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Sutter M, Kerfeld CA, Scott KM. Atypical Carboxysome Loci: JEEPs or Junk? Front Microbiol 2022; 13:872708. [PMID: 35668770 PMCID: PMC9164163 DOI: 10.3389/fmicb.2022.872708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 11/13/2022] Open
Abstract
Carboxysomes, responsible for a substantial fraction of CO2 fixation on Earth, are proteinaceous microcompartments found in many autotrophic members of domain Bacteria, primarily from the phyla Proteobacteria and Cyanobacteria. Carboxysomes facilitate CO2 fixation by the Calvin-Benson-Bassham (CBB) cycle, particularly under conditions where the CO2 concentration is variable or low, or O2 is abundant. These microcompartments are composed of an icosahedral shell containing the enzymes ribulose 1,5-carboxylase/oxygenase (RubisCO) and carbonic anhydrase. They function as part of a CO2 concentrating mechanism, in which cells accumulate HCO3 - in the cytoplasm via active transport, HCO3 - enters the carboxysomes through pores in the carboxysomal shell proteins, and carboxysomal carbonic anhydrase facilitates the conversion of HCO3 - to CO2, which RubisCO fixes. Two forms of carboxysomes have been described: α-carboxysomes and β-carboxysomes, which arose independently from ancestral microcompartments. The α-carboxysomes present in Proteobacteria and some Cyanobacteria have shells comprised of four types of proteins [CsoS1 hexamers, CsoS4 pentamers, CsoS2 assembly proteins, and α-carboxysomal carbonic anhydrase (CsoSCA)], and contain form IA RubisCO (CbbL and CbbS). In the majority of cases, these components are encoded in the genome near each other in a gene locus, and transcribed together as an operon. Interestingly, genome sequencing has revealed some α-carboxysome loci that are missing genes encoding one or more of these components. Some loci lack the genes encoding RubisCO, others lack a gene encoding carbonic anhydrase, some loci are missing shell protein genes, and in some organisms, genes homologous to those encoding the carboxysome-associated carbonic anhydrase are the only carboxysome-related genes present in the genome. Given that RubisCO, assembly factors, carbonic anhydrase, and shell proteins are all essential for carboxysome function, these absences are quite intriguing. In this review, we provide an overview of the most recent studies of the structural components of carboxysomes, describe the genomic context and taxonomic distribution of atypical carboxysome loci, and propose functions for these variants. We suggest that these atypical loci are JEEPs, which have modified functions based on the presence of Just Enough Essential Parts.
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Affiliation(s)
| | | | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrated Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, FL, United States
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Tullman-Ercek D, Warren M. Editorial overview: Bacterial microcompartments to the fore as metabolism is put in its place. Curr Opin Microbiol 2021; 64:159-161. [PMID: 34740525 DOI: 10.1016/j.mib.2021.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Technological Institute E136, Evanston, IL, 60208, USA.
| | - Martin Warren
- Quadram Institute Bioscience, Norwich Research Park, NR4 7UQ, UK
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MacCready JS, Tran L, Basalla JL, Hakim P, Vecchiarelli AG. The McdAB system positions α-carboxysomes in proteobacteria. Mol Microbiol 2021; 116:277-297. [PMID: 33638215 PMCID: PMC8359340 DOI: 10.1111/mmi.14708] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 02/06/2023]
Abstract
Carboxysomes are protein-based organelles essential for carbon fixation in cyanobacteria and proteobacteria. Previously, we showed that the cyanobacterial nucleoid is used to equally space out β-carboxysomes across cell lengths by a two-component system (McdAB) in the model cyanobacterium Synechococcus elongatus PCC 7942. More recently, we found that McdAB systems are widespread among β-cyanobacteria, which possess β-carboxysomes, but are absent in α-cyanobacteria, which possess structurally and phyletically distinct α-carboxysomes. Cyanobacterial α-carboxysomes are thought to have arisen in proteobacteria and then horizontally transferred into cyanobacteria, which suggests that α-carboxysomes in proteobacteria may also lack the McdAB system. Here, using the model chemoautotrophic proteobacterium Halothiobacillus neapolitanus, we show that a McdAB system distinct from that of β-cyanobacteria operates to position α-carboxysomes across cell lengths. We further show that this system is widespread among α-carboxysome-containing proteobacteria and that cyanobacteria likely inherited an α-carboxysome operon from a proteobacterium lacking the mcdAB locus. These results demonstrate that McdAB is a cross-phylum two-component system necessary for positioning both α- and β-carboxysomes. The findings have further implications for understanding the positioning of other protein-based bacterial organelles involved in diverse metabolic processes. PLAIN LANGUAGE SUMMARY: Cyanobacteria are well known to fix atmospheric CO2 into sugars using the enzyme Rubisco. Less appreciated are the carbon-fixing abilities of proteobacteria with diverse metabolisms. Bacterial Rubisco is housed within organelles called carboxysomes that increase enzymatic efficiency. Here we show that proteobacterial carboxysomes are distributed in the cell by two proteins, McdA and McdB. McdA on the nucleoid interacts with McdB on carboxysomes to equidistantly space carboxysomes from one another, ensuring metabolic homeostasis and a proper inheritance of carboxysomes following cell division. This study illuminates how widespread carboxysome positioning systems are among diverse bacteria. Carboxysomes significantly contribute to global carbon fixation; therefore, understanding the spatial organization mechanism shared across the bacterial world is of great interest.
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Affiliation(s)
- Joshua S. MacCready
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
| | - Lisa Tran
- Department of Microbiology and ImmunologyUniversity of MichiganAnn ArborMIUSA
| | - Joseph L. Basalla
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
| | - Pusparanee Hakim
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
| | - Anthony G. Vecchiarelli
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMIUSA
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Apparent size and morphology of bacterial microcompartments varies with technique. PLoS One 2020; 15:e0226395. [PMID: 32150579 PMCID: PMC7062276 DOI: 10.1371/journal.pone.0226395] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 02/25/2020] [Indexed: 12/30/2022] Open
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that encapsulate metabolic pathways. Metabolic engineers have recently sought to repurpose MCPs to encapsulate heterologous pathways to increase flux through pathways of interest. As MCP engineering becomes more common, standardized methods for analyzing changes to MCPs and interpreting results across studies will become increasingly important. In this study, we demonstrate that different imaging techniques yield variations in the apparent size of purified MCPs from Salmonella enterica serovar Typhimurium LT2, likely due to variations in sample preparation methods. We provide guidelines for preparing samples for MCP imaging and outline expected variations in apparent size and morphology between methods. With this report we aim to establish an aid for comparing results across studies.
