1
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Zhou B, Zheng L, Wu B, Tan Y, Lv O, Yi K, Fan G, Hong L. Protein Engineering with Lightweight Graph Denoising Neural Networks. J Chem Inf Model 2024; 64:3650-3661. [PMID: 38630581 DOI: 10.1021/acs.jcim.4c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Protein engineering faces challenges in finding optimal mutants from a massive pool of candidate mutants. In this study, we introduce a deep-learning-based data-efficient fitness prediction tool to steer protein engineering. Our methodology establishes a lightweight graph neural network scheme for protein structures, which efficiently analyzes the microenvironment of amino acids in wild-type proteins and reconstructs the distribution of the amino acid sequences that are more likely to pass natural selection. This distribution serves as a general guidance for scoring proteins toward arbitrary properties on any order of mutations. Our proposed solution undergoes extensive wet-lab experimental validation spanning diverse physicochemical properties of various proteins, including fluorescence intensity, antigen-antibody affinity, thermostability, and DNA cleavage activity. More than 40% of ProtLGN-designed single-site mutants outperform their wild-type counterparts across all studied proteins and targeted properties. More importantly, our model can bypass the negative epistatic effect to combine single mutation sites and form deep mutants with up to seven mutation sites in a single round, whose physicochemical properties are significantly improved. This observation provides compelling evidence of the structure-based model's potential to guide deep mutations in protein engineering. Overall, our approach emerges as a versatile tool for protein engineering, benefiting both the computational and bioengineering communities.
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Affiliation(s)
- Bingxin Zhou
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai 200240, China
| | - Lirong Zheng
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Banghao Wu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yang Tan
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - Outongyi Lv
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Kai Yi
- School of Mathematics and Statistics, University of New South Wales, Sydney 2052, Australia
| | - Guisheng Fan
- School of Information Science and Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
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2
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Li Z, Shen Q, Usher ET, Anderson AP, Iburg M, Lin R, Zimmer B, Meyer MD, Holehouse AS, You L, Chilkoti A, Dai Y, Lu GJ. Phase transition of GvpU regulates gas vesicle clustering in bacteria. Nat Microbiol 2024; 9:1021-1035. [PMID: 38553608 DOI: 10.1038/s41564-024-01648-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 02/20/2024] [Indexed: 04/06/2024]
Abstract
Gas vesicles (GVs) are microbial protein organelles that support cellular buoyancy. GV engineering has multiple applications, including reporter gene imaging, acoustic control and payload delivery. GVs often cluster into a honeycomb pattern to minimize occupancy of the cytosol. The underlying molecular mechanism and the influence on cellular physiology remain unknown. Using genetic, biochemical and imaging approaches, here we identify GvpU from Priestia megaterium as a protein that regulates GV clustering in vitro and upon expression in Escherichia coli. GvpU binds to the C-terminal tail of the core GV shell protein and undergoes a phase transition to form clusters in subsaturated solution. These properties of GvpU tune GV clustering and directly modulate bacterial fitness. GV variants can be designed with controllable sensitivity to GvpU-mediated clustering, enabling design of genetically tunable biosensors. Our findings elucidate the molecular mechanisms and functional roles of GV clustering, enabling its programmability for biomedical applications.
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Affiliation(s)
- Zongru Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Qionghua Shen
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Emery T Usher
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, Saint Louis, MO, USA
| | | | - Manuel Iburg
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Richard Lin
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Brandon Zimmer
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Matthew D Meyer
- Shared Equipment Authority, Rice University, Houston, TX, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, Saint Louis, MO, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
- Center for Quantitative BioDesign, Duke University, Durham, NC, USA.
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - Yifan Dai
- Department of Biomedical Engineering, Center for Biomolecular Condensates, Washington University in St. Louis, Saint Louis, MO, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
| | - George J Lu
- Department of Bioengineering, Rice University, Houston, TX, USA.
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3
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Li S, Wang F, Xing X, Yue X, Sun S, Lin H, Xu C. Activation-Induced Senescent Cell Death based on Chiral CoHAu Nanoassemblies with Enantioselective Cascade-Catalytic Ability. Adv Healthc Mater 2024; 13:e2303476. [PMID: 38161211 DOI: 10.1002/adhm.202303476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/15/2023] [Indexed: 01/03/2024]
Abstract
Chirality is common in nature, which determines the high enantioselectivity of living systems. Selecting suitable chiral configurations is of great meaning for nanostructures to function better in biological systems. In this study, chiral Co3O4-H2TPPS-Au (CoHAu) nanoassemblies are constructed to accelerate the production ∙OH by consuming D-glucose (D-Glu, widely spread in nature) based on their outstanding enantioselective cascade-catalytic abilities. In particular, D-CoHAu nanoassemblies are more effective in the catalytic conversion of D-Glu than L-CoHAu nanoassemblies. This phenomenon is due to the stronger binding affinity of D-CoHAu nanoassemblies indicated by the lower Km value. Moreover, D-CoHAu nanoassemblies display excellent consumption-ability of D-Glu and production of ∙OH in living cells, which can eliminate senescent cells effectively based on their intracellular enantioselective cascade-catalysis. This research establishes the foundation for bio-mimicking nanostructures with unique functionalities to regulate abnormal biological activities better.
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Affiliation(s)
- Si Li
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, P. R. China
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
| | - Fang Wang
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Xinhe Xing
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Xiaoyong Yue
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Shan Sun
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Hengwei Lin
- International Joint Research Center for Photo-responsive Molecules and Materials, School of Chemical and Material Engineering, Jiangnan University, Wuxi, 214122, P. R. China
| | - Chuanlai Xu
- State Key Lab of Food Science and Technology, International Joint Research Laboratory for Biointerface and Biodetection School of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China
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4
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Kang W, Ma X, Zhang H, Ma J, Liu C, Li J, Guo H, Wang D, Wang R, Li B, Xue C. Dynamic Metabolons Using Stimuli-Responsive Protein Cages. J Am Chem Soc 2024; 146:6686-6696. [PMID: 38425051 DOI: 10.1021/jacs.3c12876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Naturally evolved metabolons have the ability to assemble and disassemble in response to environmental stimuli, allowing for the rapid reorganization of chemical reactions in living cells to meet changing cellular needs. However, replicating such capability in synthetic metabolons remains a challenge due to our limited understanding of the mechanisms by which the assembly and disassembly of such naturally occurring multienzyme complexes are controlled. Here, we report the synthesis of chemical- and light-responsive protein cages for assembling synthetic metabolons, enabling the dynamic regulation of enzymatic reactions in living cells. Particularly, a chemically responsive domain was fused to a self-assembled protein cage subunit, generating engineered protein cages capable of displaying proteins containing cognate interaction domains on their surfaces in response to small molecular cues. Chemical-induced colocalization of sequential enzymes on protein cages enhances the specificity of the branched deoxyviolacein biosynthetic reactions by 2.6-fold. Further, by replacing the chemical-inducible domain with a light-inducible dimerization domain, we created an optogenetic protein cage capable of reversibly recruiting and releasing targeted proteins onto and from the exterior of the protein cages in tens of seconds by on-off of blue light. Tethering the optogenetic protein cages to membranes enables the formation of light-switchable, membrane-bound metabolons, which can repeatably recruit-release enzymes, leading to the manipulation of substrate utilization across membranes on demand. Our work demonstrates a powerful and versatile strategy for constructing dynamic metabolons in engineered living cells for efficient and controllable biocatalysis.
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Affiliation(s)
- Wei Kang
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
- Ningbo Institute of Dalian University of Technology, Ningbo 315016, China
| | - Xiao Ma
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Huawei Zhang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Southern University of Science and Technology, Shenzhen 518055, China
| | - Juncai Ma
- School of Life Sciences, Centre for Cell & Developmental Biology and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, China
| | - Chunxue Liu
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jiani Li
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Hanhan Guo
- Southern University of Science and Technology, Shenzhen 518055, China
| | - Daping Wang
- Southern University of Science and Technology, Shenzhen 518055, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, China
| | - Bo Li
- Department of Mechanical Engineering, Kennesaw State University, Marietta, Georgia 30060, United States
| | - Chuang Xue
- MOE Key Laboratory of Bio-Intelligent Manufacturing, School of Bioengineering, Dalian University of Technology, Dalian 116024, China
- Ningbo Institute of Dalian University of Technology, Ningbo 315016, China
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5
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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6
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Liao J, Yeong V, Obermeyer AC. Charge-Patterned Disordered Peptides Tune Intracellular Phase Separation in Bacteria. ACS Synth Biol 2024; 13:598-612. [PMID: 38308651 DOI: 10.1021/acssynbio.3c00564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Subcellular phase-separated compartments, known as biomolecular condensates, play an important role in the spatiotemporal organization of cells. To understand the sequence-determinants of phase separation in bacteria, we engineered protein-based condensates in Escherichia coli using electrostatic interactions as the main driving force. Minimal cationic disordered peptides were used to supercharge negative, neutral, and positive globular model proteins, enabling their phase separation with anionic biomacromolecules in the cell. The phase behavior was governed by the interaction strength between the cationic proteins and anionic biopolymers, in addition to the protein concentration. The interaction strength primarily depended on the overall net charge of the protein, but the distribution of charge between the globular and disordered domains also had an impact. Notably, the protein charge distribution between domains could tune mesoscale attributes such as the size, number, and subcellular localization of condensates within E. coli cells. The length and charge density of the disordered peptides had significant effects on protein expression levels, ultimately influencing the formation of condensates. Taken together, charge-patterned disordered peptides provide a platform for understanding the molecular grammar underlying phase separation in bacteria.
