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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.
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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.
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2
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Lin F, Xiang L, Wu L, Liu Y, Jiang Q, Deng L, Cui W. Positioning regulation of organelle network via Chinese microneedle. SCIENCE ADVANCES 2024; 10:eadl3063. [PMID: 38640234 PMCID: PMC11029808 DOI: 10.1126/sciadv.adl3063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
The organelle network is a key factor in the repair and regeneration of lesion. However, effectively intervening in the organelle network which has complex interaction mechanisms is challenging. In this study, on the basis of electromagnetic laws, we constructed a biomaterial-based physical/chemical restraint device. This device was designed to jointly constrain electrical and biological factors in a conductive screw-threaded microneedle (ST-needle) system, identifying dual positioning regulation of the organelle network. The unique physical properties of this system could accurately locate the lesion and restrict the current path to the lesion cells through electromagnetic laws, and dynamic Van der Waals forces were activated to release functionalized hydrogel microspheres. Subsequently, the mitochondria-endoplasmic reticulum (ER) complex was synergistically targeted by increasing mitochondrial ATP supply to the ER via electrical stimulation and by blocking calcium current from the ER to the mitochondria using microspheres, and then the life activity of the lesion cells was effectively restored.
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Affiliation(s)
| | | | - Longxi Wu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
| | - Yupu Liu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
| | - Qinzhe Jiang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
| | - Lianfu Deng
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, P. R. China
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3
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Trettel DS, Winkler WC. In Vitro Analysis of Bacterial Microcompartments and Shell Protein Superstructures by Confocal Microscopy. Microbiol Spectr 2023; 11:e0335722. [PMID: 36786617 PMCID: PMC10100840 DOI: 10.1128/spectrum.03357-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/18/2023] [Indexed: 02/15/2023] Open
Abstract
The shell proteins that comprise bacterial microcompartments (BMCs) can self-assemble into an array of superstructures such as nanotubes, flat sheets, and icosahedra. The physical characterization of BMCs and these superstructures typically relies on electron microscopy, which decouples samples from their solution context. We hypothesize that an investigation of fluorescently tagged BMCs and shell protein superstructures in vitro using high-resolution confocal microscopy will lead to new insights into the solution behavior of these entities. We find that confocal imaging is able to capture nanotubes and sheets previously reported by transmission electron microscopy (TEM). Using a combination of fluorescent tags, we present qualitative evidence that these structures intermix with one another in a hetero- and homotypic fashion. Complete BMCs are also able to accomplish intermixing as evidenced by colocalization data. Finally, a simple colocalization experiment suggests that fluorescently modified encapsulation peptides (EPs) may prefer certain shell protein binding partners. Together, these data demonstrate that high-resolution confocal microscopy is a powerful tool for investigating microcompartment-related structures in vitro, particularly for colocalization analyses. These results also support the notion that BMCs may intermix protein components, presumably from the outer shell. IMPORTANCE Microcompartments are large, organelle-like structures that help bacteria catabolize targeted metabolites while also protecting the cytosol against highly reactive metabolic intermediates. Their protein shell self-assembles into a polyhedral structure of approximately 100 to 200 nm in diameter. Inside the shell are thousands of copies of cargo enzymes, which are responsible for a specific metabolic pathway. While different approaches have revealed high-resolution structures of individual microcompartment proteins, it is less clear how these factors self-assemble to form the full native structure. In this study, we show that laser scanning confocal microscopy can be used to study microcompartment proteins. We find that this approach allows researchers to investigate the interactions and potential exchange of shell protein subunits in solution. From this, we conclude that confocal microscopy offers advantages for studying the in vitro structures of other microcompartments as well as carboxysomes and other bacterial organelles.
