1
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Kong WW, Zhu Y, Zhao HR, Du K, Zhou RQ, Li B, Yang F, Hou P, Huang XH, Chen Y, Wang YC, Sun F, Jiang YL, Zhou CZ. Cryo-electron tomography reveals the packaging pattern of RuBisCOs in Synechococcus β-carboxysome. Structure 2024; 32:1110-1120.e4. [PMID: 38823379 DOI: 10.1016/j.str.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Carboxysomes are large self-assembled microcompartments that serve as the central machinery of a CO2-concentrating mechanism (CCM). Biogenesis of carboxysome requires the fine organization of thousands of individual proteins; however, the packaging pattern of internal RuBisCOs remains largely unknown. Here we purified the intact β-carboxysomes from Synechococcus elongatus PCC 7942 and identified the protein components by mass spectrometry. Cryo-electron tomography combined with subtomogram averaging revealed the general organization pattern of internal RuBisCOs, in which the adjacent RuBisCOs are mainly arranged in three distinct manners: head-to-head, head-to-side, and side-by-side. The RuBisCOs in the outermost layer are regularly aligned along the shell, the majority of which directly interact with the shell. Moreover, statistical analysis enabled us to propose an ideal packaging model of RuBisCOs in the β-carboxysome. These results provide new insights into the biogenesis of β-carboxysomes and also advance our understanding of the efficient carbon fixation functionality of carboxysomes.
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Affiliation(s)
- Wen-Wen Kong
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Heng-Rui Zhao
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Kang Du
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Rui-Qian Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Bo Li
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Feng Yang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Pu Hou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Xia-He Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Ying-Chun Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
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2
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Basalla JL, Ghalmi M, Hoang Y, Dow RE, Vecchiarelli AG. An invariant C-terminal tryptophan in McdB mediates its interaction and positioning function with carboxysomes. Mol Biol Cell 2024; 35:ar107. [PMID: 38922842 PMCID: PMC11321042 DOI: 10.1091/mbc.e23-11-0443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024] Open
Abstract
Bacterial microcompartments (BMCs) are widespread, protein-based organelles that regulate metabolism. The model for studying BMCs is the carboxysome, which facilitates carbon fixation in several autotrophic bacteria. Carboxysomes can be distinguished as type α or β, which are structurally and phyletically distinct. We recently characterized the maintenance of carboxysome distribution (Mcd) systems responsible for spatially regulating α- and β-carboxysomes, consisting of the proteins McdA and McdB. McdA is an ATPase that drives carboxysome positioning, and McdB is the adaptor protein that directly interacts with carboxysomes to provide cargo specificity. The molecular features of McdB proteins that specify their interactions with carboxysomes, and whether these are similar between α- and β-carboxysomes, remain unknown. Here, we identify C-terminal motifs containing an invariant tryptophan necessary for α- and β-McdBs to associate with α- and β-carboxysomes, respectively. Substituting this tryptophan with other aromatic residues reveals corresponding gradients in the efficiency of carboxysome colocalization and positioning by McdB in vivo. Intriguingly, these gradients also correlate with the ability of McdB to form condensates in vitro. The results reveal a shared mechanism underlying McdB adaptor protein binding to carboxysomes, and potentially other BMCs. Our findings also implicate condensate formation as playing a key role in this association.
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Affiliation(s)
- Joseph L. Basalla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Y. Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Rachel E. Dow
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
| | - Anthony G. Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109
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3
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de Pins B, Greenspoon L, Bar-On YM, Shamshoum M, Ben-Nissan R, Milshtein E, Davidi D, Sharon I, Mueller-Cajar O, Noor E, Milo R. A systematic exploration of bacterial form I rubisco maximal carboxylation rates. EMBO J 2024; 43:3072-3083. [PMID: 38806660 PMCID: PMC11251275 DOI: 10.1038/s44318-024-00119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/26/2024] [Accepted: 04/22/2024] [Indexed: 05/30/2024] Open
Abstract
Autotrophy is the basis for complex life on Earth. Central to this process is rubisco-the enzyme that catalyzes almost all carbon fixation on the planet. Yet, with only a small fraction of rubisco diversity kinetically characterized so far, the underlying biological factors driving the evolution of fast rubiscos in nature remain unclear. We conducted a high-throughput kinetic characterization of over 100 bacterial form I rubiscos, the most ubiquitous group of rubisco sequences in nature, to uncover the determinants of rubisco's carboxylation velocity. We show that the presence of a carboxysome CO2 concentrating mechanism correlates with faster rubiscos with a median fivefold higher rate. In contrast to prior studies, we find that rubiscos originating from α-cyanobacteria exhibit the highest carboxylation rates among form I enzymes (≈10 s-1 median versus <7 s-1 in other groups). Our study systematically reveals biological and environmental properties associated with kinetic variation across rubiscos from nature.
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Affiliation(s)
- Benoit de Pins
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lior Greenspoon
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yinon M Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Melina Shamshoum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Roee Ben-Nissan
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Eliya Milshtein
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
- Aleph, Tel Aviv-Yafo, 6688210, Israel
| | - Itai Sharon
- Migal Galilee Research Institute, Kiryat Shmona, 11016, Israel
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.
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4
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Pulsford SB, Outram MA, Förster B, Rhodes T, Williams SJ, Badger MR, Price GD, Jackson CJ, Long BM. Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP. SCIENCE ADVANCES 2024; 10:eadk7283. [PMID: 38728392 PMCID: PMC11086599 DOI: 10.1126/sciadv.adk7283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024]
Abstract
Cyanobacterial CO2 concentrating mechanisms (CCMs) sequester a globally consequential proportion of carbon into the biosphere. Proteinaceous microcompartments, called carboxysomes, play a critical role in CCM function, housing two enzymes to enhance CO2 fixation: carbonic anhydrase (CA) and Rubisco. Despite its importance, our current understanding of the carboxysomal CAs found in α-cyanobacteria, CsoSCA, remains limited, particularly regarding the regulation of its activity. Here, we present a structural and biochemical study of CsoSCA from the cyanobacterium Cyanobium sp. PCC7001. Our results show that the Cyanobium CsoSCA is allosterically activated by the Rubisco substrate ribulose-1,5-bisphosphate and forms a hexameric trimer of dimers. Comprehensive phylogenetic and mutational analyses are consistent with this regulation appearing exclusively in cyanobacterial α-carboxysome CAs. These findings clarify the biologically relevant oligomeric state of α-carboxysomal CAs and advance our understanding of the regulation of photosynthesis in this globally dominant lineage.