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Affiliation(s)
- Jane Liao
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Vivian Yeong
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Allie C Obermeyer
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
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7
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Fang Z, Zhu YJ, Qian ZG, Xia XX. Designer protein compartments for microbial metabolic engineering. Curr Opin Biotechnol 2024; 85:103062. [PMID: 38199036 DOI: 10.1016/j.copbio.2023.103062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Protein compartments are distinct structures assembled in living cells via self-assembly or phase separation of specific proteins. Significant efforts have been made to discover their molecular structures and formation mechanisms, as well as their fundamental roles in spatiotemporal control of cellular metabolism. Here, we review the design and construction of synthetic protein compartments for spatial organization of target metabolic pathways toward increased efficiency and specificity. In particular, we highlight the compartmentalization strategies and recent examples to speed up desirable metabolic reactions, to reduce the accumulation of toxic metabolic intermediates, and to switch competing metabolic pathways. We also identify the most important challenges that need to be addressed for exploitation of these designer compartments as a versatile toolkit in metabolic reprogramming.
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Affiliation(s)
- Zhen Fang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Ya-Jiao Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
| | - Xiao-Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
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8
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Shang W, Lichtenberg E, Mlesnita AM, Wilde A, Koch HG. The contribution of mRNA targeting to spatial protein localization in bacteria. FEBS J 2024. [PMID: 38226707 DOI: 10.1111/febs.17054] [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: 10/16/2023] [Revised: 11/27/2023] [Accepted: 01/08/2024] [Indexed: 01/17/2024]
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and must be inserted into or translocated across the cytoplasmic membrane. This requires efficient targeting systems that recognize N-terminal signal sequences in client proteins and deliver them to protein transport complexes in the membrane. While the importance of these protein transport machineries for the spatial organization of the bacterial cell is well documented in multiple studies, the contribution of mRNA targeting and localized translation to protein transport is only beginning to emerge. mRNAs can exhibit diverse subcellular localizations in the bacterial cell and can accumulate at sites where new protein is required. This is frequently observed for mRNAs encoding membrane proteins, but the physiological importance of membrane enrichment of mRNAs and the consequences it has for the insertion of the encoded protein have not been explored in detail. Here, we briefly highlight some basic concepts of signal sequence-based protein targeting and describe in more detail strategies that enable the monitoring of mRNA localization in bacterial cells and potential mechanisms that route mRNAs to particular positions within the cell. Finally, we summarize some recent developments that demonstrate that mRNA targeting and localized translation can sustain membrane protein insertion under stress conditions when the protein-targeting machinery is compromised. Thus, mRNA targeting likely acts as a back-up strategy and complements the canonical signal sequence-based protein targeting.
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Affiliation(s)
- Wenkang Shang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | | | - Andreea Mihaela Mlesnita
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
| | - Annegret Wilde
- Faculty of Biology, Albert-Ludwigs University Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs University Freiburg, Germany
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9
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Zhou P, Gao C, Song W, Wei W, Wu J, Liu L, Chen X. Engineering status of protein for improving microbial cell factories. Biotechnol Adv 2024; 70:108282. [PMID: 37939975 DOI: 10.1016/j.biotechadv.2023.108282] [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: 05/12/2023] [Revised: 10/23/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023]
Abstract
With the development of metabolic engineering and synthetic biology, microbial cell factories (MCFs) have provided an efficient and sustainable method to synthesize a series of chemicals from renewable feedstocks. However, the efficiency of MCFs is usually limited by the inappropriate status of protein. Thus, engineering status of protein is essential to achieve efficient bioproduction with high titer, yield and productivity. In this review, we summarize the engineering strategies for metabolic protein status, including protein engineering for boosting microbial catalytic efficiency, protein modification for regulating microbial metabolic capacity, and protein assembly for enhancing microbial synthetic capacity. Finally, we highlight future challenges and prospects of improving microbial cell factories by engineering status of protein.
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Affiliation(s)
- Pei Zhou
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China.
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10
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Baum B, Spang A. On the origin of the nucleus: a hypothesis. Microbiol Mol Biol Rev 2023; 87:e0018621. [PMID: 38018971 PMCID: PMC10732040 DOI: 10.1128/mmbr.00186-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
SUMMARYIn this hypothesis article, we explore the origin of the eukaryotic nucleus. In doing so, we first look afresh at the nature of this defining feature of the eukaryotic cell and its core functions-emphasizing the utility of seeing the eukaryotic nucleoplasm and cytoplasm as distinct regions of a common compartment. We then discuss recent progress in understanding the evolution of the eukaryotic cell from archaeal and bacterial ancestors, focusing on phylogenetic and experimental data which have revealed that many eukaryotic machines with nuclear activities have archaeal counterparts. In addition, we review the literature describing the cell biology of representatives of the TACK and Asgardarchaeaota - the closest known living archaeal relatives of eukaryotes. Finally, bringing these strands together, we propose a model for the archaeal origin of the nucleus that explains much of the current data, including predictions that can be used to put the model to the test.
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Affiliation(s)
- Buzz Baum
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, the Netherlands
- Department of Marine Microbiology and Biogeochemistry, NIOZ, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands
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11
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Schaible GA, Jay ZJ, Cliff J, Schulz F, Gauvin C, Goudeau D, Malmstrom RR, Emil Ruff S, Edgcomb V, Hatzenpichler R. Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568837. [PMID: 38076927 PMCID: PMC10705294 DOI: 10.1101/2023.11.27.568837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing eight new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nano-scale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal non-canonical amino acid tagging (BONCAT) we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.
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Affiliation(s)
- George A. Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
| | - Zackary J. Jay
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - Colin Gauvin
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - Rex R. Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720
| | - S. Emil Ruff
- Ecosystems Center and Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, 02543
| | | | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717
- Thermal Biology Institute, Montana State University, Bozeman, MT 59717
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717
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12
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Rudd SR, Miranda LS, Curtis HR, Bigot Y, Diaz-Mendoza M, Hice R, Nizet V, Park HW, Blaha G, Federici BA, Bideshi DK. The Parasporal Body of Bacillus thuringiensis subsp. israelensis: A Unique Phage Capsid-Associated Prokaryotic Insecticidal Organelle. BIOLOGY 2023; 12:1421. [PMID: 37998020 PMCID: PMC10669011 DOI: 10.3390/biology12111421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023]
Abstract
The three most important commercial bacterial insecticides are all derived from subspecies of Bacillus thuringiensis (Bt). Specifically, Bt subsp. kurstaki (Btk) and Bt subsp. aizawai (Bta) are used to control larval lepidopteran pests. The third, Bt subsp. israelensis (Bti), is primarily used to control mosquito and blackfly larvae. All three subspecies produce a parasporal body (PB) during sporulation. The PB is composed of insecticidal proteins that damage the midgut epithelium, initiating a complex process that results in the death of the insect. Among these three subspecies of Bt, Bti is unique as it produces the most complex PB consisting of three compartments. Each compartment is bound by a multilaminar fibrous matrix (MFM). Two compartments contain one protein each, Cry11Aa1 and Cyt1Aa1, while the third contains two, Cry4Aa1/Cry4Ba1. Each compartment is packaged independently before coalescing into the mature spherical PB held together by additional layers of the MFM. This distinctive packaging process is unparalleled among known bacterial organelles, although the underlying molecular biology is yet to be determined. Here, we present structural and molecular evidence that the MFM has a hexagonal pattern to which Bti proteins Bt152 and Bt075 bind. Bt152 binds to a defined spot on the MFM during the development of each compartment, yet its function remains unknown. Bt075 appears to be derived from a bacteriophage major capsid protein (MCP), and though its sequence has markedly diverged, it shares striking 3-D structural similarity to the Escherichia coli phage HK97 Head 1 capsid protein. Both proteins are encoded on Bti's pBtoxis plasmid. Additionally, we have also identified a six-amino acid motif that appears to be part of a novel molecular process responsible for targeting the Cry and Cyt proteins to their cytoplasmic compartments. This paper describes several previously unknown features of the Bti organelle, representing a first step to understanding the biology of a unique process of sorting and packaging of proteins into PBs. The insights from this research suggest a potential for future applications in nanotechnology.
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Affiliation(s)
- Sarah R. Rudd
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
- School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA;
| | - Leticia Silva Miranda
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
| | - Hannah R. Curtis
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
- School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Yves Bigot
- UMR CNRS7247, Centre INRA Val de Loire, 37380 Nouzilly, France;
| | - Mercedes Diaz-Mendoza
- Department of Biochemistry and Molecular Biology, Faculty of Chemical and Biological Sciences, University Complutense of Madrid, 28040 Madrid, Spain;
| | - Robert Hice
- Department of Entomology, University of California, Riverside, CA 92521, USA;
| | - Victor Nizet
- Department of Pediatrics, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA;
| | - Hyun-Woo Park
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
| | - Gregor Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA;
| | - Brian A. Federici
- Department of Entomology, University of California, Riverside, CA 92521, USA;
| | - Dennis K. Bideshi
- Program in Biomedical Sciences, Department of Biological Sciences, California Baptist University, Riverside, CA 92504, USA; (S.R.R.); (L.S.M.); (H.R.C.); (H.-W.P.)
