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Wan L, Zhu Y, Zhang W, Mu W. Recent advances in design and application of synthetic membraneless organelles. Biotechnol Adv 2024; 73:108355. [PMID: 38588907 DOI: 10.1016/j.biotechadv.2024.108355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 02/26/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Membraneless organelles (MLOs) formed by liquid-liquid phase separation (LLPS) have been extensively studied due to their spatiotemporal control of biochemical and cellular processes in living cells. These findings have provided valuable insights into the physicochemical principles underlying the formation and functionalization of biomolecular condensates, which paves the way for the development of versatile phase-separating systems capable of addressing a variety of application scenarios. Here, we highlight the potential of constructing synthetic MLOs with programmable and functional properties. Notably, we organize how these synthetic membraneless compartments have been capitalized to manipulate enzymatic activities and metabolic reactions. The aim of this review is to inspire readerships to deeply comprehend the widespread roles of synthetic MLOs in the regulation enzymatic reactions and control of metabolic processes, and to encourage the rational design of controllable and functional membraneless compartments for a broad range of bioengineering applications.
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Affiliation(s)
- Li Wan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi, Jiangsu 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu 214122, China.
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2
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Doron L, Kerfeld CA. Bacterial microcompartments as a next-generation metabolic engineering tool: utilizing nature's solution for confining challenging catabolic pathways. Biochem Soc Trans 2024; 52:997-1010. [PMID: 38813858 DOI: 10.1042/bst20230229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 05/31/2024]
Abstract
Advancements in synthetic biology have facilitated the incorporation of heterologous metabolic pathways into various bacterial chassis, leading to the synthesis of targeted bioproducts. However, total output from heterologous production pathways can suffer from low flux, enzyme promiscuity, formation of toxic intermediates, or intermediate loss to competing reactions, which ultimately hinder their full potential. The self-assembling, easy-to-modify, protein-based bacterial microcompartments (BMCs) offer a sophisticated way to overcome these obstacles by acting as an autonomous catalytic module decoupled from the cell's regulatory and metabolic networks. More than a decade of fundamental research on various types of BMCs, particularly structural studies of shells and their self-assembly, the recruitment of enzymes to BMC shell scaffolds, and the involvement of ancillary proteins such as transporters, regulators, and activating enzymes in the integration of BMCs into the cell's metabolism, has significantly moved the field forward. These advances have enabled bioengineers to design synthetic multi-enzyme BMCs to promote ethanol or hydrogen production, increase cellular polyphosphate levels, and convert glycerol to propanediol or formate to pyruvate. These pioneering efforts demonstrate the enormous potential of synthetic BMCs to encapsulate non-native multi-enzyme biochemical pathways for the synthesis of high-value products.
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Affiliation(s)
- Lior Doron
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, U.S.A
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA, U.S.A
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, U.S.A
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3
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Trettel DS, Kerfeld CA, Gonzalez-Esquer CR. Dynamic structural determinants in bacterial microcompartment shells. Curr Opin Microbiol 2024; 80:102497. [PMID: 38909546 DOI: 10.1016/j.mib.2024.102497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/07/2024] [Accepted: 06/03/2024] [Indexed: 06/25/2024]
Abstract
Bacterial microcompartments (BMCs) are polyhedral structures that segregate enzymatic cargo from the cytosol via encapsulation within a protein shell. Unlike other biological polyhedra, such as viral capsids and encapsulins, BMC shells can exhibit a highly advantageous structural and functional plasticity, conforming to a variety of anabolic (CO2 fixation in carboxysomes) and catabolic (nutrient assimilation in metabolosomes) roles. Consequently, understanding the subunit properties and associated protein-protein interaction processes that guide shell assembly and function is a necessary step to fully harness BMCs as modular, biotechnological nanomachines. Here, we describe the recent insights into the dynamics of structural features of the key BMC domain (Pfam00936)-containing proteins, which serve as a structural template for BMC-H and BMC-T shell building blocks.
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Affiliation(s)
- Daniel S Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences group, Los Alamos, NM, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Cesar R Gonzalez-Esquer
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences group, Los Alamos, NM, USA.