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Affiliation(s)
- Daniel S. Trettel
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, College Park, Maryland, USA
| | - Wade C. Winkler
- Department of Chemistry and Biochemistry, The University of Maryland, College Park, College Park, Maryland, USA
- Department of Cell Biology and Molecular Genetics, The University of Maryland, College Park, College Park, Maryland, USA
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4
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Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB. J Bacteriol 2022; 204:e0057621. [PMID: 35575582 DOI: 10.1128/jb.00576-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here, we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is critical for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy, we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and system-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis. IMPORTANCE MCPs are unique, genetically encoded organelles used by many bacteria to survive in resource-limited environments. There is significant interest in understanding the biogenesis and function of these organelles, both as potential antibiotic targets in enteric pathogens and also as useful tools for overcoming metabolic engineering bottlenecks. However, the mechanism by which these organelles are formed natively is still not completely understood. Here, we provide evidence of a potential mechanism in S. enterica by which a single protein, PduB, links the MCP shell and metabolic core. This finding is critical for those seeking to disrupt MCPs during pathogenic infections or for those seeking to harness MCPs as nanobioreactors in industrial settings.
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5
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Trettel DS, Resager W, Ueberheide BM, Jenkins CC, Winkler WC. Chemical probing provides insight into the native assembly state of a bacterial microcompartment. Structure 2022; 30:537-550.e5. [PMID: 35216657 PMCID: PMC8995372 DOI: 10.1016/j.str.2022.02.002] [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: 10/06/2021] [Revised: 12/08/2021] [Accepted: 01/28/2022] [Indexed: 11/28/2022]
Abstract
Bacterial microcompartments (BMCs) are widespread in bacteria and are used for a variety of metabolic purposes, including catabolism of host metabolites. A suite of proteins self-assembles into the shell and cargo layers of BMCs. However, the native assembly state of these large complexes remains to be elucidated. Herein, chemical probes were used to observe structural features of a native BMC. While the exterior could be demarcated with fluorophores, the interior was unexpectedly permeable, suggesting that the shell layer may be more dynamic than previously thought. This allowed access to cross-linking chemical probes, which were analyzed to uncover the protein interactome. These cross-links revealed a complex multivalent network among cargo proteins that contained encapsulation peptides and demonstrated that the shell layer follows discrete rules in its assembly. These results are consistent overall with a model in which biomolecular condensation drives interactions of cargo proteins before envelopment by shell layer proteins.
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Affiliation(s)
- Daniel S Trettel
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - William Resager
- New York University Grossman School of Health, NYU Langone Health, New York, NY 10016, USA
| | - Beatrix M Ueberheide
- New York University Grossman School of Health, NYU Langone Health, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Neurology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Conor C Jenkins
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | - Wade C Winkler
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA.
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6
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Chen H, Wilson J, Ottinger S, Gan Q, Fan C. Introducing noncanonical amino acids for studying and engineering bacterial microcompartments. Curr Opin Microbiol 2021; 61:67-72. [PMID: 33813159 PMCID: PMC8169543 DOI: 10.1016/j.mib.2021.03.004] [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: 12/05/2020] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
Bacterial microcompartments (BMCs) with selectively permeable shells and encapsulated enzyme cores are well-suited candidates for nano-bioreactors because of their advantages of enhancing pathway flux and protection against toxic products. To better study and engineer protein-based BMCs, a series of protein chemistry approaches are adopted. As one of the most advanced techniques, genetic code expansion can introduce various noncanonical amino acids (ncAAs) with diverse functional groups into target proteins, thus providing powerful tools for protein studies and engineering. This review summarizes and proposes useful tools based on current development of the genetic code expansion technique towards challenges in BMC studies and engineering.
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Affiliation(s)
- Hao Chen
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Jessica Wilson
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
| | - Sara Ottinger
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA
| | - Chenguang Fan
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA; Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR, USA.
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7
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Probe into a multi-protein prokaryotic organelle using thermal scanning assay reveals distinct properties of the core and the shell. Biochim Biophys Acta Gen Subj 2020; 1864:129680. [DOI: 10.1016/j.bbagen.2020.129680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022]
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8
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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.