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13
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Sneideris T, Erkamp NA, Ausserwöger H, Saar KL, Welsh TJ, Qian D, Katsuya-Gaviria K, Johncock MLLY, Krainer G, Borodavka A, Knowles TPJ. Targeting nucleic acid phase transitions as a mechanism of action for antimicrobial peptides. Nat Commun 2023; 14:7170. [PMID: 37935659 PMCID: PMC10630377 DOI: 10.1038/s41467-023-42374-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Antimicrobial peptides (AMPs), which combat bacterial infections by disrupting the bacterial cell membrane or interacting with intracellular targets, are naturally produced by a number of different organisms, and are increasingly also explored as therapeutics. However, the mechanisms by which AMPs act on intracellular targets are not well understood. Using machine learning-based sequence analysis, we identified a significant number of AMPs that have a strong tendency to form liquid-like condensates in the presence of nucleic acids through phase separation. We demonstrate that this phase separation propensity is linked to the effectiveness of the AMPs in inhibiting transcription and translation in vitro, as well as their ability to compact nucleic acids and form clusters with bacterial nucleic acids in bacterial cells. These results suggest that the AMP-driven compaction of nucleic acids and modulation of their phase transitions constitute a previously unrecognised mechanism by which AMPs exert their antibacterial effects. The development of antimicrobials that target nucleic acid phase transitions may become an attractive route to finding effective and long-lasting antibiotics.
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Affiliation(s)
- Tomas Sneideris
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Nadia A Erkamp
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Hannes Ausserwöger
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Kadi L Saar
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Timothy J Welsh
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Daoyuan Qian
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Kai Katsuya-Gaviria
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Margaret L L Y Johncock
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Georg Krainer
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
| | - Alexander Borodavka
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK.
- Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Ave, Cambridge, UK.
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14
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Ni T, Jiang Q, Ng PC, Shen J, Dou H, Zhu Y, Radecke J, Dykes GF, Huang F, Liu LN, Zhang P. Intrinsically disordered CsoS2 acts as a general molecular thread for α-carboxysome shell assembly. Nat Commun 2023; 14:5512. [PMID: 37679318 PMCID: PMC10484944 DOI: 10.1038/s41467-023-41211-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 08/27/2023] [Indexed: 09/09/2023] Open
Abstract
Carboxysomes are a paradigm of self-assembling proteinaceous organelles found in nature, offering compartmentalisation of enzymes and pathways to enhance carbon fixation. In α-carboxysomes, the disordered linker protein CsoS2 plays an essential role in carboxysome assembly and Rubisco encapsulation. Its mechanism of action, however, is not fully understood. Here we synthetically engineer α-carboxysome shells using minimal shell components and determine cryoEM structures of these to decipher the principle of shell assembly and encapsulation. The structures reveal that the intrinsically disordered CsoS2 C-terminus is well-structured and acts as a universal "molecular thread" stitching through multiple shell protein interfaces. We further uncover in CsoS2 a highly conserved repetitive key interaction motif, [IV]TG, which is critical to the shell assembly and architecture. Our study provides a general mechanism for the CsoS2-governed carboxysome shell assembly and cargo encapsulation and further advances synthetic engineering of carboxysomes for diverse biotechnological applications.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Pei Cing Ng
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Juan Shen
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Hao Dou
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Julika Radecke
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fang Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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15
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Lipiński WP, Zehnder J, Abbas M, Güntert P, Spruijt E, Wiegand T. Fibrils Emerging from Droplets: Molecular Guiding Principles behind Phase Transitions of a Short Peptide-Based Condensate Studied by Solid-State NMR. Chemistry 2023; 29:e202301159. [PMID: 37310801 DOI: 10.1002/chem.202301159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/15/2023]
Abstract
Biochemical reactions occurring in highly crowded cellular environments require different means of control to ensure productivity and specificity. Compartmentalization of reagents by liquid-liquid phase separation is one of these means. However, extremely high local protein concentrations of up to 400 mg/ml can result in pathological aggregation into fibrillar amyloid structures, a phenomenon that has been linked to various neurodegenerative diseases. Despite its relevance, the process of liquid-to-solid transition inside condensates is still not well understood at the molecular level. We thus herein use small peptide derivatives that can undergo both liquid-liquid and subsequent liquid-to-solid phase transition as model systems to study both processes. Using solid-state nuclear magnetic resonance (NMR) and transmission electron microscopy (TEM), we compare the structure of condensed states of leucine, tryptophan and phenylalanine containing derivatives, distinguishing between liquid-like condensates, amorphous aggregates and fibrils, respectively. A structural model for the fibrils formed by the phenylalanine derivative was obtained by an NMR-based structure calculation. The fibrils are stabilised by hydrogen bonds and side-chain π-π interactions, which are likely much less pronounced or absent in the liquid and amorphous state. Such noncovalent interactions are equally important for the liquid-to-solid transition of proteins, particularly those related to neurodegenerative diseases.
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Affiliation(s)
- Wojciech P Lipiński
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Johannes Zehnder
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Manzar Abbas
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Peter Güntert
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
- Institute of Biophysical Chemistry Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji-shi, 192-0397, Tokyo, Japan
| | - Evan Spruijt
- Radboud University, Institute of Molecules and Materials (IMM), Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands
| | - Thomas Wiegand
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470, Mülheim an der Ruhr, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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16
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Ionescu D, Volland JM, Contarini PE, Gros O. Genomic Mysteries of Giant Bacteria: Insights and Implications. Genome Biol Evol 2023; 15:evad163. [PMID: 37708391 PMCID: PMC10519445 DOI: 10.1093/gbe/evad163] [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: 03/27/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/16/2023] Open
Abstract
Bacteria and Archaea are traditionally regarded as organisms with a simple morphology constrained to a size of 2-3 µm. Nevertheless, the history of microbial research is rich in the description of giant bacteria exceeding tens and even hundreds of micrometers in length or diameter already from its early days, for example, Beggiatoa spp., to the present, for example, Candidatus Thiomargarita magnifica. While some of these giants are still being studied, some were lost to science, with merely drawings and photomicrographs as evidence for their existence. The physiology and biogeochemical role of giant bacteria have been studied, with a large focus on those involved in the sulfur cycle. With the onset of the genomic era, no special emphasis has been given to this group, in an attempt to gain a novel, evolutionary, and molecular understanding of the phenomenon of bacterial gigantism. The few existing genomic studies reveal a mysterious world of hyperpolyploid bacteria with hundreds to hundreds of thousands of chromosomes that are, in some cases, identical and in others, extremely different. These studies on giant bacteria reveal novel organelles, cellular compartmentalization, and novel mechanisms to combat the accumulation of deleterious mutations in polyploid bacteria. In this perspective paper, we provide a brief overview of what is known about the genomics of giant bacteria and build on that to highlight a few burning questions that await to be addressed.
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Affiliation(s)
- Danny Ionescu
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Jean-Marie Volland
- Laboratory for Research in Complex Systems, Menlo Park, California, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul-Emile Contarini
- Laboratory for Research in Complex Systems, Menlo Park, California, USA
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Pointe-à-Pitre, France
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Pointe-à-Pitre, France
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17
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Zambelli B. Intracellular phase separation and its role in nickel sensing. Trends Cell Biol 2023; 33:732-733. [PMID: 37433710 DOI: 10.1016/j.tcb.2023.06.008] [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: 06/22/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023]
Abstract
Nickel homeostasis in many bacteria is controlled by the nickel-sensor NikR. A recent study by Cao et al. found that Escherichia coli NikR undergoes phase separation and that this event enhances its function as a nickel-dependent transcriptional repressor. The results suggest that phase separation is functional for bacterial metal homeostasis.
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Affiliation(s)
- Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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18
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Nicholls JWF, Chin JP, Williams TA, Lenton TM, O’Flaherty V, McGrath JW. On the potential roles of phosphorus in the early evolution of energy metabolism. Front Microbiol 2023; 14:1239189. [PMID: 37601379 PMCID: PMC10433651 DOI: 10.3389/fmicb.2023.1239189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.
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Affiliation(s)
- Jack W. F. Nicholls
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Jason P. Chin
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Timothy M. Lenton
- Global Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - John W. McGrath
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
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19
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Cao K, Li S, Wang Y, Hu H, Xiang S, Zhang Q, Liu Y. Cellular uptake of nickel by NikR is regulated by phase separation. Cell Rep 2023; 42:112518. [PMID: 37210726 DOI: 10.1016/j.celrep.2023.112518] [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: 05/19/2022] [Revised: 02/02/2023] [Accepted: 05/01/2023] [Indexed: 05/23/2023] Open
Abstract
Bacterial cells were long thought to be "bags of enzymes" with minimal internal structures. In recent years, membrane-less organelles formed by liquid-liquid phase separation (LLPS) of proteins or nucleic acids have been found to be involved in many important biological processes, although most of them were studied on eukaryotic cells. Here, we report that NikR, a bacterial nickel-responsive regulatory protein, exhibits LLPS both in solution and inside cells. Analyses of cellular nickel uptake and cell growth of E. coli confirm that LLPS enhances the regulatory function of NikR, while disruption of LLPS in cells promotes the expression of nickel transporter (nik) genes, which are negatively regulated by NikR. Mechanistic study shows that Ni(II) ions induces the accumulation of nik promoter DNA into the condensates formed by NikR. This result suggests that the formation of membrane-less compartments can be a regulatory mechanism of metal transporter proteins in bacterial cells.