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Hinzpeter F, Gerland U, Tostevin F. Optimal Compartmentalization Strategies for Metabolic Microcompartments. Biophys J 2017; 112:767-779. [PMID: 28256236 PMCID: PMC5340097 DOI: 10.1016/j.bpj.2016.11.3194] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/18/2016] [Accepted: 11/28/2016] [Indexed: 11/16/2022] Open
Abstract
Intracellular compartmentalization of cooperating enzymes is a strategy that is frequently used by cells. Segregation of enzymes that catalyze sequential reactions can alleviate challenges such as toxic pathway intermediates, competing metabolic reactions, and slow reaction rates. Inspired by nature, synthetic biologists also seek to encapsulate engineered metabolic pathways within vesicles or proteinaceous shells to enhance the yield of industrially and pharmaceutically useful products. Although enzymatic compartments have been extensively studied experimentally, a quantitative understanding of the underlying design principles is still lacking. Here, we study theoretically how the size and enzymatic composition of compartments should be chosen so as to maximize the productivity of a model metabolic pathway. We find that maximizing productivity requires compartments larger than a certain critical size. The enzyme density within each compartment should be tuned according to a power-law scaling in the compartment size. We explain these observations using an analytically solvable, well-mixed approximation. We also investigate the qualitatively different compartmentalization strategies that emerge in parameter regimes where this approximation breaks down. Our results suggest that the different sizes and enzyme packings of α- and β-carboxysomes each constitute an optimal compartmentalization strategy given the properties of their respective protein shells.
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Affiliation(s)
- Florian Hinzpeter
- Department of Physics, Technische Universität München, Garching, Germany.
| | - Ulrich Gerland
- Department of Physics, Technische Universität München, Garching, Germany
| | - Filipe Tostevin
- Department of Physics, Technische Universität München, Garching, Germany
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Abstract
This review summarizes research performed over the last 23 years on the genetics, enzyme structures and functions, and regulation of the expression of the genes encoding functions involved in adenosylcobalamin (AdoCbl, or coenzyme B12) biosynthesis. It also discusses the role of coenzyme B12 in the physiology of Salmonella enterica serovar Typhimurium LT2 and Escherichia coli. John Roth's seminal contributions to the field of coenzyme B12 biosynthesis research brought the power of classical and molecular genetic, biochemical, and structural approaches to bear on the extremely challenging problem of dissecting the steps of what has turned out to be one of the most complex biosynthetic pathways known. In E. coli and serovar Typhimurium, uro'gen III represents the first branch point in the pathway, where the routes for cobalamin and siroheme synthesis diverge from that for heme synthesis. The cobalamin biosynthetic pathway in P. denitrificans was the first to be elucidated, but it was soon realized that there are at least two routes for cobalamin biosynthesis, representing aerobic and anaerobic variations. The expression of the AdoCbl biosynthetic operon is complex and is modulated at different levels. At the transcriptional level, a sensor response regulator protein activates the transcription of the operon in response to 1,2-Pdl in the environment. Serovar Typhimurium and E. coli use ethanolamine as a source of carbon, nitrogen, and energy. In addition, and unlike E. coli, serovar Typhimurium can also grow on 1,2-Pdl as the sole source of carbon and energy.
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Huber MC, Schreiber A, von Olshausen P, Varga BR, Kretz O, Joch B, Barnert S, Schubert R, Eimer S, Kele P, Schiller SM. Designer amphiphilic proteins as building blocks for the intracellular formation of organelle-like compartments. NATURE MATERIALS 2015; 14:125-32. [PMID: 25362355 DOI: 10.1038/nmat4118] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 09/22/2014] [Indexed: 05/24/2023]
Abstract
Nanoscale biological materials formed by the assembly of defined block-domain proteins control the formation of cellular compartments such as organelles. Here, we introduce an approach to intentionally 'program' the de novo synthesis and self-assembly of genetically encoded amphiphilic proteins to form cellular compartments, or organelles, in Escherichia coli. These proteins serve as building blocks for the formation of artificial compartments in vivo in a similar way to lipid-based organelles. We investigated the formation of these organelles using epifluorescence microscopy, total internal reflection fluorescence microscopy and transmission electron microscopy. The in vivo modification of these protein-based de novo organelles, by means of site-specific incorporation of unnatural amino acids, allows the introduction of artificial chemical functionalities. Co-localization of membrane proteins results in the formation of functionalized artificial organelles combining artificial and natural cellular function. Adding these protein structures to the cellular machinery may have consequences in nanobiotechnology, synthetic biology and materials science, including the constitution of artificial cells and bio-based metamaterials.