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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
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9
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Decoding the stoichiometric composition and organisation of bacterial metabolosomes. Nat Commun 2020; 11:1976. [PMID: 32332738 PMCID: PMC7181861 DOI: 10.1038/s41467-020-15888-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 03/31/2020] [Indexed: 01/08/2023] Open
Abstract
Some enteric bacteria including Salmonella have evolved the propanediol-utilising microcompartment (Pdu MCP), a specialised proteinaceous organelle that is essential for 1,2-propanediol degradation and enteric pathogenesis. Pdu MCPs are a family of bacterial microcompartments that are self-assembled from hundreds of proteins within the bacterial cytosol. Here, we seek a comprehensive understanding of the stoichiometric composition and organisation of Pdu MCPs. We obtain accurate stoichiometry of shell proteins and internal enzymes of the natural Pdu MCP by QconCAT-driven quantitative mass spectrometry. Genetic deletion of the major shell protein and absolute quantification reveal the stoichiometric and structural remodelling of metabolically functional Pdu MCPs. Decoding the precise protein stoichiometry allows us to develop an organisational model of the Pdu metabolosome. The structural insights into the Pdu MCP are critical for both delineating the general principles underlying bacterial organelle formation, structural robustness and function, and repurposing natural microcompartments using synthetic biology for biotechnological applications. Enteric pathogens such as Salmonella depend on propanediol-utilising microcompartments (Pdu MCP), which self-assemble from cytosolic proteins. Using mass spectrometry-based absolute quantification, the authors here define the protein stoichiometry and propose an organizational model of a Salmonella Pdu MCP.
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10
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Wade Y, Daniel RA, Leak DJ. Heterologous Microcompartment Assembly in Bacillaceae: Establishing the Components Necessary for Scaffold Formation. ACS Synth Biol 2019; 8:1642-1654. [PMID: 31242391 DOI: 10.1021/acssynbio.9b00155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Bacterial microcompartments (BMCs) are organelles that host specific biochemical reactions for both anabolic and catabolic functions. Engineered morphologically diverse BMCs bearing heterologous enzymatic pathways have shown enhanced productivity for commodity chemicals, which makes BMCs an important focus for metabolic engineering. Gaining control of BMC assembly and incorporation of a heterologous enzymatic cargo has yet to be achieved in thermophiles. Herein, we address this by first conducting a detailed bioinformatic analysis of the propanediol utilization (pdu) operon in the thermophile Parageobacillus thermoglucosidasius. We then demonstrated, in vivo, the ability to assemble the native BMCs at an elevated temperature of 60 °C. Heterologous expression of Pdu shell proteins from P. thermoglucosidasius in Bacillus subtilis resulted in the assembly of a single tubular BMC with an average length of 1.4 μm; BMCs assembled after a 20 min induction of expression of the shell operons. Moreover, we show that it is possible to target the monomeric superfolder GFP (msfGFP) to the interior of the compartment by fusion of an N-terminal sequence of the propanediol utilization protein (PduP) of at least 24 amino acids. This study establishes the feasibility of constructing cell factories for small molecules in industrially important Bacillus and Geobacillus spp. by heterologous cargo-carrying BMC production and assembly. Additionally, the study provides experimental confirmation that BMCs are produced in thermophilic bacteria, which opens a path for future research on repurposing the native organelles to provide new functionality at elevated temperatures.
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Affiliation(s)
- Yana Wade
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne, NE2 4AX, U.K
| | - Richard A. Daniel
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle-upon-Tyne, NE2 4AX, U.K
| | - David J. Leak
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, U.K
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11
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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.