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Affiliation(s)
- Sacha B. Pulsford
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Megan A. Outram
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Britta Förster
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Timothy Rhodes
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Simon J. Williams
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Murray R. Badger
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - G. Dean Price
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Colin J. Jackson
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| | - Benedict M. Long
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW, Australia
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
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5
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Nguyen ND, Pulsford SB, Förster B, Rottet S, Rourke L, Long BM, Price GD. A carboxysome-based CO 2 concentrating mechanism for C 3 crop chloroplasts: advances and the road ahead. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:940-952. [PMID: 38321620 DOI: 10.1111/tpj.16667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/08/2024]
Abstract
The introduction of the carboxysome-based CO2 concentrating mechanism (CCM) into crop plants has been modelled to significantly increase crop yields. This projection serves as motivation for pursuing this strategy to contribute to global food security. The successful implementation of this engineering challenge is reliant upon the transfer of a microcompartment that encapsulates cyanobacterial Rubisco, known as the carboxysome, alongside active bicarbonate transporters. To date, significant progress has been achieved with respect to understanding various aspects of the cyanobacterial CCM, and more recently, different components of the carboxysome have been successfully introduced into plant chloroplasts. In this Perspective piece, we summarise recent findings and offer new research avenues that will accelerate research in this field to ultimately and successfully introduce the carboxysome into crop plants for increased crop yields.
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Affiliation(s)
- Nghiem D Nguyen
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sacha B Pulsford
- Research School of Chemistry, Australian National University, 137 Sullivan's Ck Rd, Acton, Australian Capital Territory, 2601, Australia
| | - Britta Förster
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Sarah Rottet
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Loraine Rourke
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
| | - Benedict M Long
- Discipline of Biological Sciences, School of Environmental and Life Sciences, ARC Centre of Excellence in Synthetic Biology, The University of Newcastle, University Drive, Callaghan, New South Wales, 2308, Australia
| | - G Dean Price
- Plant Science Division, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory, 2601, Australia
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6
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Long BM, Matsuda Y, Moroney JV. Algal chloroplast pyrenoids: Evidence for convergent evolution. Proc Natl Acad Sci U S A 2024; 121:e2402546121. [PMID: 38513078 PMCID: PMC10998615 DOI: 10.1073/pnas.2402546121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Affiliation(s)
- Benedict Michael Long
- Discipline of Biological Sciences, School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Yusuke Matsuda
- Department of Bioscience, School of Biological and Environmental Sciences, Kansei Gakuin University, Sanda, Hyogo669-1330, Japan
| | - James V. Moroney
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA70803
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7
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Zhou RQ, Jiang YL, Li H, Hou P, Kong WW, Deng JX, Chen Y, Zhou CZ, Zeng Q. Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus. NATURE PLANTS 2024; 10:661-672. [PMID: 38589484 DOI: 10.1038/s41477-024-01660-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/29/2024] [Indexed: 04/10/2024]
Abstract
Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant 'outside-in' assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency.
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Affiliation(s)
- Rui-Qian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Pu Hou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jia-Xin Deng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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8
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Pulsford SB, Nguyen ND, Long BM. The ties that bind. Disordered linkers underpin carboxysome construction. Proc Natl Acad Sci U S A 2023; 120:e2316828120. [PMID: 37889932 PMCID: PMC10636299 DOI: 10.1073/pnas.2316828120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023] Open
Affiliation(s)
- Sacha B. Pulsford
- Research School of Chemistry, Australian National University, Acton, ACT2601, Australia
| | - Nghiem D. Nguyen
- Plant Science Division, Research School of Biology, Australian National University, Acton, ACT2601, Australia
| | - Benedict M. Long
- Discipline of Biological Sciences, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW2308, Australia
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9
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Blikstad C, Dugan EJ, Laughlin TG, Turnšek JB, Liu MD, Shoemaker SR, Vogiatzi N, Remis JP, Savage DF. Identification of a carbonic anhydrase-Rubisco complex within the alpha-carboxysome. Proc Natl Acad Sci U S A 2023; 120:e2308600120. [PMID: 37862384 PMCID: PMC10614612 DOI: 10.1073/pnas.2308600120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/28/2023] [Indexed: 10/22/2023] Open
Abstract
Carboxysomes are proteinaceous organelles that encapsulate key enzymes of CO2 fixation-Rubisco and carbonic anhydrase-and are the centerpiece of the bacterial CO2 concentrating mechanism (CCM). In the CCM, actively accumulated cytosolic bicarbonate diffuses into the carboxysome and is converted to CO2 by carbonic anhydrase, producing a high CO2 concentration near Rubisco and ensuring efficient carboxylation. Self-assembly of the α-carboxysome is orchestrated by the intrinsically disordered scaffolding protein, CsoS2, which interacts with both Rubisco and carboxysomal shell proteins, but it is unknown how the carbonic anhydrase, CsoSCA, is incorporated into the α-carboxysome. Here, we present the structural basis of carbonic anhydrase encapsulation into α-carboxysomes from Halothiobacillus neapolitanus. We find that CsoSCA interacts directly with Rubisco via an intrinsically disordered N-terminal domain. A 1.98 Å single-particle cryoelectron microscopy structure of Rubisco in complex with this peptide reveals that CsoSCA binding is predominantly mediated by a network of hydrogen bonds. CsoSCA's binding site overlaps with that of CsoS2, but the two proteins utilize substantially different motifs and modes of binding, revealing a plasticity of the Rubisco binding site. Our results advance the understanding of carboxysome biogenesis and highlight the importance of Rubisco, not only as an enzyme but also as a central hub for mediating assembly through protein interactions.