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Affiliation(s)
- Kaiming Cao
- College of Chemistry and Environmental Engineering, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China; Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Shixuan Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Yu Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Hongze Hu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Sijia Xiang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Qianling Zhang
- College of Chemistry and Environmental Engineering, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
| | - Yangzhong Liu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China.
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20
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Dunstan RA, Bamert RS, Tan KS, Imbulgoda U, Barlow CK, Taiaroa G, Pickard DJ, Schittenhelm RB, Dougan G, Short FL, Lithgow T. Epitopes in the capsular polysaccharide and the porin OmpK36 receptors are required for bacteriophage infection of Klebsiella pneumoniae. Cell Rep 2023; 42:112551. [PMID: 37224021 DOI: 10.1016/j.celrep.2023.112551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/09/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
To kill bacteria, bacteriophages (phages) must first bind to a receptor, triggering the release of the phage DNA into the bacterial cell. Many bacteria secrete polysaccharides that had been thought to shield bacterial cells from phage attack. We use a comprehensive genetic screen to distinguish that the capsule is not a shield but is instead a primary receptor enabling phage predation. Screening of a transposon library to select phage-resistant Klebsiella shows that the first receptor-binding event docks to saccharide epitopes in the capsule. We discover a second step of receptor binding, dictated by specific epitopes in an outer membrane protein. This additional and necessary event precedes phage DNA release to establish a productive infection. That such discrete epitopes dictate two essential binding events for phages has profound implications for understanding the evolution of phage resistance and what dictates host range, two issues critically important to translating knowledge of phage biology into phage therapies.
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Affiliation(s)
- Rhys A Dunstan
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
| | - Rebecca S Bamert
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Kher Shing Tan
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Uvini Imbulgoda
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Christopher K Barlow
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Clayton, VIC, Australia
| | - Derek J Pickard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Francesca L Short
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia; Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
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21
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Wang R, Liu X, Lv B, Sun W, Li C. Designing Intracellular Compartments for Efficient Engineered Microbial Cell Factories. ACS Synth Biol 2023; 12:1378-1395. [PMID: 37083286 DOI: 10.1021/acssynbio.2c00671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
With the rapid development of synthetic biology, various kinds of microbial cell factories (MCFs) have been successfully constructed to produce high-value-added compounds. However, the complexity of metabolic regulation and pathway crosstalk always cause issues such as intermediate metabolite accumulation, byproduct generation, and metabolic burden in MCFs, resulting in low efficiencies and low yields of industrial biomanufacturing. Such issues could be solved by spatially rearranging the pathways using intracellular compartments. In this review, design strategies are summarized and discussed based on the types and characteristics of natural and artificial subcellular compartments. This review systematically presents information for the construction of efficient MCFs with intracellular compartments in terms of four aspects of design strategy goals: (1) improving local reactant concentration; (2) intercepting and isolating competing pathways; (3) providing specific reaction substances and environments; and (4) storing and accumulating products.
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Affiliation(s)
- Ruwen Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Xin Liu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Bo Lv
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
| | - Wentao Sun
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, PR China
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, PR China
- Center for Synthetic and System Biology, Tsinghua University, Beijing, 100084, PR China
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22
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Howley E, Mangus A, Williams D, Torres CI. Intracytoplasmic membranes develop in Geobacter sulfurreducens under thermodynamically limiting conditions. NPJ Biofilms Microbiomes 2023; 9:18. [PMID: 37029136 PMCID: PMC10082016 DOI: 10.1038/s41522-023-00384-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 03/17/2023] [Indexed: 04/09/2023] Open
Abstract
Geobacter sulfurreducens is an electroactive bacterium capable of reducing metal oxides in the environment and electrodes in engineered systems1,2. Geobacter sp. are the keystone organisms in electrogenic biofilms, as their respiration consumes fermentation products produced by other organisms and reduces a terminal electron acceptor e.g. iron oxide or an electrode. To respire extracellular electron acceptors with a wide range of redox potentials, G. sulfurreducens has a complex network of respiratory proteins, many of which are membrane-bound3-5. We have identified intracytoplasmic membrane (ICM) structures in G. sulfurreducens. This ICM is an invagination of the inner membrane that has folded and organized by an unknown mechanism, often but not always located near the tip of a cell. Using confocal microscopy, we can identify that at least half of the cells contain an ICM when grown on low potential anode surfaces, whereas cells grown at higher potential anode surfaces or using fumarate as electron acceptor had significantly lower ICM frequency. 3D models developed from cryo-electron tomograms show the ICM to be a continuous extension of the inner membrane in contact with the cytoplasmic and periplasmic space. The differential abundance of ICM in cells grown under different thermodynamic conditions supports the hypothesis that it is an adaptation to limited energy availability, as an increase in membrane-bound respiratory proteins could increase electron flux. Thus, the ICM provides extra inner-membrane surface to increase the abundance of these proteins. G. sulfurreducens is the first Thermodesulfobacterium or metal-oxide reducer found to produce ICMs.
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Affiliation(s)
- Ethan Howley
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Anna Mangus
- School for Engineering Mass Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Dewight Williams
- Eyring Materials Center, Arizona State University, Tempe, AZ, USA
| | - César I Torres
- School for Engineering Mass Transport and Energy, Arizona State University, Tempe, AZ, USA.
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23
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Zhou P, Liu H, Meng X, Zuo H, Qi M, Guo L, Gao C, Song W, Wu J, Chen X, Chen W, Liu L. Engineered Artificial Membraneless Organelles in Saccharomyces cerevisiae To Enhance Chemical Production. Angew Chem Int Ed Engl 2023; 62:e202215778. [PMID: 36762978 DOI: 10.1002/anie.202215778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/11/2023]
Abstract
Microbial cell factories provide a green and sustainable opportunity to produce value-added products from renewable feedstock. However, the leakage of toxic or volatile intermediates decreases the efficiency of microbial cell factories. In this study, membraneless organelles (MLOs) were reconstructed in Saccharomyces cerevisiae by the disordered protein sequence A-IDPs. A regulation system was designed to spatiotemporally regulate the size and rigidity of MLOs. Manipulating the MLO size of strain ZP03-FM, the amounts of assimilated methanol and malate were increased by 162 % and 61 %, respectively. Furthermore, manipulating the MLO rigidity in strain ZP04-RB made acetyl-coA synthesis from oxidative glycolysis change to non-oxidative glycolysis; consequently, CO2 release decreased by 35 % and the n-butanol yield increased by 20 %. This artificial MLO provides a strategy for the co-localization of enzymes to channel C1 starting materials into value-added chemicals.
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Affiliation(s)
- Pei Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Hui Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xin Meng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Huiyun Zuo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Mengya Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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24
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Muñoz-Gómez SA, Cadena LR, Gardiner AT, Leger MM, Sheikh S, Connell LB, Bilý T, Kopejtka K, Beatty JT, Koblížek M, Roger AJ, Slamovits CH, Lukeš J, Hashimi H. Intracytoplasmic-membrane development in alphaproteobacteria involves the homolog of the mitochondrial crista-developing protein Mic60. Curr Biol 2023; 33:1099-1111.e6. [PMID: 36921606 DOI: 10.1016/j.cub.2023.02.059] [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: 11/06/2022] [Revised: 02/06/2023] [Accepted: 02/16/2023] [Indexed: 03/16/2023]
Abstract
Mitochondrial cristae expand the surface area of respiratory membranes and ultimately allow for the evolutionary scaling of respiration with cell volume across eukaryotes. The discovery of Mic60 homologs among alphaproteobacteria, the closest extant relatives of mitochondria, suggested that cristae might have evolved from bacterial intracytoplasmic membranes (ICMs). Here, we investigated the predicted structure and function of alphaproteobacterial Mic60, and a protein encoded by an adjacent gene Orf52, in two distantly related purple alphaproteobacteria, Rhodobacter sphaeroides and Rhodopseudomonas palustris. In addition, we assessed the potential physical interactors of Mic60 and Orf52 in R. sphaeroides. We show that the three α helices of mitochondrial Mic60's mitofilin domain, as well as its adjacent membrane-binding amphipathic helix, are present in alphaproteobacterial Mic60. The disruption of Mic60 and Orf52 caused photoheterotrophic growth defects, which are most severe under low light conditions, and both their disruption and overexpression led to enlarged ICMs in both studied alphaproteobacteria. We also found that alphaproteobacterial Mic60 physically interacts with BamA, the homolog of Sam50, one of the main physical interactors of eukaryotic Mic60. This interaction, responsible for making contact sites at mitochondrial envelopes, has been conserved in modern alphaproteobacteria despite more than a billion years of evolutionary divergence. Our results suggest a role for Mic60 in photosynthetic ICM development and contact site formation at alphaproteobacterial envelopes. Overall, we provide support for the hypothesis that mitochondrial cristae evolved from alphaproteobacterial ICMs and have therefore improved our understanding of the nature of the mitochondrial ancestor.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
| | - Lawrence Rudy Cadena
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Alastair T Gardiner
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Michelle M Leger
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, 08003 Catalonia, Spain
| | - Shaghayegh Sheikh
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Louise B Connell
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tomáš Bilý
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Karel Kopejtka
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - J Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michal Koblížek
- Center Algatech, Institute of Microbiology, Czech Academy of Sciences, 37901 Třeboň, Czech Republic
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Julius Lukeš
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic
| | - Hassan Hashimi
- Institute of Parasitology, Biology Center, Czech Academy of Sciences, 37005 České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice (Budweis), Czech Republic.