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12
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Wang Y, Wang F, Bao X, Fu L. Systematic analysis of lysine acetylome reveals potential functions of lysine acetylation in Shewanella baltica, the specific spoilage organism of aquatic products. J Proteomics 2019; 205:103419. [PMID: 31212084 DOI: 10.1016/j.jprot.2019.103419] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 05/19/2019] [Accepted: 06/11/2019] [Indexed: 01/24/2023]
Abstract
Protein lysine acetylation is a major post-translational modification and plays a critical regulatory role in almost every aspect in both eukaryotes and prokaryotes, yet there have been no data on Shewanella baltica, which is one of the specific spoilage organism (SSO) of aquatic products. Here, we performed the first global acetylproteome analysis of S. baltica. 2929 lysine acetylation sites were identified in 1103 proteins, accounting for 26.1% of the total proteins which participate in a wide variety of biological processes, especially in the constituent of ribosome, the biosynthesis of aminoacyl-tRNA, the amino acids and fatty acid metabolism. Besides, 14 conserved acetylation motifs were detected in S. baltica. Notably, various directly or indirectly spoilage-related proteins were prevalently acetylated, including enzymes involved in the unsaturated fatty acids biosynthesis closely related to the cold adaptability, cold shock proteins, pivotal enzymes involved in the putrescine biosynthesis, and a LuxR-type protein in quorum sensing system. The acetylome analysis in Shewanella can supplement the database and provide new insight into uncovering the spoilage mechanisms of S. baltica. The provided dataset illuminates the potential role of reversible acetylation in S. baltica, and serves as an important resource for exploring the physiological role of lysine acetylation in prokaryotes. SIGNIFICANCE: The psychrotrophic nature and the ability of S. baltica to make good use of "habitat" nutrients explain its importance in spoilage of seafood stored at low temperatures. However, the underlying mechanism of spoilage potential from the perspective of protein post-translational modification was rarely studied. This work identifies the first comprehensive survey of a lysine acetylome in S. baltica and uncovers the involvement of lysine acetylation in the diverse biological processes, especially in the closely spoilage-related pathways. This study provides a resource for functional analysis of acetylated proteins and creates opportunities for in-depth elucidation of the physiological role of protein acetylation in Shewanella spp.
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Affiliation(s)
- Yangbo Wang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; Zhejiang Engineering Institute of Food Quality and Safety, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Feifei Wang
- Key Laboratory for Food Microbial Technology of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Xingyue Bao
- Key Laboratory for Food Microbial Technology of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Linglin Fu
- Key Laboratory for Food Microbial Technology of Zhejiang Province, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou 310018, China; Zhejiang Engineering Institute of Food Quality and Safety, Zhejiang Gongshang University, Hangzhou 310018, China.
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13
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Lee MJ, Mantell J, Brown IR, Fletcher JM, Verkade P, Pickersgill RW, Woolfson DN, Frank S, Warren MJ. De novo targeting to the cytoplasmic and luminal side of bacterial microcompartments. Nat Commun 2018; 9:3413. [PMID: 30143644 PMCID: PMC6109187 DOI: 10.1038/s41467-018-05922-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/31/2018] [Indexed: 01/05/2023] Open
Abstract
Bacterial microcompartments, BMCs, are proteinaceous organelles that encase a specific metabolic pathway within a semi-permeable protein shell. Short encapsulation peptides can direct cargo proteins to the lumen of the compartments. However, the fusion of such peptides to non-native proteins does not guarantee encapsulation and often causes aggregation. Here, we report an approach for targeting recombinant proteins to BMCs that utilizes specific de novo coiled-coil protein–protein interactions. Attachment of one coiled-coil module to PduA (a component of the BMC shell) allows targeting of a fluorescent protein fused to a cognate coiled-coil partner. This interaction takes place on the outer surface of the BMC. The redesign of PduA to generate an N-terminus on the luminal side of the BMC results in intact compartments to which proteins can still be targeted via the designed coiled-coil system. This study provides a strategy to display proteins on the surface or within the lumen of the BMCs. Bacterial microcompartments (BMCs) are protein-bound organelles encapsulating segments of metabolic pathways. Here the authors utilize specific de novo coiled-coil protein-protein interactions to display proteins on the outer or inner surface of BMCs.
