927
- Resource Type:
- Published Article
- Journal Name:
- Frontiers in Bioengineering and Biotechnology
- Additional Journal Information:
- Journal Name: Frontiers in Bioengineering and Biotechnology Journal Volume: 12; Journal ID: ISSN 2296-4185
- Publisher:
- Frontiers Media SA
- Country of Publication:
- Switzerland
- Language:
- English
Citation Formats
Doron, Lior, Raval, Dhairya, and Kerfeld, Cheryl A. Towards using bacterial microcompartments as a platform for spatial metabolic engineering in the industrially important and metabolically versatile Zymomonas mobilis. Switzerland: N. p., 2024.
Web. doi:10.3389/fbioe.2024.1344260.
Doron, Lior, Raval, Dhairya, & Kerfeld, Cheryl A. Towards using bacterial microcompartments as a platform for spatial metabolic engineering in the industrially important and metabolically versatile Zymomonas mobilis. Switzerland. https://doi.org/10.3389/fbioe.2024.1344260
Doron, Lior, Raval, Dhairya, and Kerfeld, Cheryl A. Fri .
"Towards using bacterial microcompartments as a platform for spatial metabolic engineering in the industrially important and metabolically versatile Zymomonas mobilis". Switzerland. https://doi.org/10.3389/fbioe.2024.1344260.
@article{osti_2282927,
title = {Towards using bacterial microcompartments as a platform for spatial metabolic engineering in the industrially important and metabolically versatile Zymomonas mobilis},
author = {Doron, Lior and Raval, Dhairya and Kerfeld, Cheryl A.},
abstractNote = {Advances in synthetic biology have enabled the incorporation of novel biochemical pathways for the production of high-value products into industrially important bacterial hosts. However, attempts to redirect metabolic fluxes towards desired products often lead to the buildup of toxic or undesirable intermediates or, more generally, unwanted metabolic cross-talk. The use of shells derived from self-assembling protein-based prokaryotic organelles, referred to as bacterial microcompartments (BMCs), as a scaffold for metabolic enzymes represents a sophisticated approach that can both insulate and integrate the incorporation of challenging metabolic pathways into industrially important bacterial hosts. Here we took a synthetic biology approach and introduced the model shell system derived from the myxobacterium Haliangium ochraceum (HO shell) into the industrially relevant organism Zymomonas mobilis with the aim of constructing a BMC-based spatial scaffolding platform. SDS-PAGE, transmission electron microscopy, and dynamic light scattering analyses collectively demonstrated the ability to express and purify empty capped and uncapped HO shells from Z. mobilis . As a proof of concept to internally load or externally decorate the shell surface with enzyme cargo, we have successfully targeted fluorophores to the surfaces of the BMC shells. Overall, our results provide the foundation for incorporating enzymes and constructing BMCs with synthetic biochemical pathways for the future production of high-value products in Z. mobilis .},
doi = {10.3389/fbioe.2024.1344260},
journal = {Frontiers in Bioengineering and Biotechnology},
number = ,
volume = 12,
place = {Switzerland},
year = {Fri Jan 26 00:00:00 EST 2024},
month = {Fri Jan 26 00:00:00 EST 2024}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.3389/fbioe.2024.1344260
https://doi.org/10.3389/fbioe.2024.1344260
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Programmable polyproteams built using twin peptide superglues
journal, January 2016
- Veggiani, Gianluca; Nakamura, Tomohiko; Brenner, Michael D.
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 5
Characterization of a novel aromatic substrate-processing microcompartment in Actinobacteria
journal, July 2023
- Doron, Lior; Sutter, Markus; Kerfeld, Cheryl A.
- mBio
Heterologous Microcompartment Assembly in Bacillaceae: Establishing the Components Necessary for Scaffold Formation
journal, June 2019
- Wade, Yana; Daniel, Richard A.; Leak, David J.