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25
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An B, Wang Y, Huang Y, Wang X, Liu Y, Xun D, Church GM, Dai Z, Yi X, Tang TC, Zhong C. Engineered Living Materials For Sustainability. Chem Rev 2023; 123:2349-2419. [PMID: 36512650 DOI: 10.1021/acs.chemrev.2c00512] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recent advances in synthetic biology and materials science have given rise to a new form of materials, namely engineered living materials (ELMs), which are composed of living matter or cell communities embedded in self-regenerating matrices of their own or artificial scaffolds. Like natural materials such as bone, wood, and skin, ELMs, which possess the functional capabilities of living organisms, can grow, self-organize, and self-repair when needed. They also spontaneously perform programmed biological functions upon sensing external cues. Currently, ELMs show promise for green energy production, bioremediation, disease treatment, and fabricating advanced smart materials. This review first introduces the dynamic features of natural living systems and their potential for developing novel materials. We then summarize the recent research progress on living materials and emerging design strategies from both synthetic biology and materials science perspectives. Finally, we discuss the positive impacts of living materials on promoting sustainability and key future research directions.
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Affiliation(s)
- Bolin An
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yanyi Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuanyuan Huang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yuzhu Liu
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dongmin Xun
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - George M Church
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Zhuojun Dai
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiao Yi
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tzu-Chieh Tang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston 02115, Massachusetts United States.,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston 02115, Massachusetts United States
| | - Chao Zhong
- Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.,CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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26
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Dziuba MV, Paulus A, Schramm L, Awal RP, Pósfai M, Monteil CL, Fouteau S, Uebe R, Schüler D. Silent gene clusters encode magnetic organelle biosynthesis in a non-magnetotactic phototrophic bacterium. THE ISME JOURNAL 2023; 17:326-339. [PMID: 36517527 PMCID: PMC9938234 DOI: 10.1038/s41396-022-01348-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022]
Abstract
Horizontal gene transfer is a powerful source of innovations in prokaryotes that can affect almost any cellular system, including microbial organelles. The formation of magnetosomes, one of the most sophisticated microbial mineral-containing organelles synthesized by magnetotactic bacteria for magnetic navigation in the environment, was also shown to be a horizontally transferrable trait. However, the mechanisms determining the fate of such genes in new hosts are not well understood, since non-adaptive gene acquisitions are typically rapidly lost and become unavailable for observation. This likely explains why gene clusters encoding magnetosome biosynthesis have never been observed in non-magnetotactic bacteria. Here, we report the first discovery of a horizontally inherited dormant gene clusters encoding biosynthesis of magnetosomes in a non-magnetotactic phototrophic bacterium Rhodovastum atsumiense. We show that these clusters were inactivated through transcriptional silencing and antisense RNA regulation, but retain functionality, as several genes were able to complement the orthologous deletions in a remotely related magnetotactic bacterium. The laboratory transfer of foreign magnetosome genes to R. atsumiense was found to endow the strain with magnetosome biosynthesis, but strong negative selection led to rapid loss of this trait upon subcultivation, highlighting the trait instability in this organism. Our results provide insight into the horizontal dissemination of gene clusters encoding complex prokaryotic organelles and illuminate the potential mechanisms of their genomic preservation in a dormant state.
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Affiliation(s)
- M. V. Dziuba
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany
| | - A. Paulus
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany ,grid.7384.80000 0004 0467 6972Department of Microbial Biochemistry, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, Bayreuth, Germany
| | - L. Schramm
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany
| | - R. P. Awal
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany
| | - M. Pósfai
- ELKH-PE Environmental Mineralogy Research Group, Veszprém, Hungary ,grid.7336.10000 0001 0203 5854Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, Veszprém, Hungary
| | - C. L. Monteil
- grid.5399.60000 0001 2176 4817Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France
| | - S. Fouteau
- grid.8390.20000 0001 2180 5818LABGeM, Genomique Metabolique, CEA, Genoscope, Institut Francois Jacob, CNRS, Universite d’Evry, Universite Paris- Saclay, Evry, France
| | - R. Uebe
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany ,grid.7384.80000 0004 0467 6972Department of Microbial Biochemistry, Faculty of Life Sciences: Food, Nutrition and Health, University of Bayreuth, Bayreuth, Germany
| | - D. Schüler
- grid.7384.80000 0004 0467 6972Department of Microbiology, Faculty of Biology, Chemistry and Geosciences, University of Bayreuth, Bayreuth, Germany
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27
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Live-Cell Fluorescence Imaging of Magnetosome Organelle for Magnetotaxis Motility. Methods Mol Biol 2023; 2646:133-146. [PMID: 36842112 DOI: 10.1007/978-1-0716-3060-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
The assessment of intracellular dynamics is crucial for understanding the function and formation process of bacterial organelle, just as it is for the inquisition of their eukaryotic counterparts. The methods for imaging magnetosome organelles in a magnetotactic bacterial cell using live-cell fluorescence imaging by highly inclined and laminated optical sheet (HILO) microscopy are presented in this chapter. Furthermore, we introduce methods for pH imaging in magnetosome lumen as an application of fluorescence magnetosome imaging.
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28
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Surveying membrane landscapes: a new look at the bacterial cell surface. Nat Rev Microbiol 2023:10.1038/s41579-023-00862-w. [PMID: 36828896 DOI: 10.1038/s41579-023-00862-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 02/26/2023]
Abstract
Recent studies applying advanced imaging techniques are changing the way we understand bacterial cell surfaces, bringing new knowledge on everything from single-cell heterogeneity in bacterial populations to their drug sensitivity and mechanisms of antimicrobial resistance. In both Gram-positive and Gram-negative bacteria, the outermost surface of the bacterial cell is being imaged at nanoscale; as a result, topographical maps of bacterial cell surfaces can be constructed, revealing distinct zones and specific features that might uniquely identify each cell in a population. Functionally defined assembly precincts for protein insertion into the membrane have been mapped at nanoscale, and equivalent lipid-assembly precincts are suggested from discrete lipopolysaccharide patches. As we review here, particularly for Gram-negative bacteria, the applications of various modalities of nanoscale imaging are reawakening our curiosity about what is conceptually a 3D cell surface landscape: what it looks like, how it is made and how it provides resilience to respond to environmental impacts.
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29
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Wang H, Hayer-Hartl M. Phase Separation of Rubisco by the Folded SSUL Domains of CcmM in Beta-Carboxysome Biogenesis. Methods Mol Biol 2023; 2563:269-296. [PMID: 36227479 DOI: 10.1007/978-1-0716-2663-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Carboxysomes are large, cytosolic bodies present in all cyanobacteria and many proteobacteria that function as the sites of photosynthetic CO2 fixation by the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The carboxysome lumen is enriched with Rubisco and carbonic anhydrase (CA). The polyhedral proteinaceous shell allows the passage of HCO3- ions into the carboxysome, where they are converted to CO2 by CA. Thus, the carboxysome functions as a CO2-concentrating mechanism (CCM), enhancing the efficiency of Rubisco in CO2 fixation. In β-cyanobacteria, carboxysome biogenesis first involves the aggregation of Rubisco by CcmM, a scaffolding protein that exists in two isoforms. Both isoforms contain a minimum of three Rubisco small subunit-like (SSUL) domains, connected by flexible linkers. Multivalent interaction between these linked SSUL domains with Rubisco results in phase separation and condensate formation. Here, we use Rubisco and the short isoform of CcmM (M35) of the β-cyanobacterium Synechococcus elongatus PCC7942 to describe the methods used for in vitro analysis of the mechanism of condensate formation driven by the SSUL domains. The methods include turbidity assays, bright-field and fluorescence microscopy, as well as transmission electron microscopy (TEM) in both negative staining and cryo-conditions.
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Affiliation(s)
- Huping Wang
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany
- Membrane Protein Biosynthesis and Quality Control, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
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30
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Spang A. Is an archaeon the ancestor of eukaryotes? Environ Microbiol 2022; 25:775-779. [PMID: 36562617 DOI: 10.1111/1462-2920.16323] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022]
Abstract
The origin of complex cellular life is a key puzzle in evolutionary research, which has broad implications for various neighbouring scientific disciplines. Naturally, views on this topic vary widely depending on the world view and context from which this topic is approached. In the following, I will share my perspective about our current scientific knowledge on the origin of eukaryotic cells, that is, eukaryogenesis, from a biological point of view focusing on the question as to whether an archaeon was the ancestor of eukaryotes.
