1
|
Doron L, Kerfeld CA. Bacterial microcompartments as a next-generation metabolic engineering tool: utilizing nature's solution for confining challenging catabolic pathways. Biochem Soc Trans 2024; 52:997-1010. [PMID: 38813858 DOI: 10.1042/bst20230229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Advancements in synthetic biology have facilitated the incorporation of heterologous metabolic pathways into various bacterial chassis, leading to the synthesis of targeted bioproducts. However, total output from heterologous production pathways can suffer from low flux, enzyme promiscuity, formation of toxic intermediates, or intermediate loss to competing reactions, which ultimately hinder their full potential. The self-assembling, easy-to-modify, protein-based bacterial microcompartments (BMCs) offer a sophisticated way to overcome these obstacles by acting as an autonomous catalytic module decoupled from the cell's regulatory and metabolic networks. More than a decade of fundamental research on various types of BMCs, particularly structural studies of shells and their self-assembly, the recruitment of enzymes to BMC shell scaffolds, and the involvement of ancillary proteins such as transporters, regulators, and activating enzymes in the integration of BMCs into the cell's metabolism, has significantly moved the field forward. These advances have enabled bioengineers to design synthetic multi-enzyme BMCs to promote ethanol or hydrogen production, increase cellular polyphosphate levels, and convert glycerol to propanediol or formate to pyruvate. These pioneering efforts demonstrate the enormous potential of synthetic BMCs to encapsulate non-native multi-enzyme biochemical pathways for the synthesis of high-value products.
Collapse
Affiliation(s)
- Lior Doron
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, U.S.A
| |
Collapse
|
2
|
Trettel DS, Kerfeld CA, Gonzalez-Esquer CR. Dynamic structural determinants in bacterial microcompartment shells. Curr Opin Microbiol 2024; 80:102497. [PMID: 38909546 DOI: 10.1016/j.mib.2024.102497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/07/2024] [Accepted: 06/03/2024] [Indexed: 06/25/2024]
Abstract
Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO2 fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein-protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks.
Collapse
Affiliation(s)
- Daniel S Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences group, Los Alamos, NM, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Cesar R Gonzalez-Esquer
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences group, Los Alamos, NM, USA.
| |
Collapse
|
3
|
Gu S, Bradley-Clarke J, Rose RS, Warren MJ, Pickersgill RW. Enzyme-cargo encapsulation peptides bind between tessellating tiles of the bacterial microcompartment shell. J Biol Chem 2024; 300:107357. [PMID: 38735476 PMCID: PMC11157265 DOI: 10.1016/j.jbc.2024.107357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 05/14/2024] Open
Abstract
Bacterial microcompartments are prokaryotic organelles comprising encapsulated enzymes within a thin protein shell. They facilitate metabolic processing including propanediol, choline, glycerol, and ethanolamine utilization, and they accelerate carbon fixation in cyanobacteria. Enzymes targeted to the inside of the microcompartment frequently possess a cargo-encapsulation peptide, but the site to which the peptide binds is unclear. We provide evidence that the encapsulation peptides bind to the hydrophobic groove formed between tessellating subunits of the shell proteins. In silico docking studies provide a compelling model of peptide binding to this prominent hydrophobic groove. This result is consistent with the now widely accepted view that the convex side of the shell oligomers faces the lumen of the microcompartment. The binding of the encapsulation peptide to the groove between tessellating shell protein tiles explains why it has been difficult to define the peptide binding site using other methods, provides a mechanism by which encapsulation-peptide bearing enzymes can promote shell assembly, and explains how the presence of cargo affects the size and shape of the bacterial microcompartment. This knowledge may be exploited in engineering microcompartments or disease prevention by hampering cargo encapsulation.
Collapse
Affiliation(s)
- Shuang Gu
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Jack Bradley-Clarke
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Ruth-Sarah Rose
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK
| | - Martin J Warren
- School of Biosciences, University of Kent, Canterbury, Kent, UK
| | - Richard W Pickersgill
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, UK.
| |
Collapse
|
4
|
Kong WW, Zhu Y, Zhao HR, Du K, Zhou RQ, Li B, Yang F, Hou P, Huang XH, Chen Y, Wang YC, Sun F, Jiang YL, Zhou CZ. Cryo-electron tomography reveals the packaging pattern of RuBisCOs in Synechococcus β-carboxysome. Structure 2024:S0969-2126(24)00184-9. [PMID: 38823379 DOI: 10.1016/j.str.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/01/2024] [Accepted: 05/07/2024] [Indexed: 06/03/2024]
Abstract
Carboxysomes are large self-assembled microcompartments that serve as the central machinery of a CO2-concentrating mechanism (CCM). Biogenesis of carboxysome requires the fine organization of thousands of individual proteins; however, the packaging pattern of internal RuBisCOs remains largely unknown. Here we purified the intact β-carboxysomes from Synechococcus elongatus PCC 7942 and identified the protein components by mass spectrometry. Cryo-electron tomography combined with subtomogram averaging revealed the general organization pattern of internal RuBisCOs, in which the adjacent RuBisCOs are mainly arranged in three distinct manners: head-to-head, head-to-side, and side-by-side. The RuBisCOs in the outermost layer are regularly aligned along the shell, the majority of which directly interact with the shell. Moreover, statistical analysis enabled us to propose an ideal packaging model of RuBisCOs in the β-carboxysome. These results provide new insights into the biogenesis of β-carboxysomes and also advance our understanding of the efficient carbon fixation functionality of carboxysomes.
Collapse
Affiliation(s)
- Wen-Wen Kong
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Yun Zhu
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Heng-Rui Zhao
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Kang Du
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Rui-Qian Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Bo Li
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Feng Yang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Pu Hou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Xia-He Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Ying-Chun Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China.
| |
Collapse
|
5
|
Dutcher CA, Andreas MP, Giessen TW. A two-component quasi-icosahedral protein nanocompartment with variable shell composition and irregular tiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591138. [PMID: 38712103 PMCID: PMC11071501 DOI: 10.1101/2024.04.25.591138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells for varied metabolic purposes. These protein-based compartments often exhibit icosahedral symmetry and consist of a small number of structural components with defined roles. Encapsulins are a prevalent protein-based compartmentalization strategy in prokaryotes. All encapsulins studied thus far consist of a single shell protein that adopts the viral HK97-fold. Here, we report the characterization of a Family 2B two-component encapsulin from Streptomyces lydicus. We show the differential assembly behavior of the two shell components and demonstrate their ability to co-assemble into mixed shells with variable shell composition. We determined the structures of both shell proteins using cryo-electron microscopy. Using 3D-classification and crosslinking studies, we highlight the irregular tiling of mixed shells. Our work expands the known assembly modes of HK97-fold proteins and lays the foundation for future functional and engineering studies on two-component encapsulins.
Collapse
Affiliation(s)
- Cassandra A. Dutcher
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| |
Collapse
|
6
|
Zhou RQ, Jiang YL, Li H, Hou P, Kong WW, Deng JX, Chen Y, Zhou CZ, Zeng Q. Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus. NATURE PLANTS 2024; 10:661-672. [PMID: 38589484 DOI: 10.1038/s41477-024-01660-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/29/2024] [Indexed: 04/10/2024]
Abstract
Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant 'outside-in' assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency.
Collapse
Affiliation(s)
- Rui-Qian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Pu Hou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jia-Xin Deng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
| |
Collapse
|
7
|
Trettel DS, Pacheco SL, Laskie AK, Gonzalez-Esquer CR. Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation. FRONTIERS IN PLANT SCIENCE 2024; 15:1346759. [PMID: 38425792 PMCID: PMC10902431 DOI: 10.3389/fpls.2024.1346759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO2-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.