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Affiliation(s)
- Matthias C Huber
- 1] Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Str. 31 D-79104 Freiburg, Germany [2] Institute for Pharmaceutical Sciences, University of Freiburg, Albertstr. 25 D-79104 Freiburg, Germany [3] Freiburg Institute for Advanced Studies (FRIAS), School of Soft Matter Research, University of Freiburg, Albertstr. 19 D-79104 Freiburg, Germany [4] Faculty of Chemistry and Pharmacy, University of Freiburg, Fahnenbergplatz D-79104 Freiburg, Germany
| | - Andreas Schreiber
- 1] Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Str. 31 D-79104 Freiburg, Germany [2] Institute for Pharmaceutical Sciences, University of Freiburg, Albertstr. 25 D-79104 Freiburg, Germany [3] Freiburg Institute for Advanced Studies (FRIAS), School of Soft Matter Research, University of Freiburg, Albertstr. 19 D-79104 Freiburg, Germany [4] Faculty of Biology, University of Freiburg, Schänzlestrasse 1 D-79085 Freiburg, Germany
| | - Philipp von Olshausen
- 1] Bio- and Nano-Photonics, Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 102 D-79110 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18 D-79104 Freiburg, Germany
| | - Balázs R Varga
- Chemical Biology Research Group, Hungarian Academy of Sciences, CNS, IOC, Magyar tudósok krt. 2 H-1117 Budapest, Hungary
| | - Oliver Kretz
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18 D-79104 Freiburg, Germany
| | - Barbara Joch
- Institute for Neuroanatomy University of Freiburg, Albertstr. 17 D-79104 Freiburg, Germany
| | - Sabine Barnert
- 1] Faculty of Chemistry and Pharmacy, University of Freiburg, Fahnenbergplatz D-79104 Freiburg, Germany [2] Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology and Biopharmacy, University of Freiburg, Hermann-Herder-Str. 9 D-79104 Freiburg, Germany
| | - Rolf Schubert
- 1] Faculty of Chemistry and Pharmacy, University of Freiburg, Fahnenbergplatz D-79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18 D-79104 Freiburg, Germany [3] Institute of Pharmaceutical Sciences, Department of Pharmaceutical Technology and Biopharmacy, University of Freiburg, Hermann-Herder-Str. 9 D-79104 Freiburg, Germany
| | - Stefan Eimer
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18 D-79104 Freiburg, Germany
| | - Péter Kele
- Chemical Biology Research Group, Hungarian Academy of Sciences, CNS, IOC, Magyar tudósok krt. 2 H-1117 Budapest, Hungary
| | - Stefan M Schiller
- 1] Institute for Macromolecular Chemistry, University of Freiburg, Stefan-Meier-Str. 31 D-79104 Freiburg, Germany [2] Institute for Pharmaceutical Sciences, University of Freiburg, Albertstr. 25 D-79104 Freiburg, Germany [3] Freiburg Institute for Advanced Studies (FRIAS), School of Soft Matter Research, University of Freiburg, Albertstr. 19 D-79104 Freiburg, Germany [4] Faculty of Chemistry and Pharmacy, University of Freiburg, Fahnenbergplatz D-79104 Freiburg, Germany [5] Faculty of Biology, University of Freiburg, Schänzlestrasse 1 D-79085 Freiburg, Germany [6] BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18 D-79104 Freiburg, Germany [7] IMTEK Department of Microsystems Engineering, University of Freiburg, Georges-Köhler-Allee 103 D-79110 Freiburg, Germany [8] Center for Biosystems Analysis (ZBSA), University of Freiburg, Habsburger Str. 49 D-79104 Freiburg, Germany
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Axen SD, Erbilgin O, Kerfeld CA. A taxonomy of bacterial microcompartment loci constructed by a novel scoring method. PLoS Comput Biol 2014; 10:e1003898. [PMID: 25340524 PMCID: PMC4207490 DOI: 10.1371/journal.pcbi.1003898] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 09/09/2014] [Indexed: 01/21/2023] Open
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelles involved in both autotrophic and heterotrophic metabolism. All BMCs share homologous shell proteins but differ in their complement of enzymes; these are typically encoded adjacent to shell protein genes in genetic loci, or operons. To enable the identification and prediction of functional (sub)types of BMCs, we developed LoClass, an algorithm that finds putative BMC loci and inventories, weights, and compares their constituent pfam domains to construct a locus similarity network and predict locus (sub)types. In addition to using LoClass to analyze sequences in the Non-redundant Protein Database, we compared predicted BMC loci found in seven candidate bacterial phyla (six from single-cell genomic studies) to the LoClass taxonomy. Together, these analyses resulted in the identification of 23 different types of BMCs encoded in 30 distinct locus (sub)types found in 23 bacterial phyla. These include the two carboxysome types and a divergent set of metabolosomes, BMCs that share a common catalytic core and process distinct substrates via specific signature enzymes. Furthermore, many Candidate BMCs were found that lack one or more core metabolosome components, including one that is predicted to represent an entirely new paradigm for BMC-associated metabolism, joining the carboxysome and metabolosome. By placing these results in a phylogenetic context, we provide a framework for understanding the horizontal transfer of these loci, a starting point for studies aimed at understanding the evolution of BMCs. This comprehensive taxonomy of BMC loci, based on their constituent protein domains, foregrounds the functional diversity of BMCs and provides a reference for interpreting the role of BMC gene clusters encoded in isolate, single cell, and metagenomic data. Many loci encode ancillary functions such as transporters or genes for cofactor assembly; this expanded vocabulary of BMC-related functions should be useful for design of genetic modules for introducing BMCs in bioengineering applications. Some enzymatic transformations have undesirable side reactions, produce toxic or volatile intermediates, or are inefficient; these shortcomings can be alleviated through their sequestration with their substrates in a confined space, as in the membrane-bound organelles of eukaryotes. Recently, it was discovered that bacteria also form organelles–bacterial microcompartments (BMCs)–composed of a protein shell that surrounds functionally related enzymes. BMCs long evaded detection because they typically form only in the presence of the substrate they metabolize, and they can only be visualized by electron microscopy. A few BMCs have been experimentally characterized; they have diverse functions in CO2 fixation, pathogenesis, and niche colonization. While the encapsulated enzymes differ among functionally distinct BMCs, the shell architecture is conserved. This enables their detection computationally, as genes for shell proteins are typically nearby genes for the encapsulated enzymes. We developed a novel algorithm to comprehensively identify and categorize BMCs in sequenced bacterial genomes. We show that BMCs are often encoded adjacent to genes that play supporting roles to the organelle's function. Our results provide the first glimpse of the extent of BMC metabolic diversity and will inform design of genetic modules encoding BMCs for introduction of new metabolic functions in a plug-and-play approach.
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Affiliation(s)
- Seth D. Axen
- DOE Joint Genome Institute, Walnut Creek, California, United States of America
| | - Onur Erbilgin
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Cheryl A. Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, United States of America
- DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Berkeley Synthetic Biology Institute, Berkeley, California, United States of America
- * E-mail: ,
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Characterization of a planctomycetal organelle: a novel bacterial microcompartment for the aerobic degradation of plant saccharides. Appl Environ Microbiol 2014; 80:2193-205. [PMID: 24487526 DOI: 10.1128/aem.03887-13] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial microcompartments (BMCs) are organelles that encapsulate functionally linked enzymes within a proteinaceous shell. The prototypical example is the carboxysome, which functions in carbon fixation in cyanobacteria and some chemoautotrophs. It is increasingly apparent that diverse heterotrophic bacteria contain BMCs that are involved in catabolic reactions, and many of the BMCs are predicted to have novel functions. However, most of these putative organelles have not been experimentally characterized. In this study, we sought to discover the function of a conserved BMC gene cluster encoded in the majority of the sequenced planctomycete genomes. This BMC is especially notable for its relatively simple genetic composition, its remote phylogenetic position relative to characterized BMCs, and its apparent exclusivity to the enigmatic Verrucomicrobia and Planctomycetes. Members of the phylum Planctomycetes are known for their morphological dissimilarity to the rest of the bacterial domain: internal membranes, reproduction by budding, and lack of peptidoglycan. As a result, they are ripe for many discoveries, but currently the tools for genetic studies are very limited. We expanded the genetic toolbox for the planctomycetes and generated directed gene knockouts of BMC-related genes in Planctomyces limnophilus. A metabolic activity screen revealed that BMC gene products are involved in the degradation of a number of plant and algal cell wall sugars. Among these sugars, we confirmed that BMCs are formed and required for growth on l-fucose and l-rhamnose. Our results shed light on the functional diversity of BMCs as well as their ecological role in the planctomycetes, which are commonly associated with algae.