- ACS Synthetic Biology, Vol. 8, Issue 7
Regulated redirection of central carbon flux enhances anaerobic production of bioproducts in Zymomonas mobilis
journal, September 2020
- Liu, Yang; Ghosh, Indro Neil; Martien, Julia
- Metabolic Engineering, Vol. 61
Involvement of a Bacterial Microcompartment in the Metabolism of Fucose and Rhamnose by Clostridium phytofermentans
journal, January 2013
- Petit, Elsa; LaTouf, W. Greg; Coppi, Maddalena V.
- PLoS ONE, Vol. 8, Issue 1
Engineering Zymomonas mobilis for Robust Cellulosic Ethanol Production
journal, September 2019
- Xia, Juan; Yang, Yongfu; Liu, Chen-Guang
- Trends in Biotechnology, Vol. 37, Issue 9
The challenges of cellular compartmentalization in plant metabolic engineering
journal, April 2013
- Heinig, Uwe; Gutensohn, Michael; Dudareva, Natalia
- Current Opinion in Biotechnology, Vol. 24, Issue 2
Expression of Phosphofructokinase Is Not Sufficient to Enable Embden-Meyerhof-Parnas Glycolysis in Zymomonas mobilis ZM4
journal, September 2019
- Felczak, Magdalena M.; Jacobson, Tyler B.; Ong, Wai Kit
- Frontiers in Microbiology, Vol. 10
A genomic integration platform for heterologous cargo encapsulation in 1,2-propanediol utilization bacterial microcompartments
journal, April 2020
- Nichols, Taylor M.; Kennedy, Nolan W.; Tullman-Ercek, Danielle
- Biochemical Engineering Journal, Vol. 156
Improving Mobilization of Foreign DNA into Zymomonas mobilis Strain ZM4 by Removal of Multiple Restriction Systems
journal, September 2021
- Lal, Piyush Behari; Wells, Fritz; Myers, Kevin S.
- Applied and Environmental Microbiology, Vol. 87, Issue 19
Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms
journal, June 2018
- Calero, Patricia; Nikel, Pablo I.
- Microbial Biotechnology, Vol. 12, Issue 1
Impact of Expression of EMP Enzymes on Glucose Metabolism in Zymomonas mobilis
journal, April 2013
- Chen, Rachel Ruizhen; Agrawal, Manoj; Mao, Zichao
- Applied Biochemistry and Biotechnology, Vol. 170, Issue 4
Peptide tag forming a rapid covalent bond to a protein, through engineering a bacterial adhesin
journal, February 2012
- Zakeri, B.; Fierer, J. O.; Celik, E.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 12
Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia
journal, December 2021
- Burrichter, Anna G.; Dörr, Stefanie; Bergmann, Paavo
- BMC Microbiology, Vol. 21, Issue 1
Tools for Genetic Engineering and Gene Expression Control in Novosphingobium aromaticivorans and Rhodobacter sphaeroides
journal, August 2023
- Hall, Ashley N.; Hall, Benjamin W.; Kinney, Kyle J.
- bioRxiv
Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell
journal, June 2017
- Sutter, Markus; Greber, Basil; Aussignargues, Clement
- Science, Vol. 356, Issue 6344
Assembly, function and evolution of cyanobacterial carboxysomes
journal, June 2016
- Kerfeld, Cheryl A.; Melnicki, Matthew R.
- Current Opinion in Plant Biology, Vol. 31
Bacterial microcompartments
journal, March 2018
- Kerfeld, Cheryl A.; Aussignargues, Clement; Zarzycki, Jan
- Nature Reviews Microbiology, Vol. 16, Issue 5
The potential of bacterial microcompartment architectures for phytonanotechnology
journal, July 2022
- Raba, Daniel A.; Kerfeld, Cheryl A.
- Environmental Microbiology Reports, Vol. 14, Issue 5
The Propanediol Utilization (pdu) Operon ofSalmonella enterica Serovar Typhimurium LT2 Includes Genes Necessary for Formation of Polyhedral Organelles Involved in Coenzyme B12-Dependent 1,2-Propanediol Degradation
†
journal, January 1999
- Bobik, Thomas A.; Havemann, Gregory D.; Busch, Robert J.