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Affiliation(s)
- Cecilia Blikstad
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Eli J. Dugan
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Thomas G. Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Julia B. Turnšek
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Mira D. Liu
- Department of Chemistry, University of California, Berkeley, CA94720
| | - Sophie R. Shoemaker
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
| | - Nikoleta Vogiatzi
- Department of Chemistry - Ångström Laboratory, Uppsala University, Uppsala75120, Sweden
| | - Jonathan P. Remis
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA94720
| | - David F. Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, CA94720
- HHMI, University of California, Berkeley, CA94720
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10
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Ni T, Jiang Q, Ng PC, Shen J, Dou H, Zhu Y, Radecke J, Dykes GF, Huang F, Liu LN, Zhang P. Intrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly. Nat Commun 2023; 14:5512. [PMID: 37679318 PMCID: PMC10484944 DOI: 10.1038/s41467-023-41211-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineer α-carboxysome shells using minimal shell components and determine cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncover in CsoS2 a highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-governed carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Pei Cing Ng
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Juan Shen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hao Dou
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Julika Radecke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fang Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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11
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Basalla JL, Mak CA, Byrne JA, Ghalmi M, Hoang Y, Vecchiarelli AG. Dissecting the phase separation and oligomerization activities of the carboxysome positioning protein McdB. eLife 2023; 12:e81362. [PMID: 37668016 PMCID: PMC10554743 DOI: 10.7554/elife.81362] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
Across bacteria, protein-based organelles called bacterial microcompartments (BMCs) encapsulate key enzymes to regulate their activities. The model BMC is the carboxysome that encapsulates enzymes for CO2 fixation to increase efficiency and is found in many autotrophic bacteria, such as cyanobacteria. Despite their importance in the global carbon cycle, little is known about how carboxysomes are spatially regulated. We recently identified the two-factor system required for the maintenance of carboxysome distribution (McdAB). McdA drives the equal spacing of carboxysomes via interactions with McdB, which associates with carboxysomes. McdA is a ParA/MinD ATPase, a protein family well studied in positioning diverse cellular structures in bacteria. However, the adaptor proteins like McdB that connect these ATPases to their cargos are extremely diverse. In fact, McdB represents a completely unstudied class of proteins. Despite the diversity, many adaptor proteins undergo phase separation, but functional roles remain unclear. Here, we define the domain architecture of McdB from the model cyanobacterium Synechococcus elongatus PCC 7942, and dissect its mode of biomolecular condensate formation. We identify an N-terminal intrinsically disordered region (IDR) that modulates condensate solubility, a central coiled-coil dimerizing domain that drives condensate formation, and a C-terminal domain that trimerizes McdB dimers and provides increased valency for condensate formation. We then identify critical basic residues in the IDR, which we mutate to glutamines to solubilize condensates. Finally, we find that a condensate-defective mutant of McdB has altered association with carboxysomes and influences carboxysome enzyme content. The results have broad implications for understanding spatial organization of BMCs and the molecular grammar of protein condensates.
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Affiliation(s)
- Joseph L Basalla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Claudia A Mak
- Department of Biological Chemistry, University of Michigan-Ann ArborAnn ArborUnited States
| | - Jordan A Byrne
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
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12
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Cobb SJ, Dharani AM, Oliveira AR, Pereira IAC, Reisner E. Carboxysome-Inspired Electrocatalysis using Enzymes for the Reduction of CO 2 at Low Concentrations. Angew Chem Int Ed Engl 2023; 62:e202218782. [PMID: 37078435 DOI: 10.1002/anie.202218782] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/21/2023]
Abstract
The electrolysis of dilute CO2 streams suffers from low concentrations of dissolved substrate and its rapid depletion at the electrolyte-electrocatalyst interface. These limitations require first energy-intensive CO2 capture and concentration, before electrolyzers can achieve acceptable performances. For direct electrocatalytic CO2 reduction from low-concentration sources, we introduce a strategy that mimics the carboxysome in cyanobacteria by utilizing microcompartments with nanoconfined enzymes in a porous electrode. A carbonic anhydrase accelerates CO2 hydration kinetics and minimizes substrate depletion by making all dissolved carbon available for utilization, while a highly efficient formate dehydrogenase reduces CO2 cleanly to formate; down to even atmospheric concentrations of CO2 . This bio-inspired concept demonstrates that the carboxysome provides a viable blueprint for the reduction of low-concentration CO2 streams to chemicals by using all forms of dissolved carbon.
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Affiliation(s)
- Samuel J Cobb
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Azim M Dharani
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Ana Rita Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Erwin Reisner
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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13
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Nguyen ND, Pulsford SB, Hee WY, Rae BD, Rourke LM, Price GD, Long BM. Towards engineering a hybrid carboxysome. PHOTOSYNTHESIS RESEARCH 2023; 156:265-277. [PMID: 36892800 PMCID: PMC10154267 DOI: 10.1007/s11120-023-01009-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 02/17/2023] [Indexed: 05/03/2023]
Abstract
Carboxysomes are bacterial microcompartments, whose structural features enable the encapsulated Rubisco holoenzyme to operate in a high-CO2 environment. Consequently, Rubiscos housed within these compartments possess higher catalytic turnover rates relative to their plant counterparts. This particular enzymatic property has made the carboxysome, along with associated transporters, an attractive prospect to incorporate into plant chloroplasts to increase future crop yields. To date, two carboxysome types have been characterized, the α-type that has fewer shell components and the β-type that houses a faster Rubisco. While research is underway to construct a native carboxysome in planta, work investigating the internal arrangement of carboxysomes has identified conserved Rubisco amino acid residues between the two carboxysome types which could be engineered to produce a new, hybrid carboxysome. In theory, this hybrid carboxysome would benefit from the simpler α-carboxysome shell architecture while simultaneously exploiting the higher Rubisco turnover rates in β-carboxysomes. Here, we demonstrate in an Escherichia coli expression system, that the Thermosynechococcus elongatus Form IB Rubisco can be imperfectly incorporated into simplified Cyanobium α-carboxysome-like structures. While encapsulation of non-native cargo can be achieved, T. elongatus Form IB Rubisco does not interact with the Cyanobium carbonic anhydrase, a core requirement for proper carboxysome functionality. Together, these results suggest a way forward to hybrid carboxysome formation.
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Affiliation(s)
- Nghiem Dinh Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Sacha B Pulsford
- Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, The Australian National University, Building 46, Sullivan's Creek Road, Acton, ACT, 2601, Australia
| | - Wei Yi Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
| | - Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - Loraine M Rourke
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
| | - G Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia.
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia.
- Division of Plant Sciences, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Canberra, ACT, 2601, Australia.
| | - Benedict M Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Building 134, Linnaeus Way, Acton, ACT, 2601, Australia
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, 134 Linnaeus Way, Acton, ACT, 2601, Australia
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14
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Kupriyanova EV, Pronina NA, Los DA. Adapting from Low to High: An Update to CO 2-Concentrating Mechanisms of Cyanobacteria and Microalgae. PLANTS (BASEL, SWITZERLAND) 2023; 12:1569. [PMID: 37050194 PMCID: PMC10096703 DOI: 10.3390/plants12071569] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
The intracellular accumulation of inorganic carbon (Ci) by microalgae and cyanobacteria under ambient atmospheric CO2 levels was first documented in the 80s of the 20th Century. Hence, a third variety of the CO2-concentrating mechanism (CCM), acting in aquatic photoautotrophs with the C3 photosynthetic pathway, was revealed in addition to the then-known schemes of CCM, functioning in CAM and C4 higher plants. Despite the low affinity of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) of microalgae and cyanobacteria for the CO2 substrate and low CO2/O2 specificity, CCM allows them to perform efficient CO2 fixation in the reductive pentose phosphate (RPP) cycle. CCM is based on the coordinated operation of strategically located carbonic anhydrases and CO2/HCO3- uptake systems. This cooperation enables the intracellular accumulation of HCO3-, which is then employed to generate a high concentration of CO2 molecules in the vicinity of Rubisco's active centers compensating up for the shortcomings of enzyme features. CCM functions as an add-on to the RPP cycle while also acting as an important regulatory link in the interaction of dark and light reactions of photosynthesis. This review summarizes recent advances in the study of CCM molecular and cellular organization in microalgae and cyanobacteria, as well as the fundamental principles of its functioning and regulation.