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Affiliation(s)
- Matthew J Lee
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Judith Mantell
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,Wolfson Bioimaging Facility, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Ian R Brown
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK
| | - Jordan M Fletcher
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,Wolfson Bioimaging Facility, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Richard W Pickersgill
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Derek N Woolfson
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, UK.,School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Stefanie Frank
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gordon Street, London, WC1E 6BT, UK.
| | - Martin J Warren
- Industrial Biotechnology Centre, School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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14
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Abstract
Bacterial microcompartments (BMCs) are self-assembling organelles that consist of an enzymatic core that is encapsulated by a selectively permeable protein shell. The potential to form BMCs is widespread and found across the kingdom Bacteria. BMCs have crucial roles in carbon dioxide fixation in autotrophs and the catabolism of organic substrates in heterotrophs. They contribute to the metabolic versatility of bacteria, providing a competitive advantage in specific environmental niches. Although BMCs were first visualized more than 60 years ago, it is mainly in the past decade that progress has been made in understanding their metabolic diversity and the structural basis of their assembly and function. This progress has not only heightened our understanding of their role in microbial metabolism but is also beginning to enable their use in a variety of applications in synthetic biology. In this Review, we focus on recent insights into the structure, assembly, diversity and function of BMCs.
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Affiliation(s)
- Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Clement Aussignargues
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Jan Zarzycki
- Max-Planck-Institute for Terrestrial Microbiology, D-35043, Marburg, Germany
| | - Fei Cai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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15
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Thompson MC, Cascio D, Yeates TO. Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism. Acta Crystallogr D Struct Biol 2018; 74:411-421. [PMID: 29717712 PMCID: PMC5930349 DOI: 10.1107/s2059798318003479] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/28/2018] [Indexed: 11/10/2022] Open
Abstract
Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the data sets, and it was found that the 18 data sets separated into two distinct groups, with large R values (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California, USA
| | - Duilio Cascio
- UCLA–DOE Institute for Genomics and Proteomics, Los Angeles, California, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California, USA
- UCLA–DOE Institute for Genomics and Proteomics, Los Angeles, California, USA
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16
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The Wrappers of the 1,2-Propanediol Utilization Bacterial Microcompartments. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1112:333-344. [DOI: 10.1007/978-981-13-3065-0_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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17
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Graf L, Wu K, Wilson JW. Transfer and analysis of Salmonella pdu genes in a range of Gram-negative bacteria demonstrate exogenous microcompartment expression across a variety of species. Microb Biotechnol 2017; 11:199-210. [PMID: 28967207 PMCID: PMC5743805 DOI: 10.1111/1751-7915.12863] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/17/2017] [Accepted: 08/31/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial microcompartments (MCPs) are protein organelles that typically house toxic or volatile reaction intermediates involved in metabolic pathways. Engineering bacteria to express exogenous MCPs will allow these cells to gain useful functions involving molecule compartmentalization. We cloned a 38 kb region from the Salmonella enterica serovar Typhimurium genome containing the pdu 1,2 propanediol (1,2 PD) utilization and cob/cbi genes using the FRT‐Capture strategy to clone and transfer large genomic segments. We transferred this clone to a range of Gram‐negative bacteria and found the clone to be functional for 1,2 PD metabolism in a variety of species including S. Typhimurium Δpdu, Escherichia coli, Salmonella bongori, Klebsiella pneumoniae, Cronobacter sakazakii, Serratia marcescens, and different Pseudomonas species. We successfully isolated MCPs expressed from the clone from several, but not all, of these strains, and we observed this utilizing a range of different media and in the absence of protease inhibitor. We also present a mini‐prep protocol that allows rapid, small‐scale screening of strains for MCP production. To date, this is the first analysis of cloned, exogenous microcompartment expression across several different Gram‐negative backgrounds and provides a foundation for MCP use in a variety of bacterial species using a full, intact clone.