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Affiliation(s)
- Anja Spang
- NIOZ, Royal Netherlands Institute for Sea Research, Department of Marine Microbiology and Biogeochemistry, Utrecht University, AB Den Burg, The Netherlands.,Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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31
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Kang W, Ma X, Kakarla D, Zhang H, Fang Y, Chen B, Zhu K, Zheng D, Wu Z, Li B, Xue C. Organizing Enzymes on Self-Assembled Protein Cages for Cascade Reactions. Angew Chem Int Ed Engl 2022; 61:e202214001. [PMID: 36288455 DOI: 10.1002/anie.202214001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Indexed: 11/06/2022]
Abstract
Cells use self-assembled biomaterials such as lipid membranes or proteinaceous shells to coordinate thousands of reactions that simultaneously take place within crowded spaces. However, mimicking such spatial organization for synthetic applications in engineered systems remains a challenge, resulting in inferior catalytic efficiency. In this work, we show that protein cages as an ideal scaffold to organize enzymes to enhance cascade reactions both in vitro and in living cells. We demonstrate that not only enzyme-enzyme distance but also the improved Km value contribute to the enhanced reaction rate of cascade reactions. Three sequential enzymes for lycopene biosynthesis have been co-localized on the exterior of the engineered protein cages in Escherichia coli, leading to an 8.5-fold increase of lycopene production by streamlining metabolic flux towards its biosynthesis. This versatile system offers a powerful tool to achieve enzyme spatial organization for broad applications in biocatalysis.
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Affiliation(s)
- Wei Kang
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ningbo Institute of Dalian University of Technology, Ningbo, 315016, China
| | - Xiao Ma
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Deepika Kakarla
- Department of Mechanical Engineering, Kennesaw State University, GA 0060, Marietta, USA
| | - Huawei Zhang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yunming Fang
- National Energy Research Centre for Biorefinery, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Baizhu Chen
- School of Biomedical Engineering, SUN YAT-SEN University, Shenzhen, 518000, China
| | - Kongfu Zhu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Danni Zheng
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ningbo Institute of Dalian University of Technology, Ningbo, 315016, China
| | - Zhiyue Wu
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China
| | - Bo Li
- Department of Mechanical Engineering, Kennesaw State University, GA 0060, Marietta, USA
| | - Chuang Xue
- State Key Laboratory of Fine Chemicals, Frontiers Science Centre for Smart Materials Oriented Chemical Engineering, School of Bioengineering, Dalian University of Technology, Dalian, 116024, China.,Ningbo Institute of Dalian University of Technology, Ningbo, 315016, China
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32
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Howley E, Ki D, Krajmalnik-Brown R, Torres CI. Geobacter sulfurreducens' Unique Metabolism Results in Cells with a High Iron and Lipid Content. Microbiol Spectr 2022; 10:e0259322. [PMID: 36301091 PMCID: PMC9769739 DOI: 10.1128/spectrum.02593-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/24/2022] [Indexed: 01/07/2023] Open
Abstract
Geobacter sulfurreducens is a ubiquitous iron-reducing bacterium in soils, and in engineered systems, it can respire an electrode to produce measurable electric current. Its unique metabolism, heavily dependent on an extensive network of cytochromes, requires a unique cell composition. In this work, we used metallomics, cell fraction and elemental analyses, and transcriptomics to study and analyze the cell composition of G. sulfurreducens. Elemental composition studies (C, H, O, N, and ash content) showed high C:O and H:O ratios of approximately 1.7:1 and 0.25:1, indicative of more reduced cell composition that is consistent with high lipid content. Our study shows that G. sulfurreducens cells have a large amount of iron (2 ± 0.2 μg/g dry weight) and lipids (32 ± 0.5% dry weight/dry weight) and that this composition does not change whether the cells are grown with a soluble or an insoluble electron acceptor. The high iron concentration, higher than similar microorganisms, is attributed to the production of cytochromes that are abundant in transcriptomic analyses in both solid and soluble electron acceptor growth. The unique cell composition of G. sulfurreducens must be considered when growing this microorganism for lab studies and commercial applications. IMPORTANCE Geobacter sulfurreducens is an electroactive microorganism. In nature, it grows on metallic minerals by transferring electrons to them, effectively "breathing" metals. In a manmade system, it respires an electrode to produce an electric current. It has become a model organism for the study of electroactive organisms. There are potential biotechnological applications of an organism that can bridge the gap between biology and electrical signal and, as a ubiquitous iron reducer in soils around the world, G. sulfurreducens has an impact on the global iron cycle. We measured the concentrations of metals, macromolecules, and basic elements in G. sulfurreducens to define this organism's composition. We also used gene expression data to discuss which proteins those metals could be associated with. We found that G. sulfurreducens has a large amount of lipid and iron compared to other bacteria-these observations are important for future microbiologists and biotechnologists working with the organism.
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Affiliation(s)
- Ethan Howley
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - Dongwon Ki
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- Division of Living and the Built Environment Research, Seoul Institute of Technology, Seoul, South Korea
| | - Rosa Krajmalnik-Brown
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Sustainable Engineering and the Built Environment, Arizona State University, Tempe, Arizona, USA
| | - César I. Torres
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona, USA
- School for Engineering of Matter Transport and Energy, Arizona State University, Tempe, Arizona, USA
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33
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Lin X, Li Z, Bu D, Liu W, Li Z, Wei R, Yu M. Multiple organelle-targeted near-infrared fluorescent probes toward pH and viscosity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 283:121665. [PMID: 35961205 DOI: 10.1016/j.saa.2022.121665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
Organelles, including mitochondria (mito), lysosomes (lyso), endoplasmic reticulum (ER), Golgi apparatus (Golgi), and ribosome et al., play a vital role in maintaining the regular work of the cell. Viscosity is an essential parameter in the cellular microenvironment. Herein, four viscosity-sensitive near-infrared fluorescent probes DMPC, DEPC, DHDM and DHDV that can simultaneously target multiple organelles were synthesized. As the viscosity increased, the fluorescence intensity of the probes gradually increased due to the hindrance of the rotation of the carbon-carbon single bond. The fluorescence intensity of DHDV increased by about 453 times, and the fluorescence quantum yield also increased from 0.051 to 0.681. Cell experiments indicated the probes could simultaneously target four kinds of organelles, and the four probes could also track mitochondria with no dependence on membrane potential. Further experiments showed that the probes could detect viscosity changes in lyso and mito. In addition, the probes also demonstrated the advantages of low cytotoxicity, good anti-interference and stability, providing a simple and effective tool for studying the activity of organelles with changing viscosity signals.
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Affiliation(s)
- Xuemei Lin
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Zhe Li
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Dandan Bu
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Wenjing Liu
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Zhanxian Li
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China.
| | - Ruixue Wei
- Department of Cerebrovascular Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Mingming Yu
- Green Catalysis Center and College of Chemistry, Zhengzhou University, Zhengzhou 450001, China.
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34
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Berche P. A new giant bacterium reminiscent of eukaryotes. C R Biol 2022; 345:39-42. [PMID: 36847463 DOI: 10.5802/crbiol.87] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022]
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35
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Lipiński WP, Visser BS, Robu I, Fakhree MAA, Lindhoud S, Claessens MMAE, Spruijt E. Biomolecular condensates can both accelerate and suppress aggregation of α-synuclein. SCIENCE ADVANCES 2022; 8:eabq6495. [PMID: 36459561 PMCID: PMC10942789 DOI: 10.1126/sciadv.abq6495] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
Biomolecular condensates present in cells can fundamentally affect the aggregation of amyloidogenic proteins and play a role in the regulation of this process. While liquid-liquid phase separation of amyloidogenic proteins by themselves can act as an alternative nucleation pathway, interaction of partly disordered aggregation-prone proteins with preexisting condensates that act as localization centers could be a far more general mechanism of altering their aggregation behavior. Here, we show that so-called host biomolecular condensates can both accelerate and slow down amyloid formation. We study the amyloidogenic protein α-synuclein and two truncated α-synuclein variants in the presence of three types of condensates composed of nonaggregating peptides, RNA, or ATP. Our results demonstrate that condensates can markedly speed up amyloid formation when proteins localize to their interface. However, condensates can also significantly suppress aggregation by sequestering and stabilizing amyloidogenic proteins, thereby providing living cells with a possible protection mechanism against amyloid formation.
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Affiliation(s)
- Wojciech P. Lipiński
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Brent S. Visser
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Irina Robu
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
| | - Mohammad A. A. Fakhree
- Nanobiophysics, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, Netherlands
| | - Saskia Lindhoud
- Department of Molecules and Materials, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede, Netherlands
| | - Mireille M. A. E. Claessens
- Nanobiophysics, Faculty of Science and Technology, University of Twente, PO Box 217, 7500 AE Enschede, Netherlands
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, Netherlands
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36
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Different states and the associated fates of biomolecular condensates. Essays Biochem 2022; 66:849-862. [PMID: 36350032 DOI: 10.1042/ebc20220054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/20/2022] [Accepted: 10/07/2022] [Indexed: 11/11/2022]
Abstract
Abstract
Biomolecular condensates are functional assemblies, which can enrich intrinsically disordered proteins (IDPs) and/or RNAs at concentrations that are orders of magnitude higher than the bulk. In their native functional state, these structures can exist in multiple physical states including liquid-droplet phase, hydrogels, and solid assemblies. On the other hand, an aberrant transition between these physical states can result in loss-of-function or a gain-of-toxic-function. A prime example of such an aberrant transition is droplet aging—a phenomenon where some condensates may progressively transition into less dynamic material states at biologically relevant timescales. In this essay, we review structural and viscoelastic roots of aberrant liquid–solid transitions. Also, we highlight the different checkpoints and experimentally tunable handles, both active (ATP-dependent enzymes, post-translational modifications) and passive (colocalization of RNA molecules), that could alter the material state of assemblies.