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Schrewe M, Julsing MK, Bühler B, Schmid A. Whole-cell biocatalysis for selective and productive C-O functional group introduction and modification. Chem Soc Rev 2014; 42:6346-77. [PMID: 23475180 DOI: 10.1039/c3cs60011d] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
During the last decades, biocatalysis became of increasing importance for chemical and pharmaceutical industries. Regarding regio- and stereospecificity, enzymes have shown to be superior compared to traditional chemical synthesis approaches, especially in C-O functional group chemistry. Catalysts established on a process level are diverse and can be classified along a functional continuum starting with single-step biotransformations using isolated enzymes or microbial strains towards fermentative processes with recombinant microorganisms containing artificial synthetic pathways. The complex organization of respective enzymes combined with aspects such as cofactor dependency and low stability in isolated form often favors the use of whole cells over that of isolated enzymes. Based on an inventory of the large spectrum of biocatalytic C-O functional group chemistry, this review focuses on highlighting the potentials, limitations, and solutions offered by the application of self-regenerating microbial cells as biocatalysts. Different cellular functionalities are discussed in the light of their (possible) contribution to catalyst efficiency. The combined achievements in the areas of protein, genetic, metabolic, and reaction engineering enable the development of whole-cell biocatalysts as powerful tools in organic synthesis.
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Affiliation(s)
- Manfred Schrewe
- Laboratory of Chemical Biotechnology, Department of Biochemical and Chemical Engineering, TU Dortmund University, Emil-Figge-Strasse 66, 44227 Dortmund, Germany
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Schreiber A, Schiller SM. Nanobiotechnology of protein-based compartments: steps toward nanofactories. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2013. [DOI: 10.1680/bbn.13.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Ferrer-Miralles N, Rodríguez-Carmona E, Corchero JL, García-Fruitós E, Vázquez E, Villaverde A. Engineering protein self-assembling in protein-based nanomedicines for drug delivery and gene therapy. Crit Rev Biotechnol 2013; 35:209-21. [DOI: 10.3109/07388551.2013.833163] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Rae BD, Long BM, Badger MR, Price GD. Functions, compositions, and evolution of the two types of carboxysomes: polyhedral microcompartments that facilitate CO2 fixation in cyanobacteria and some proteobacteria. Microbiol Mol Biol Rev 2013; 77:357-79. [PMID: 24006469 PMCID: PMC3811607 DOI: 10.1128/mmbr.00061-12] [Citation(s) in RCA: 242] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacteria are the globally dominant photoautotrophic lineage. Their success is dependent on a set of adaptations collectively termed the CO2-concentrating mechanism (CCM). The purpose of the CCM is to support effective CO2 fixation by enhancing the chemical conditions in the vicinity of the primary CO2-fixing enzyme, D-ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), to promote the carboxylase reaction and suppress the oxygenase reaction. In cyanobacteria and some proteobacteria, this is achieved by encapsulation of RubisCO within carboxysomes, which are examples of a group of proteinaceous bodies called bacterial microcompartments. Carboxysomes encapsulate the CO2-fixing enzyme within the selectively permeable protein shell and simultaneously encapsulate a carbonic anhydrase enzyme for CO2 supply from a cytoplasmic bicarbonate pool. These bodies appear to have arisen twice and undergone a process of convergent evolution. While the gross structures of all known carboxysomes are ostensibly very similar, with shared gross features such as a selectively permeable shell layer, each type of carboxysome encapsulates a phyletically distinct form of RubisCO enzyme. Furthermore, the specific proteins forming structures such as the protein shell or the inner RubisCO matrix are not identical between carboxysome types. Each type has evolutionarily distinct forms of the same proteins, as well as proteins that are entirely unrelated to one another. In light of recent developments in the study of carboxysome structure and function, we present this review to summarize the knowledge of the structure and function of both types of carboxysome. We also endeavor to cast light on differing evolutionary trajectories which may have led to the differences observed in extant carboxysomes.
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Affiliation(s)
- Benjamin D Rae
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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Self-assembling, protein-based intracellular bacterial organelles: emerging vehicles for encapsulating, targeting and delivering therapeutical cargoes. Microb Cell Fact 2011; 10:92. [PMID: 22046962 PMCID: PMC3247854 DOI: 10.1186/1475-2859-10-92] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 11/03/2011] [Indexed: 12/23/2022] Open
Abstract
Many bacterial species contain intracellular nano- and micro-compartments consisting of self-assembling proteins that form protein-only shells. These structures are built up by combinations of a reduced number of repeated elements, from 60 repeated copies of one unique structural element self-assembled in encapsulins of 24 nm to 10,000-20,000 copies of a few protein species assembled in a organelle of around 100-150 nm in cross-section. However, this apparent simplicity does not correspond to the structural and functional sophistication of some of these organelles. They package, by not yet definitely solved mechanisms, one or more enzymes involved in specific metabolic pathways, confining such reactions and sequestering or increasing the inner concentration of unstable, toxics or volatile intermediate metabolites. From a biotechnological point of view, we can use the self assembling properties of these particles for directing shell assembling and enzyme packaging, mimicking nature to design new applications in biotechnology. Upon appropriate engineering of the building blocks, they could act as a new family of self-assembled, protein-based vehicles in Nanomedicine to encapsulate, target and deliver therapeutic cargoes to specific cell types and/or tissues. This would provide a new, intriguing platform of microbial origin for drug delivery.
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Domingo-Espín J, Unzueta U, Saccardo P, Rodríguez-Carmona E, Corchero JL, Vázquez E, Ferrer-Miralles N. Engineered biological entities for drug delivery and gene therapy protein nanoparticles. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 104:247-98. [PMID: 22093221 PMCID: PMC7173510 DOI: 10.1016/b978-0-12-416020-0.00006-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The development of genetic engineering techniques has speeded up the growth of the biotechnological industry, resulting in a significant increase in the number of recombinant protein products on the market. The deep knowledge of protein function, structure, biological interactions, and the possibility to design new polypeptides with desired biological activities have been the main factors involved in the increase of intensive research and preclinical and clinical approaches. Consequently, new biological entities with added value for innovative medicines such as increased stability, improved targeting, and reduced toxicity, among others have been obtained. Proteins are complex nanoparticles with sizes ranging from a few nanometers to a few hundred nanometers when complex supramolecular interactions occur, as for example, in viral capsids. However, even though protein production is a delicate process that imposes the use of sophisticated analytical methods and negative secondary effects have been detected in some cases as immune and inflammatory reactions, the great potential of biodegradable and tunable protein nanoparticles indicates that protein-based biotechnological products are expected to increase in the years to come.