Collapse
Affiliation(s)
- Daniel S. Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences Group, Los Alamos, NM, United States
| | | | | | | |
Collapse
|
8
|
Česle EEL, Ta Rs K, Jansons J, Kalniņš G. Modulation of Hybrid GRM2-type Bacterial Microcompartment Shells through BMC-H Shell Protein Fusion and Incorporation of Non-native BMC-T Shell Proteins. ACS Synth Biol 2023; 12:3275-3286. [PMID: 37937366 DOI: 10.1021/acssynbio.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Bacterial microcompartments (BMCs) are organelle-like structures in bacteria that facilitate a wide range of enzymatic reactions. The microcompartment shell contains an encapsulated enzymatic core and, in contrast to phospholipid-based eukaryotic organelle membranes, has a pseudoicosahedral shape composed of BMC-H, BMC-T, and BMC-P proteins with conserved structures. This semipermeable microcompartment shell delineates the enzymatic core assemblies and the intermediates from the rest of the cell. It is also thought to function as a barrier against toxic intermediates as well as to increase the reaction rate. These properties of BMCs have made them intriguing candidates for biotechnological applications, for which it is important to explore the potential scope of the BMC shell modulation possibilities. In this work, we explore two BMC shell modulation mechanisms: first, confirming the incorporation of three trimeric BMC-T shell proteins and two truncated BMC-T shell proteins into Klebsiella pneumoniae GRM2-type BMC protein shells containing no representatives of this group, and second, producing BMC particles from double- and triple-fused hexameric BMC-H shell proteins. These results reveal the potential for "mix and match" synthetic BMC shell formation to ensure shell properties specifically suited to the encapsulated cargo and show for the first time the involvement of an essentially dimeric pseudohexameric shell protein in BMC shell formation.
Collapse
Affiliation(s)
- Eva Emi Lija Česle
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
| | - Kaspars Ta Rs
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
- University of Latvia, Jelgavas 1, Riga 1004, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
| |
Collapse
|
9
|
Doron L, Sutter M, Kerfeld CA. Characterization of a novel aromatic substrate-processing microcompartment in Actinobacteria. mBio 2023; 14:e0121623. [PMID: 37462359 PMCID: PMC10470539 DOI: 10.1128/mbio.01216-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 09/02/2023] Open
Abstract
We have discovered a new cluster of genes that is found exclusively in the Actinobacteria phylum. This locus includes genes for the 2-aminophenol meta-cleavage pathway and the shell proteins of a bacterial microcompartment (BMC) and has been named aromatics (ARO) for its putative role in the breakdown of aromatic compounds. In this study, we provide details about the distribution and composition of the ARO BMC locus and conduct phylogenetic, structural, and functional analyses of the first two enzymes in the catabolic pathway: a unique 2-aminophenol dioxygenase, which is exclusively found alongside BMC shell genes in Actinobacteria, and a semialdehyde dehydrogenase, which works downstream of the dioxygenase. Genomic analysis reveals variations in the complexity of the ARO loci across different orders. Some loci are simple, containing shell proteins and enzymes for the initial steps of the catabolic pathway, while others are extensive, encompassing all the necessary genes for the complete breakdown of 2-aminophenol into pyruvate and acetyl-CoA. Furthermore, our analysis uncovers two subtypes of ARO BMC that likely degrade either 2-aminophenol or catechol, depending on the presence of a pathway-specific gene within the ARO locus. The precise precursor of 2-aminophenol, which serves as the initial substrate and/or inducer for the ARO pathway, remains unknown, as our model organism Micromonospora rosaria cannot utilize 2-aminophenol as its sole energy source. However, using enzymatic assays, we demonstrate the dioxygenase's ability to cleave both 2-aminophenol and catechol in vitro, in collaboration with the aldehyde dehydrogenase, to facilitate the rapid conversion of these unstable and toxic intermediates. IMPORTANCE Bacterial microcompartments (BMCs) are proteinaceous organelles that are widespread among bacteria and provide a competitive advantage in specific environmental niches. Studies have shown that the genetic information necessary to form functional BMCs is encoded in loci that contain genes encoding shell proteins and the enzymatic core. This allows the bioinformatic discovery of BMCs with novel functions and expands our understanding of the metabolic diversity of BMCs. ARO loci, found only in Actinobacteria, contain genes encoding for phylogenetically remote shell proteins and homologs of the meta-cleavage degradation pathway enzymes that were shown to convert central aromatic intermediates into pyruvate and acetyl-CoA in gamma Proteobacteria. By analyzing the gene composition of ARO BMC loci and characterizing two core enzymes phylogenetically, structurally, and functionally, we provide an initial functional characterization of the ARO BMC, the most unusual BMC identified to date, distinctive among the repertoire of studied BMCs.
Collapse
Affiliation(s)
- Lior Doron
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
10
|
Jackson PJ, Hitchcock A, Brindley AA, Dickman MJ, Hunter CN. Absolute quantification of cellular levels of photosynthesis-related proteins in Synechocystis sp. PCC 6803. PHOTOSYNTHESIS RESEARCH 2023; 155:219-245. [PMID: 36542271 PMCID: PMC9958174 DOI: 10.1007/s11120-022-00990-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Quantifying cellular components is a basic and important step for understanding how a cell works, how it responds to environmental changes, and for re-engineering cells to produce valuable metabolites and increased biomass. We quantified proteins in the model cyanobacterium Synechocystis sp. PCC 6803 given the general importance of cyanobacteria for global photosynthesis, for synthetic biology and biotechnology research, and their ancestral relationship to the chloroplasts of plants. Four mass spectrometry methods were used to quantify cellular components involved in the biosynthesis of chlorophyll, carotenoid and bilin pigments, membrane assembly, the light reactions of photosynthesis, fixation of carbon dioxide and nitrogen, and hydrogen and sulfur metabolism. Components of biosynthetic pathways, such as those for chlorophyll or for photosystem II assembly, range between 1000 and 10,000 copies per cell, but can be tenfold higher for CO2 fixation enzymes. The most abundant subunits are those for photosystem I, with around 100,000 copies per cell, approximately 2 to fivefold higher than for photosystem II and ATP synthase, and 5-20 fold more than for the cytochrome b6f complex. Disparities between numbers of pathway enzymes, between components of electron transfer chains, and between subunits within complexes indicate possible control points for biosynthetic processes, bioenergetic reactions and for the assembly of multisubunit complexes.
Collapse
Affiliation(s)
- Philip J Jackson
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK.
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK.
| | - Andrew Hitchcock
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Amanda A Brindley
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, S1 3JD, UK
| | - C Neil Hunter
- Plants, Photosynthesis and Soil, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Tsidilkovski L, Mohajerani F, Hagan MF. Microcompartment assembly around multicomponent fluid cargoes. J Chem Phys 2022; 156:245104. [PMID: 35778087 PMCID: PMC9249432 DOI: 10.1063/5.0089556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a complex of enzymes and other components involved in certain metabolic processes. The simulations demonstrate that the relative interaction strengths among the different cargo species play a key role in determining the amount of each species that is encapsulated, their spatial organization, and the nature of the shell assembly pathways. However, the shell protein–shell protein and shell protein–cargo component interactions that help drive assembly and encapsulation also influence cargo composition within certain parameter regimes. These behaviors are governed by a combination of thermodynamic and kinetic effects. In addition to elucidating how natural microcompartments encapsulate multiple components involved within reaction cascades, these results have implications for efforts in synthetic biology to colocalize alternative sets of molecules within microcompartments to accelerate specific reactions. More broadly, the results suggest that coupling between self-assembly and multicomponent liquid–liquid phase separation may play a role in the organization of the cellular cytoplasm.
Collapse
Affiliation(s)
- Lev Tsidilkovski
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, USA
| |
Collapse
|
13
|
Edwardson TGW, Levasseur MD, Tetter S, Steinauer A, Hori M, Hilvert D. Protein Cages: From Fundamentals to Advanced Applications. Chem Rev 2022; 122:9145-9197. [PMID: 35394752 DOI: 10.1021/acs.chemrev.1c00877] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins that self-assemble into polyhedral shell-like structures are useful molecular containers both in nature and in the laboratory. Here we review efforts to repurpose diverse protein cages, including viral capsids, ferritins, bacterial microcompartments, and designed capsules, as vaccines, drug delivery vehicles, targeted imaging agents, nanoreactors, templates for controlled materials synthesis, building blocks for higher-order architectures, and more. A deep understanding of the principles underlying the construction, function, and evolution of natural systems has been key to tailoring selective cargo encapsulation and interactions with both biological systems and synthetic materials through protein engineering and directed evolution. The ability to adapt and design increasingly sophisticated capsid structures and functions stands to benefit the fields of catalysis, materials science, and medicine.