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37
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Huang J, Jiang Q, Yang M, Dykes GF, Weetman SL, Xin W, He HL, Liu LN. Probing the Internal pH and Permeability of a Carboxysome Shell. Biomacromolecules 2022; 23:4339-4348. [PMID: 36054822 PMCID: PMC9554877 DOI: 10.1021/acs.biomac.2c00781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The carboxysome is a protein-based nanoscale organelle
in cyanobacteria
and many proteobacteria, which encapsulates the key CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco)
and carbonic anhydrase (CA) within a polyhedral protein shell. The
intrinsic self-assembly and architectural features of carboxysomes
and the semipermeability of the protein shell provide the foundation
for the accumulation of CO2 within carboxysomes and enhanced
carboxylation. Here, we develop an approach to determine the interior
pH conditions and inorganic carbon accumulation within an α-carboxysome
shell derived from a chemoautotrophic proteobacterium Halothiobacillus neapolitanus and evaluate the shell
permeability. By incorporating a pH reporter, pHluorin2, within empty
α-carboxysome shells produced in Escherichia
coli, we probe the interior pH of the protein shells
with and without CA. Our in vivo and in vitro results demonstrate a lower interior pH of α-carboxysome shells
than the cytoplasmic pH and buffer pH, as well as the modulation of
the interior pH in response to changes in external environments, indicating
the shell permeability to bicarbonate ions and protons. We further
determine the saturated HCO3– concentration
of 15 mM within α-carboxysome shells and show the CA-mediated
increase in the interior CO2 level. Uncovering the interior
physiochemical microenvironment of carboxysomes is crucial for understanding
the mechanisms underlying carboxysomal shell permeability and enhancement
of Rubisco carboxylation within carboxysomes. Such fundamental knowledge
may inform reprogramming carboxysomes to improve metabolism and recruit
foreign enzymes for enhanced catalytical performance.
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Affiliation(s)
- Jiafeng Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,School of Life Sciences, Central South University, Changsha 410017, China
| | - Qiuyao Jiang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China
| | - Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Samantha L Weetman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Wei Xin
- Department of Central Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, China.,Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 271000, China
| | - Hai-Lun He
- School of Life Sciences, Central South University, Changsha 410017, China
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom.,College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
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38
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Otoničar J, Hostnik M, Grundner M, Kostanjšek R, Gredar T, Garvas M, Arsov Z, Podlesek Z, Gostinčar C, Jakše J, Busby SJW, Butala M. A method for targeting a specified segment of DNA to a bacterial microorganelle. Nucleic Acids Res 2022; 50:e113. [PMID: 36029110 DOI: 10.1093/nar/gkac714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/28/2022] [Accepted: 08/09/2022] [Indexed: 11/14/2022] Open
Abstract
Encapsulation of a selected DNA molecule in a cell has important implications for bionanotechnology. Non-viral proteins that can be used as nucleic acid containers include proteinaceous subcellular bacterial microcompartments (MCPs) that self-assemble into a selectively permeable protein shell containing an enzymatic core. Here, we adapted a propanediol utilization (Pdu) MCP into a synthetic protein cage to package a specified DNA segment in vivo, thereby enabling subsequent affinity purification. To this end, we engineered the LacI transcription repressor to be routed, together with target DNA, into the lumen of a Strep-tagged Pdu shell. Sequencing of extracted DNA from the affinity-isolated MCPs shows that our strategy results in packaging of a DNA segment carrying multiple LacI binding sites, but not the flanking regions. Furthermore, we used LacI to drive the encapsulation of a DNA segment containing operators for LacI and for a second transcription factor.
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Affiliation(s)
- Jan Otoničar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Hostnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Grundner
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Rok Kostanjšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Tajda Gredar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Maja Garvas
- Jožef Stefan Institute, Condensed Matter Physics Department, 1000 Ljubljana, Slovenia
| | - Zoran Arsov
- Jožef Stefan Institute, Condensed Matter Physics Department, 1000 Ljubljana, Slovenia
| | - Zdravko Podlesek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Matej Butala
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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39
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Ramos-Martín F, D'Amelio N. Biomembrane lipids: When physics and chemistry join to shape biological activity. Biochimie 2022; 203:118-138. [PMID: 35926681 DOI: 10.1016/j.biochi.2022.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/13/2022] [Accepted: 07/21/2022] [Indexed: 11/02/2022]
Abstract
Biomembranes constitute the first lines of defense of cells. While small molecules can often permeate cell walls in bacteria and plants, they are generally unable to penetrate the barrier constituted by the double layer of phospholipids, unless specific receptors or channels are present. Antimicrobial or cell-penetrating peptides are in fact highly specialized molecules able to bypass this barrier and even discriminate among different cell types. This capacity is made possible by the intrinsic properties of its phospholipids, their distribution between the internal and external leaflet, and their ability to mutually interact, modulating the membrane fluidity and the exposition of key headgroups. Although common phospholipids can be found in the membranes of most organisms, some are characteristic of specific cell types. Here, we review the properties of the most common lipids and describe how they interact with each other in biomembrane. We then discuss how their assembly in bilayers determines some key physical-chemical properties such as permeability, potential and phase status. Finally, we describe how the exposition of specific phospholipids determines the recognition of cell types by membrane-targeting molecules.
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Affiliation(s)
- Francisco Ramos-Martín
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, 80039, France.
| | - Nicola D'Amelio
- Unité de Génie Enzymatique et Cellulaire UMR 7025 CNRS, Université de Picardie Jules Verne, Amiens, 80039, France.
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40
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Schwartzman JA, Ebrahimi A, Chadwick G, Sato Y, Roller BRK, Orphan VJ, Cordero OX. Bacterial growth in multicellular aggregates leads to the emergence of complex life cycles. Curr Biol 2022; 32:3059-3069.e7. [PMID: 35777363 PMCID: PMC9496226 DOI: 10.1016/j.cub.2022.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/03/2022] [Accepted: 06/07/2022] [Indexed: 01/12/2023]
Abstract
Facultative multicellular behaviors expand the metabolic capacity and physiological resilience of bacteria. Despite their ubiquity in nature, we lack an understanding of how these behaviors emerge from cellular-scale phenomena. Here, we show how the coupling between growth and resource gradient formation leads to the emergence of multicellular lifecycles in a marine bacterium. Under otherwise carbon-limited growth conditions, Vibrio splendidus 12B01 forms clonal multicellular groups to collectively harvest carbon from soluble polymers of the brown-algal polysaccharide alginate. As they grow, groups phenotypically differentiate into two spatially distinct sub-populations: a static "shell" surrounding a motile, carbon-storing "core." Differentiation of these two sub-populations coincides with the formation of a gradient in nitrogen-source availability within clusters. Additionally, we find that populations of cells containing a high proportion of carbon-storing individuals propagate and form new clusters more readily on alginate than do populations with few carbon-storing cells. Together, these results suggest that local metabolic activity and differential partitioning of resources leads to the emergence of reproductive cycles in a facultatively multicellular bacterium.
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Affiliation(s)
- Julia A Schwartzman
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Ali Ebrahimi
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Grayson Chadwick
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuya Sato
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan
| | - Benjamin R K Roller
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Center for Microbiology and Environmental Systems Science, University of Vienna, Djerassiplatz 1, Vienna 1030, Austria; Department of Environmental Systems Sciences, ETH Zürich, Universitätsstrasse 16, Zürich 8092, Switzerland; Department of Environmental Microbiology, Eawag, Ueberlandstrasse 133, Dübendorf 8600, Switzerland
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Otto X Cordero
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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41
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Ni T, Sun Y, Burn W, Al-Hazeem MMJ, Zhu Y, Yu X, Liu LN, Zhang P. Structure and assembly of cargo Rubisco in two native α-carboxysomes. Nat Commun 2022; 13:4299. [PMID: 35879301 PMCID: PMC9314367 DOI: 10.1038/s41467-022-32004-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/11/2022] [Indexed: 01/13/2023] Open
Abstract
Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase catalyzing carbon fixation inside a proteinaceous shell. How Rubisco complexes pack within the carboxysomes is unknown. Using cryo-electron tomography, we determine the distinct 3D organization of Rubisco inside two distant α-carboxysomes from a marine α-cyanobacterium Cyanobium sp. PCC 7001 where Rubiscos are organized in three concentric layers, and from a chemoautotrophic bacterium Halothiobacillus neapolitanus where they form intertwining spirals. We further resolve the structures of native Rubisco as well as its higher-order assembly at near-atomic resolutions by subtomogram averaging. The structures surprisingly reveal that the authentic intrinsically disordered linker protein CsoS2 interacts with Rubiscos in native carboxysomes but functions distinctively in the two α-carboxysomes. In contrast to the uniform Rubisco-CsoS2 association in the Cyanobium α-carboxysome, CsoS2 binds only to the Rubiscos close to the shell in the Halo α-carboxysome. Our findings provide critical knowledge of the assembly principles of α-carboxysomes, which may aid in the rational design and repurposing of carboxysome structures for new functions.
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Affiliation(s)
- Tao Ni
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Will Burn
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Monsour M J Al-Hazeem
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Yanan Zhu
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Xiulian Yu
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China.
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK.
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK.