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15
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Badger MR, Sharwood RE. Rubisco, the imperfect winner: it's all about the base. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:562-580. [PMID: 36412307 DOI: 10.1093/jxb/erac458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Rubisco catalysis is complex and includes an activation step through the formation of a carbamate at the conserved active site lysine residue and the formation of a highly reactive enediol that is the key to its catalytic reaction. The formation of this enediol is both the basis of its success and its Achilles' heel, creating imperfections to its catalytic efficiency. While Rubisco originally evolved in an atmosphere of high CO2, the earth's multiple oxidation events provided challenges to Rubisco through the fixation of O2 that competes with CO2 at the active site. Numerous catalytic screens across the Rubisco superfamily have identified significant variation in catalytic properties that have been linked to large and small subunit sequences. Despite this, we still have a rudimentary understanding of Rubisco's catalytic mechanism and how the evolution of kinetic properties has occurred. This review identifies the lysine base that functions both as an activator and a proton abstractor to create the enediol as a key to understanding how Rubisco may optimize its kinetic properties. The ways in which Rubisco and its partners have overcome catalytic and activation imperfections and thrived in a world of high O2, low CO2, and variable climatic regimes is remarkable.
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Affiliation(s)
- Murray R Badger
- Research School of Biology, Building 134 Linnaeus Way, Canberra ACT, 2601, Australia
| | - Robert E Sharwood
- Hawkesbury Institute for the Environment, Western Sydney University, Bourke St, Richmond, NSW, 2753, Australia
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16
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Wang H, Hayer-Hartl M. Phase Separation of Rubisco by the Folded SSUL Domains of CcmM in Beta-Carboxysome Biogenesis. Methods Mol Biol 2023; 2563:269-296. [PMID: 36227479 DOI: 10.1007/978-1-0716-2663-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Carboxysomes are large, cytosolic bodies present in all cyanobacteria and many proteobacteria that function as the sites of photosynthetic CO2 fixation by the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The carboxysome lumen is enriched with Rubisco and carbonic anhydrase (CA). The polyhedral proteinaceous shell allows the passage of HCO3- ions into the carboxysome, where they are converted to CO2 by CA. Thus, the carboxysome functions as a CO2-concentrating mechanism (CCM), enhancing the efficiency of Rubisco in CO2 fixation. In β-cyanobacteria, carboxysome biogenesis first involves the aggregation of Rubisco by CcmM, a scaffolding protein that exists in two isoforms. Both isoforms contain a minimum of three Rubisco small subunit-like (SSUL) domains, connected by flexible linkers. Multivalent interaction between these linked SSUL domains with Rubisco results in phase separation and condensate formation. Here, we use Rubisco and the short isoform of CcmM (M35) of the β-cyanobacterium Synechococcus elongatus PCC7942 to describe the methods used for in vitro analysis of the mechanism of condensate formation driven by the SSUL domains. The methods include turbidity assays, bright-field and fluorescence microscopy, as well as transmission electron microscopy (TEM) in both negative staining and cryo-conditions.
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Affiliation(s)
- Huping Wang
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- Membrane Protein Biosynthesis and Quality Control, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
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17
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Garcia A, Gaju O, Bowerman AF, Buck SA, Evans JR, Furbank RT, Gilliham M, Millar AH, Pogson BJ, Reynolds MP, Ruan Y, Taylor NL, Tyerman SD, Atkin OK. Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration. THE NEW PHYTOLOGIST 2023; 237:60-77. [PMID: 36251512 PMCID: PMC10100352 DOI: 10.1111/nph.18545] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/15/2022] [Indexed: 06/06/2023]
Abstract
The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential (Y p ) of crops is vital to address these challenges. In this review, we explore a component ofY p that has yet to be optimised - that being improvements in the efficiency with which light energy is converted into biomass (ε c ) via modifications to CO2 fixed per unit quantum of light (α), efficiency of respiratory ATP production (ε prod ) and efficiency of ATP use (ε use ). For α, targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential forε prod to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improveε use via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high-throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step-change in yield potential of globally important crops.
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Affiliation(s)
- Andres Garcia
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Oorbessy Gaju
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- College of Science, Lincoln Institute for Agri‐Food TechnologyUniversity of LincolnLincolnshireLN2 2LGUK
| | - Andrew F. Bowerman
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Sally A. Buck
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - John R. Evans
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Robert T. Furbank
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
- ARC Centre of Excellence for Translational Photosynthesis, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
| | - Matthew Gilliham
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research InstituteUniversity of AdelaideGlen OsmondSA5064Australia
| | - A. Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences & Institute of AgricultureThe University of Western AustraliaCrawleyWA6009Australia
| | - Barry J. Pogson
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Matthew P. Reynolds
- International Maize and Wheat Improvement Center (CIMMYT)Km. 45, Carretera Mexico, El BatanTexcoco56237Mexico
| | - Yong‐Ling Ruan
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
| | - Nicolas L. Taylor
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences & Institute of AgricultureThe University of Western AustraliaCrawleyWA6009Australia
| | - Stephen D. Tyerman
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research InstituteUniversity of AdelaideGlen OsmondSA5064Australia
| | - Owen K. Atkin
- ARC Centre of Excellence in Plant Energy Biology, Research School of BiologyThe Australian National UniversityCanberraACT2601Australia
- Division of Plant Sciences, Research School of BiologyAustralian National UniversityCanberraACT2601Australia
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18
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Abstract
Cyanobacteria rely on CO2-concentrating mechanisms (CCMs) to grow in today's atmosphere (0.04% CO2). These complex physiological adaptations require ≈15 genes to produce two types of protein complexes: inorganic carbon (Ci) transporters and 100+ nm carboxysome compartments that encapsulate rubisco with a carbonic anhydrase (CA) enzyme. Mutations disrupting any of these genes prohibit growth in ambient air. If any plausible ancestral form-i.e., lacking a single gene-cannot grow, how did the CCM evolve? Here, we test the hypothesis that evolution of the bacterial CCM was "catalyzed" by historically high CO2 levels that decreased over geologic time. Using an E. coli reconstitution of a bacterial CCM, we constructed strains lacking one or more CCM components and evaluated their growth across CO2 concentrations. We expected these experiments to demonstrate the importance of the carboxysome. Instead, we found that partial CCMs expressing CA or Ci uptake genes grew better than controls in intermediate CO2 levels (≈1%) and observed similar phenotypes in two autotrophic bacteria, Halothiobacillus neapolitanus and Cupriavidus necator. To understand how CA and Ci uptake improve growth, we model autotrophy as colimited by CO2 and HCO3-, as both are required to produce biomass. Our experiments and model delineated a viable trajectory for CCM evolution where decreasing atmospheric CO2 induces an HCO3- deficiency that is alleviated by acquisition of CA or Ci uptake, thereby enabling the emergence of a modern CCM. This work underscores the importance of considering physiology and environmental context when studying the evolution of biological complexity.
