1
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Li T, Chen T, Chang P, Ge X, Chriscoli V, Dykes GF, Wang Q, Liu LN. Uncovering the roles of the scaffolding protein CsoS2 in mediating the assembly and shape of the α-carboxysome shell. mBio 2024:e0135824. [PMID: 39207096 DOI: 10.1128/mbio.01358-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
Carboxysomes are proteinaceous organelles featuring icosahedral protein shells that enclose the carbon-fixing enzymes, ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco), along with carbonic anhydrase. The intrinsically disordered scaffolding protein CsoS2 plays a vital role in the construction of α-carboxysomes through bridging the shell and cargo enzymes. The N-terminal domain of CsoS2 binds Rubisco and facilitates Rubisco packaging within the α-carboxysome, whereas the C-terminal domain of CsoS2 (CsoS2-C) anchors to the shell and promotes shell assembly. However, the role of the middle region of CsoS2 (CsoS2-M) has remained elusive. Here, we conducted in-depth examinations on the function of CsoS2-M in the assembly of the α-carboxysome shell by generating a series of recombinant shell variants in the absence of cargos. Our results reveal that CsoS2-M assists CsoS2-C in the assembly of the α-carboxysome shell and plays an important role in shaping the α-carboxysome shell through enhancing the association of shell proteins on both the facet-facet interfaces and flat shell facets. Moreover, CsoS2-M is responsible for recruiting the C-terminal truncated isoform of CsoS2, CsoS2A, into α-carboxysomes, which is crucial for Rubisco encapsulation and packaging. This study not only deepens our knowledge of how the carboxysome shell is constructed and regulated but also lays the groundwork for engineering and repurposing carboxysome-based nanostructures for diverse biotechnological purposes. IMPORTANCE Carboxysomes are a paradigm of organelle-like structures in cyanobacteria and many proteobacteria. These nanoscale compartments enclose Rubisco and carbonic anhydrase within an icosahedral virus-like shell to improve CO2 fixation, playing a vital role in the global carbon cycle. Understanding how the carboxysomes are formed is not only important for basic research studies but also holds promise for repurposing carboxysomes in bioengineering applications. In this study, we focuses on a specific scaffolding protein called CsoS2, which is involved in facilitating the assembly of α-type carboxysomes. By deciphering the functions of different parts of CsoS2, especially its middle region, we provide new insights into how CsoS2 drives the stepwise assembly of the carboxysome at the molecular level. This knowledge will guide the rational design and reprogramming of carboxysome nanostructures for many biotechnological applications.
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Affiliation(s)
- Tianpei Li
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Ping Chang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Xingwu Ge
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Vincent Chriscoli
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
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2
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Li T, Chang P, Chen W, Shi Z, Xue C, Dykes GF, Huang F, Wang Q, Liu LN. Nanoengineering Carboxysome Shells for Protein Cages with Programmable Cargo Targeting. ACS NANO 2024; 18:7473-7484. [PMID: 38326220 PMCID: PMC10938918 DOI: 10.1021/acsnano.3c11559] [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: 11/20/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Protein nanocages have emerged as promising candidates for enzyme immobilization and cargo delivery in biotechnology and nanotechnology. Carboxysomes are natural proteinaceous organelles in cyanobacteria and proteobacteria and have exhibited great potential in creating versatile nanocages for a wide range of applications given their intrinsic characteristics of self-assembly, cargo encapsulation, permeability, and modularity. However, how to program intact carboxysome shells with specific docking sites for tunable and efficient cargo loading is a key question in the rational design and engineering of carboxysome-based nanostructures. Here, we generate a range of synthetically engineered nanocages with site-directed cargo loading based on an α-carboxysome shell in conjunction with SpyTag/SpyCatcher and Coiled-coil protein coupling systems. The systematic analysis demonstrates that the cargo-docking sites and capacities of the carboxysome shell-based protein nanocages could be precisely modulated by selecting specific anchoring systems and shell protein domains. Our study provides insights into the encapsulation principles of the α-carboxysome and establishes a solid foundation for the bioengineering and manipulation of nanostructures capable of capturing cargos and molecules with exceptional efficiency and programmability, thereby enabling applications in catalysis, delivery, and medicine.
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Affiliation(s)
- Tianpei Li
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Ping Chang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Weixian Chen
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Zhaoyang Shi
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Chunling Xue
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Gregory F. Dykes
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Fang Huang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Qiang Wang
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Lu-Ning Liu
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
- MOE
Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science
Center for Deep Ocean Multispheres and Earth System & College
of Marine Life Sciences, Ocean University
of China, Qingdao 266003, China
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3
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Oltrogge LM, Chen AW, Chaijarasphong T, Turnšek JB, Savage DF. α-Carboxysome Size Is Controlled by the Disordered Scaffold Protein CsoS2. Biochemistry 2024; 63:219-229. [PMID: 38085650 PMCID: PMC10795168 DOI: 10.1021/acs.biochem.3c00403] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 01/17/2024]
Abstract
Carboxysomes are protein microcompartments that function in the bacterial CO2 concentrating mechanism (CCM) to facilitate CO2 assimilation. To do so, carboxysomes assemble from thousands of constituent proteins into an icosahedral shell, which encapsulates the enzymes Rubisco and carbonic anhydrase to form structures typically > 100 nm and > 300 megadaltons. Although many of the protein interactions driving the assembly process have been determined, it remains unknown how size and composition are precisely controlled. Here, we show that the size of α-carboxysomes is controlled by the disordered scaffolding protein CsoS2. CsoS2 contains two classes of related peptide repeats that bind to the shell in a distinct fashion, and our data indicate that size is controlled by the relative number of these interactions. We propose an energetic and structural model wherein the two repeat classes bind at the junction of shell hexamers but differ in their preferences for the shell contact angles, and thus the local curvature. In total, this model suggests that a set of specific and repeated interactions between CsoS2 and shell proteins collectively achieve the large size and monodispersity of α-carboxysomes.
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Affiliation(s)
- Luke M. Oltrogge
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of California, Berkeley, California 94720, United States
| | - Allen W. Chen
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | | | - Julia B. Turnšek
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
| | - David F. Savage
- Department
of Molecular and Cell Biology, University
of California, Berkeley, California 94720, United States
- Howard
Hughes Medical Institute, University of California, Berkeley, California 94720, United States
- Innovative
Genomics Institute, University of California, Berkeley, California 94720, United States
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4
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Ang WSL, How JA, How JB, Mueller-Cajar O. The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:612-626. [PMID: 35903998 DOI: 10.1093/jxb/erac321] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme's active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid-liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid-liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure-function relationship of phase separation in biology.
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Affiliation(s)
- Warren Shou Leong Ang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Ann How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jian Boon How
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oliver Mueller-Cajar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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5
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [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: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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6
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Yang M, Wenner N, Dykes GF, Li Y, Zhu X, Sun Y, Huang F, Hinton JCD, Liu LN. Biogenesis of a bacterial metabolosome for propanediol utilization. Nat Commun 2022; 13:2920. [PMID: 35614058 PMCID: PMC9132943 DOI: 10.1038/s41467-022-30608-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial metabolosomes are a family of protein organelles in bacteria. Elucidating how thousands of proteins self-assemble to form functional metabolosomes is essential for understanding their significance in cellular metabolism and pathogenesis. Here we investigate the de novo biogenesis of propanediol-utilization (Pdu) metabolosomes and characterize the roles of the key constituents in generation and intracellular positioning of functional metabolosomes. Our results demonstrate that the Pdu metabolosome undertakes both "Shell first" and "Cargo first" assembly pathways, unlike the β-carboxysome structural analog which only involves the "Cargo first" strategy. Shell and cargo assemblies occur independently at the cell poles. The internal cargo core is formed through the ordered assembly of multiple enzyme complexes, and exhibits liquid-like properties within the metabolosome architecture. Our findings provide mechanistic insight into the molecular principles driving bacterial metabolosome assembly and expand our understanding of liquid-like organelle biogenesis.