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Affiliation(s)
- Laura Graf
- Biology Department, Villanova University, Mendel Hall, 800 Lancaster Avenue, Villanova, PA, 19085, USA
| | - Kent Wu
- Biology Department, Villanova University, Mendel Hall, 800 Lancaster Avenue, Villanova, PA, 19085, USA
| | - James W Wilson
- Biology Department, Villanova University, Mendel Hall, 800 Lancaster Avenue, Villanova, PA, 19085, USA
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18
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The N Terminus of the PduB Protein Binds the Protein Shell of the Pdu Microcompartment to Its Enzymatic Core. J Bacteriol 2017; 199:JB.00785-16. [PMID: 28138097 DOI: 10.1128/jb.00785-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/20/2017] [Indexed: 12/12/2022] Open
Abstract
Bacterial microcompartments (MCPs) are extremely large proteinaceous organelles that consist of an enzymatic core encapsulated within a complex protein shell. A key question in MCP biology is the nature of the interactions that guide the assembly of thousands of protein subunits into a well-ordered metabolic compartment. In this report, we show that the N-terminal 37 amino acids of the PduB protein have a critical role in binding the shell of the 1,2-propanediol utilization (Pdu) microcompartment to its enzymatic core. Several mutations were constructed that deleted short regions of the N terminus of PduB. Growth tests indicated that three of these deletions were impaired MCP assembly. Attempts to purify MCPs from these mutants, followed by gel electrophoresis and enzyme assays, indicated that the protein complexes isolated consisted of MCP shells depleted of core enzymes. Electron microscopy substantiated these findings by identifying apparently empty MCP shells but not intact MCPs. Analyses of 13 site-directed mutants indicated that the key region of the N terminus of PduB required for MCP assembly is a putative helix spanning residues 6 to 18. Considering the findings presented here together with prior work, we propose a new model for MCP assembly.IMPORTANCE Bacterial microcompartments consist of metabolic enzymes encapsulated within a protein shell and are widely used to optimize metabolic process. Here, we show that the N-terminal 37 amino acids of the PduB shell protein are essential for assembly of the 1,2-propanediol utilization microcompartment. The results indicate that it plays a key role in binding the outer shell to the enzymatic core. We propose that this interaction might be used to define the relative orientation of the shell with respect to the core. This finding is of fundamental importance to our understanding of microcompartment assembly and may have application to engineering microcompartments as nanobioreactors for chemical production.
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19
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Held M, Kolb A, Perdue S, Hsu SY, Bloch SE, Quin MB, Schmidt-Dannert C. Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli. Sci Rep 2016; 6:24359. [PMID: 27063436 PMCID: PMC4827028 DOI: 10.1038/srep24359] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/29/2016] [Indexed: 01/17/2023] Open
Abstract
Compartmentalization of designed metabolic pathways within protein based nanocompartments has the potential to increase reaction efficiency in multi-step biosynthetic reactions. We previously demonstrated proof-of-concept of this aim by targeting a functional enzyme to single cellular protein nanocompartments, which were formed upon recombinant expression of the Salmonella enterica LT2 ethanolamine utilization bacterial microcompartment shell proteins EutS or EutSMNLK in Escherichia coli. To optimize this system, increasing overall encapsulated enzyme reaction efficiency, factor(s) required for the production of more than one nanocompartment per cell must be identified. In this work we report that the cupin domain protein EutQ is required for assembly of more than one nanocompartment per cell. Overexpression of EutQ results in multiple nanocompartment assembly in our recombinant system. EutQ specifically interacts with the shell protein EutM in vitro via electrostatic interactions with the putative cytosolic face of EutM. These findings lead to the theory that EutQ could facilitate multiple nanocompartment biogenesis by serving as an assembly hub for shell proteins. This work offers insights into the biogenesis of Eut bacterial microcompartments, and also provides an improved platform for the production of protein based nanocompartments for targeted encapsulation of enzyme pathways.