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19
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Mehta AK, Chakraborty S. Multiscale modelling of mixotrophic algal growth in pilot-scale photobioreactors and its application to microalgal cultivation using wastewater. ENVIRONMENTAL RESEARCH 2022; 214:113952. [PMID: 35934141 DOI: 10.1016/j.envres.2022.113952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/20/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
This multiscale model quantifies transport and reaction processes in mixotrophic microalgal growth at three characteristic length scales, namely, macro (photobioreactor), meso (algal cell), micro (organelles). The macro and the meso scale equations capture the temporal dynamics of the transport of CO2, O2, H+, organic carbon and nitrogen sources in the photobioreactor and the cell, respectively, while the micro scale quantifies the reaction rates of CO2 fixation and photorespiration in the chloroplast, and mitochondrial respiration. Our model is validated using our experiments (R2 = 0.96-0.99) on urea, CO2 (0.04-5%), and acetic acid-mediated mixotrophic cultivation of Chlorella sorokiniana for 138 h using municipal wastewater (with and without media) at 11,000 lx light in 25-liter pilot-scale bubble-column photobioreactors, which produces 0.47-2.74 g/L biomass with 22.8-29.6% lipids, while reducing the COD, ammonium, phosphate, nickel, and H+ concentrations by 65-89%. The alga assimilates the ammonium and the phosphates present in wastewater into amino acids and ATP, respectively. Our simulations quantify the autotrophic and heterotrophic components of mixotrophic biomass yield to find the optimal inlet CO2 concentration (of 3%) that synergizes autotrophic CO2 sequestration with heterotrophic assimilation of organic carbon, thereby maximizing both autotrophic and heterotrophic growths. Super-optimal levels of inlet CO2 acidify the stroma of the chloroplast, inhibit RuBisCo's enzymatic activity for CO2 fixation in the Calvin Cycle, decelerate carrier-mediated uptake of acetate, and reduce biomass yields. Our harvesting process drastically reduces the algal harvesting time to less than 29 min. This multiscale reaction-transport model provides a useful tool for further scaling up this pilot-scale technology that synergistically integrates CO2 sequestration and wastewater treatment with rapid microalgal cultivation (using municipal wastewater without autoclaving) and cost-effective harvesting.
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Affiliation(s)
- Arun Kumar Mehta
- Department of Chemical Engineering, Indian Institute of Technology, Kharagpur, 721302, India
| | - Saikat Chakraborty
- Department of Chemical Engineering, Indian Institute of Technology, Kharagpur, 721302, India; Biological Systems Engineering, Plaksha University, Mohali, 140306, India.
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20
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Adler L, Díaz-Ramos A, Mao Y, Pukacz KR, Fei C, McCormick AJ. New horizons for building pyrenoid-based CO2-concentrating mechanisms in plants to improve yields. PLANT PHYSIOLOGY 2022; 190:1609-1627. [PMID: 35961043 PMCID: PMC9614477 DOI: 10.1093/plphys/kiac373] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/06/2022] [Indexed: 05/06/2023]
Abstract
Many photosynthetic species have evolved CO2-concentrating mechanisms (CCMs) to improve the efficiency of CO2 assimilation by Rubisco and reduce the negative impacts of photorespiration. However, the majority of plants (i.e. C3 plants) lack an active CCM. Thus, engineering a functional heterologous CCM into important C3 crops, such as rice (Oryza sativa) and wheat (Triticum aestivum), has become a key strategic ambition to enhance yield potential. Here, we review recent advances in our understanding of the pyrenoid-based CCM in the model green alga Chlamydomonas reinhardtii and engineering progress in C3 plants. We also discuss recent modeling work that has provided insights into the potential advantages of Rubisco condensation within the pyrenoid and the energetic costs of the Chlamydomonas CCM, which, together, will help to better guide future engineering approaches. Key findings include the potential benefits of Rubisco condensation for carboxylation efficiency and the need for a diffusional barrier around the pyrenoid matrix. We discuss a minimal set of components for the CCM to function and that active bicarbonate import into the chloroplast stroma may not be necessary for a functional pyrenoid-based CCM in planta. Thus, the roadmap for building a pyrenoid-based CCM into plant chloroplasts to enhance the efficiency of photosynthesis now appears clearer with new challenges and opportunities.
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Affiliation(s)
| | | | - Yuwei Mao
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Krzysztof Robin Pukacz
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Chenyi Fei
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA
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21
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Huang J, Jiang Q, Yang M, Dykes GF, Weetman SL, Xin W, He HL, Liu LN. Probing the Internal pH and Permeability of a Carboxysome Shell. Biomacromolecules 2022; 23:4339-4348. [PMID: 36054822 PMCID: PMC9554877 DOI: 10.1021/acs.biomac.2c00781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The carboxysome is a protein-based nanoscale organelle
in cyanobacteria
and many proteobacteria, which encapsulates the key CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)
and carbonic anhydrase (CA) within a polyhedral protein shell. The
intrinsic self-assembly and architectural features of carboxysomes
and the semipermeability of the protein shell provide the foundation
for the accumulation of CO2 within carboxysomes and enhanced
carboxylation. Here, we develop an approach to determine the interior
pH conditions and inorganic carbon accumulation within an α-carboxysome
shell derived from a chemoautotrophic proteobacterium Halothiobacillus neapolitanus and evaluate the shell
permeability. By incorporating a pH reporter, pHluorin2, within empty
α-carboxysome shells produced in Escherichia
coli, we probe the interior pH of the protein shells
with and without CA. Our in vivo and in vitro results demonstrate a lower interior pH of α-carboxysome shells
than the cytoplasmic pH and buffer pH, as well as the modulation of
the interior pH in response to changes in external environments, indicating
the shell permeability to bicarbonate ions and protons. We further
determine the saturated HCO3– concentration
of 15 mM within α-carboxysome shells and show the CA-mediated
increase in the interior CO2 level. Uncovering the interior
physiochemical microenvironment of carboxysomes is crucial for understanding
the mechanisms underlying carboxysomal shell permeability and enhancement
of Rubisco carboxylation within carboxysomes. Such fundamental knowledge
may inform reprogramming carboxysomes to improve metabolism and recruit
foreign enzymes for enhanced catalytical performance.