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Affiliation(s)
- Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, 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
| | - Yan Li
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Xiaojun Zhu
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Fang Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - 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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7
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Sutter M, Kerfeld CA, Scott KM. Atypical Carboxysome Loci: JEEPs or Junk? Front Microbiol 2022; 13:872708. [PMID: 35668770 PMCID: PMC9164163 DOI: 10.3389/fmicb.2022.872708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Carboxysomes, responsible for a substantial fraction of CO2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria, primarily from the phyla Proteobacteria and Cyanobacteria. Carboxysomes facilitate CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO2 concentration is variable or low, or O2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO2 concentrating mechanism, in which cells accumulate HCO3 - in the cytoplasm via active transport, HCO3 - enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO3 - to CO2, which RubisCO fixes. Two forms of carboxysomes have been described: α-carboxysomes and β-carboxysomes, which arose independently from ancestral microcompartments. The α-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and α-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some α-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysome-related genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts.
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Affiliation(s)
| | | | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, FL, United States
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8
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Abstract
Carbon dioxide is a major greenhouse gas, and its fixation and transformation are receiving increasing attention. Biofixation of CO2 is an eco–friendly and efficient way to reduce CO2, and six natural CO2 fixation pathways have been identified in microorganisms and plants. In this review, the six pathways along with the most recent identified variant pathway were firstly comparatively characterized. The key metabolic process and enzymes of the CO2 fixation pathways were also summarized. Next, the enzymes of Rubiscos, biotin-dependent carboxylases, CO dehydrogenase/acetyl-CoA synthase, and 2-oxoacid:ferredoxin oxidoreductases, for transforming inorganic carbon (CO2, CO, and bicarbonate) to organic chemicals, were specially analyzed. Then, the factors including enzyme properties, CO2 concentrating, energy, and reducing power requirements that affect the efficiency of CO2 fixation were discussed. Recent progress in improving CO2 fixation through enzyme and metabolic engineering was then summarized. The artificial CO2 fixation pathways with thermodynamical and/or energetical advantages or benefits and their applications in biosynthesis were included as well. The challenges and prospects of CO2 biofixation and conversion are discussed.
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9
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Gavrilov SN, Potapov EG, Prokof’eva MI, Klyukina AA, Merkel AY, Maslov AA, Zavarzina DG. Diversity of Novel Uncultured Prokaryotes in Microbial Communities of the Yessentukskoye Underground Mineral Water Deposit. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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10
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Melnicki MR, Sutter M, Kerfeld CA. Evolutionary relationships among shell proteins of carboxysomes and metabolosomes. Curr Opin Microbiol 2021; 63:1-9. [PMID: 34098411 PMCID: PMC8525121 DOI: 10.1016/j.mib.2021.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/16/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
Bacterial microcompartments (BMCs) are self-assembling prokaryotic organelles which encapsulate enzymes within a polyhedral protein shell. The shells are comprised of only two structural modules, distinct domains that form pentagonal and hexagonal building blocks, which occupy the vertices and facets, respectively. As all BMC loci encode at least one hexamer-forming and one pentamer-forming protein, the evolutionary history of BMCs can be interrogated from the perspective of their shells. Here, we discuss how structures of intact shells and detailed phylogenies of their building blocks from a recent phylogenomic survey distinguish families of these domains and reveal clade-specific structural features. These features suggest distinct functional roles that recur across diverse BMCs. For example, it is clear that carboxysomes independently arose twice from metabolosomes, yet the principles of shell assembly are remarkably conserved.
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Affiliation(s)
- Matthew R Melnicki
- Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Markus Sutter
- Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology Division and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Cheryl A Kerfeld
- Michigan State University-U.S. Department of Energy (MSU-DOE) Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology Division and Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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11
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Borden JS, Savage DF. New discoveries expand possibilities for carboxysome engineering. Curr Opin Microbiol 2021; 61:58-66. [PMID: 33798818 DOI: 10.1016/j.mib.2021.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/06/2021] [Accepted: 03/11/2021] [Indexed: 12/19/2022]
Abstract
Carboxysomes are CO2-fixing protein compartments present in all cyanobacteria and some proteobacteria. These structures are attractive candidates for carbon assimilation bioengineering because they concentrate carbon, allowing the fixation reaction to occur near its maximum rate, and because they self-assemble in diverse organisms with a set of standard biological parts. Recent discoveries have expanded our understanding of how the carboxysome assembles, distributes itself, and sustains its metabolism. These studies have already led to substantial advances in engineering the carboxysome and carbon concentrating mechanism into recombinant organisms, with an eye towards establishing the system in industrial microbes and plants. Future studies may also consider the potential of in vitro carboxysomes for both discovery and applied science.
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Affiliation(s)
- Julia S Borden
- Department of Molecular & Cellular Biology, UC Berkeley, Berkeley, CA 94720, USA
| | - David F Savage
- Department of Molecular & Cellular Biology, UC Berkeley, Berkeley, CA 94720, USA.
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12
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Panich J, Fong B, Singer SW. Metabolic Engineering of Cupriavidus necator H16 for Sustainable Biofuels from CO 2. Trends Biotechnol 2021; 39:412-424. [PMID: 33518389 DOI: 10.1016/j.tibtech.2021.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/05/2021] [Accepted: 01/06/2021] [Indexed: 02/08/2023]
Abstract
Decelerating global warming is one of the predominant challenges of our time and will require conversion of CO2 to usable products and commodity chemicals. Of particular interest is the production of fuels, because the transportation sector is a major source of CO2 emissions. Here, we review recent technological advances in metabolic engineering of the hydrogen-oxidizing bacterium Cupriavidus necator H16, a chemolithotroph that naturally consumes CO2 to generate biomass. We discuss recent successes in biofuel production using this organism, and the implementation of electrolysis/artificial photosynthesis approaches that enable growth of C. necator using renewable electricity and CO2. Last, we discuss prospects of improving the nonoptimal growth of C. necator in ambient concentrations of CO2.
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Affiliation(s)
- Justin Panich
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Bonnie Fong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven W Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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13
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Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production. Nat Commun 2020; 11:5448. [PMID: 33116131 PMCID: PMC7595155 DOI: 10.1038/s41467-020-19280-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/07/2020] [Indexed: 11/30/2022] Open
Abstract
Compartmentalization is a ubiquitous building principle in cells, which permits segregation of biological elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diameter) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the production of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen production of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions. The extreme oxygen sensitive character of hydrogenases is a longstanding issue for hydrogen production in bacteria. Here, the authors build carboxysome shells in E. coli and incorporate catalytically active hydrogenases and functional partners within the empty shell for the production of hydrogen.
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14
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Perazzoli S, de Santana Neto JP, Soares HM. Anoxic-biocathode microbial desalination cell as a new approach for wastewater remediation and clean water production. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2020; 81:550-563. [PMID: 32385209 DOI: 10.2166/wst.2020.134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bioelectrochemical systems are emerging as a promising and friendly alternative to convert the energy stored in wastewater directly into electricity by microorganisms and utilize it in situ to drive desalination. To better understand such processes, we propose the development of an anoxic biocathode microbial desalination Cell for the conversion of carbon- and nitrogen-rich wastewaters into bioenergy and to perform salt removal. Our results demonstrate a power output of 0.425 W m-3 with desalination, organic matter removal and nitrate conversion efficiencies of 43.69, 99.85 and 92.11% respectively. Microbiological analysis revealed Proteobacteria as the dominant phylum in the anode (88.45%) and biocathode (97.13%). While a relatively higher bacterial abundance was developed in the anode chamber, the biocathode showed a greater variety of microorganisms, with a predominance of Paracoccus (73.2%), which are related to the denitrification process. These findings are promising and provide new opportunities for the development and application of this technology in the field of wastewater treatment to produce cleaner water and conserve natural resources.