Collapse
Affiliation(s)
| | | | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Mao Hori
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| |
Collapse
|
14
|
Toward a glycyl radical enzyme containing synthetic bacterial microcompartment to produce pyruvate from formate and acetate. Proc Natl Acad Sci U S A 2022; 119:2116871119. [PMID: 35193962 PMCID: PMC8872734 DOI: 10.1073/pnas.2116871119] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 12/15/2022] Open
Abstract
The enormous complexity of metabolic pathways, in both their regulation and propensity for metabolite cross-talk, represents a major obstacle for metabolic engineering. Self-assembling, catalytically programmable and genetically transferable bacterial microcompartments (BMCs) offer solutions to decrease this complexity through compartmentalization of enzymes within a selectively permeable protein shell. Synthetic BMCs can operate as autonomous metabolic modules decoupled from the cell’s regulatory network, only interfacing with the cell’s metabolism via the highly engineerable proteinaceous shell. Here, we build a synthetic, modular, multienzyme BMC. It functions not only as a proof-of-concept for next-generation metabolic engineering, but also provides the foundation for subsequent tuning, with the goal to create a microanaerobic environment protecting an oxygen-sensitive reaction in aerobic growth conditions that could be deployed. Formate has great potential to function as a feedstock for biorefineries because it can be sustainably produced by a variety of processes that don’t compete with agricultural production. However, naturally formatotrophic organisms are unsuitable for large-scale cultivation, difficult to engineer, or have inefficient native formate assimilation pathways. Thus, metabolic engineering needs to be developed for model industrial organisms to enable efficient formatotrophic growth. Here, we build a prototype synthetic formate utilizing bacterial microcompartment (sFUT) encapsulating the oxygen-sensitive glycyl radical enzyme pyruvate formate lyase and a phosphate acyltransferase to convert formate and acetyl-phosphate into the central biosynthetic intermediate pyruvate. This metabolic module offers a defined environment with a private cofactor coenzyme A that can cycle efficiently between the encapsulated enzymes. To facilitate initial design-build-test-refine cycles to construct an active metabolic core, we used a “wiffleball” architecture, defined as an icosahedral bacterial microcompartment (BMC) shell with unoccupied pentameric vertices to freely permit substrate and product exchange. The resulting sFUT prototype wiffleball is an active multi enzyme synthetic BMC functioning as platform technology.
Collapse
|
15
|
Liu LN. Advances in the bacterial organelles for CO 2 fixation. Trends Microbiol 2021; 30:567-580. [PMID: 34802870 DOI: 10.1016/j.tim.2021.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/19/2021] [Accepted: 10/22/2021] [Indexed: 02/08/2023]
Abstract
Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concentration mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biology to repurpose the metabolic module in diverse applications.
Collapse
Affiliation(s)
- Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, 266003 Qingdao, China.
| |
Collapse
|
16
|
Sutter M, Melnicki MR, Schulz F, Woyke T, Kerfeld CA. A catalog of the diversity and ubiquity of bacterial microcompartments. Nat Commun 2021; 12:3809. [PMID: 34155212 PMCID: PMC8217296 DOI: 10.1038/s41467-021-24126-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 05/28/2021] [Indexed: 12/25/2022] Open
Abstract
Bacterial microcompartments (BMCs) are organelles that segregate segments of metabolic pathways which are incompatible with surrounding metabolism. BMCs consist of a selectively permeable shell, composed of three types of structurally conserved proteins, together with sequestered enzymes that vary among functionally distinct BMCs. Genes encoding shell proteins are typically clustered with those for the encapsulated enzymes. Here, we report that the number of identifiable BMC loci has increased twenty-fold since the last comprehensive census of 2014, and the number of distinct BMC types has doubled. The new BMC types expand the range of compartmentalized catalysis and suggest that there is more BMC biochemistry yet to be discovered. Our comprehensive catalog of BMCs provides a framework for their identification, correlation with bacterial niche adaptation, experimental characterization, and development of BMC-based nanoarchitectures for biomedical and bioengineering applications. Bacterial microcompartments (BMCs) are organelles consisting of a protein shell in which certain metabolic reactions take place separated from the cytoplasm. Here, Sutter et al. present a comprehensive catalog of BMC loci, substantially expanding the number of known BMCs and describing distinct types and compartmentalized reactions.
Collapse
Affiliation(s)
- Markus Sutter
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Matthew R Melnicki
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA
| | - Frederik Schulz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|
17
|
Abstract
Bacterial microcompartments (BMCs) confine a diverse array of metabolic reactions within a selectively permeable protein shell, allowing for specialized biochemistry that would be less efficient or altogether impossible without compartmentalization. BMCs play critical roles in carbon fixation, carbon source utilization, and pathogenesis. Despite their prevalence and importance in bacterial metabolism, little is known about BMC “homeostasis,” a term we use here to encompass BMC assembly, composition, size, copy-number, maintenance, turnover, positioning, and ultimately, function in the cell. The carbon-fixing carboxysome is one of the most well-studied BMCs with regard to mechanisms of self-assembly and subcellular organization. In this minireview, we focus on the only known BMC positioning system to date—the maintenance of carboxysome distribution (Mcd) system, which spatially organizes carboxysomes. We describe the two-component McdAB system and its proposed diffusion-ratchet mechanism for carboxysome positioning. We then discuss the prevalence of McdAB systems among carboxysome-containing bacteria and highlight recent evidence suggesting how liquid-liquid phase separation (LLPS) may play critical roles in carboxysome homeostasis. We end with an outline of future work on the carboxysome distribution system and a perspective on how other BMCs may be spatially regulated. We anticipate that a deeper understanding of BMC organization, including nontraditional homeostasis mechanisms involving LLPS and ATP-driven organization, is on the horizon.
Collapse
|
18
|
Sun H, Cui N, Han SJ, Chen ZP, Xia LY, Chen Y, Jiang YL, Zhou CZ. Complex structure reveals CcmM and CcmN form a heterotrimeric adaptor in β-carboxysome. Protein Sci 2021; 30:1566-1576. [PMID: 33928692 DOI: 10.1002/pro.4090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/09/2022]
Abstract
Carboxysome is an icosahedral self-assembled microcompartment that sequesters RuBisCO and carbonic anhydrases within a selectively permeable protein shell. The scaffolding proteins, CcmM, and CcmN were proposed to act as adaptors that crosslink the enzymatic core to shell facets. However, the details of interaction pattern remain unknown. Here we obtained a stable heterotrimeric complex of CcmM γ-carbonic anhydrase domain (termed CcmMNT ) and CcmN, with a 1:2 stoichiometry, which interacts with the shell proteins CcmO and CcmL in vitro. The 2.9 Å crystal structure of this heterotrimer revealed an asymmetric bundle composed of one CcmMNT and two CcmN subunits, all of which adopt a triangular left-handed β-helical barrel structure. The central CcmN subunit packs against CcmMNT and another CcmN subunit via a wall-to-edge or wall-to-wall pattern, respectively. Together with previous findings, we propose CcmMNT -CcmN functions as an adaptor to facilitate the recruitment of shell proteins and the assembly of intact β-carboxysome.
Collapse
Affiliation(s)
- Hui Sun
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ning Cui
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Shu-Jing Han
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Zhi-Peng Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Ling-Yun Xia
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China
| |
Collapse
|
19
|
Cesle EE, Filimonenko A, Tars K, Kalnins G. Variety of size and form of GRM2 bacterial microcompartment particles. Protein Sci 2021; 30:1035-1043. [PMID: 33763934 PMCID: PMC8040866 DOI: 10.1002/pro.4069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Bacterial microcompartments (BMCs) are bacterial organelles involved in enzymatic processes, such as carbon fixation, choline, ethanolamine and propanediol degradation, and others. Formed of a semi-permeable protein shell and an enzymatic core, they can enhance enzyme performance and protect the cell from harmful intermediates. With the ability to encapsulate non-native enzymes, BMCs show high potential for applied use. For this goal, a detailed look into shell form variability is significant to predict shell adaptability. Here we present four novel 3D cryo-EM maps of recombinant Klebsiella pneumoniae GRM2 BMC shell particles with the resolution in range of 9 to 22 Å and nine novel 2D classes corresponding to discrete BMC shell forms. These structures reveal icosahedral, elongated, oblate, multi-layered and polyhedral traits of BMCs, indicating considerable variation in size and form as well as adaptability during shell formation processes.
Collapse
Affiliation(s)
- Eva Emilija Cesle
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
| | - Anatolij Filimonenko
- CEITEC‐Central European Institute of TechnologyMasaryk UniversityBrnoCzech Republic
| | - Kaspars Tars
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
- Faculty of BiologyUniversity of LatviaRigaLatvia
| | - Gints Kalnins
- Structural Biology, Biotechnology and Virusology LaboratoryLatvian Biomedical Research and Study CentreRigaLatvia
| |
Collapse
|
20
|
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.