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Affiliation(s)
- Jiafeng Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,School of Life Sciences, Central South University, Changsha 410017, China
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Samantha L Weetman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Wei Xin
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271000, China
| | - Hai-Lun He
- School of Life Sciences, Central South University, Changsha 410017, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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22
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Lin JY, Sri Wahyu Effendi S, Ng IS. Enhanced carbon capture and utilization (CCU) using heterologous carbonic anhydrase in Chlamydomonas reinhardtii for lutein and lipid production. BIORESOURCE TECHNOLOGY 2022; 351:127009. [PMID: 35304253 DOI: 10.1016/j.biortech.2022.127009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/11/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Chlamydomonas reinhardtii is a model microalga that has a higher growth rate and produces high levels of lutein and lipids, but biomass production is limited. Carbonic anhydrase (CA) converts atmospheric CO2 to bicarbonate which is crucial for carbon-concentrating mechanism (CCM) in microalgae and boosts cell density. Therefore, C. reinhardtii harboring the heterologous CA from Mesorhizobium loti (MlCA) and Sulfurihydrogenibium yellowstonense (SyCA) were explored to increase CO2 capture and utilization (CCU) through different culture devices. Genetically modified C. reinhardtii was able to grow from mixotrophic to autotrophic conditions. Subsequently, biomass, lutein, and lipid were maximized to OD680 of 4.56, 21.32 mg/L and 672 mg/L using photo-bioreactor (PBR) with 5% CO2. Moreover, CO2 assimilation rate was 2.748 g-CO2/g-DCW and 2.792 g-CO2/g-DCW under mixotrophic and autotrophic conditions, respectively. The biomass accumulation correlated with CA activity. In addition, the transcript levels of major genes in metabolic pathways of lutein and lipid were dramatically increased.
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Affiliation(s)
- Jia-Yi Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | | | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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23
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Fei C, Wilson AT, Mangan NM, Wingreen NS, Jonikas MC. Modelling the pyrenoid-based CO 2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops. NATURE PLANTS 2022; 8:583-595. [PMID: 35596080 PMCID: PMC9122830 DOI: 10.1038/s41477-022-01153-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 04/11/2022] [Indexed: 05/19/2023]
Abstract
Many eukaryotic photosynthetic organisms enhance their carbon uptake by supplying concentrated CO2 to the CO2-fixing enzyme Rubisco in an organelle called the pyrenoid. Ongoing efforts seek to engineer this pyrenoid-based CO2-concentrating mechanism (PCCM) into crops to increase yields. Here we develop a computational model for a PCCM on the basis of the postulated mechanism in the green alga Chlamydomonas reinhardtii. Our model recapitulates all Chlamydomonas PCCM-deficient mutant phenotypes and yields general biophysical principles underlying the PCCM. We show that an effective and energetically efficient PCCM requires a physical barrier to reduce pyrenoid CO2 leakage, as well as proper enzyme localization to reduce futile cycling between CO2 and HCO3-. Importantly, our model demonstrates the feasibility of a purely passive CO2 uptake strategy at air-level CO2, while active HCO3- uptake proves advantageous at lower CO2 levels. We propose a four-step engineering path to increase the rate of CO2 fixation in the plant chloroplast up to threefold at a theoretical cost of only 1.3 ATP per CO2 fixed, thereby offering a framework to guide the engineering of a PCCM into land plants.
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Affiliation(s)
- Chenyi Fei
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Alexandra T Wilson
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Niall M Mangan
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL, USA.
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ, USA.
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24
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Kędzior M, Garcia AK, Li M, Taton A, Adam ZR, Young JN, Kaçar B. Resurrected Rubisco suggests uniform carbon isotope signatures over geologic time. Cell Rep 2022; 39:110726. [PMID: 35476992 DOI: 10.1016/j.celrep.2022.110726] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/26/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022] Open
Abstract
The earliest geochemical indicators of microbes-and the enzymes that powered them-extend back ∼3.8 Ga on Earth. Paleobiologists often attempt to understand these indicators by assuming that the behaviors of extant microbes and enzymes are uniform with those of their predecessors. This consistency in behavior seems at odds with our understanding of the inherent variability of living systems. Here, we examine whether a uniformitarian assumption for an enzyme thought to generate carbon isotope indicators of biological activity, RuBisCO, can be corroborated by independently studying the history of changes recorded within RuBisCO's genetic sequences. We resurrected a Precambrian-age RuBisCO by engineering its ancient DNA inside a cyanobacterium genome and measured the engineered organism's fitness and carbon-isotope-discrimination profile. Results indicate that Precambrian uniformitarian assumptions may be warranted but with important caveats. Experimental studies illuminating early innovations are crucial to explore the molecular foundations of life's earliest traces.
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Affiliation(s)
- Mateusz Kędzior
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amanda K Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Meng Li
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Arnaud Taton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zachary R Adam
- NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Geosciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jodi N Young
- School of Oceanography, University of Washington, Seattle, WA 98195, USA
| | - Betül Kaçar
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; NASA Center for Early Life and Evolution, University of Wisconsin-Madison, Madison, WI 53706, USA.