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Affiliation(s)
- Joan Domingo-Espín
- Institute for Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona, Spain
| | - Ugutz Unzueta
- Institute for Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona, Spain
| | - Paolo Saccardo
- Institute for Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona, Spain
| | - Escarlata Rodríguez-Carmona
- Institute for Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona, Spain
| | - José Luís Corchero
- Institute for Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona, Spain
| | - Esther Vázquez
- Institute for Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona, Spain
| | - Neus Ferrer-Miralles
- Institute for Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain,CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona, Spain
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16
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Abstract
Bacterial microcompartments (BMCs) are polyhedral organelles found in an increasingly wide variety of bacterial species. These structures, typified by carboxysomes of cyanobacteria and many chemoautotrophs, function to compartmentalize important reaction sequences of metabolic pathways. Unlike their eukaryotic counterparts, which are surrounded by lipid bilayer membranes, these microbial organelles are bounded by a thin protein shell that is assembled from multiple copies of a few different polypeptides. The main shell proteins form hexamers whose edges interact to create the thin sheets that form the facets of the polyhedral BMCs. Each hexamer contains a central pore hypothesized to mediate flux of metabolites into and out of the organelle. Because several distinctly different metabolic processes are found in the various BMCs studied to date, it has been proposed that a common advantage to packaging these pathways within shell-bound compartments is to optimize the concentration of volatile metabolites in the BMC by maintaining an interior pH that is lower than that of the cytoplasm. We have tested this idea by recombinantly fusing a pH-sensitive green fluorescent protein (GFP) to ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), the major enzyme component inside the carboxysome. Our results suggest that the carboxysomal pH is similar to that of its external environment and that the protein shell does not constitute a proton barrier. The explanation for the sundry BMC functions must therefore be sought in the characteristics of the pores that traverse their shells.
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17
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Southam G, Beveridge TJ. Examination of Lipopolysaccharide (O-Antigen) Populations of Thiobacillus ferrooxidans from Two Mine Tailings. Appl Environ Microbiol 2010; 59:1283-8. [PMID: 16348925 PMCID: PMC182078 DOI: 10.1128/aem.59.5.1283-1288.1993] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Net acid-generating capacities of 39.74 kg of H(2)SO(4) per ton (ca. 0.05 kg/kg) (pH 2.68) for the Lemoine copper mine tailings (closed ca. 8 years ago; located 40 km west of Chibougamau, Quebec, Canada) and 16.07 kg of H(2)SO(4) per ton (ca. 0.02 kg/kg) (pH 3.01) for the Copper Rand tailings (in current use and 50 km distant [east] from those of Lemoine) demonstrate that these sulfide tailings can support populations of acidophilic thiobacilli. Oxidized regions in both tailings environments were readily visible, were extremely acidic (Lemoine, pH 2.36; Copper Rand, pH 3.07), and provided natural isolates for our study. A 10% (wt/vol) oxalic acid treatment, which solubilizes both ferric sulfate and ferric hydroxide precipitates (B. Ramsay, J. Ramsay, M. deTremblay, and C. Chavarie, Geomicrobiol. J. 6:171-177, 1988), enabled the recovery of intact bacterial cells from the tailings material and from liquid synthetic medium for lipopolysaccharide analysis. No viable cells could be cultured after this oxalic acid treatment. Sodium dodecyl sulfate-polyacrylamide gel electro-phoretic profiles of lipopolysaccharides extracted from the Lemoine tailings were complex, indicating a heterogeneous population of Thiobacillus ferrooxidans. Six T. ferrooxidans subspecies as identified by lipopolysaccharide analysis (i.e., lipopolysaccharide chemotypes) were eventually isolated from a total of 112 cultures from the Lemoine tailings. Using the same isolate and lipopolysaccharide typing techniques, we identified only a single lipopolysaccharide chemotype from 20 cultures of T. ferrooxidans isolated from the Copper Rand tailings. This homogeneity of lipopolysaccharide chemotype was much different from what was found for the older Lemoine tailings and may reflect a progressive lipopolysaccharide heterogeneity of Thiobacillus isolates as tailings leach and age.
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Affiliation(s)
- G Southam
- Department of Microbiology, College of Biological Science, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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18
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Abstract
Some bacteria contain organelles or microcompartments consisting of a large virion-like protein shell encapsulating sequentially acting enzymes. These organized microcompartments serve to enhance or protect key metabolic pathways inside the cell. The variety of bacterial microcompartments provide diverse metabolic functions, ranging from CO(2) fixation to the degradation of small organic molecules. Yet they share an evolutionarily related shell, which is defined by a conserved protein domain that is widely distributed across the bacterial kingdom. Structural studies on a number of these bacterial microcompartment shell proteins are illuminating the architecture of the shell and highlighting its critical role in controlling molecular transport into and out of microcompartments. Current structural, evolutionary, and mechanistic ideas are discussed, along with genomic studies for exploring the function and diversity of this family of bacterial organelles.
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Affiliation(s)
- Todd O Yeates
- Department of Chemistry and Biochemistry, Institute of Genomics and Proteomics, University of California, Los Angeles, California 90095, USA.