Collapse
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.
| |
Collapse
|
21
|
Mohajerani F, Sayer E, Neil C, Inlow K, Hagan MF. Mechanisms of Scaffold-Mediated Microcompartment Assembly and Size Control. ACS NANO 2021; 15:4197-4212. [PMID: 33683101 PMCID: PMC8058603 DOI: 10.1021/acsnano.0c05715] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This article describes a theoretical and computational study of the dynamical assembly of a protein shell around a complex consisting of many cargo molecules and long, flexible scaffold molecules. Our study is motivated by bacterial microcompartments, which are proteinaceous organelles that assemble around a condensed droplet of enzymes and reactants. As in many examples of cytoplasmic liquid-liquid phase separation, condensation of the microcompartment interior cargo is driven by flexible scaffold proteins that have weak multivalent interactions with the cargo. Our results predict that the shell size, amount of encapsulated cargo, and assembly pathways depend sensitively on properties of the scaffold, including its length and valency of scaffold-cargo interactions. Moreover, the ability of self-assembling protein shells to change their size to accommodate scaffold molecules of different lengths depends crucially on whether the spontaneous curvature radius of the protein shell is smaller or larger than a characteristic elastic length scale of the shell. Beyond natural microcompartments, these results have important implications for synthetic biology efforts to target alternative molecules for encapsulation by microcompartments or viral shells. More broadly, the results elucidate how cells exploit coupling between self-assembly and liquid-liquid phase separation to organize their interiors.
Collapse
Affiliation(s)
- Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Evan Sayer
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Christopher Neil
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Koe Inlow
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Michael F Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts 02453, United States
| |
Collapse
|
22
|
Stewart AM, Stewart KL, Yeates TO, Bobik TA. Advances in the World of Bacterial Microcompartments. Trends Biochem Sci 2021; 46:406-416. [PMID: 33446424 DOI: 10.1016/j.tibs.2020.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 12/20/2022]
Abstract
Bacterial microcompartments (MCPs) are extremely large (100-400 nm) and diverse proteinaceous organelles that compartmentalize multistep metabolic pathways, increasing their efficiency and sequestering toxic and/or volatile intermediates. This review highlights recent studies that have expanded our understanding of the diversity, structure, function, and potential biotechnological uses of MCPs. Several new types of MCPs have been identified and characterized revealing new functions and potential new associations with human disease. Recent structural studies of MCP proteins and recombinant MCP shells have provided new insights into MCP assembly and mechanisms and raised new questions about MCP structure. We also discuss recent work on biotechnology applications that use MCP principles to develop nanobioreactors, nanocontainers, and molecular scaffolds.
Collapse
Affiliation(s)
- Andrew M Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Katie L Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Todd O Yeates
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA; UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA.
| | - Thomas A Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.
| |
Collapse
|
23
|
Scaffolding protein CcmM directs multiprotein phase separation in β-carboxysome biogenesis. Nat Struct Mol Biol 2021; 28:909-922. [PMID: 34759380 PMCID: PMC8580825 DOI: 10.1038/s41594-021-00676-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/28/2021] [Indexed: 12/01/2022]
Abstract
Carboxysomes in cyanobacteria enclose the enzymes Rubisco and carbonic anhydrase to optimize photosynthetic carbon fixation. Understanding carboxysome assembly has implications in agricultural biotechnology. Here we analyzed the role of the scaffolding protein CcmM of the β-cyanobacterium Synechococcus elongatus PCC 7942 in sequestrating the hexadecameric Rubisco and the tetrameric carbonic anhydrase, CcaA. We find that the trimeric CcmM, consisting of γCAL oligomerization domains and linked small subunit-like (SSUL) modules, plays a central role in mediation of pre-carboxysome condensate formation through multivalent, cooperative interactions. The γCAL domains interact with the C-terminal tails of the CcaA subunits and additionally mediate a head-to-head association of CcmM trimers. Interestingly, SSUL modules, besides their known function in recruiting Rubisco, also participate in intermolecular interactions with the γCAL domains, providing further valency for network formation. Our findings reveal the mechanism by which CcmM functions as a central organizer of the pre-carboxysome multiprotein matrix, concentrating the core components Rubisco and CcaA before β-carboxysome shell formation.
Collapse
|
24
|
Chowdhury NP, Moon J, Müller V. Adh4, an alcohol dehydrogenase controls alcohol formation within bacterial microcompartments in the acetogenic bacterium Acetobacterium woodii. Environ Microbiol 2020; 23:499-511. [PMID: 33283462 DOI: 10.1111/1462-2920.15340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/18/2020] [Accepted: 11/30/2020] [Indexed: 01/23/2023]
Abstract
Acetobacterium woodii utilizes the Wood-Ljungdahl pathway for reductive synthesis of acetate from carbon dioxide. However, A. woodii can also perform non-acetogenic growth on 1,2-propanediol (1,2-PD) where instead of acetate, equal amounts of propionate and propanol are produced as metabolic end products. Metabolism of 1,2-PD occurs via encapsulated metabolic enzymes within large proteinaceous bodies called bacterial microcompartments. While the genome of A. woodii harbours 11 genes encoding putative alcohol dehydrogenases, the BMC-encapsulated propanol-generating alcohol dehydrogenase remains unidentified. Here, we show that Adh4 of A. woodii is the alcohol dehydrogenase required for propanol/ethanol formation within these microcompartments. It catalyses the NADH-dependent reduction of propionaldehyde or acetaldehyde to propanol or ethanol and primarily functions to recycle NADH within the BMC. Removal of adh4 gene from the A. woodii genome resulted in slow growth on 1,2-PD and the mutant displayed reduced propanol and enhanced propionate formation as a metabolic end product. In sum, the data suggest that Adh4 is responsible for propanol formation within the BMC and is involved in redox balancing in the acetogen, A. woodii.
Collapse
Affiliation(s)
- Nilanjan Pal Chowdhury
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Jimyung Moon
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology and Bioenergetics, Institute of Molecular Biosciences, Johann Wolfgang Goethe University Frankfurt/Main, Frankfurt, Germany
| |
Collapse
|
25
|
Stewart KL, Stewart AM, Bobik TA. Prokaryotic Organelles: Bacterial Microcompartments in E. coli and Salmonella. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0025-2019. [PMID: 33030141 PMCID: PMC7552817 DOI: 10.1128/ecosalplus.esp-0025-2019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Indexed: 02/07/2023]
Abstract
Bacterial microcompartments (MCPs) are proteinaceous organelles consisting of a metabolic pathway encapsulated within a selectively permeable protein shell. Hundreds of species of bacteria produce MCPs of at least nine different types, and MCP metabolism is associated with enteric pathogenesis, cancer, and heart disease. This review focuses chiefly on the four types of catabolic MCPs (metabolosomes) found in Escherichia coli and Salmonella: the propanediol utilization (pdu), ethanolamine utilization (eut), choline utilization (cut), and glycyl radical propanediol (grp) MCPs. Although the great majority of work done on catabolic MCPs has been carried out with Salmonella and E. coli, research outside the group is mentioned where necessary for a comprehensive understanding. Salient characteristics found across MCPs are discussed, including enzymatic reactions and shell composition, with particular attention paid to key differences between classes of MCPs. We also highlight relevant research on the dynamic processes of MCP assembly, protein targeting, and the mechanisms that underlie selective permeability. Lastly, we discuss emerging biotechnology applications based on MCP principles and point out challenges, unanswered questions, and future directions.
Collapse
Affiliation(s)
- Katie L. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Andrew M. Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| | - Thomas A. Bobik
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA 50011
| |
Collapse
|
26
|
Kerfeld CA, Sutter M. Engineered bacterial microcompartments: apps for programming metabolism. Curr Opin Biotechnol 2020; 65:225-232. [PMID: 32554213 PMCID: PMC7719235 DOI: 10.1016/j.copbio.2020.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/04/2020] [Accepted: 05/06/2020] [Indexed: 12/12/2022]
Abstract
Bacterial Microcompartments (BMCs) are used by diverse bacteria to compartmentalize enzymatic reactions, functioning analogously to the organelles of eukaryotes. The bounding membrane and encapsulated components are composed entirely of protein, which makes them ideal targets for modification by genetic engineering. In contrast to viruses, in which generally only one protein forms the capsid, the shells of BMCs consist of a variety of shell proteins, each a potential unit of selection. Despite their differences in permeability, the shell proteins are surprisingly interchangeable. Recent developments have shown that they are also highly amenable to engineered modifications which poise them for a variety of biotechnological applications. Given their modular structure, with a module defined as a semi-autonomous functional unit, BMCs can be considered apps for programming metabolism that can be de-bugged by adaptive evolution.