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Affiliation(s)
- Simone Perazzoli
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, 88034-001 Florianópolis, SC, Brazil E-mail:
| | - José Pedro de Santana Neto
- Department of Mechanical Engineering, Federal University of Santa Catarina, 88034-001 Florianópolis, SC, Brazil
| | - Hugo M Soares
- Department of Chemical and Food Engineering, Federal University of Santa Catarina, 88034-001 Florianópolis, SC, Brazil E-mail:
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15
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Sun Y, Wollman AJM, Huang F, Leake MC, Liu LN. Single-Organelle Quantification Reveals Stoichiometric and Structural Variability of Carboxysomes Dependent on the Environment. THE PLANT CELL 2019; 31:1648-1664. [PMID: 31048338 PMCID: PMC6635877 DOI: 10.1105/tpc.18.00787] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 05/02/2019] [Indexed: 05/25/2023]
Abstract
The carboxysome is a complex, proteinaceous organelle that plays essential roles in carbon assimilation in cyanobacteria and chemoautotrophs. It comprises hundreds of protein homologs that self-assemble in space to form an icosahedral structure. Despite its significance in enhancing CO2 fixation and potentials in bioengineering applications, the formation of carboxysomes and their structural composition, stoichiometry, and adaptation to cope with environmental changes remain unclear. Here we use live-cell single-molecule fluorescence microscopy, coupled with confocal and electron microscopy, to decipher the absolute protein stoichiometry and organizational variability of single β-carboxysomes in the model cyanobacterium Synechococcus elongatus PCC7942. We determine the physiological abundance of individual building blocks within the icosahedral carboxysome. We further find that the protein stoichiometry, diameter, localization, and mobility patterns of carboxysomes in cells depend sensitively on the microenvironmental levels of CO2 and light intensity during cell growth, revealing cellular strategies of dynamic regulation. These findings, also applicable to other bacterial microcompartments and macromolecular self-assembling systems, advance our knowledge of the principles that mediate carboxysome formation and structural modulation. It will empower rational design and construction of entire functional metabolic factories in heterologous organisms, for example crop plants, to boost photosynthesis and agricultural productivity.
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Affiliation(s)
- Yaqi Sun
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Adam J M Wollman
- Biological Physical Sciences Institute, Departments of Physics and Biology, University of York, YO10 5DD, United Kingdom
| | - Fang Huang
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Mark C Leake
- Biological Physical Sciences Institute, Departments of Physics and Biology, University of York, YO10 5DD, United Kingdom
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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16
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de Ruiter MV, Klem R, Luque D, Cornelissen JJLM, Castón JR. Structural nanotechnology: three-dimensional cryo-EM and its use in the development of nanoplatforms for in vitro catalysis. NANOSCALE 2019; 11:4130-4146. [PMID: 30793729 DOI: 10.1039/c8nr09204d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The organization of enzymes into different subcellular compartments is essential for correct cell function. Protein-based cages are a relatively recently discovered subclass of structurally dynamic cellular compartments that can be mimicked in the laboratory to encapsulate enzymes. These synthetic structures can then be used to improve our understanding of natural protein-based cages, or as nanoreactors in industrial catalysis, metabolic engineering, and medicine. Since the function of natural protein-based cages is related to their three-dimensional structure, it is important to determine this at the highest possible resolution if viable nanoreactors are to be engineered. Cryo-electron microscopy (cryo-EM) is ideal for undertaking such analyses within a feasible time frame and at near-native conditions. This review describes how three-dimensional cryo-EM is used in this field and discusses its advantages. An overview is also given of the nanoreactors produced so far, their structure, function, and applications.
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Affiliation(s)
- Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands.
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17
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Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W. Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 2018; 430:4156-4167. [PMID: 30138616 DOI: 10.1016/j.jmb.2018.08.013.visualizing] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/29/2018] [Accepted: 08/13/2018] [Indexed: 05/19/2023]
Abstract
Cyanobacteria are photosynthetic organisms responsible for ~25% of the organic carbon fixation on earth. A key step in carbon fixation is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme in the biosphere. Applying Zernike phase-contrast electron cryo-tomography and automated annotation, we identified individual RuBisCO molecules and their assembly intermediates leading to the formation of carboxysomes inside Syn5 cyanophage infected cyanobacteria Synechococcus sp. WH8109 cells. Surprisingly, more RuBisCO molecules were found to be present as cytosolic free-standing complexes or clusters than as packaged assemblies inside carboxysomes. Cytosolic RuBisCO clusters and partially assembled carboxysomes identified in the cell tomograms support a concurrent assembly model involving both the protein shell and the enclosed RuBisCO. In mature carboxysomes, RuBisCO is neither randomly nor strictly icosahedrally packed within protein shells of variable sizes. A time-averaged molecular dynamics simulation showed a semi-liquid probability distribution of the RuBisCO in carboxysomes and correlated well with carboxysome subtomogram averages. Our structural observations reveal the various stages of RuBisCO assemblies, which could be important for understanding cellular function.
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Affiliation(s)
- Wei Dai
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Muyuan Chen
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Myers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven J Ludtke
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA; Departments of Bioengineering and of Microbiology and Immunoplogy, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
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18
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Jäger VD, Lamm R, Kloß R, Kaganovitch E, Grünberger A, Pohl M, Büchs J, Jaeger KE, Krauss U. A Synthetic Reaction Cascade Implemented by Colocalization of Two Proteins within Catalytically Active Inclusion Bodies. ACS Synth Biol 2018; 7:2282-2295. [PMID: 30053372 DOI: 10.1021/acssynbio.8b00274] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In nature, enzymatic reaction cascades, i.e., realized in metabolic networks, operate with unprecedented efficacy, with the reactions often being spatially and temporally orchestrated. The principle of "learning from nature" has in recent years inspired the setup of synthetic reaction cascades combining biocatalytic reaction steps to artificial cascades. Hereby, the spatial organization of multiple enzymes, e.g., by coimmobilization, remains a challenging task, as currently no generic principles are available that work for every enzyme. We here present a tunable, genetically programmed coimmobilization strategy that relies on the fusion of a coiled-coil domain as aggregation inducing-tag, resulting in the formation of catalytically active inclusion body coimmobilizates (Co-CatIBs). Coexpression and coimmobilization was proven using two fluorescent proteins, and the strategy was subsequently extended to two enzymes, which enabled the realization of an integrated enzymatic two-step cascade for the production of (1 R,2 R)-1-phenylpropane-1,2-diol (PPD), a precursor of the calicum channel blocker diltiazem. In particular, the easy production and preparation of Co-CatIBs, readily yielding a biologically produced enzyme immobilizate renders the here presented strategy an interesting alternative to existing cascade immobilization techniques.
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Affiliation(s)
- Vera D. Jäger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Robin Lamm
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, D-52074 Aachen, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ramona Kloß
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Eugen Kaganovitch
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Alexander Grünberger
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Multiscale Bioengineering group, Bielefeld University, D-33615 Bielefeld, Germany
| | - Martina Pohl
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Jochen Büchs
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, D-52074 Aachen, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Ulrich Krauss
- Institut für Molekulare Enzymtechnologie, Heinrich-Heine-Universität Düsseldorf, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
- Bioeconomy Science Center (BioSc), Forschungszentrum Jülich, D-52425 Jülich, Germany
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19
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Dai W, Chen M, Myers C, Ludtke SJ, Pettitt BM, King JA, Schmid MF, Chiu W. Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography. J Mol Biol 2018; 430:4156-4167. [PMID: 30138616 DOI: 10.1016/j.jmb.2018.08.013] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 07/29/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022]
Abstract
Cyanobacteria are photosynthetic organisms responsible for ~25% of the organic carbon fixation on earth. A key step in carbon fixation is catalyzed by ribulose bisphosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme in the biosphere. Applying Zernike phase-contrast electron cryo-tomography and automated annotation, we identified individual RuBisCO molecules and their assembly intermediates leading to the formation of carboxysomes inside Syn5 cyanophage infected cyanobacteria Synechococcus sp. WH8109 cells. Surprisingly, more RuBisCO molecules were found to be present as cytosolic free-standing complexes or clusters than as packaged assemblies inside carboxysomes. Cytosolic RuBisCO clusters and partially assembled carboxysomes identified in the cell tomograms support a concurrent assembly model involving both the protein shell and the enclosed RuBisCO. In mature carboxysomes, RuBisCO is neither randomly nor strictly icosahedrally packed within protein shells of variable sizes. A time-averaged molecular dynamics simulation showed a semi-liquid probability distribution of the RuBisCO in carboxysomes and correlated well with carboxysome subtomogram averages. Our structural observations reveal the various stages of RuBisCO assemblies, which could be important for understanding cellular function.