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19
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Cai F, Menon BB, Cannon GC, Curry KJ, Shively JM, Heinhorst S. The pentameric vertex proteins are necessary for the icosahedral carboxysome shell to function as a CO2 leakage barrier. PLoS One 2009; 4:e7521. [PMID: 19844578 PMCID: PMC2760150 DOI: 10.1371/journal.pone.0007521] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Accepted: 10/02/2009] [Indexed: 11/18/2022] Open
Abstract
Background Carboxysomes are polyhedral protein microcompartments found in many autotrophic bacteria; they encapsulate the CO2 fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) within a thin protein shell and provide an environment that enhances the catalytic capabilities of the enzyme. Two types of shell protein constituents are common to carboxysomes and related microcompartments of heterotrophic bacteria, and the genes for these proteins are found in a large variety of bacteria. Methodology/Principal Findings We have created a Halothiobacillus neapolitanus knockout mutant that does not produce the two paralogous CsoS4 proteins thought to occupy the vertices of the icosahedral carboxysomes and related microcompartments. Biochemical and ultrastructural analyses indicated that the mutant predominantly forms carboxysomes of normal appearance, in addition to some elongated microcompartments. Despite their normal shape, purified mutant carboxysomes are functionally impaired, although the activities of the encapsulated enzymes are not negatively affected. Conclusions/Significance In the absence of the CsoS4 proteins the carboxysome shell loses its limited permeability to CO2 and is no longer able to provide the catalytic advantage RubisCO derives from microcompartmentalization. This study presents direct evidence that the diffusion barrier property of the carboxysome shell contributes significantly to the biological function of the carboxysome.
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Affiliation(s)
- Fei Cai
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Balaraj B. Menon
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Gordon C. Cannon
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Kenneth J. Curry
- Department of Biological Sciences, The University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
| | - Jessup M. Shively
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Sabine Heinhorst
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, United States of America
- * E-mail:
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Merroun M, Hennig C, Rossberg A, Reich T, Selenska-Pobell S. Characterization of U(VI)-Acidithiobacillus ferrooxidans complexes using EXAFS, transmission electron microscopy, and energy-dispersive X-ray analysis. RADIOCHIM ACTA 2009. [DOI: 10.1524/ract.91.10.583.22477] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Summary
We used a combination of Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy, Transmission Electron Microscopy (TEM) and Energy-Dispersive X-ray (EDX) analysis to conduct molecular scale studies on U(VI) interaction with three recently described eco-types of Acidithiobacillus ferrooxidans. On the basis of the information obtained by using these methods, we concluded that uranyl phosphate complexes were formed by the cells of the three eco-types studied. The uranium accumulated by A. ferrooxidans cells was located mainly within the extracellular polysaccharides, and on the cell wall. Smaller amounts were also observed in the cytoplasm.
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21
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Crowley CS, Sawaya MR, Bobik TA, Yeates TO. Structure of the PduU shell protein from the Pdu microcompartment of Salmonella. Structure 2008; 16:1324-32. [PMID: 18786396 PMCID: PMC5878062 DOI: 10.1016/j.str.2008.05.013] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Revised: 05/29/2008] [Accepted: 05/30/2008] [Indexed: 01/07/2023]
Abstract
The Pdu microcompartment is a proteinaceous, subcellular structure that serves as an organelle for the metabolism of 1,2-propanediol in Salmonella enterica. It encapsulates several related enzymes within a shell composed of a few thousand protein subunits. Recent structural studies on the carboxysome, a related microcompartment involved in CO(2) fixation, have concluded that the major shell proteins from that microcompartment form hexamers that pack into layers comprising the facets of the shell. Here we report the crystal structure of PduU, a protein from the Pdu microcompartment, representing the first structure of a shell protein from a noncarboxysome microcompartment. Though PduU is a hexamer like other characterized shell proteins, it has undergone a circular permutation leading to dramatic differences in the hexamer pore. In view of the hypothesis that microcompartment metabolites diffuse across the outer shell through these pores, the unique structure of PduU suggests the possibility of a special functional role.
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Affiliation(s)
- Christopher S. Crowley
- UCLA Molecular Biology Institute; University of California, Los Angeles (UCLA); Los Angeles, CA, 90095; USA
| | - Michael R. Sawaya
- UCLA-DOE Institute for Genomics and Proteomics; UCLA; Los Angeles, CA, 90095; USA
| | - Thomas A. Bobik
- Department of Biochemistry, Biophysics and Molecular Biology; Iowa State University; Ames, IA, 50011; USA
| | - Todd O. Yeates
- UCLA Molecular Biology Institute; University of California, Los Angeles (UCLA); Los Angeles, CA, 90095; USA,UCLA-DOE Institute for Genomics and Proteomics; UCLA; Los Angeles, CA, 90095; USA,UCLA Department of Chemistry and Biochemistry; UCLA; Los Angeles, CA, 90095; USA
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22
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Bobik TA. Polyhedral organelles compartmenting bacterial metabolic processes. Appl Microbiol Biotechnol 2006; 70:517-25. [PMID: 16525780 DOI: 10.1007/s00253-005-0295-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2005] [Revised: 12/05/2005] [Accepted: 12/07/2005] [Indexed: 11/29/2022]
Abstract
Bacterial polyhedral organelles are extremely large macromolecular complexes consisting of metabolic enzymes encased within a multiprotein shell that is somewhat reminiscent of a viral capsid. Recent investigations suggest that polyhedral organelles are widely used by bacteria for optimizing metabolic processes. The distribution and diversity of these unique structures has been underestimated because many are not formed during growth on standard laboratory media and because electron microscopy is required for their observation. However, recent physiological studies and genomic analyses tentatively indicate seven functionally distinct organelles distributed among over 40 genera of bacteria. Functional studies conducted thus far are consistent with the idea that polyhedral organelles act as microcompartments that enhance metabolic processes by selectively concentrating specific metabolites. Relatively little is known about how this is achieved at the molecular level. Possible mechanisms include regulation of enzyme activity or efficiency, substrate channeling, a selectively permeable protein shell, and/or differential solubility of metabolites within the organelle. Given their complexity and distinctive structure, it would not be surprising if aspects of their biochemical mechanism are unique. Therefore, the unusual structure of polyhedral organelles raises intriguing questions about their assembly, turnover, and molecular evolution, very little of which is understood.