Collapse
Affiliation(s)
- Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory and Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory and Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| |
Collapse
|
27
|
Rubisco accumulation factor 1 (Raf1) plays essential roles in mediating Rubisco assembly and carboxysome biogenesis. Proc Natl Acad Sci U S A 2020; 117:17418-17428. [PMID: 32636267 PMCID: PMC7382273 DOI: 10.1073/pnas.2007990117] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Carboxysomes are membrane-free organelles for carbon assimilation in cyanobacteria. The carboxysome consists of a proteinaceous shell that structurally resembles virus capsids and internal enzymes including ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco), the primary carbon-fixing enzyme in photosynthesis. The formation of carboxysomes requires hierarchical self-assembly of thousands of protein subunits, initiated from Rubisco assembly and packaging to shell encapsulation. Here we study the role of Rubisco assembly factor 1 (Raf1) in Rubisco assembly and carboxysome formation in a model cyanobacterium, Synechococcus elongatus PCC7942 (Syn7942). Cryo-electron microscopy reveals that Raf1 facilitates Rubisco assembly by mediating RbcL dimer formation and dimer-dimer interactions. Syn7942 cells lacking Raf1 are unable to form canonical intact carboxysomes but generate a large number of intermediate assemblies comprising Rubisco, CcaA, CcmM, and CcmN without shell encapsulation and a low abundance of carboxysome-like structures with reduced dimensions and irregular shell shapes and internal organization. As a consequence, the Raf1-depleted cells exhibit reduced Rubisco content, CO2-fixing activity, and cell growth. Our results provide mechanistic insight into the chaperone-assisted Rubisco assembly and biogenesis of carboxysomes. Advanced understanding of the biogenesis and stepwise formation process of the biogeochemically important organelle may inform strategies for heterologous engineering of functional CO2-fixing modules to improve photosynthesis.
Collapse
|
28
|
Rohnke BA, Rodríguez Pérez KJ, Montgomery BL. Linking the Dynamic Response of the Carbon Dioxide-Concentrating Mechanism to Carbon Assimilation Behavior in Fremyella diplosiphon. mBio 2020; 11:e01052-20. [PMID: 32457252 PMCID: PMC7251215 DOI: 10.1128/mbio.01052-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/31/2022] Open
Abstract
Cyanobacteria use a carbon dioxide (CO2)-concentrating mechanism (CCM) that enhances their carbon fixation efficiency and is regulated by many environmental factors that impact photosynthesis, including carbon availability, light levels, and nutrient access. Efforts to connect the regulation of the CCM by these factors to functional effects on carbon assimilation rates have been complicated by the aqueous nature of cyanobacteria. Here, we describe the use of cyanobacteria in a semiwet state on glass fiber filtration discs-cyanobacterial discs-to establish dynamic carbon assimilation behavior using gas exchange analysis. In combination with quantitative PCR (qPCR) and transmission electron microscopy (TEM) analyses, we linked the regulation of CCM components to corresponding carbon assimilation behavior in the freshwater, filamentous cyanobacterium Fremyella diplosiphon Inorganic carbon (Ci) levels, light quantity, and light quality have all been shown to influence carbon assimilation behavior in F. diplosiphon Our results suggest a biphasic model of cyanobacterial carbon fixation. While behavior at low levels of CO2 is driven mainly by the Ci uptake ability of the cyanobacterium, at higher CO2 levels, carbon assimilation behavior is multifaceted and depends on Ci availability, carboxysome morphology, linear electron flow, and cell shape. Carbon response curves (CRCs) generated via gas exchange analysis enable rapid examination of CO2 assimilation behavior in cyanobacteria and can be used for cells grown under distinct conditions to provide insight into how CO2 assimilation correlates with the regulation of critical cellular functions, such as the environmental control of the CCM and downstream photosynthetic capacity.IMPORTANCE Environmental regulation of photosynthesis in cyanobacteria enhances organismal fitness, light capture, and associated carbon fixation under dynamic conditions. Concentration of carbon dioxide (CO2) near the carbon-fixing enzyme RubisCO occurs via the CO2-concentrating mechanism (CCM). The CCM is also tuned in response to carbon availability, light quality or levels, or nutrient access-cues that also impact photosynthesis. We adapted dynamic gas exchange methods generally used with plants to investigate environmental regulation of the CCM and carbon fixation capacity using glass fiber-filtered cells of the cyanobacterium Fremyella diplosiphon We describe a breakthrough in measuring real-time carbon uptake and associated assimilation capacity for cells grown in distinct conditions (i.e., light quality, light quantity, or carbon status). These measurements demonstrate that the CCM modulates carbon uptake and assimilation under low-Ci conditions and that light-dependent regulation of pigmentation, cell shape, and downstream stages of carbon fixation are critical for tuning carbon uptake and assimilation.
Collapse
Affiliation(s)
- Brandon A Rohnke
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Kiara J Rodríguez Pérez
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- University of Puerto Rico at Arecibo, Arecibo, Puerto Rico
| | - Beronda L Montgomery
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| |
Collapse
|
29
|
Hennacy JH, Jonikas MC. Prospects for Engineering Biophysical CO 2 Concentrating Mechanisms into Land Plants to Enhance Yields. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:461-485. [PMID: 32151155 PMCID: PMC7845915 DOI: 10.1146/annurev-arplant-081519-040100] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Although cyanobacteria and algae represent a small fraction of the biomass of all primary producers, their photosynthetic activity accounts for roughly half of the daily CO2 fixation that occurs on Earth. These microorganisms are able to accomplish this feat by enhancing the activity of the CO2-fixing enzyme Rubisco using biophysical CO2 concentrating mechanisms (CCMs). Biophysical CCMs operate by concentrating bicarbonate and converting it into CO2 in a compartment that houses Rubisco (in contrast with other CCMs that concentrate CO2 via an organic intermediate, such as malate in the case of C4 CCMs). This activity provides Rubisco with a high concentration of its substrate, thereby increasing its reaction rate. The genetic engineering of a biophysical CCM into land plants is being pursued as a strategy to increase crop yields. This review focuses on the progress toward understanding the molecular components of cyanobacterial and algal CCMs, as well as recent advances toward engineering these components into land plants.
Collapse
Affiliation(s)
- Jessica H Hennacy
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA; ,
| |
Collapse
|
30
|
Oltrogge LM, Chaijarasphong T, Chen AW, Bolin ER, Marqusee S, Savage DF. Multivalent interactions between CsoS2 and Rubisco mediate α-carboxysome formation. Nat Struct Mol Biol 2020; 27:281-287. [PMID: 32123388 PMCID: PMC7337323 DOI: 10.1038/s41594-020-0387-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 01/24/2020] [Indexed: 11/23/2022]
Abstract
Carboxysomes are bacterial microcompartments that function as the centerpiece of the bacterial CO2-concentrating mechanism by facilitating high CO2 concentrations near the carboxylase Rubisco. The carboxysome self-assembles from thousands of individual proteins into icosahedral-like particles with a dense enzyme cargo encapsulated within a proteinaceous shell. In the case of the α-carboxysome, there is little molecular insight into protein-protein interactions that drive the assembly process. Here, studies on the α-carboxysome from Halothiobacillus neapolitanus demonstrate that Rubisco interacts with the N-terminus of CsoS2, a multivalent, intrinsically disordered protein. X-ray structural analysis of the CsoS2 interaction motif bound to Rubisco reveals a series of conserved electrostatic interactions that are only made with properly assembled hexadecameric Rubisco. Although biophysical measurements indicate this single interaction is weak, its implicit multivalency induces high-affinity binding through avidity. Taken together, our results indicate CsoS2 acts as an interaction hub to condense Rubisco and enable efficient α-carboxysome formation.