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Affiliation(s)
- Wei Dai
- Department of Cell Biology and Neuroscience & Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA.
| | - Muyuan Chen
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Myers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven J Ludtke
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B Montgomery Pettitt
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jonathan A King
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA; Departments of Bioengineering and of Microbiology and Immunoplogy, James H. Clark Center, Stanford University, Stanford, CA 94305, USA.
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20
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Qiu XY, Xie SS, Min L, Wu XM, Zhu LY, Zhu L. Spatial organization of enzymes to enhance synthetic pathways in microbial chassis: a systematic review. Microb Cell Fact 2018; 17:120. [PMID: 30064437 PMCID: PMC6066912 DOI: 10.1186/s12934-018-0965-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/19/2018] [Indexed: 01/29/2023] Open
Abstract
For years, microbes have been widely applied as chassis in the construction of synthetic metabolic pathways. However, the lack of in vivo enzyme clustering of heterologous metabolic pathways in these organisms often results in low local concentrations of enzymes and substrates, leading to a low productive efficacy. In recent years, multiple methods have been applied to the construction of small metabolic clusters by spatial organization of heterologous metabolic enzymes. These methods mainly focused on using engineered molecules to bring the enzymes into close proximity via different interaction mechanisms among proteins and nucleotides and have been applied in various heterologous pathways with different degrees of success while facing numerous challenges. In this paper, we mainly reviewed some of those notable advances in designing and creating approaches to achieve spatial organization using different intermolecular interactions. Current challenges and future aspects in the further application of such approaches are also discussed in this paper.
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Affiliation(s)
- Xin-Yuan Qiu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Si-Si Xie
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Lu Min
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Xiao-Min Wu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China
| | - Lv-Yun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China.
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Liberal Arts and Sciences, National University of Defense Technology, Changsha, 410073, Hunan, China.
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21
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Abstract
Cyanobacteria sequester photosynthetic enzymes into microcompartments which facilitate the conversion of carbon dioxide into sugars. Geometric similarities between these structures and self-assembling viral capsids have inspired models that posit microcompartments as stable equilibrium arrangements of the constituent proteins. Here we describe a different mechanism for microcompartment assembly, one that is fundamentally nonequilibrium and yet highly reliable. This pathway is revealed by simulations of a molecular model resolving the size and shape of a cargo droplet and the extent and topography of an elastic shell. The resulting metastable microcompartment structures closely resemble those of carboxysomes, with a narrow size distribution and faceted shells. The essence of their assembly dynamics can be understood from a simpler mathematical model that combines elements of classical nucleation theory with continuum elasticity. These results highlight important control variables for achieving nanoscale encapsulation in general and for modulating the size and shape of carboxysomes in particular.
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22
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Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.
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Affiliation(s)
- Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Clement Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jan Zarzycki
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Fei Cai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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23
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Scott KM, Williams J, Porter CMB, Russel S, Harmer TL, Paul JH, Antonen KM, Bridges MK, Camper GJ, Campla CK, Casella LG, Chase E, Conrad JW, Cruz MC, Dunlap DS, Duran L, Fahsbender EM, Goldsmith DB, Keeley RF, Kondoff MR, Kussy BI, Lane MK, Lawler S, Leigh BA, Lewis C, Lostal LM, Marking D, Mancera PA, McClenthan EC, McIntyre EA, Mine JA, Modi S, Moore BD, Morgan WA, Nelson KM, Nguyen KN, Ogburn N, Parrino DG, Pedapudi AD, Pelham RP, Preece AM, Rampersad EA, Richardson JC, Rodgers CM, Schaffer BL, Sheridan NE, Solone MR, Staley ZR, Tabuchi M, Waide RJ, Wanjugi PW, Young S, Clum A, Daum C, Huntemann M, Ivanova N, Kyrpides N, Mikhailova N, Palaniappan K, Pillay M, Reddy TBK, Shapiro N, Stamatis D, Varghese N, Woyke T, Boden R, Freyermuth SK, Kerfeld CA. Genomes of ubiquitous marine and hypersaline Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira spp. encode a diversity of mechanisms to sustain chemolithoautotrophy in heterogeneous environments. Environ Microbiol 2018. [PMID: 29521452 DOI: 10.1111/1462-2920.14090] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemolithoautotrophic bacteria from the genera Hydrogenovibrio, Thiomicrorhabdus and Thiomicrospira are common, sometimes dominant, isolates from sulfidic habitats including hydrothermal vents, soda and salt lakes and marine sediments. Their genome sequences confirm their membership in a deeply branching clade of the Gammaproteobacteria. Several adaptations to heterogeneous habitats are apparent. Their genomes include large numbers of genes for sensing and responding to their environment (EAL- and GGDEF-domain proteins and methyl-accepting chemotaxis proteins) despite their small sizes (2.1-3.1 Mbp). An array of sulfur-oxidizing complexes are encoded, likely to facilitate these organisms' use of multiple forms of reduced sulfur as electron donors. Hydrogenase genes are present in some taxa, including group 1d and 2b hydrogenases in Hydrogenovibrio marinus and H. thermophilus MA2-6, acquired via horizontal gene transfer. In addition to high-affinity cbb3 cytochrome c oxidase, some also encode cytochrome bd-type quinol oxidase or ba3 -type cytochrome c oxidase, which could facilitate growth under different oxygen tensions, or maintain redox balance. Carboxysome operons are present in most, with genes downstream encoding transporters from four evolutionarily distinct families, which may act with the carboxysomes to form CO2 concentrating mechanisms. These adaptations to habitat variability likely contribute to the cosmopolitan distribution of these organisms.
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Affiliation(s)
- Kathleen M Scott
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - John Williams
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Cody M B Porter
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Sydney Russel
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Tara L Harmer
- Biology Program, Stockton University, Galloway, NJ, USA
| | - John H Paul
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kirsten M Antonen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Megan K Bridges
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Gary J Camper
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christie K Campla
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Leila G Casella
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Eva Chase
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - James W Conrad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Mercedez C Cruz
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Darren S Dunlap
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Laura Duran
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth M Fahsbender
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Dawn B Goldsmith
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ryan F Keeley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Matthew R Kondoff
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Breanna I Kussy
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Marannda K Lane
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Stephanie Lawler
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittany A Leigh
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Courtney Lewis
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Lygia M Lostal
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Devon Marking
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Paola A Mancera
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Evan C McClenthan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Emily A McIntyre
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jessica A Mine
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Swapnil Modi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brittney D Moore
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - William A Morgan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kaleigh M Nelson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Kimmy N Nguyen
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nicholas Ogburn
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - David G Parrino
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Anangamanjari D Pedapudi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Rebecca P Pelham
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Amanda M Preece
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Elizabeth A Rampersad
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Jason C Richardson
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Christina M Rodgers
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Brent L Schaffer
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Nancy E Sheridan
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Michael R Solone
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Zachery R Staley
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Maki Tabuchi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Ramond J Waide
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Pauline W Wanjugi
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Suzanne Young
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL, 33620, USA
| | - Alicia Clum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Chris Daum
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | - Manoj Pillay
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Nicole Shapiro
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | - Neha Varghese
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Rich Boden
- School of Biological & Marine Sciences, University of Plymouth, Drake Circus, Plymouth, UK.,Sustainable Earth Institute, University of Plymouth, Drake Circus, Plymouth, UK
| | | | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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24
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Chaijarasphong T, Savage DF. Sequestered: Design and Construction of Synthetic Organelles. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Thawatchai Chaijarasphong
- Mahidol University; Faculty of Science, Department of Biotechnology; Rama VI Rd. Bangkok 10400 Thailand
| | - David F. Savage
- University of California; Department of Molecular and Cell Biology; 2151 Berkeley Way, Berkeley CA 94720 USA
- University of California; Department of Chemistry; 2151 Berkeley Way, Berkeley CA 94720 USA
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25
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Scott K. Spotlight on… Kathleen Scott. FEMS Microbiol Lett 2018. [PMID: 29514289 DOI: 10.1093/femsle/fny022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kathleen Scott
- Department of Integrative Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620-9951, USA
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26
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Fang Y, Huang F, Faulkner M, Jiang Q, Dykes GF, Yang M, Liu LN. Engineering and Modulating Functional Cyanobacterial CO 2-Fixing Organelles. FRONTIERS IN PLANT SCIENCE 2018; 9:739. [PMID: 29922315 PMCID: PMC5996877 DOI: 10.3389/fpls.2018.00739] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/15/2018] [Indexed: 05/12/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles widespread among bacterial phyla and provide a means for compartmentalizing specific metabolic pathways. They sequester catalytic enzymes from the cytoplasm, using an icosahedral proteinaceous shell with selective permeability to metabolic molecules and substrates, to enhance metabolic efficiency. Carboxysomes were the first BMCs discovered and their unprecedented capacity of CO2 fixation allows cyanobacteria to make a significant contribution to global carbon fixation. There is an increasing interest in utilizing synthetic biology to construct synthetic carboxysomes in new hosts, i.e., higher plants, to enhance carbon fixation and productivity. Here, we report the construction of a synthetic operon of the β-carboxysome from the cyanobacterium Synechococcus elongatus PCC7942 to generate functional β-carboxysome-like structures in Escherichia coli. The protein expression, structure, assembly, and activity of synthetic β-carboxysomes were characterized in depth using confocal, electron and atomic force microscopy, proteomics, immunoblot analysis, and enzymatic assays. Furthermore, we examined the in vivo interchangeability of β-carboxysome building blocks with other BMC components. To our knowledge, this is the first production of functional β-carboxysome-like structures in heterologous organisms. It provides important information for the engineering of fully functional carboxysomes and CO2-fixing modules in higher plants. The study strengthens our synthetic biology toolbox for generating BMC-based organelles with tunable activities and new scaffolding biomaterials for metabolic improvement and molecule delivery.