- Journal of Bacteriology, Vol. 181, Issue 19
Zymomonas mobilis as a model system for production of biofuels and biochemicals
journal, September 2016
- Yang, Shihui; Fei, Qiang; Zhang, Yaoping
- Microbial Biotechnology, Vol. 9, Issue 6
Enzymatic assembly of DNA molecules up to several hundred kilobases
journal, April 2009
- Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
- Nature Methods, Vol. 6, Issue 5, p. 343-345
Pathway Compartmentalization in Peroxisome of Saccharomyces cerevisiae to Produce Versatile Medium Chain Fatty Alcohols
journal, May 2016
- Sheng, Jiayuan; Stevens, Joseph; Feng, Xueyang
- Scientific Reports, Vol. 6, Issue 1
Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering
journal, October 2019
- Kirst, Henning; Kerfeld, Cheryl A.
- BMC Biology, Vol. 17, Issue 1
De novo targeting to the cytoplasmic and luminal side of bacterial microcompartments
journal, August 2018
- Lee, Matthew J.; Mantell, Judith; Brown, Ian R.
- Nature Communications, Vol. 9, Issue 1
Unusual transformations in the biosynthesis of the antibiotic phosphinothricin tripeptide
journal, July 2007
- Blodgett, Joshua A. V.; Thomas, Paul M.; Li, Gongyong
- Nature Chemical Biology, Vol. 3, Issue 8
Toward a glycyl radical enzyme containing synthetic bacterial microcompartment to produce pyruvate from formate and acetate
journal, February 2022
- Kirst, Henning; Ferlez, Bryan H.; Lindner, Steffen N.
- Proceedings of the National Academy of Sciences, Vol. 119, Issue 8
Programmed loading and rapid purification of engineered bacterial microcompartment shells
journal, July 2018
- Hagen, Andrew; Sutter, Markus; Sloan, Nancy
- Nature Communications, Vol. 9, Issue 1
Advances in the World of Bacterial Microcompartments
journal, May 2021
- Stewart, Andrew M.; Stewart, Katie L.; Yeates, Todd O.
- Trends in Biochemical Sciences, Vol. 46, Issue 5
Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides
journal, January 2014
- Erbilgin, Onur; McDonald, Kent L.; Kerfeld, Cheryl A.
- Applied and Environmental Microbiology, Vol. 80, Issue 7
Heterologous expression of the Halothiobacillus neapolitanus carboxysomal gene cluster in Corynebacterium glutamicum
journal, September 2017
- Baumgart, Meike; Huber, Isabel; Abdollahzadeh, Iman
- Journal of Biotechnology, Vol. 258
Redirection of cytosolic or plastidic isoprenoid precursors elevates terpene production in plants
journal, October 2006
- Wu, Shuiqin; Schalk, Michel; Clark, Anthony
- Nature Biotechnology, Vol. 24, Issue 11, p. 1441-1447
Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles
journal, January 2020
- Kalnins, Gints; Cesle, Eva-Emilija; Jansons, Juris
- Nature Communications, Vol. 11, Issue 1
Embracing Biological Solutions to the Sustainable Energy Challenge
journal, January 2017
- Adesina, Oluwakemi; Anzai, Isao A.; Avalos, José L.
- Chem, Vol. 2, Issue 1
New technologies provide more metabolic engineering strategies for bioethanol production in Zymomonas mobilis
journal, January 2019
- Zhang, Kun; Lu, Xinxin; Li, Yi
- Applied Microbiology and Biotechnology, Vol. 103, Issue 5
Bacterial microcompartment assembly: The key role of encapsulation peptides
journal, May 2015
- Aussignargues, Clément; Paasch, Bradley C.; Gonzalez-Esquer, Raul
- Communicative & Integrative Biology, Vol. 8, Issue 3
The industrial yeast Pichia pastoris is converted from a heterotroph into an autotroph capable of growth on CO2
journal, December 2019
- Gassler, Thomas; Sauer, Michael; Gasser, Brigitte
- Nature Biotechnology, Vol. 38, Issue 2
Dual regulation of cytoplasmic and mitochondrial acetyl-CoA utilization for improved isoprene production in Saccharomyces cerevisiae
journal, September 2016
- Lv, Xiaomei; Wang, Fan; Zhou, Pingping
- Nature Communications, Vol. 7, Issue 1
Structure of a Synthetic β -Carboxysome Shell
journal, September 2019
- Sutter, Markus; Laughlin, Thomas G.; Sloan, Nancy B.