Collapse
Affiliation(s)
- Luke M Oltrogge
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
| | - Thawatchai Chaijarasphong
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.,Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Allen W Chen
- Department of Chemistry, University of California Berkeley, Berkeley, CA, USA
| | - Eric R Bolin
- Biophysics Graduate Program, University of California Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, USA
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.,Department of Chemistry, University of California Berkeley, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA.
| |
Collapse
|
31
|
Chowdhury C, Bobik TA. Engineering the PduT shell protein to modify the permeability of the 1,2-propanediol microcompartment of Salmonella. MICROBIOLOGY-SGM 2020; 165:1355-1364. [PMID: 31674899 DOI: 10.1099/mic.0.000872] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that consist of metabolic enzymes encapsulated within a protein shell. The function of MCPs is to optimize metabolic pathways by increasing reaction rates and sequestering toxic pathway intermediates. A substantial amount of effort has been directed toward engineering synthetic MCPs as intracellular nanoreactors for the improved production of renewable chemicals. A key challenge in this area is engineering protein shells that allow the entry of desired substrates. In this study, we used site-directed mutagenesis of the PduT shell protein to remove its central iron-sulfur cluster and create openings (pores) in the shell of the Pdu MCP that have varied chemical properties. Subsequently, in vivo and in vitro studies were used to show that PduT-C38S and PduT-C38A variants increased the diffusion of 1,2-propanediol, propionaldehyde, NAD+ and NADH across the shell of the MCP. In contrast, PduT-C38I and PduT-C38W eliminated the iron-sulfur cluster without altering the permeability of the Pdu MCP, suggesting that the side-chains of C38I and C38W occluded the opening formed by removal of the iron-sulfur cluster. Thus, genetic modification offers an approach to engineering the movement of larger molecules (such as NAD/H) across MCP shells, as well as a method for blocking transport through trimeric bacterial microcompartment (BMC) domain shell proteins.
Collapse
Affiliation(s)
- Chiranjit Chowdhury
- Present address: Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Campus, Sector-125, Noida, UP-201313, India.,Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Thomas A Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
32
|
Juodeikis R, Lee MJ, Mayer M, Mantell J, Brown IR, Verkade P, Woolfson DN, Prentice MB, Frank S, Warren MJ. Effect of metabolosome encapsulation peptides on enzyme activity, coaggregation, incorporation, and bacterial microcompartment formation. Microbiologyopen 2020; 9:e1010. [PMID: 32053746 PMCID: PMC7221423 DOI: 10.1002/mbo3.1010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/17/2020] [Accepted: 01/21/2020] [Indexed: 01/21/2023] Open
Abstract
Metabolosomes, catabolic bacterial microcompartments (BMCs), are proteinaceous organelles that are associated with the breakdown of metabolites such as propanediol and ethanolamine. They are composed of an outer multicomponent protein shell that encases a specific metabolic pathway. Protein cargo found within BMCs is directed by the presence of an encapsulation peptide that appears to trigger aggregation before the formation of the outer shell. We investigated the effect of three distinct encapsulation peptides on foreign cargo in a recombinant BMC system. Our data demonstrate that these peptides cause variations in enzyme activity and protein aggregation. We observed that the level of protein aggregation generally correlates with the size of metabolosomes, while in the absence of cargo BMCs self‐assemble into smaller compartments. The results agree with a flexible model for BMC formation based around the ability of the BMC shell to associate with an aggregate formed due to the interaction of encapsulation peptides.
Collapse
Affiliation(s)
- Rokas Juodeikis
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| | - Matthew J Lee
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| | - Matthias Mayer
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| | - Judith Mantell
- School of Biochemistry, University of Bristol, Bristol, UK.,Wolfson Bioimaging Facility, University of Bristol, Bristol, UK
| | - Ian R Brown
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, UK.,Wolfson Bioimaging Facility, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Bristol, UK.,BrisSynBio, University of Bristol, Bristol, UK.,School of Chemistry, University of Bristol, Bristol, UK
| | | | - Stefanie Frank
- Department of Biochemical Engineering, University College London, London, UK
| | - Martin J Warren
- Centre for Industrial Biotechnology, School of Biosciences, University of Kent, Canterbury, UK
| |
Collapse
|
33
|
Kalnins G, Cesle EE, Jansons J, Liepins J, Filimonenko A, Tars K. Encapsulation mechanisms and structural studies of GRM2 bacterial microcompartment particles. Nat Commun 2020; 11:388. [PMID: 31959751 PMCID: PMC6971018 DOI: 10.1038/s41467-019-14205-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 12/18/2019] [Indexed: 11/08/2022] Open
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles consisting of a protein shell and an encapsulated enzymatic core. BMCs are involved in several biochemical processes, such as choline, glycerol and ethanolamine degradation and carbon fixation. Since non-native enzymes can also be encapsulated in BMCs, an improved understanding of BMC shell assembly and encapsulation processes could be useful for synthetic biology applications. Here we report the isolation and recombinant expression of BMC structural genes from the Klebsiella pneumoniae GRM2 locus, the investigation of mechanisms behind encapsulation of the core enzymes, and the characterization of shell particles by cryo-EM. We conclude that the enzymatic core is encapsulated in a hierarchical manner and that the CutC choline lyase may play a secondary role as an adaptor protein. We also present a cryo-EM structure of a pT = 4 quasi-symmetric icosahedral shell particle at 3.3 Å resolution, and demonstrate variability among the minor shell forms.
Collapse
Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia.
| | - Eva-Emilija Cesle
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| | - Anatolij Filimonenko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites 1, Riga, 1067, Latvia
- University of Latvia, Jelgavas 1, Riga, 1004, Latvia
| |
Collapse
|
34
|
Garcia-Alles LF, Root K, Maveyraud L, Aubry N, Lesniewska E, Mourey L, Zenobi R, Truan G. Occurrence and stability of hetero-hexamer associations formed by β-carboxysome CcmK shell components. PLoS One 2019; 14:e0223877. [PMID: 31603944 PMCID: PMC6788708 DOI: 10.1371/journal.pone.0223877] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
The carboxysome is a bacterial micro-compartment (BMC) subtype that encapsulates enzymatic activities necessary for carbon fixation. Carboxysome shells are composed of a relatively complex cocktail of proteins, their precise number and identity being species dependent. Shell components can be classified in two structural families, the most abundant class associating as hexamers (BMC-H) that are supposed to be major players for regulating shell permeability. Up to recently, these proteins were proposed to associate as homo-oligomers. Genomic data, however, demonstrated the existence of paralogs coding for multiple shell subunits. Here, we studied cross-association compatibilities among BMC-H CcmK proteins of Synechocystis sp. PCC6803. Co-expression in Escherichia coli proved a consistent formation of hetero-hexamers combining CcmK1 and CcmK2 or, remarkably, CcmK3 and CcmK4 subunits. Unlike CcmK1/K2 hetero-hexamers, the stoichiometry of incorporation of CcmK3 in associations with CcmK4 was low. Cross-interactions implicating other combinations were weak, highlighting a structural segregation of the two groups that could relate to gene organization. Sequence analysis and structural models permitted the localization of interactions that would favor formation of CcmK3/K4 hetero-hexamers. The crystallization of these CcmK3/K4 associations conducted to the elucidation of a structure corresponding to the CcmK4 homo-hexamer. Yet, subunit exchange could not be demonstrated in vitro. Biophysical measurements showed that hetero-hexamers are thermally less stable than homo-hexamers, and impeded in forming larger assemblies. These novel findings are discussed within the context of reported data to propose a functional scenario in which minor CcmK3/K4 incorporation in shells would introduce sufficient local disorder as to allow shell remodeling necessary to adapt rapidly to environmental changes.
Collapse
Affiliation(s)
- Luis F. Garcia-Alles
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- * E-mail:
| | - Katharina Root
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Laurent Maveyraud
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Nathalie Aubry
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Eric Lesniewska
- ICB UMR CNRS 6303, University of Bourgogne Franche-Comte, Dijon, France
| | - Lionel Mourey
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Gilles Truan
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| |
Collapse
|
35
|
Kirst H, Kerfeld CA. Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering. BMC Biol 2019; 17:79. [PMID: 31601225 PMCID: PMC6787980 DOI: 10.1186/s12915-019-0691-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 08/23/2019] [Indexed: 12/15/2022] Open
Abstract
Bacterial cells have long been thought to be simple cells with little spatial organization, but recent research has shown that they exhibit a remarkable degree of subcellular differentiation. Indeed, bacteria even have organelles such as magnetosomes for sensing magnetic fields or gas vesicles controlling cell buoyancy. A functionally diverse group of bacterial organelles are the bacterial microcompartments (BMCs) that fulfill specialized metabolic needs. Modification and reengineering of these BMCs enable innovative approaches for metabolic engineering and nanomedicine.
Collapse
Affiliation(s)
- Henning Kirst
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA.,Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA. .,Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA.