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27
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Garcia-Alles LF, Lesniewska E, Root K, Aubry N, Pocholle N, Mendoza CI, Bourillot E, Barylyuk K, Pompon D, Zenobi R, Reguera D, Truan G. Spontaneous non-canonical assembly of CcmK hexameric components from β-carboxysome shells of cyanobacteria. PLoS One 2017; 12:e0185109. [PMID: 28934279 PMCID: PMC5608322 DOI: 10.1371/journal.pone.0185109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/06/2017] [Indexed: 02/07/2023] Open
Abstract
CcmK proteins are major constituents of icosahedral shells of β-carboxysomes, a bacterial microcompartment that plays a key role for CO2 fixation in nature. Supported by the characterization of bidimensional (2D) layers of packed CcmK hexamers in crystal and electron microscopy structures, CcmK are assumed to be the major components of icosahedral flat facets. Here, we reassessed the validity of this model by studying CcmK isoforms from Synechocystis sp. PCC6803. Native mass spectrometry studies confirmed that CcmK are hexamers in solution. Interestingly, potential pre-assembled intermediates were also detected with CcmK2. Atomic-force microscopy (AFM) imaging under quasi-physiological conditions confirmed the formation of canonical flat sheets with CcmK4. Conversely, CcmK2 formed both canonical and striped-patterned patches, while CcmK1 assembled into remarkable supra-hexameric curved honeycomb-like mosaics. Mutational studies ascribed the propensity of CcmK1 to form round assemblies to a combination of two features shared by at least one CcmK isoform in most β-cyanobacteria: a displacement of an α helical portion towards the hexamer edge, where a potential phosphate binding funnel forms between packed hexamers, and the presence of a short C-terminal extension in CcmK1. All-atom molecular dynamics supported a contribution of phosphate molecules sandwiched between hexamers to bend CcmK1 assemblies. Formation of supra-hexameric curved structures could be reproduced in coarse-grained simulations, provided that adhesion forces to the support were weak. Apart from uncovering unprecedented CcmK self-assembly features, our data suggest the possibility that transitions between curved and flat assemblies, following cargo maturation, could be important for the biogenesis of β-carboxysomes, possibly also of other BMC.
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Affiliation(s)
- Luis F. Garcia-Alles
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
- * E-mail: (LFGA); (GT)
| | - Eric Lesniewska
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Nathalie Aubry
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
| | - Nicolas Pocholle
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Carlos I. Mendoza
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Cd Mx, México
| | - Eric Bourillot
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Denis Pompon
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - David Reguera
- Departament de Física de la Matèria Condensada, Universitat de Barcelona, Barcelona, Spain
| | - Gilles Truan
- LISBP, CNRS, INRA, INSA, University of Toulouse, Toulouse, France
- * E-mail: (LFGA); (GT)
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28
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Baumgart M, Huber I, Abdollahzadeh I, Gensch T, Frunzke J. Heterologous expression of the Halothiobacillus neapolitanus carboxysomal gene cluster in Corynebacterium glutamicum. J Biotechnol 2017; 258:126-135. [DOI: 10.1016/j.jbiotec.2017.03.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/16/2017] [Accepted: 03/18/2017] [Indexed: 12/20/2022]
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29
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Turmo A, Gonzalez-Esquer CR, Kerfeld CA. Carboxysomes: metabolic modules for CO2 fixation. FEMS Microbiol Lett 2017; 364:4082729. [DOI: 10.1093/femsle/fnx176] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/12/2017] [Indexed: 11/13/2022] Open
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30
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Faulkner M, Rodriguez-Ramos J, Dykes GF, Owen SV, Casella S, Simpson DM, Beynon RJ, Liu LN. Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes. NANOSCALE 2017; 9:10662-10673. [PMID: 28616951 PMCID: PMC5708340 DOI: 10.1039/c7nr02524f] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Carboxysomes are proteinaceous organelles that play essential roles in enhancing carbon fixation in cyanobacteria and some proteobacteria. These self-assembling organelles encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase using a protein shell structurally resembling an icosahedral viral capsid. The protein shell serves as a physical barrier to protect enzymes from the cytosol and a selectively permeable membrane to mediate transport of enzyme substrates and products. The structural and mechanical nature of native carboxysomes remain unclear. Here, we isolate functional β-carboxysomes from the cyanobacterium Synechococcus elongatus PCC7942 and perform the first characterization of the macromolecular architecture and inherent physical mechanics of single β-carboxysomes using electron microscopy, atomic force microscopy (AFM) and proteomics. Our results illustrate that the intact β-carboxysome comprises three structural domains, a single-layered icosahedral shell, an inner layer and paracrystalline arrays of interior Rubisco. We also observe the protein organization of the shell and partial β-carboxysomes that likely serve as the β-carboxysome assembly intermediates. Furthermore, the topography and intrinsic mechanics of functional β-carboxysomes are determined in native conditions using AFM and AFM-based nanoindentation, revealing the flexible organization and soft mechanical properties of β-carboxysomes compared to rigid viruses. Our study provides new insights into the natural characteristics of β-carboxysome organization and nanomechanics, which can be extended to diverse bacterial microcompartments and are important considerations for the design and engineering of functional carboxysomes in other organisms to supercharge photosynthesis. It offers an approach for inspecting the structural and mechanical features of synthetic metabolic organelles and protein scaffolds in bioengineering.
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Affiliation(s)
- Matthew Faulkner
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | | | - Gregory F Dykes
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Siân V Owen
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Selene Casella
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Deborah M Simpson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Robert J Beynon
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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31
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Rae BD, Long BM, Förster B, Nguyen ND, Velanis CN, Atkinson N, Hee WY, Mukherjee B, Price GD, McCormick AJ. Progress and challenges of engineering a biophysical CO2-concentrating mechanism into higher plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:3717-3737. [PMID: 28444330 DOI: 10.1093/jxb/erx133] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Growth and productivity in important crop plants is limited by the inefficiencies of the C3 photosynthetic pathway. Introducing CO2-concentrating mechanisms (CCMs) into C3 plants could overcome these limitations and lead to increased yields. Many unicellular microautotrophs, such as cyanobacteria and green algae, possess highly efficient biophysical CCMs that increase CO2 concentrations around the primary carboxylase enzyme, Rubisco, to enhance CO2 assimilation rates. Algal and cyanobacterial CCMs utilize distinct molecular components, but share several functional commonalities. Here we outline the recent progress and current challenges of engineering biophysical CCMs into C3 plants. We review the predicted requirements for a functional biophysical CCM based on current knowledge of cyanobacterial and algal CCMs, the molecular engineering tools and research pipelines required to translate our theoretical knowledge into practice, and the current challenges to achieving these goals.
