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Huffine CA, Zhao R, Tang YJ, Cameron JC. Role of carboxysomes in cyanobacterial CO 2 assimilation: CO 2 concentrating mechanisms and metabolon implications. Environ Microbiol 2023; 25:219-228. [PMID: 36367380 DOI: 10.1111/1462-2920.16283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Many carbon-fixing organisms have evolved CO2 concentrating mechanisms (CCMs) to enhance the delivery of CO2 to RuBisCO, while minimizing reactions with the competitive inhibitor, molecular O2 . These distinct types of CCMs have been extensively studied using genetics, biochemistry, cell imaging, mass spectrometry, and metabolic flux analysis. Highlighted in this paper, the cyanobacterial CCM features a bacterial microcompartment (BMC) called 'carboxysome' in which RuBisCO is co-encapsulated with the enzyme carbonic anhydrase (CA) within a semi-permeable protein shell. The cyanobacterial CCM is capable of increasing CO2 around RuBisCO, leading to one of the most efficient processes known for fixing ambient CO2 . The carboxysome life cycle is dynamic and creates a unique subcellular environment that promotes activity of the Calvin-Benson (CB) cycle. The carboxysome may function within a larger cellular metabolon, physical association of functionally coupled proteins, to enhance metabolite channelling and carbon flux. In light of CCMs, synthetic biology approaches have been used to improve enzyme complex for CO2 fixations. Research on CCM-associated metabolons has also inspired biologists to engineer multi-step pathways by providing anchoring points for enzyme cascades to channel intermediate metabolites towards valuable products.
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Affiliation(s)
- Clair A Huffine
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, USA
- Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, Colorado, USA
| | - Runyu Zhao
- Department of Energy, Environmental and Chemical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University in Saint Louis, Saint Louis, Missouri, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
- Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, USA
- National Renewable Energy Laboratory, Golden, Colorado, USA
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Liu AK, Pereira JH, Kehl AJ, Rosenberg DJ, Orr DJ, Chu SKS, Banda DM, Hammel M, Adams PD, Siegel JB, Shih PM. Structural plasticity enables evolution and innovation of RuBisCO assemblies. Sci Adv 2022; 8:eadc9440. [PMID: 36026446 PMCID: PMC9417184 DOI: 10.1126/sciadv.adc9440] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Oligomerization is a core structural feature that defines the form and function of many proteins. Most proteins form molecular complexes; however, there remains a dearth of diversity-driven structural studies investigating the evolutionary trajectory of these assemblies. Ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is one such enzyme that adopts multiple assemblies, although the origins and distribution of its different oligomeric states remain cryptic. Here, we retrace the evolution of ancestral and extant form II RuBisCOs, revealing a complex and diverse history of oligomerization. We structurally characterize a newly discovered tetrameric RuBisCO, elucidating how solvent-exposed surfaces can readily adopt new interactions to interconvert or give rise to new oligomeric states. We further use these principles to engineer and demonstrate how changes in oligomerization can be mediated by relatively few mutations. Our findings yield insight into how structural plasticity may give rise to new oligomeric states.
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Affiliation(s)
- Albert K. Liu
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, CA 95616, USA
| | - Jose H. Pereira
- Technology Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alexander J. Kehl
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Daniel J. Rosenberg
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Douglas J. Orr
- Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
| | - Simon K. S. Chu
- Biophysics Graduate Group, University of California, Davis, Davis, CA, USA
| | - Douglas M. Banda
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Paul D. Adams
- Technology Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Justin B. Siegel
- Genome Center, University of California, Davis, Davis, CA 95616, USA
- Chemistry Department, University of California, Davis, Davis, CA 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Sacramento, Sacramento, CA 95616, USA
| | - Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
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