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Affiliation(s)
- Thomas A Bobik
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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23
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Beller HR, Chain PSG, Letain TE, Chakicherla A, Larimer FW, Richardson PM, Coleman MA, Wood AP, Kelly DP. The genome sequence of the obligately chemolithoautotrophic, facultatively anaerobic bacterium Thiobacillus denitrificans. J Bacteriol 2006; 188:1473-88. [PMID: 16452431 PMCID: PMC1367237 DOI: 10.1128/jb.188.4.1473-1488.2006] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2005] [Accepted: 11/30/2005] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of Thiobacillus denitrificans ATCC 25259 is the first to become available for an obligately chemolithoautotrophic, sulfur-compound-oxidizing, beta-proteobacterium. Analysis of the 2,909,809-bp genome will facilitate our molecular and biochemical understanding of the unusual metabolic repertoire of this bacterium, including its ability to couple denitrification to sulfur-compound oxidation, to catalyze anaerobic, nitrate-dependent oxidation of Fe(II) and U(IV), and to oxidize mineral electron donors. Notable genomic features include (i) genes encoding c-type cytochromes totaling 1 to 2 percent of the genome, which is a proportion greater than for almost all bacterial and archaeal species sequenced to date, (ii) genes encoding two [NiFe]hydrogenases, which is particularly significant because no information on hydrogenases has previously been reported for T. denitrificans and hydrogen oxidation appears to be critical for anaerobic U(IV) oxidation by this species, (iii) a diverse complement of more than 50 genes associated with sulfur-compound oxidation (including sox genes, dsr genes, and genes associated with the AMP-dependent oxidation of sulfite to sulfate), some of which occur in multiple (up to eight) copies, (iv) a relatively large number of genes associated with inorganic ion transport and heavy metal resistance, and (v) a paucity of genes encoding organic-compound transporters, commensurate with obligate chemolithoautotrophy. Ultimately, the genome sequence of T. denitrificans will enable elucidation of the mechanisms of aerobic and anaerobic sulfur-compound oxidation by beta-proteobacteria and will help reveal the molecular basis of this organism's role in major biogeochemical cycles (i.e., those involving sulfur, nitrogen, and carbon) and groundwater restoration.
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Affiliation(s)
- Harry R Beller
- Lawrence Livermore National Laboratory, P.O. Box 808, L-542, Livermore, California 94551-0808, USA.
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24
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25
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Electron microscopic studies on Zoothamnium niveum (Hemprich & Ehrenberg, 1831) Ehrenberg 1838 (Oligohymenophora, Peritrichida), a ciliate with ectosymbiotic, chemoautotrophic bacteria. Eur J Protistol 1996. [DOI: 10.1016/s0932-4739(96)80020-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Hine PM. Intracellular crystal formation in Bacteroides nodosus. JOURNAL OF ULTRASTRUCTURE AND MOLECULAR STRUCTURE RESEARCH 1988; 100:263-8. [PMID: 2854148 DOI: 10.1016/0889-1605(88)90043-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
An intracellular crystalline structure was found in at least two strains of Bacteroides nodosus. The inclusion appeared to be associated with good growth of the organism under optimum conditions following selective passage of rough colonies containing highly fimbriate cells. Several morphological forms of the inclusion were noted. Indiscriminate subculture of crystal-forming cultures led to the loss of this particular property indicating a genetically controlled system of either bacterial or bacteriophage origin.
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Affiliation(s)
- P M Hine
- Wellcome Biotechnology, Beckenham, Kent, England
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27
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Affiliation(s)
- G A Codd
- Department of Biological Sciences, University of Dundee, UK
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28
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Couche GA, Gregson RP. Protein inclusions produced by the entomopathogenic bacterium Xenorhabdus nematophilus subsp. nematophilus. J Bacteriol 1987; 169:5279-88. [PMID: 3667532 PMCID: PMC213937 DOI: 10.1128/jb.169.11.5279-5288.1987] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The entomopathogenic bacterium Xenorhabdus nematophilus subsp. nematophilus produces two types of intracellular inclusion bodies during in vitro culture. Large cigar-shaped inclusions (designated type 1) and smaller ovoid inclusions (designated type 2) were purified from cell lysates, using differential centrifugation in discontinuous glycerol gradients and isopycnic density gradient centrifugation in sodium diatrizoate. The inclusions, composed almost exclusively of protein, are readily soluble at high and low pH values and in the presence of cation chelators such as EDTA, anionic detergents (sodium dodecyl sulfate), or protein denaturants (urea, NaBr). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified inclusions revealed a single 26-kilodalton protein (IP-1) in type 1 inclusions and a 22-kilodalton protein (IP-2) in type 2 inclusions. Analysis of these proteins by isoelectric focusing in the presence of 8 M urea showed that IP-1 is acidic and IP-2 is neutral. Furthermore, each protein occurred in multiple forms differing slightly in isoelectric point. Other variations in peptides released by trypsin digestion, immunological properties, and amino acid composition revealed significant structural differences between IP-1 and IP-2. Kinetic studies using light microscopy, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and immunoblotting procedures showed that inclusion protein synthesis occurs only during the second half of exponential culture growth. Synthesis of inclusion proteins and their aggregation to form inclusions occurred concurrently. Possible functions for these abundant proteins are discussed.
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Affiliation(s)
- G A Couche
- Biotechnology Australia Pty Ltd., Roseville, New South Wales
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29
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Shively J, Devore W, Stratford L, Porter L, Medlin L, Stevens S. Molecular evolution of the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). FEMS Microbiol Lett 1986. [DOI: 10.1111/j.1574-6968.1986.tb01804.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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30
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Giere O. Structure and position of bacterial endosymbionts in the gill filaments of lucinidae from bermuda (Mollusca, Bivalvia). ZOOMORPHOLOGY 1985. [DOI: 10.1007/bf00312060] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Peschek GA. Structure and function of respiratory membranes in cyanobacteria (blue-green algae). Subcell Biochem 1984; 10:85-191. [PMID: 6433519 DOI: 10.1007/978-1-4613-2709-7_2] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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32
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Remsen CC. Structural attributes of membraneous organelles in bacteria. INTERNATIONAL REVIEW OF CYTOLOGY 1982; 76:195-223. [PMID: 6749745 DOI: 10.1016/s0074-7696(08)61791-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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33
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Lanaras T, Codd GA. Ribulose 1,5-bisphosphate carboxylase and polyhedral bodies of Chlorogloeopsis fritschii. PLANTA 1981; 153:279-285. [PMID: 24276834 DOI: 10.1007/bf00383900] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/1981] [Accepted: 07/23/1981] [Indexed: 06/02/2023]
Abstract
Ribulose 1,5-bisphosphate (RuBP) carboxylase (EC 4.1.1.39) activity was approximately equally distributed between supernatant and pellet fractions produced by differential centrifugation of disrupted cells of Chlorogloeopsis fritschii. Low ionic strength buffer favoured the recovery of particulate RuBP carboxylase. Density gradient centrifugation of resuspended cell-free particulate material produced a single band of RuBP carboxylase activity, which was associated with the polyhedral body fraction, rather than with the thylakoids or other observable particles. Isolated polyhedral body stability was improved by density gradient centrifugation through gradients of Percoll plus sucrose in buffer, which yielded apparently intact polyhedral bodies. These were 100 to 150 nm in diameter and contained ring-shaped, 12 nm diameter particles. It is inferred that the C. fritschii polyhedral bodies are carboxysomes. Sodium dodecyl sulphate (SDS) polyacrylamide gel electrophoresis of SDS-dissociated polyhedral bodies revealed 8 major polypeptides. The most abundant, with molecular weights of 52,000 and 13,000, correspond with the large and small subunits, respectively, of RuBP carboxylase.