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Affiliation(s)
- Benjamin D Rae
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Benedict M Long
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Britta Förster
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Nghiem D Nguyen
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Christos N Velanis
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nicky Atkinson
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Wei Yih Hee
- Research School of Biology, The Australian National University, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Bratati Mukherjee
- Australian Research Council Centre of Excellence for Translational Photosynthesis
- Research School of Biology, The Australian National University, 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, 134 Linnaeus Way, Acton ACT 2601, Australia
| | - Alistair J McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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32
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Bernadotte A, Semenova V, Musial VAM, Kasprzykowska A, Zubarev RA. Self-assembly of Deinococcus radiodurans supports nanocell scenario of life origin. Discoveries (Craiova) 2017; 5:e72. [PMID: 32309590 PMCID: PMC6941539 DOI: 10.15190/d.2017.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In many origin-of-life scenarios, first a kit of elements and simple compounds emerges, then a primitive membrane and then a nanocell with a minimal genome is self-assembled, which then proceeds to multiply by copying itself while mutating. Testing this scenario, we selected Deinococcus Radiodurans known for its exceptional self-repair properties as a model system, separated its bacterial lysis into DNA, RNA and protein fractions, while lipids were used for liposome formation. The fractions were sealed in glass tubes individually and in combinations and stored for three weeks. Upon seeding on Petri dishes, the fractions containing liposomes together with nucleic acid and/or proteins gave in total 19 colonies of Deinococcus radiodurans (confirmed by proteomics), while liposome-free fractions as well as liposome-only fractions gave no colonies. The self-assembly of viable cells from essentially dead mixtures validates the lyposome-based origin-of-life scenario.
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Affiliation(s)
- Alexandra Bernadotte
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Valeriya Semenova
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Vitor A M Musial
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Anna Kasprzykowska
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,SciLifeLab, Stockholm, Sweden
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33
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The N Terminus of the PduB Protein Binds the Protein Shell of the Pdu Microcompartment to Its Enzymatic Core. J Bacteriol 2017; 199:JB.00785-16. [PMID: 28138097 DOI: 10.1128/jb.00785-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/20/2017] [Indexed: 12/12/2022] Open
Abstract
Bacterial microcompartments (MCPs) are extremely large proteinaceous organelles that consist of an enzymatic core encapsulated within a complex protein shell. A key question in MCP biology is the nature of the interactions that guide the assembly of thousands of protein subunits into a well-ordered metabolic compartment. In this report, we show that the N-terminal 37 amino acids of the PduB protein have a critical role in binding the shell of the 1,2-propanediol utilization (Pdu) microcompartment to its enzymatic core. Several mutations were constructed that deleted short regions of the N terminus of PduB. Growth tests indicated that three of these deletions were impaired MCP assembly. Attempts to purify MCPs from these mutants, followed by gel electrophoresis and enzyme assays, indicated that the protein complexes isolated consisted of MCP shells depleted of core enzymes. Electron microscopy substantiated these findings by identifying apparently empty MCP shells but not intact MCPs. Analyses of 13 site-directed mutants indicated that the key region of the N terminus of PduB required for MCP assembly is a putative helix spanning residues 6 to 18. Considering the findings presented here together with prior work, we propose a new model for MCP assembly.IMPORTANCE Bacterial microcompartments consist of metabolic enzymes encapsulated within a protein shell and are widely used to optimize metabolic process. Here, we show that the N-terminal 37 amino acids of the PduB shell protein are essential for assembly of the 1,2-propanediol utilization microcompartment. The results indicate that it plays a key role in binding the outer shell to the enzymatic core. We propose that this interaction might be used to define the relative orientation of the shell with respect to the core. This finding is of fundamental importance to our understanding of microcompartment assembly and may have application to engineering microcompartments as nanobioreactors for chemical production.
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34
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Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem 2017; 15:4260-4271. [DOI: 10.1039/c7ob00391a] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multi-enzyme cascades provide a wealth of valuable chemicals. Efficiency of reaction schemes can be improved by spatial organization of biocatalysts. This review will highlight various methods of spatial organization of biocatalysts: fusion, immobilization, scaffolding and encapsulation.
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Affiliation(s)
- M. B. Quin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - K. K. Wallin
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - G. Zhang
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
| | - C. Schmidt-Dannert
- University of Minnesota
- Dept. of Biochemistry
- Molecular Biology and Biophysics
- St Paul
- USA
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35
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Bhaskar S, Lim S. Engineering protein nanocages as carriers for biomedical applications. NPG ASIA MATERIALS 2017; 9:e371. [PMID: 32218880 PMCID: PMC7091667 DOI: 10.1038/am.2016.128] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/26/2016] [Accepted: 04/12/2016] [Indexed: 05/02/2023]
Abstract
Protein nanocages have been explored as potential carriers in biomedicine. Formed by the self-assembly of protein subunits, the caged structure has three surfaces that can be engineered: the interior, the exterior and the intersubunit. Therapeutic and diagnostic molecules have been loaded in the interior of nanocages, while their external surfaces have been engineered to enhance their biocompatibility and targeting abilities. Modifications of the intersubunit interactions have been shown to modulate the self-assembly profile with implications for tuning the molecular release. We review natural and synthetic protein nanocages that have been modified using chemical and genetic engineering techniques to impart non-natural functions that are responsive to the complex cellular microenvironment of malignant cells while delivering molecular cargos with improved efficiencies and minimal toxicity.
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Affiliation(s)
- Sathyamoorthy Bhaskar
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
| | - Sierin Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
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36
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Gonzalez-Esquer CR, Newnham SE, Kerfeld CA. Bacterial microcompartments as metabolic modules for plant synthetic biology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:66-75. [PMID: 26991644 DOI: 10.1111/tpj.13166] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 03/04/2016] [Accepted: 03/08/2016] [Indexed: 05/28/2023]
Abstract
Bacterial microcompartments (BMCs) are megadalton-sized protein assemblies that enclose segments of metabolic pathways within cells. They increase the catalytic efficiency of the encapsulated enzymes while sequestering volatile or toxic intermediates from the bulk cytosol. The first BMCs discovered were the carboxysomes of cyanobacteria. Carboxysomes compartmentalize the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) with carbonic anhydrase. They enhance the carboxylase activity of RuBisCO by increasing the local concentration of CO2 in the vicinity of the enzyme's active site. As a metabolic module for carbon fixation, carboxysomes could be transferred to eukaryotic organisms (e.g. plants) to increase photosynthetic efficiency. Within the scope of synthetic biology, carboxysomes and other BMCs hold even greater potential when considered a source of building blocks for the development of nanoreactors or three-dimensional scaffolds to increase the efficiency of either native or heterologously expressed enzymes. The carboxysome serves as an ideal model system for testing approaches to engineering BMCs because their expression in cyanobacteria provides a sensitive screen for form (appearance of polyhedral bodies) and function (ability to grow on air). We recount recent progress in the re-engineering of the carboxysome shell and core to offer a conceptual framework for the development of BMC-based architectures for applications in plant synthetic biology.