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Affiliation(s)
- Mark Held
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Alexander Kolb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah Perdue
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Szu-Yi Hsu
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Sarah E Bloch
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Maureen B Quin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA
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20
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Bobik TA, Lehman BP, Yeates TO. Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways. Mol Microbiol 2015; 98:193-207. [PMID: 26148529 PMCID: PMC4718714 DOI: 10.1111/mmi.13117] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2015] [Indexed: 12/15/2022]
Abstract
Prokaryotes use subcellular compartments for a variety of purposes. An intriguing example is a family of complex subcellular organelles known as bacterial microcompartments (MCPs). MCPs are widely distributed among bacteria and impact processes ranging from global carbon fixation to enteric pathogenesis. Overall, MCPs consist of metabolic enzymes encased within a protein shell, and their function is to optimize biochemical pathways by confining toxic or volatile metabolic intermediates. MCPs are fundamentally different from other organelles in having a complex protein shell rather than a lipid-based membrane as an outer barrier. This unusual feature raises basic questions about organelle assembly, protein targeting and metabolite transport. In this review, we discuss the three best-studied MCPs highlighting atomic-level models for shell assembly, targeting sequences that direct enzyme encapsulation, multivalent proteins that organize the lumen enzymes, the principles of metabolite movement across the shell, internal cofactor recycling, a potential system of allosteric regulation of metabolite transport and the mechanism and rationale behind the functional diversification of the proteins that form the shell. We also touch on some potential biotechnology applications of an unusual compartment designed by nature to optimize metabolic processes within a cellular context.
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Affiliation(s)
- Thomas A. Bobik
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Brent P. Lehman
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011
| | - Todd O. Yeates
- Molecular Biology Institute, University of California, Los Angeles
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles
- Department of Chemistry and Biochemistry, University of California, Los Angeles
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21
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Jakobson CM, Kim EY, Slininger MF, Chien A, Tullman-Ercek D. Localization of proteins to the 1,2-propanediol utilization microcompartment by non-native signal sequences is mediated by a common hydrophobic motif. J Biol Chem 2015; 290:24519-33. [PMID: 26283792 DOI: 10.1074/jbc.m115.651919] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 12/14/2022] Open
Abstract
Various bacteria localize metabolic pathways to proteinaceous organelles known as bacterial microcompartments (MCPs), enabling the metabolism of carbon sources to enhance survival and pathogenicity in the gut. There is considerable interest in exploiting bacterial MCPs for metabolic engineering applications, but little is known about the interactions between MCP signal sequences and the protein shells of different MCP systems. We found that the N-terminal sequences from the ethanolamine utilization (Eut) and glycyl radical-generating protein MCPs are able to target reporter proteins to the 1,2-propanediol utilization (Pdu) MCP, and that this localization is mediated by a conserved hydrophobic residue motif. Recapitulation of this motif by the addition of a single amino acid conferred targeting function on an N-terminal sequence from the ethanol utilization MCP system that previously did not act as a Pdu signal sequence. Moreover, the Pdu-localized signal sequences competed with native Pdu targeting sequences for encapsulation in the Pdu MCP. Salmonella enterica natively possesses both the Pdu and Eut operons, and our results suggest that Eut proteins might be localized to the Pdu MCP in vivo. We further demonstrate that S. enterica LT2 retained the ability to grow on 1,2-propanediol as the sole carbon source when a Pdu enzyme was replaced with its Eut homolog. Although the relevance of this finding to the native system remains to be explored, we show that the Pdu-localized signal sequences described herein allow control over the ratio of heterologous proteins encapsulated within Pdu MCPs.
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Affiliation(s)
| | - Edward Y Kim
- From the Department of Chemical and Biomolecular Engineering and
| | | | - Alex Chien
- Biophysics Graduate Group, University of California, Berkeley, California 94720
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