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Affiliation(s)
- T Lanaras
- Department of Biological Sciences, The University, DD1 4HN, Dundee, U.K
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34
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Endo BY. The ultrastructure and distribution of an intracellular bacterium-like microorganism in tissue of larvae of the soybean cyst nematode, Heterodera glycines. JOURNAL OF ULTRASTRUCTURE RESEARCH 1979; 67:1-14. [PMID: 571920 DOI: 10.1016/s0022-5320(79)80012-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Caldwell DE, Overbeck J. The planktonic microflora of lakes. CRC CRITICAL REVIEWS IN MICROBIOLOGY 1977; 5:305-70. [PMID: 407052 DOI: 10.3109/10408417709102809] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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36
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Smith AJ, Hoare DS. Specialist phototrophs, lithotrophs, and methylotrophs: a unity among a diversity of procaryotes? BACTERIOLOGICAL REVIEWS 1977; 41:419-48. [PMID: 329833 PMCID: PMC414007 DOI: 10.1128/br.41.2.419-448.1977] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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37
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Wullenweber M, Koops HP, Harms H. Polyhedral inclusion bodies in cells of Nitrosomonas spec. Arch Microbiol 1977; 112:69-72. [PMID: 190964 DOI: 10.1007/bf00446656] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polyhedral inclusion bodies were observed in cells of a Nitrosomonas species. They were present in growing cells as well as in resting cells. In thin sections their size was about 130 nm in growing cells and about 185 nm in diameter in resting cells. The bodies were commonly located in the nucleoplasm. They appeared to be bounded by a nonunit membrane and had a granular substructure. In thin sections about 70% of the exponentially grown cells and about 20% of the resting cells of the investigated strain showed 1-7 respectively 1-3 inclusion bodies.
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Purohit K, McFadden BA, Shaykh MM. D-Ribulose-1,5-bisphosphate carboxylase and polyhedral inclusion bodies in Thiobacillus intermedius. J Bacteriol 1976; 127:516-22. [PMID: 179979 PMCID: PMC233085 DOI: 10.1128/jb.127.1.516-522.1976] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The growth-related parameters of Thiobacillus intermedius, cultured in glutamate-CO2-S2O32- medium, have been determined. After centrifugation at 48,000 X g for 1 h, 24% of the D-ribulose-1,5-bisphosphate carboxylase (RuBPCase) activity of the disrupted-cell suspensions obtained from CO2-S2O32--and glutamate-CO2-S2O3(3)- grown cells could be sedimented, and the specific activities of this enzyme in the supernatant fractions were almost equivalent. The enzyme was stable in T. intermedius starved of thiosulfate in the presence and absence of glutamate, but a progressive decrease was evident in several growth cycles, each cycle supported by resupplementation of cells with thiosulfate. Polyhedral inclusion bodies were present in CO2-S2O3(2)- and glutamate-CO2S2O3(2)- grown cells. The number of polyhedral bodies per cell increased during mixotrophic growth approximately in proportion to the observed increase in the specific activity of RuBPCase. RuBPCase could not be detected in T. intermedius grown heterotrophically on yeast extract, nor could polyhedral bodies be found.
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Bock E, Düvel D, Peters KR. [Characterization of a phage-like particle from cells of Nitrobacter. I. Host-particle correlation and particle isolation (author's transl)]. Arch Microbiol 1974; 97:115-27. [PMID: 4836295 DOI: 10.1007/bf00403051] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Westphal K, Bock E. [Characterization of a phage-like particle from cells of Nitrobacter. III. On the DNA-content]. Arch Microbiol 1974; 101:121-30. [PMID: 4614734 DOI: 10.1007/bf00455932] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Shively JM, Ball FL, Kline BW. Electron microscopy of the carboxysomes (polyhedral bodies) of Thiobacillus neapolitanus. J Bacteriol 1973; 116:1405-11. [PMID: 4127632 PMCID: PMC246500 DOI: 10.1128/jb.116.3.1405-1411.1973] [Citation(s) in RCA: 100] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The carboxysomes of Thiobacillus neapolitanus are shown, by electron microscopy, to consist of a paracrystalline array of 10-nm particles surrounded by a "membrane." The 10-nm particles have a center hole or depression and have been previously identified as ribulose diphosphate carboxylase. The membrane is a monolayer approximately 3.5-nm thick.
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Shively JM, Ball F, Brown DH, Saunders RE. Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of Thiobacillus neapolitanus. Science 1973; 182:584-6. [PMID: 4355679 DOI: 10.1126/science.182.4112.584] [Citation(s) in RCA: 201] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The polyhedral inclusions of Thiobacillus neapolitanus have been isolated; they contain ribulose diphosphate carboxylase.
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McFadden BA. Autotrophic CO2 assimilation and the evolution of ribulose diphosphate carboxylase. BACTERIOLOGICAL REVIEWS 1973; 37:289-319. [PMID: 4357017 PMCID: PMC413820 DOI: 10.1128/br.37.3.289-319.1973] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Batzing BL, Claus GW. Fine structural changes of Acetobacter suboxydans during growth in a defined medium. J Bacteriol 1973; 113:1455-61. [PMID: 4120607 PMCID: PMC251717 DOI: 10.1128/jb.113.3.1455-1461.1973] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cytological differences were observed between stationary- and exponentialphase cells of Acetobacter suboxydans grown in a defined medium. Unstained cells observed with the light microscope just after entering the stationary phase differed from exponentially growing cells in that the former exhibited localized increases in density, particularly in the polar regions. Electron microscopy of thin sections revealed that early stationary-phase cells possessed predominantly polar complexes of intracytoplasmic membranes accompanied by polar increases in ribosomal material. When cultures were allowed to continue far into the stationary phase, cells contained extensive aggregations of membrane-like material as the predominant fine-structural feature. In contrast, thin sections of exponentially growing cells exhibited only occasional indications of intracytoplasmic membranes. Intracytoplasmic membranes heretofore have been observed only rarely in the heterotrophic Pseudomonadales.
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Craig AS, Williamson KI. Three inclusions of rhizobial bacteroids and their cytochemical character. Arch Microbiol 1972. [DOI: 10.1007/bf00424997] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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