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Affiliation(s)
| | - Sarah E Newnham
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Berkeley Synthetic Biology Institute, UC Berkeley, Berkeley, CA, USA
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA
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37
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Kerfeld CA, Melnicki MR. Assembly, function and evolution of cyanobacterial carboxysomes. CURRENT OPINION IN PLANT BIOLOGY 2016; 31:66-75. [PMID: 27060669 DOI: 10.1016/j.pbi.2016.03.009] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 05/19/2023]
Abstract
All cyanobacteria contain carboxysomes, RuBisCO-encapsulating bacterial microcompartments that function as prokaryotic organelles. The two carboxysome types, alpha and beta, differ fundamentally in components, assembly, and species distribution. Alpha carboxysomes share a highly-conserved gene organization, with evidence of horizontal gene transfer from chemoautotrophic proteobacteria to the picocyanobacteria, and seem to co-assemble shells concomitantly with aggregation of cargo enzymes. In contrast, beta carboxysomes assemble an enzymatic core first, with an encapsulation peptide playing a critical role in formation of the surrounding shell. Based on similarities in assembly, and phylogenetic analysis of the pentameric shell protein conserved across all bacterial microcompartments, beta carboxysomes appear to be more closely related to the microcompartments of heterotrophic bacteria (metabolosomes) than to alpha carboxysomes, which appear deeply divergent. Beta carboxysomes can be found in the basal cyanobacterial clades that diverged before the ancestor of the chloroplast and have recently been shown to be able to encapsulate functional RuBisCO enzymes resurrected from ancestrally-reconstructed sequences, consistent with an ancient origin. Alpha and beta carboxysomes are not only distinct units of evolution, but are now emerging as genetic/metabolic modules for synthetic biology; heterologous expression and redesign of both the shell and the enzymatic core have recently been achieved.
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Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Matthew R Melnicki
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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Held M, Kolb A, Perdue S, Hsu SY, Bloch SE, Quin MB, Schmidt-Dannert C. Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli. Sci Rep 2016; 6:24359. [PMID: 27063436 PMCID: PMC4827028 DOI: 10.1038/srep24359] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/29/2016] [Indexed: 01/17/2023] Open
Abstract
Compartmentalization of designed metabolic pathways within protein based nanocompartments has the potential to increase reaction efficiency in multi-step biosynthetic reactions. We previously demonstrated proof-of-concept of this aim by targeting a functional enzyme to single cellular protein nanocompartments, which were formed upon recombinant expression of the Salmonella enterica LT2 ethanolamine utilization bacterial microcompartment shell proteins EutS or EutSMNLK in Escherichia coli. To optimize this system, increasing overall encapsulated enzyme reaction efficiency, factor(s) required for the production of more than one nanocompartment per cell must be identified. In this work we report that the cupin domain protein EutQ is required for assembly of more than one nanocompartment per cell. Overexpression of EutQ results in multiple nanocompartment assembly in our recombinant system. EutQ specifically interacts with the shell protein EutM in vitro via electrostatic interactions with the putative cytosolic face of EutM. These findings lead to the theory that EutQ could facilitate multiple nanocompartment biogenesis by serving as an assembly hub for shell proteins. This work offers insights into the biogenesis of Eut bacterial microcompartments, and also provides an improved platform for the production of protein based nanocompartments for targeted encapsulation of enzyme pathways.
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Affiliation(s)
- Mark Held
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Alexander Kolb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah Perdue
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Szu-Yi Hsu
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah E Bloch
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Maureen B Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
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Shih PM, Occhialini A, Cameron JC, Andralojc PJ, Parry MAJ, Kerfeld CA. Biochemical characterization of predicted Precambrian RuBisCO. Nat Commun 2016; 7:10382. [PMID: 26790750 PMCID: PMC4735906 DOI: 10.1038/ncomms10382] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 12/04/2015] [Indexed: 01/02/2023] Open
Abstract
The antiquity and global abundance of the enzyme, RuBisCO, attests to the crucial and longstanding role it has played in the biogeochemical cycles of Earth over billions of years. The counterproductive oxygenase activity of RuBisCO has persisted over billions of years of evolution, despite its competition with the carboxylase activity necessary for carbon fixation, yet hypotheses regarding the selective pressures governing RuBisCO evolution have been limited to speculation. Here we report the resurrection and biochemical characterization of ancestral RuBisCOs, dating back to over one billion years ago (Gyr ago). Our findings provide an ancient point of reference revealing divergent evolutionary paths taken by eukaryotic homologues towards improved specificity for CO2, versus the evolutionary emphasis on increased rates of carboxylation observed in bacterial homologues. Consistent with these distinctions, in vivo analysis reveals the propensity of ancestral RuBisCO to be encapsulated into modern-day carboxysomes, bacterial organelles central to the cyanobacterial CO2 concentrating mechanism.
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Affiliation(s)
- Patrick M. Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA
| | - Alessandro Occhialini
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Jeffrey C. Cameron
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA
| | - P John Andralojc
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
| | - Martin A. J. Parry
- Department of Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts AL5 2JQ, UK
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1, 4YQ, UK
| | - Cheryl A. Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720-3102, USA
- Department of Biochemistry and Molecular Biology, DOE Plant Research Laboratories, Michigan State University, East Lansing, Michigan 488242, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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40
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Chaijarasphong T, Nichols RJ, Kortright KE, Nixon CF, Teng PK, Oltrogge LM, Savage DF. Programmed Ribosomal Frameshifting Mediates Expression of the α-Carboxysome. J Mol Biol 2016; 428:153-164. [DOI: 10.1016/j.jmb.2015.11.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/04/2015] [Accepted: 11/12/2015] [Indexed: 01/24/2023]
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41
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Abstract
Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.
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42
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Cai F, Dou Z, Bernstein SL, Leverenz R, Williams EB, Heinhorst S, Shively J, Cannon GC, Kerfeld CA. Advances in Understanding Carboxysome Assembly in Prochlorococcus and Synechococcus Implicate CsoS2 as a Critical Component. Life (Basel) 2015; 5:1141-71. [PMID: 25826651 PMCID: PMC4499774 DOI: 10.3390/life5021141] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/09/2015] [Accepted: 03/16/2015] [Indexed: 11/16/2022] Open
Abstract
The marine Synechococcus and Prochlorococcus are the numerically dominant cyanobacteria in the ocean and important in global carbon fixation. They have evolved a CO2-concentrating-mechanism, of which the central component is the carboxysome, a self-assembling proteinaceous organelle. Two types of carboxysome, α and β, encapsulating form IA and form IB d-ribulose-1,5-bisphosphate carboxylase/oxygenase, respectively, differ in gene organization and associated proteins. In contrast to the β-carboxysome, the assembly process of the α-carboxysome is enigmatic. Moreover, an absolutely conserved α-carboxysome protein, CsoS2, is of unknown function and has proven recalcitrant to crystallization. Here, we present studies on the CsoS2 protein in three model organisms and show that CsoS2 is vital for α-carboxysome biogenesis. The primary structure of CsoS2 appears tripartite, composed of an N-terminal, middle (M)-, and C-terminal region. Repetitive motifs can be identified in the N- and M-regions. Multiple lines of evidence suggest CsoS2 is highly flexible, possibly an intrinsically disordered protein. Based on our results from bioinformatic, biophysical, genetic and biochemical approaches, including peptide array scanning for protein-protein interactions, we propose a model for CsoS2 function and its spatial location in the α-carboxysome. Analogies between the pathway for β-carboxysome biogenesis and our model for α-carboxysome assembly are discussed.
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Affiliation(s)
- Fei Cai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Zhicheng Dou
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Susan L Bernstein
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Ryan Leverenz
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
| | - Eric B Williams
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Sabine Heinhorst
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Jessup Shively
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA.
| | - Gordon C Cannon
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
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43
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Bacterial microcompartments and the modular construction of microbial metabolism. Trends Microbiol 2015; 23:22-34. [DOI: 10.1016/j.tim.2014.10.003] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/07/2014] [Accepted: 10/08/2014] [Indexed: 01/22/2023]
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44
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Production of bacterial microcompartments. Methods Mol Biol 2014. [PMID: 25358774 DOI: 10.1007/978-1-4939-2131-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Bacterial microcompartments (BMCs) are protein-based organelles that allow specific metabolic steps to be sequestered from the cytoplasmic environment. Compartmentalization of enzymes and pathway intermediates can increase flux through a metabolic pathway and protect the cell from toxic intermediates. BMCs thus offer the potential to increase the efficiency of engineered metabolic pathways. Moreover, as protein cages, BMCs may enable various other applications in biotechnology. These future applications of BMCs will require the ability to rapidly and efficiently produce BMCs for physical characterization and protein engineering. This chapter presents an analysis of approaches to expression and purification of BMCs and outlines a generalized strategy based on these approaches that can be used as a starting point for production of new BMCs.