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25
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Abstract
Carboxysomes are anabolic bacterial microcompartments that play an essential role in carbon fixation in cyanobacteria and some chemoautotrophs. This self-assembling organelle encapsulates the key CO2-fixing enzymes, Rubisco, and carbonic anhydrase using a polyhedral protein shell that is constructed by hundreds of shell protein paralogs. The α-carboxysome from the chemoautotroph Halothiobacillus neapolitanus serves as a model system in fundamental studies and synthetic engineering of carboxysomes. In this study, we adopted a QconCAT-based quantitative mass spectrometry approach to determine the stoichiometric composition of native α-carboxysomes from H. neapolitanus. We further performed an in-depth comparison of the protein stoichiometry of native α-carboxysomes and their recombinant counterparts heterologously generated in Escherichia coli to evaluate the structural variability and remodeling of α-carboxysomes. Our results provide insight into the molecular principles that mediate carboxysome assembly, which may aid in rational design and reprogramming of carboxysomes in new contexts for biotechnological applications. IMPORTANCE A wide range of bacteria use special protein-based organelles, termed bacterial microcompartments, to encase enzymes and reactions to increase the efficiency of biological processes. As a model bacterial microcompartment, the carboxysome contains a protein shell filled with the primary carbon fixation enzyme Rubisco. The self-assembling organelle is generated by hundreds of proteins and plays important roles in converting carbon dioxide to sugar, a process known as carbon fixation. In this study, we uncovered the exact stoichiometry of all building components and the structural plasticity of the functional α-carboxysome, using newly developed quantitative mass spectrometry together with biochemistry, electron microscopy, and enzymatic assay. The study advances our understanding of the architecture and modularity of natural carboxysomes. The knowledge learned from natural carboxysomes will suggest feasible ways to produce functional carboxysomes in other hosts, such as crop plants, with the overwhelming goal of boosting cell metabolism and crop yields.
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26
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Evolution of Phytoplankton in Relation to Their Physiological Traits. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10020194] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Defining the physiological traits that characterise phytoplankton involves comparison with related organisms in benthic habitats. Comparison of survival time in darkness under natural conditions requires more information. Gas vesicles and flagella as mechanisms of upward movement relative to surrounding water, allowing periodic vertical migration, are not confined to plankton, although buoyancy changes related to compositional changes of a large central vacuole may be restricted to plankton. Benthic microalgae have the same range of photosynthetic pigments as phytoplankton; it is not clear if there are differences in the rate of regulation and acclimation of photosynthetic machinery to variations in irradiance for phytoplankton and for microphytobenthos. There are inadequate data to determine if responses to variations in frequency or magnitude of changes in the supply of inorganic carbon, nitrogen or phosphorus differ between phytoplankton and benthic microalgae. Phagophotomixotrophy and osmophotomixotrophy occur in both phytoplankton and benthic microalgae. Further progress in identifying physiological traits specific to phytoplankton requires more experimentation on benthic microalgae that are closely related to planktonic microalgae, with attention to whether the benthic algae examined have, as far as can be determined, never been planktonic during their evolution or are derived from planktonic ancestors.
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27
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Chen T, Fang Y, Jiang Q, Dykes GF, Lin Y, Price GD, Long BM, Liu LN. Incorporation of Functional Rubisco Activases into Engineered Carboxysomes to Enhance Carbon Fixation. ACS Synth Biol 2022; 11:154-161. [PMID: 34664944 PMCID: PMC8787814 DOI: 10.1021/acssynbio.1c00311] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
The carboxysome is
a versatile paradigm of prokaryotic organelles
and is a proteinaceous self-assembling microcompartment that plays
essential roles in carbon fixation in all cyanobacteria and some chemoautotrophs.
The carboxysome encapsulates
the central CO2-fixing enzyme, ribulose-1,5-bisphosphate
carboxylase/oxygenase (Rubisco), using a polyhedral protein shell
that is selectively permeable to specific metabolites in favor of
Rubisco carboxylation. There is tremendous interest in repurposing
carboxysomes to boost carbon fixation in heterologous organisms. Here,
we develop the design and engineering of α-carboxysomes by coexpressing
the Rubisco activase components CbbQ and CbbO with α-carboxysomes
in Escherichia coli. Our results show
that CbbQ and CbbO could assemble into the reconstituted α-carboxysome
as intrinsic components. Incorporation of both CbbQ and CbbO within
the carboxysome promotes activation of Rubisco and enhances the CO2-fixation activities of recombinant carboxysomes. We also
show that the structural composition of these carboxysomes could be
modified in different expression systems, representing the plasticity
of the carboxysome architecture. In translational terms, our study
informs strategies for engineering and modulating carboxysomes in
diverse biotechnological applications.
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Affiliation(s)
- Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Fang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Gregory F. Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - G. Dean Price
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Benedict M. Long
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, Australian National University, 134 Linnaeus Way, Acton, Australian Capital Territory 2601, Australia
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, U.K
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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28
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Liu LN. Advances in the bacterial organelles for CO 2 fixation. Trends Microbiol 2021; 30:567-580. [PMID: 34802870 DOI: 10.1016/j.tim.2021.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concentration mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biology to repurpose the metabolic module in diverse applications.
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Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003 Qingdao, China.
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29
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Huffine CA, Wheeler LC, Wing B, Cameron JC. Computational modeling and evolutionary implications of biochemical reactions in bacterial microcompartments. Curr Opin Microbiol 2021; 65:15-23. [PMID: 34717259 DOI: 10.1016/j.mib.2021.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/02/2021] [Indexed: 11/19/2022]
Abstract
Bacterial microcompartments (BMCs) are protein-encapsulated compartments found across at least 23 bacterial phyla. BMCs contain a variety of metabolic processes that share the commonality of toxic or volatile intermediates, oxygen-sensitive enzymes and cofactors, or increased substrate concentration for magnified reaction rates. These compartmentalized reactions have been computationally modeled to explore the encapsulated dynamics, ask evolutionary-based questions, and develop a more systematic understanding required for the engineering of novel BMCs. Many crucial aspects of these systems remain unknown or unmeasured, such as substrate permeabilities across the protein shell, feasibility of pH gradients, and transport rates of associated substrates into the cell. This review explores existing BMC models, dominated in the literature by cyanobacterial carboxysomes, and highlights potentially important areas for exploration.
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Affiliation(s)
- Clair A Huffine
- BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA; Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA; Interdisciplinary Quantitative Biology Program (IQ Biology), BioFrontiers Institute, University of Colorado, Boulder, CO 80309, USA
| | - Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Boswell Wing
- Department of Geological Sciences, Boulder, CO 80309, USA
| | - Jeffrey C Cameron
- Department of Biochemistry, University of Colorado, Boulder, CO 80309, USA; Renewable and Sustainable Energy Institute, University of Colorado, Boulder, CO 80309, USA; National Renewable Energy Laboratory, Golden, CO 80401, USA.