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42
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Abstract
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases form in a system of many interacting components, like in cells. Here we introduce a numerical method based on physical relaxation dynamics to study the coexisting phases in such systems. We use our approach to optimize interactions between components, similar to how evolution might have optimized the interactions of proteins. These evolved interactions robustly lead to a defined number of phases, despite substantial uncertainties in the initial composition, while random or designed interactions perform much worse. Moreover, the optimized interactions are robust to perturbations, and they allow fast adaption to new target phase counts. We thus show that genetically encoded interactions of proteins provide versatile control of phase behavior. The phases forming in our system are also a concrete example of a robust emergent property that does not rely on fine-tuning the parameters of individual constituents.
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43
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Revealing bacterial cell biology using cryo-electron tomography. Curr Opin Struct Biol 2022; 75:102419. [PMID: 35820259 DOI: 10.1016/j.sbi.2022.102419] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Visualizing macromolecules inside bacteria at a high spatial resolution has remained a challenge owing to their small size and limited resolution of optical microscopy techniques. Recent advances in cryo-electron tomography (cryo-ET) imaging methods have revealed the spatial and temporal assemblies of many macromolecules involved in different cellular processes in bacteria at a resolution of a few nanometers in their native milieu. Specifically, the application of cryo-focused ion beam (cryo-FIB) milling to thin bacterial specimens makes them amenable for high-resolution cryo-ET data collection. In this review, we highlight recent research in three emerging areas of bacterial cell biology that have benefited from the cryo-FIB-ET technology - cytoskeletal filament assembly, intracellular organelles, and multicellularity.
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44
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Schaible GA, Kohtz AJ, Cliff J, Hatzenpichler R. Correlative SIP-FISH-Raman-SEM-NanoSIMS links identity, morphology, biochemistry, and physiology of environmental microbes. ISME COMMUNICATIONS 2022; 2:52. [PMID: 37938730 PMCID: PMC9723565 DOI: 10.1038/s43705-022-00134-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 06/09/2022] [Indexed: 05/08/2023]
Abstract
Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial microbial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. This workflow was then applied to a sample of yet uncultured multicellular magnetotactic bacteria (MMB). In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes on a single-cell level.
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Affiliation(s)
- George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - Anthony J Kohtz
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA
| | - John Cliff
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, 59717, USA.
- Thermal Biology Institute, Montana State University, Bozeman, MT, 59717, USA.
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA.
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45
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Volland JM, Gonzalez-Rizzo S, Gros O, Tyml T, Ivanova N, Schulz F, Goudeau D, Elisabeth NH, Nath N, Udwary D, Malmstrom RR, Guidi-Rontani C, Bolte-Kluge S, Davies KM, Jean MR, Mansot JL, Mouncey NJ, Angert ER, Woyke T, Date SV. A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles. Science 2022; 376:1453-1458. [PMID: 35737788 DOI: 10.1126/science.abb3634] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cells of most bacterial species are around 2 micrometers in length, with some of the largest specimens reaching 750 micrometers. Using fluorescence, x-ray, and electron microscopy in conjunction with genome sequencing, we characterized Candidatus (Ca.) Thiomargarita magnifica, a bacterium that has an average cell length greater than 9000 micrometers and is visible to the naked eye. These cells grow orders of magnitude over theoretical limits for bacterial cell size, display unprecedented polyploidy of more than half a million copies of a very large genome, and undergo a dimorphic life cycle with asymmetric segregation of chromosomes into daughter cells. These features, along with compartmentalization of genomic material and ribosomes in translationally active organelles bound by bioenergetic membranes, indicate gain of complexity in the Thiomargarita lineage and challenge traditional concepts of bacterial cells.
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Affiliation(s)
- Jean-Marie Volland
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Silvina Gonzalez-Rizzo
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France
| | - Olivier Gros
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France.,Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane, Université des Antilles, UFR des Sciences Exactes et Naturelles, Pointe-à-Pitre, Guadeloupe, France
| | - Tomáš Tyml
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Frederik Schulz
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Danielle Goudeau
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nathalie H Elisabeth
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nandita Nath
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Daniel Udwary
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chantal Guidi-Rontani
- Institut de Systématique, Evolution, Biodiversité CNRS UMR 7205, Museum National d'Histoire Naturelle, Paris, France
| | - Susanne Bolte-Kluge
- Sorbonne Universités, UPMC Univ. Paris 06, CNRS FRE3631, Institut de Biologie Paris Seine, Paris, France
| | - Karen M Davies
- Department of Energy Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Maïtena R Jean
- Institut de Systématique, Evolution, Biodiversité, Université des Antilles, Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Campus de Fouillole, Pointe-à-Pitre, France
| | - Jean-Louis Mansot
- Centre Commun de Caractérisation des Matériaux des Antilles et de la Guyane, Université des Antilles, UFR des Sciences Exactes et Naturelles, Pointe-à-Pitre, Guadeloupe, France
| | - Nigel J Mouncey
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Esther R Angert
- Cornell University, College of Agriculture and Life Sciences, Department of Microbiology, Ithaca, NY, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Laboratory for Research in Complex Systems, Menlo Park, CA, USA.,University of California Merced, School of Natural Sciences, Merced, CA, USA
| | - Shailesh V Date
- Laboratory for Research in Complex Systems, Menlo Park, CA, USA.,University of California San Francisco, San Francisco, CA, USA.,San Francisco State University, San Francisco, CA, USA
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46
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Abstract
Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.
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Affiliation(s)
- Tobias W. Giessen
- Departments of Biomedical Engineering and Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
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47
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Padmanabhan S, Monera-Girona AJ, Pajares-Martínez E, Bastida-Martínez E, Del Rey Navalón I, Pérez-Castaño R, Galbis-Martínez ML, Fontes M, Elías-Arnanz M. Plasmalogens and Photooxidative Stress Signaling in Myxobacteria, and How it Unmasked CarF/TMEM189 as the Δ1'-Desaturase PEDS1 for Human Plasmalogen Biosynthesis. Front Cell Dev Biol 2022; 10:884689. [PMID: 35646900 PMCID: PMC9131029 DOI: 10.3389/fcell.2022.884689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/25/2022] [Indexed: 11/18/2022] Open
Abstract
Plasmalogens are glycerophospholipids with a hallmark sn-1 vinyl ether bond that endows them with unique physical-chemical properties. They have proposed biological roles in membrane organization, fluidity, signaling, and antioxidative functions, and abnormal plasmalogen levels correlate with various human pathologies, including cancer and Alzheimer’s disease. The presence of plasmalogens in animals and in anaerobic bacteria, but not in plants and fungi, is well-documented. However, their occurrence in the obligately aerobic myxobacteria, exceptional among aerobic bacteria, is often overlooked. Tellingly, discovery of the key desaturase indispensable for vinyl ether bond formation, and therefore fundamental in plasmalogen biogenesis, emerged from delving into how the soil myxobacterium Myxococcus xanthus responds to light. A recent pioneering study unmasked myxobacterial CarF and its human ortholog TMEM189 as the long-sought plasmanylethanolamine desaturase (PEDS1), thus opening a crucial door to study plasmalogen biogenesis, functions, and roles in disease. The findings demonstrated the broad evolutionary sweep of the enzyme and also firmly established a specific signaling role for plasmalogens in a photooxidative stress response. Here, we will recount our take on this fascinating story and its implications, and review the current state of knowledge on plasmalogens, their biosynthesis and functions in the aerobic myxobacteria.
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Affiliation(s)
- S Padmanabhan
- Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Antonio J Monera-Girona
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Elena Pajares-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Eva Bastida-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Irene Del Rey Navalón
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Ricardo Pérez-Castaño
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - María Luisa Galbis-Martínez
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Marta Fontes
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Montserrat Elías-Arnanz
- Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain
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48
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Carreira LAM, Szadkowski D, Müller F, Søgaard-Andersen L. Spatiotemporal regulation of switching front–rear cell polarity. Curr Opin Cell Biol 2022; 76:102076. [DOI: 10.1016/j.ceb.2022.102076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
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49
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Yang M, Wenner N, Dykes GF, Li Y, Zhu X, Sun Y, Huang F, Hinton JCD, Liu LN. Biogenesis of a bacterial metabolosome for propanediol utilization. Nat Commun 2022; 13:2920. [PMID: 35614058 PMCID: PMC9132943 DOI: 10.1038/s41467-022-30608-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 04/22/2022] [Indexed: 12/24/2022] Open
Abstract
Bacterial metabolosomes are a family of protein organelles in bacteria. Elucidating how thousands of proteins self-assemble to form functional metabolosomes is essential for understanding their significance in cellular metabolism and pathogenesis. Here we investigate the de novo biogenesis of propanediol-utilization (Pdu) metabolosomes and characterize the roles of the key constituents in generation and intracellular positioning of functional metabolosomes. Our results demonstrate that the Pdu metabolosome undertakes both "Shell first" and "Cargo first" assembly pathways, unlike the β-carboxysome structural analog which only involves the "Cargo first" strategy. Shell and cargo assemblies occur independently at the cell poles. The internal cargo core is formed through the ordered assembly of multiple enzyme complexes, and exhibits liquid-like properties within the metabolosome architecture. Our findings provide mechanistic insight into the molecular principles driving bacterial metabolosome assembly and expand our understanding of liquid-like organelle biogenesis.
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Affiliation(s)
- Mengru Yang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Nicolas Wenner
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Yan Li
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Xiaojun Zhu
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Fang Huang
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Jay C D Hinton
- Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom
| | - Lu-Ning Liu
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, United Kingdom.
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China.
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50
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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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