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
Ferlez B, Sutter M, Kerfeld CA. A designed bacterial microcompartment shell with tunable composition and precision cargo loading. Metab Eng 2019; 54:286-291. [PMID: 31075444 PMCID: PMC6884132 DOI: 10.1016/j.ymben.2019.04.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/09/2019] [Accepted: 04/24/2019] [Indexed: 12/31/2022]
Abstract
Microbes often augment their metabolism by conditionally constructing proteinaceous organelles, known as bacterial microcompartments (BMCs), that encapsulate enzymes to degrade organic compounds or assimilate CO2. BMCs self-assemble and are spatially delimited by a semi-permeable shell made up of hexameric, trimeric, and pentameric shell proteins. Bioengineers aim to recapitulate the organization and efficiency of these complex biological architectures by redesigning the shell to incorporate non-native enzymes from biotechnologically relevant pathways. To meet this challenge, a diverse set of synthetic biology tools are required, including methods to manipulate the properties of the shell as well as target and organize cargo encapsulation. We designed and determined the crystal structure of a synthetic shell protein building block with an inverted sidedness of its N- and C-terminal residues relative to its natural counterpart; the inversion targets genetically fused protein cargo to the lumen of the shell. Moreover, the titer of fluorescent protein cargo encapsulated using this strategy is controllable using an inducible tetracycline promoter. These results expand the available set of building blocks for precision engineering of BMC-based nanoreactors and are compatible with orthogonal methods which will facilitate the installation and organization of multi-enzyme pathways.
Collapse
Affiliation(s)
- Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
| |
Collapse
|
38
|
Bio-engineering of bacterial microcompartments: a mini review. Biochem Soc Trans 2019; 47:765-777. [DOI: 10.1042/bst20170564] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/30/2022]
Abstract
AbstractBacterial microcompartments (BMCs) are protein-bound prokaryotic organelles, discovered in cyanobacteria more than 60 years ago. Functionally similar to eukaryotic cellular organelles, BMCs compartment metabolic activities in the cytoplasm, foremost to increase local enzyme concentration and prevent toxic intermediates from damaging the cytosolic content. Advanced knowledge of the functional and structural properties of multiple types of BMCs, particularly over the last 10 years, have highlighted design principles of microcompartments. This has prompted new research into their potential to function as programmable synthetic nano-bioreactors and novel bio-materials with biotechnological and medical applications. Moreover, due to the involvement of microcompartments in bacterial pathogenesis and human health, BMCs have begun to gain attention as potential novel drug targets. This mini-review gives an overview of important synthetic biology developments in the bioengineering of BMCs and a perspective on future directions in the field.
Collapse
|
39
|
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.
Collapse
Affiliation(s)
- Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands.
| | | | | | | | | |
Collapse
|
40
|
Vedalankar P, Tripathy BC. Evolution of light-independent protochlorophyllide oxidoreductase. PROTOPLASMA 2019; 256:293-312. [PMID: 30291443 DOI: 10.1007/s00709-018-1317-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/27/2018] [Indexed: 06/08/2023]
Abstract
The nonhomologous enzymes, the light-independent protochlorophyllide reductase (DPOR) and the light-dependent protochlorophyllide oxidoreductase (LPOR), catalyze the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide) in the penultimate step of biosynthesis of chlorophyll (Chl) required for photosynthetic light absorption and energy conversion. The two enzymes differ with respect to the requirement of light for catalysis and oxygen sensitivity. DPOR and LPOR initially evolved in the ancestral prokaryotic genome perhaps at different times. DPOR originated in the anoxygenic environment of the Earth from nitrogenase-like enzyme of methanogenic archaea. Due to the transition from anoxygenic to oxygenic photosynthesis in the prokaryote, the DPOR was mostly inactivated in the daytime by photosynthetic O2 leading to the evolution of oxygen-insensitive LPOR that could function in the light. The primary endosymbiotic event transferred the DPOR and LPOR genes to the eukaryotic phototroph; the DPOR remained in the genome of the ancestor that turned into the plastid, whereas LPOR was transferred to the host nuclear genome. From an evolutionary point of view, several compelling theories that explain the disappearance of DPOR from several species cutting across different phyla are as follows: (i) pressure of the oxygenic environment; (ii) change in the light conditions and temperature; and (iii) lineage-specific gene losses, RNA editing, and nonsynonymous substitution. Certain primary amino acid sequence and the physiochemical properties of the ChlL subunit of DPOR have similarity with that of LPOR suggesting a convergence of these two enzymes in certain evolutionary event. The newly obtained sequence data from different phototrophs will further enhance the width of the phylogenetic information on DPOR.
Collapse
Affiliation(s)
| | - Baishnab C Tripathy
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| |
Collapse
|
41
|
Ferlez B, Sutter M, Kerfeld CA. Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles. mBio 2019; 10:e02327-18. [PMID: 30622187 PMCID: PMC6325248 DOI: 10.1128/mbio.02327-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 11/28/2018] [Indexed: 12/31/2022] Open
Abstract
An increasing number of microbes are being identified that organize catabolic pathways within self-assembling proteinaceous structures known as bacterial microcompartments (BMCs). Most BMCs are characterized by their singular substrate specificity and commonly employ B12-dependent radical mechanisms. In contrast, a less-well-known BMC type utilizes the B12-independent radical chemistry of glycyl radical enzymes (GREs). Unlike B12-dependent enzymes, GREs require an activating enzyme (AE) as well as an external source of electrons to generate an adenosyl radical and form their catalytic glycyl radical. Organisms encoding these glycyl radical enzyme-associated microcompartments (GRMs) confront the challenge of coordinating the activation and maintenance of their GREs with the assembly of a multienzyme core that is encapsulated in a protein shell. The GRMs appear to enlist redox proteins to either generate reductants internally or facilitate the transfer of electrons from the cytosol across the shell. Despite this relative complexity, GRMs are one of the most widespread types of BMC, with distinct subtypes to catabolize different substrates. Moreover, they are encoded by many prominent gut-associated and pathogenic bacteria. In this review, we will focus on the diversity, function, and physiological importance of GRMs, with particular attention given to their associated and enigmatic redox proteins.
Collapse
Affiliation(s)
- Bryan Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| |
Collapse
|
42
|
Ryan P, Forrester TJB, Wroblewski C, Kenney TMG, Kitova EN, Klassen JS, Kimber MS. The small RbcS-like domains of the β-carboxysome structural protein CcmM bind RubisCO at a site distinct from that binding the RbcS subunit. J Biol Chem 2018; 294:2593-2603. [PMID: 30591587 DOI: 10.1074/jbc.ra118.006330] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/13/2018] [Indexed: 12/26/2022] Open
Abstract
Carboxysomes are compartments in bacterial cells that promote efficient carbon fixation by sequestering RubisCO and carbonic anhydrase within a protein shell that impedes CO2 escape. The key to assembling this protein complex is CcmM, a multidomain protein whose C-terminal region is required for RubisCO recruitment. This CcmM region is built as a series of copies (generally 3-5) of a small domain, CcmMS, joined by unstructured linkers. CcmMS domains have weak, but significant, sequence identity to RubisCO's small subunit, RbcS, suggesting that CcmM binds RubisCO by displacing RbcS. We report here the 1.35-Å structure of the first Thermosynechococcus elongatus CcmMS domain, revealing that it adopts a compact, well-defined structure that resembles that of RbcS. CcmMS, however, lacked key RbcS RubisCO-binding determinants, most notably an extended N-terminal loop. Nevertheless, individual CcmMS domains are able to bind RubisCO in vitro with 1.16 μm affinity. Two or four linked CcmMS domains did not exhibit dramatic increases in this affinity, implying that short, disordered linkers may frustrate successive CcmMS domains attempting to simultaneously bind a single RubisCO oligomer. Size-exclusion chromatography-coupled right-angled light scattering (SEC-RALS) and native MS experiments indicated that multiple CcmMS domains can bind a single RubisCO holoenzyme and, moreover, that RbcS is not released from these complexes. CcmMS bound equally tightly to a RubisCO variant in which the α/β domain of RbcS was deleted, suggesting that CcmMS binds RubisCO independently of its RbcS subunit. We propose that, instead, the electropositive CcmMS may bind to an extended electronegative pocket between RbcL dimers.