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30
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Joun J, Hong ME, Sirohi R, Sim SJ. Enhanced biomass production through a repeated sequential auto-and heterotrophic culture mode in Chlorella protothecoides. BIORESOURCE TECHNOLOGY 2021; 338:125532. [PMID: 34274588 DOI: 10.1016/j.biortech.2021.125532] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 05/05/2023]
Abstract
A repeated sequential auto-and heterotrophic (RSAH) culture mode was designed to enhancebiomass ofChlorella protothecoides. Based on the result that the photosynthesis system may receive damage if the light period is more than 16 h, autotrophy was applied in the 16 h of the light cycle and mixotrophy using acetic acid and glucose in the 8 h of dark cycle. In the dark cycle, an organic carbon source was added according to the Monod equation to maintain activation of the TCA cycle and organic carbon source-to-cell conversion. When acetic acid and glucose were used as organic carbon sources, this culture method was found to be 32.3% and 12.6% higher in biomass, 2.59 and 2.67 times higher in the organic carbon source-to-cell conversion factor, and 2.17 and 2.32 times higher in ATP/ADP ratio, respectively, compared to mixotrophy. Through this new culture method, economic feasibility and carbon reduction capabilities in large-scale cultures can be achieved.
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Affiliation(s)
- Jaemin Joun
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seoungbuk-gu, Seoul 02841, Republic of Korea
| | - Min Eui Hong
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seoungbuk-gu, Seoul 02841, Republic of Korea
| | - Ranjna Sirohi
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seoungbuk-gu, Seoul 02841, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seoungbuk-gu, Seoul 02841, Republic of Korea.
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31
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Nocentini A, Supuran CT, Capasso C. An overview on the recently discovered iota-carbonic anhydrases. J Enzyme Inhib Med Chem 2021; 36:1988-1995. [PMID: 34482770 PMCID: PMC8425729 DOI: 10.1080/14756366.2021.1972995] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Carbonic anhydrases (CAs, EC 4.2.1.1) have been studied for decades and have been classified as a superfamily of enzymes which includes, up to date, eight gene families or classes indicated with the Greek letters α, β, γ, δ, ζ, η, θ, ι. This versatile enzyme superfamily is involved in multiple physiological processes, catalysing a fundamental reaction for all living organisms, the reversible hydration of carbon dioxide to bicarbonate and a proton. Recently, the ι-CA (LCIP63) from the diatom Thalassiosira pseudonana and a bacterial ι-CA (BteCAι) identified in the genome of Burkholderia territorii were characterised. The recombinant BteCAι was observed to act as an excellent catalyst for the physiologic reaction. Very recently, the discovery of a novel ι-CAs (COG4337) in the eukaryotic microalga Bigelowiella natans and the cyanobacterium Anabaena sp. PCC7120 has brought to light an unexpected feature for this ancient superfamily: this ι-CAs was catalytically active without a metal ion cofactor, unlike the previous reported ι-CAs as well as all known CAs investigated so far. This review reports recent investigations on ι-CAs obtained in these last three years, highlighting their peculiar features, and hypothesising that possibly this new CA family shows catalytic activity without the need of metal ions.
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Affiliation(s)
- Alessio Nocentini
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Firenze, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, Institute of Biosciences and Bioresources, CNR, Napoli, Italy
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32
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Rottet S, Förster B, Hee WY, Rourke LM, Price GD, Long BM. Engineered Accumulation of Bicarbonate in Plant Chloroplasts: Known Knowns and Known Unknowns. FRONTIERS IN PLANT SCIENCE 2021; 12:727118. [PMID: 34531888 PMCID: PMC8438413 DOI: 10.3389/fpls.2021.727118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/06/2021] [Indexed: 05/10/2023]
Abstract
Heterologous synthesis of a biophysical CO2-concentrating mechanism (CCM) in plant chloroplasts offers significant potential to improve the photosynthetic efficiency of C3 plants and could translate into substantial increases in crop yield. In organisms utilizing a biophysical CCM, this mechanism efficiently surrounds a high turnover rate Rubisco with elevated CO2 concentrations to maximize carboxylation rates. A critical feature of both native biophysical CCMs and one engineered into a C3 plant chloroplast is functional bicarbonate (HCO3 -) transporters and vectorial CO2-to-HCO3 - converters. Engineering strategies aim to locate these transporters and conversion systems to the C3 chloroplast, enabling elevation of HCO3 - concentrations within the chloroplast stroma. Several CCM components have been identified in proteobacteria, cyanobacteria, and microalgae as likely candidates for this approach, yet their successful functional expression in C3 plant chloroplasts remains elusive. Here, we discuss the challenges in expressing and regulating functional HCO3 - transporter, and CO2-to-HCO3 - converter candidates in chloroplast membranes as an essential step in engineering a biophysical CCM within plant chloroplasts. We highlight the broad technical and physiological concerns which must be considered in proposed engineering strategies, and present our current status of both knowledge and knowledge-gaps which will affect successful engineering outcomes.
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Affiliation(s)
- Sarah Rottet
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
| | - Britta Förster
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Wei Yih Hee
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
| | - Loraine M. Rourke
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
| | - G. Dean Price
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Benedict M. Long
- Realizing Increased Photosynthetic Efficiency (RIPE), The Australian National University, Canberra, ACT, Australia
- Australian Research Council Centre of Excellence for Translational Photosynthesis, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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33
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Abstract
Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.
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34
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Rubisco proton production can drive the elevation of CO 2 within condensates and carboxysomes. Proc Natl Acad Sci U S A 2021; 118:2014406118. [PMID: 33931502 PMCID: PMC8106323 DOI: 10.1073/pnas.2014406118] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Membraneless organelles containing the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) are a common feature of organisms utilizing CO2 concentrating mechanisms to enhance photosynthetic carbon acquisition. In cyanobacteria and proteobacteria, the Rubisco condensate is encapsulated in a proteinaceous shell, collectively termed a carboxysome, while some algae and hornworts have evolved Rubisco condensates known as pyrenoids. In both cases, CO2 fixation is enhanced compared with the free enzyme. Previous mathematical models have attributed the improved function of carboxysomes to the generation of elevated CO2 within the organelle via a colocalized carbonic anhydrase (CA) and inwardly diffusing HCO3 -, which have accumulated in the cytoplasm via dedicated transporters. Here, we present a concept in which we consider the net of two protons produced in every Rubisco carboxylase reaction. We evaluate this in a reaction-diffusion compartment model to investigate functional advantages these protons may provide Rubisco condensates and carboxysomes, prior to the evolution of HCO3 - accumulation. Our model highlights that diffusional resistance to reaction species within a condensate allows Rubisco-derived protons to drive the conversion of HCO3 - to CO2 via colocalized CA, enhancing both condensate [CO2] and Rubisco rate. Protonation of Rubisco substrate (RuBP) and product (phosphoglycerate) plays an important role in modulating internal pH and CO2 generation. Application of the model to putative evolutionary ancestors, prior to contemporary cellular HCO3 - accumulation, revealed photosynthetic enhancements along a logical sequence of advancements, via Rubisco condensation, to fully formed carboxysomes. Our model suggests that evolution of Rubisco condensation could be favored under low CO2 and low light environments.
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