- Plant Physiology, Vol. 181, Issue 3
A Markerless Method for Genome Engineering in Zymomonas mobilis ZM4
journal, October 2019
- Lal, Piyush Behari; Wells, Fritz M.; Lyu, Yucai
- Frontiers in Microbiology, Vol. 10
Advances in the bacterial organelles for CO2 fixation
journal, June 2022
- Liu, Lu-Ning
- Trends in Microbiology, Vol. 30, Issue 6
Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production
journal, October 2020
- Li, Tianpei; Jiang, Qiuyao; Huang, Jiafeng
- Nature Communications, Vol. 11, Issue 1
Theoretical and Practical Aspects of Multienzyme Organization and Encapsulation
journal, May 2023
- Abrahamson, Charlotte H.; Palmero, Brett J.; Kennedy, Nolan W.
- Annual Review of Biophysics, Vol. 52, Issue 1
Solution Structure of a Bacterial Microcompartment Targeting Peptide and Its Application in the Construction of an Ethanol Bioreactor
journal, November 2013
- Lawrence, Andrew D.; Frank, Stefanie; Newnham, Sarah
- ACS Synthetic Biology, Vol. 3, Issue 7
A designed bacterial microcompartment shell with tunable composition and precision cargo loading
journal, July 2019
- Ferlez, Bryan; Sutter, Markus; Kerfeld, Cheryl A.
- Metabolic Engineering, Vol. 54
Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement
journal, April 2010
- Parsons, Joshua B.; Frank, Stefanie; Bhella, David
- Molecular Cell, Vol. 38, Issue 2
Transfer and analysis of Salmonella pdu genes in a range of Gram-negative bacteria demonstrate exogenous microcompartment expression across a variety of species
journal, October 2017
- Graf, Laura; Wu, Kent; Wilson, James W.
- Microbial Biotechnology, Vol. 11, Issue 1
Assembly of Robust Bacterial Microcompartment Shells Using Building Blocks from an Organelle of Unknown Function
journal, May 2014
- Lassila, Jonathan K.; Bernstein, Susan L.; Kinney, James N.
- Journal of Molecular Biology, Vol. 426, Issue 11
Employing bacterial microcompartment technology to engineer a shell-free enzyme-aggregate for enhanced 1,2-propanediol production in Escherichia coli
journal, July 2016
- Lee, Matthew J.; Brown, Ian R.; Juodeikis, Rokas
- Metabolic Engineering, Vol. 36
Inducible-Expression Plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans
journal, August 2009
- Ind, Alice C.; Porter, Steven L.; Brown, Mostyn T.
- Applied and Environmental Microbiology, Vol. 75, Issue 20
Construction of Recombinant Pdu Metabolosome Shells for Small Molecule Production in Corynebacterium glutamicum
journal, August 2017
- Huber, Isabel; Palmer, David J.; Ludwig, Kira N.
- ACS Synthetic Biology, Vol. 6, Issue 11
Engineered bacterial microcompartments: apps for programming metabolism
journal, October 2020
- Kerfeld, Cheryl A.; Sutter, Markus
- Current Opinion in Biotechnology, Vol. 65
The 17-Gene Ethanolamine (eut) Operon ofSalmonella typhimurium Encodes Five Homologues of Carboxysome Shell Proteins
journal, September 1999
- Kofoid, Eric; Rappleye, Chad; Stojiljkovic, Igor
- Journal of Bacteriology, Vol. 181, Issue 17
A catalog of the diversity and ubiquity of bacterial microcompartments
journal, June 2021
- Sutter, Markus; Melnicki, Matthew R.; Schulz, Frederik
- Nature Communications, Vol. 12, Issue 1