Collapse
Affiliation(s)
- Patrick Ryan
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Taylor J B Forrester
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Charles Wroblewski
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Tristan M G Kenney
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Matthew S Kimber
- From the Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada and
| |
Collapse
|
43
|
MacCready JS, Hakim P, Young EJ, Hu L, Liu J, Osteryoung KW, Vecchiarelli AG, Ducat DC. Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria. eLife 2018; 7:39723. [PMID: 30520729 PMCID: PMC6328274 DOI: 10.7554/elife.39723] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/19/2018] [Indexed: 12/25/2022] Open
Abstract
Carboxysomes are protein-based bacterial organelles encapsulating key enzymes of the Calvin-Benson-Bassham cycle. Previous work has implicated a ParA-like protein (hereafter McdA) as important for spatially organizing carboxysomes along the longitudinal axis of the model cyanobacterium Synechococcus elongatus PCC 7942. Yet, how self-organization of McdA emerges and contributes to carboxysome positioning is unknown. Here, we identify a small protein, termed McdB that localizes to carboxysomes and drives emergent oscillatory patterning of McdA on the nucleoid. Our results demonstrate that McdB directly stimulates McdA ATPase activity and its release from DNA, driving carboxysome-dependent depletion of McdA locally on the nucleoid and promoting directed motion of carboxysomes towards increased concentrations of McdA. We propose that McdA and McdB are a previously unknown class of self-organizing proteins that utilize a Brownian-ratchet mechanism to position carboxysomes in cyanobacteria, rather than a cytoskeletal system. These results have broader implications for understanding spatial organization of protein mega-complexes and organelles in bacteria. Cyanobacteria are tiny organisms that can harness the energy of the sun to power their cells. Many of the tools required for this complex photosynthetic process are packaged into small compartments inside the cell, the carboxysomes. In Synechococcus elongatus, a cyanobacterium that is shaped like a rod, the carboxysomes are positioned at regular intervals along the length of the cell. This ensures that, when the bacterium splits itself in half to reproduce, both daughter cells have the same number of carboxysomes. Researchers know that, in S. elongatus, a protein called McdA can oscillate from one end of the cell to the other. This protein is responsible for the carboxysomes being in the right place, and some scientists believe that it helps to create an internal skeleton that anchors and drags the compartments into position. Here, MacCready et al. propose another mechanism and, by combining various approaches, identify a new partner for McdA. This protein, called McdB, is present on the carboxysomes. McdB also binds to McdA, which itself attaches to the nucleoid – the region in the cell that contains the DNA. McdB forces McdA to release itself from DNA, causing the protein to reposition itself along the nucleoid. Because McdB attaches to McdA, the carboxysomes then follow suit, constantly seeking the highest concentrations of McdA bound to nearby DNA. Instead of relying on a cellular skeleton, these two proteins can organize themselves on their own using the nucleoid as a scaffold; in turn, they distribute carboxysomes evenly along the length of a cell. Plants also obtain their energy from the sun via photosynthesis, but they do not carry carboxysomes. Scientists have tried to introduce these compartments inside plant cells, hoping that it could generate crops with higher yields. Knowing how carboxysomes are organized so they can be passed down from one generation to the next could be important for these experiments.
Collapse
Affiliation(s)
- Joshua S MacCready
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
| | - Pusparanee Hakim
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Michigan, United States
| | - Eric J Young
- Department of Biochemistry, Michigan State University, East Lansing, United States
| | - Longhua Hu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jian Liu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | | | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Michigan, United States
| | - Daniel C Ducat
- Department of Biochemistry, Michigan State University, East Lansing, United States.,MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
| |
Collapse
|
44
|
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.
Collapse
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.
| |
Collapse
|
45
|
Liu Y, He X, Lim W, Mueller J, Lawrie J, Kramer L, Guo J, Niu W. Deciphering molecular details in the assembly of alpha-type carboxysome. Sci Rep 2018; 8:15062. [PMID: 30305640 PMCID: PMC6180065 DOI: 10.1038/s41598-018-33074-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/12/2018] [Indexed: 01/25/2023] Open
Abstract
Bacterial microcompartments (BMCs) are promising natural protein structures for applications that require the segregation of certain metabolic functions or molecular species in a defined microenvironment. To understand how endogenous cargos are packaged inside the protein shell is key for using BMCs as nano-scale reactors or delivery vesicles. In this report, we studied the encapsulation of RuBisCO into the α-type carboxysome from Halothiobacillus neapolitan. Our experimental data revealed that the CsoS2 scaffold proteins engage RuBisCO enzyme through an interaction with the small subunit (CbbS). In addition, the N domain of the large subunit (CbbL) of RuBisCO interacts with all shell proteins that can form the hexamers. The binding affinity between the N domain of CbbL and one of the major shell proteins, CsoS1C, is within the submicromolar range. The absence of the N domain also prevented the encapsulation of the rest of the RuBisCO subunits. Our findings complete the picture of how RuBisCOs are encapsulated into the α-type carboxysome and provide insights for future studies and engineering of carboxysome as a protein shell.
Collapse
Affiliation(s)
- Yilan Liu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Xinyuan He
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Weiping Lim
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Joshua Mueller
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Justin Lawrie
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Levi Kramer
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Jiantao Guo
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States
| | - Wei Niu
- Department of Chemical & Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States.
| |
Collapse
|
46
|
Biotechnological Advances in Bacterial Microcompartment Technology. Trends Biotechnol 2018; 37:325-336. [PMID: 30236905 DOI: 10.1016/j.tibtech.2018.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/22/2018] [Accepted: 08/23/2018] [Indexed: 12/22/2022]
Abstract
Bacterial microcompartments (BMCs) represent proteinaceous macromolecular nanobioreactors that are found in a broad range of bacteria, and which are associated with either anabolic or catabolic processes. They consist of a semipermeable outer shell that packages a central metabolic enzyme or pathway, providing both enhanced flux and protection against toxic intermediates. Recombinant production of BMCs has led to their repurposing with the incorporation of altogether new pathways. Deconstructing BMCs into their component parts has shown that some individual shell proteins self-associate into filaments that can be further modified into a cytoplasmic scaffold, or cytoscaffold, to which enzymes/proteins can be targeted. BMCs therefore represent a modular system that is highly suited for engineering biological systems for useful purposes.
Collapse
|
47
|
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.
Collapse
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.
| |
Collapse
|
48
|
Hagen A, Sutter M, Sloan N, Kerfeld CA. Programmed loading and rapid purification of engineered bacterial microcompartment shells. Nat Commun 2018; 9:2881. [PMID: 30038362 PMCID: PMC6056538 DOI: 10.1038/s41467-018-05162-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/15/2018] [Indexed: 12/30/2022] Open
Abstract
Bacterial microcompartments (BMCs) are selectively permeable proteinaceous organelles which encapsulate segments of metabolic pathways across bacterial phyla. They consist of an enzymatic core surrounded by a protein shell composed of multiple distinct proteins. Despite great potential in varied biotechnological applications, engineering efforts have been stymied by difficulties in their isolation and characterization and a dearth of robust methods for programming cores and shell permeability. We address these challenges by functionalizing shell proteins with affinity handles, enabling facile complementation-based affinity purification (CAP) and specific cargo docking sites for efficient encapsulation via covalent-linkage (EnCo). These shell functionalizations extend our knowledge of BMC architectural principles and enable the development of minimal shell systems of precisely defined structure and composition. The generalizability of CAP and EnCo will enable their application to functionally diverse microcompartment systems to facilitate both characterization of natural functions and the development of bespoke shells for selectively compartmentalizing proteins.
Collapse
Affiliation(s)
- Andrew Hagen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Markus Sutter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA.,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Nancy Sloan
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Cheryl A Kerfeld
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA. .,MSU-DOE Plant Research Laboratory, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA. .,Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Road, East Lansing, MI, 48824, USA.
| |
Collapse
|
49
|
Volke DC, Nikel PI. Getting Bacteria in Shape: Synthetic Morphology Approaches for the Design of Efficient Microbial Cell Factories. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800111] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel C. Volke
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability; Technical University of Denmark; Kemitorvet 2800 Kgs. Lyngby Denmark
| |
Collapse
|
50
|
Mohajerani F, Hagan MF. The role of the encapsulated cargo in microcompartment assembly. PLoS Comput Biol 2018; 14:e1006351. [PMID: 30063715 PMCID: PMC6086489 DOI: 10.1371/journal.pcbi.1006351] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/10/2018] [Accepted: 07/10/2018] [Indexed: 11/19/2022] Open
Abstract
Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and theoretical modeling to study the factors that control the size and morphology of a protein shell assembling around hundreds to thousands of molecules. We perform dynamical simulations of shell assembly in the presence and absence of cargo over a range of interaction strengths, subunit and cargo stoichiometries, and the shell spontaneous curvature. Depending on these parameters, we find that the presence of a cargo can either increase or decrease the size of a shell relative to its intrinsic spontaneous curvature, as seen in recent experiments. These features are controlled by a balance of kinetic and thermodynamic effects, and the shell size is assembly pathway dependent. We discuss implications of these results for synthetic biology efforts to target new enzymes to microcompartment interiors.
Collapse
Affiliation(s)
- Farzaneh Mohajerani
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, Massachusetts, United States of America
| |
Collapse
|