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45
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Keeling TJ, Samborska B, Demers RW, Kimber MS. Interactions and structural variability of β-carboxysomal shell protein CcmL. PHOTOSYNTHESIS RESEARCH 2014; 121:125-133. [PMID: 24504539 DOI: 10.1007/s11120-014-9973-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 01/14/2014] [Indexed: 06/03/2023]
Abstract
CcmL is a small, pentameric protein that is argued to fill the vertices of β-carboxysomal shell. Here we report the structures of two CcmL orthologs, those from Nostoc sp. PCC 7120 and Thermosynechococcus elongatus BP-1. These structures broadly resemble those previously reported for other strains. However, the Nostoc CcmL structure shows an interesting pattern of behavior where two loops that map to the base of the pentamer adopt either an out or in conformation, with a consistent (over six pentamers) out-in-out-in-in pattern of protomers. The pentamers in this structure are also consistently organized into a back-to-back decamer, though evidence suggests that this is likely not present in solution. Förster resonance energy transfer experiments were able to show a weak interaction between CcmL and CcmK2 when CcmK2 was present at >100 μM. Since CcmK2 forms defined bodies with approximately 200 nm diameter at this concentration, this would support the idea that CcmL can only interact with CcmK2 at rare defect points in the growing shell.
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Affiliation(s)
- Thomas J Keeling
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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46
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Chowdhury C, Sinha S, Chun S, Yeates TO, Bobik TA. Diverse bacterial microcompartment organelles. Microbiol Mol Biol Rev 2014. [PMID: 25184561 DOI: 10.1128/mmbr.00009–14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Bacterial microcompartments (MCPs) are sophisticated protein-based organelles used to optimize metabolic pathways. They consist of metabolic enzymes encapsulated within a protein shell, which creates an ideal environment for catalysis and facilitates the channeling of toxic/volatile intermediates to downstream enzymes. The metabolic processes that require MCPs are diverse and widely distributed and play important roles in global carbon fixation and bacterial pathogenesis. The protein shells of MCPs are thought to selectively control the movement of enzyme cofactors, substrates, and products (including toxic or volatile intermediates) between the MCP interior and the cytoplasm of the cell using both passive electrostatic/steric and dynamic gated mechanisms. Evidence suggests that specialized shell proteins conduct electrons between the cytoplasm and the lumen of the MCP and/or help rebuild damaged iron-sulfur centers in the encapsulated enzymes. The MCP shell is elaborated through a family of small proteins whose structural core is known as a bacterial microcompartment (BMC) domain. BMC domain proteins oligomerize into flat, hexagonally shaped tiles, which assemble into extended protein sheets that form the facets of the shell. Shape complementarity along the edges allows different types of BMC domain proteins to form mixed sheets, while sequence variation provides functional diversification. Recent studies have also revealed targeting sequences that mediate protein encapsulation within MCPs, scaffolding proteins that organize lumen enzymes and the use of private cofactor pools (NAD/H and coenzyme A [HS-CoA]) to facilitate cofactor homeostasis. Although much remains to be learned, our growing understanding of MCPs is providing a basis for bioengineering of protein-based containers for the production of chemicals/pharmaceuticals and for use as molecular delivery vehicles.
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Affiliation(s)
- Chiranjit Chowdhury
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Sharmistha Sinha
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Sunny Chun
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - Todd O Yeates
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, USA Department of Energy Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, USA Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
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47
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Lin MT, Occhialini A, Andralojc JP, Devonshire J, Hines KM, Parry MAJ, Hanson MR. β-Carboxysomal proteins assemble into highly organized structures in Nicotiana chloroplasts. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:1-12. [PMID: 24810513 PMCID: PMC4080790 DOI: 10.1111/tpj.12536] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 04/15/2014] [Indexed: 05/18/2023]
Abstract
The photosynthetic efficiency of C3 plants suffers from the reaction of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) with O2 instead of CO2 , leading to the costly process of photorespiration. Increasing the concentration of CO2 around Rubisco is a strategy used by photosynthetic prokaryotes such as cyanobacteria for more efficient incorporation of inorganic carbon. Engineering the cyanobacterial CO2 -concentrating mechanism, the carboxysome, into chloroplasts is an approach to enhance photosynthesis or to compartmentalize other biochemical reactions to confer new capabilities on transgenic plants. We have chosen to explore the possibility of producing β-carboxysomes from Synechococcus elongatus PCC7942, a model freshwater cyanobacterium. Using the agroinfiltration technique, we have transiently expressed multiple β-carboxysomal proteins (CcmK2, CcmM, CcmL, CcmO and CcmN) in Nicotiana benthamiana with fusions that target these proteins into chloroplasts, and that provide fluorescent labels for visualizing the resultant structures. By confocal and electron microscopic analysis, we have observed that the shell proteins of the β-carboxysome are able to assemble in plant chloroplasts into highly organized assemblies resembling empty microcompartments. We demonstrate that a foreign protein can be targeted with a 17-amino-acid CcmN peptide to the shell proteins inside chloroplasts. Our experiments establish the feasibility of introducing carboxysomes into chloroplasts for the potential compartmentalization of Rubisco or other proteins.
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Affiliation(s)
- Myat T. Lin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | | | - John P. Andralojc
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Jean Devonshire
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Kevin M. Hines
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Martin A. J. Parry
- Plant Biology and Crop Science, Rothamsted Research, Harpenden, Herts, AL5 2JQ, UK
| | - Maureen R. Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
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48
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Whitehead L, Long BM, Price GD, Badger MR. Comparing the in vivo function of α-carboxysomes and β-carboxysomes in two model cyanobacteria. PLANT PHYSIOLOGY 2014; 165:398-411. [PMID: 24642960 PMCID: PMC4012598 DOI: 10.1104/pp.114.237941] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 03/10/2014] [Indexed: 05/19/2023]
Abstract
The carbon dioxide (CO2)-concentrating mechanism of cyanobacteria is characterized by the occurrence of Rubisco-containing microcompartments called carboxysomes within cells. The encapsulation of Rubisco allows for high-CO2 concentrations at the site of fixation, providing an advantage in low-CO2 environments. Cyanobacteria with Form-IA Rubisco contain α-carboxysomes, and cyanobacteria with Form-IB Rubisco contain β-carboxysomes. The two carboxysome types have arisen through convergent evolution, and α-cyanobacteria and β-cyanobacteria occupy different ecological niches. Here, we present, to our knowledge, the first direct comparison of the carboxysome function from α-cyanobacteria (Cyanobium spp. PCC7001) and β-cyanobacteria (Synechococcus spp. PCC7942) with similar inorganic carbon (Ci; as CO2 and HCO3-) transporter systems. Despite evolutionary and structural differences between α-carboxysomes and β-carboxysomes, we found that the two strains are remarkably similar in many physiological parameters, particularly the response of photosynthesis to light and external Ci and their modulation of internal ribulose-1,5-bisphosphate, phosphoglycerate, and Ci pools when grown under comparable conditions. In addition, the different Rubisco forms present in each carboxysome had almost identical kinetic parameters. The conclusions indicate that the possession of different carboxysome types does not significantly influence the physiological function of these species and that similar carboxysome function may be possessed by each carboxysome type. Interestingly, both carboxysome types showed a response to cytosolic Ci, which is of higher affinity than predicted by current models, being saturated by 5 to 15 mm Ci. This finding has bearing on the viability of transplanting functional carboxysomes into the C3 chloroplast.
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Affiliation(s)
- Lynne Whitehead
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 0200, Australia
| | - Benedict M. Long
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 0200, Australia
| | - G. Dean Price
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 0200, Australia
| | - Murray R. Badger
- Research School of Biology, Australian National University, Acton, Australian Capital Territory 0200, Australia
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49
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Carboxysomes – Sequestering RubisCO for Efficient Carbon Fixation. THE STRUCTURAL BASIS OF BIOLOGICAL ENERGY GENERATION 2014. [DOI: 10.1007/978-94-017-8742-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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50
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Ferrer-Miralles N, Rodríguez-Carmona E, Corchero JL, García-Fruitós E, Vázquez E, Villaverde A. Engineering protein self-assembling in protein-based nanomedicines for drug delivery and gene therapy. Crit Rev Biotechnol 2013; 35:209-21. [DOI: 10.3109/07388551.2013.833163] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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