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4
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Chatterjee A, Kaval KG, Garsin DA. Role of ethanolamine utilization and bacterial microcompartment formation in Listeria monocytogenes intracellular infection. Infect Immun 2024; 92:e0016224. [PMID: 38752742 DOI: 10.1128/iai.00162-24] [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: 04/10/2024] [Accepted: 04/18/2024] [Indexed: 05/28/2024] Open
Abstract
Ethanolamine (EA) affects the colonization and pathogenicity of certain human bacterial pathogens in the gastrointestinal tract. However, EA can also affect the intracellular survival and replication of host cell invasive bacteria such as Listeria monocytogenes (LMO) and Salmonella enterica serovar Typhimurium (S. Typhimurium). The EA utilization (eut) genes can be categorized as regulatory, enzymatic, or structural, and previous work in LMO showed that loss of genes encoding functions for the enzymatic breakdown of EA inhibited LMO intracellular replication. In this work, we sought to further characterize the role of EA utilization during LMO infection of host cells. Unlike what was previously observed for S. Typhimurium, in LMO, an EA regulator mutant (ΔeutV) was equally deficient in intracellular replication compared to an EA metabolism mutant (ΔeutB), and this was consistent across Caco-2, RAW 264.7, and THP-1 cell lines. The structural genes encode proteins that self-assemble into bacterial microcompartments (BMCs) that encase the enzymes necessary for EA metabolism. For the first time, native EUT BMCs were fluorescently tagged, and EUT BMC formation was observed in vitro and in vivo. Interestingly, BMC formation was observed in bacteria infecting Caco-2 cells, but not the macrophage cell lines. Finally, the cellular immune response of Caco-2 cells to infection with eut mutants was examined, and it was discovered that ΔeutB and ΔeutV mutants similarly elevated the expression of inflammatory cytokines. In conclusion, EA sensing and utilization during LMO intracellular infection are important for optimal LMO replication and immune evasion but are not always concomitant with BMC formation.IMPORTANCEListeria monocytogenes (LMO) is a bacterial pathogen that can cause severe disease in immunocompromised individuals when consumed in contaminated food. It can replicate inside of mammalian cells, escaping detection by the immune system. Therefore, understanding the features of this human pathogen that contribute to its infectiousness and intracellular lifestyle is important. In this work we demonstrate that genes encoding both regulators and enzymes of EA metabolism are important for optimal growth inside mammalian cells. Moreover, the formation of specialized compartments to enable EA metabolism were visualized by tagging with a fluorescent protein and found to form when LMO infects some mammalian cell types, but not others. Interestingly, the formation of the compartments was associated with features consistent with an early stage of the intracellular infection. By characterizing bacterial metabolic pathways that contribute to survival in host environments, we hope to positively impact knowledge and facilitate new treatment strategies.
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Affiliation(s)
- Ayan Chatterjee
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Karan Gautam Kaval
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
| | - Danielle A Garsin
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center, Houston, Texas, USA
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Yu X, Li H, Xu C, Xu Z, Chen S, Liu W, Zhang T, Sun H, Ge Y, Qi Z, Liu J. Liquid-Liquid Phase Separation-Mediated Photocatalytic Subcellular Hybrid System for Highly Efficient Hydrogen Production. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400097. [PMID: 38572522 PMCID: PMC11165473 DOI: 10.1002/advs.202400097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/28/2024] [Indexed: 04/05/2024]
Abstract
Plant chloroplasts have a highly compartmentalized interior, essential for executing photocatalytic functions. However, the construction of a photocatalytic reaction compartment similar to chloroplasts in inorganic-biological hybrid systems (IBS) has not been reported. Drawing inspiration from the compartmentalized chloroplast and the phenomenon of liquid-liquid phase separation, herein, a new strategy is first developed for constructing a photocatalytic subcellular hybrid system through liquid-liquid phase separation technology in living cells. Photosensitizers and in vivo expressed hydrogenases are designed to coassemble within the cell to create subcellular compartments for synergetic photocatalysis. This compartmentalization facilitates efficient electron transfer and light energy utilization, resulting in highly effective H2 production. The subcellular compartments hybrid system (HM/IBSCS) exhibits a nearly 87-fold increase in H2 production compared to the bare bacteria/hybrid system. Furthermore, the intracellular compartments of the photocatalytic reactor enhance the system's stability obviously, with the bacteria maintaining approximately 81% of their H2 production activity even after undergoing five cycles of photocatalytic hydrogen production. The research brings forward visionary prospects for the field of semi-artificial photosynthesis, offering new possibilities for advancements in areas such as renewable energy, biomanufacturing, and genetic engineering.
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Affiliation(s)
- Xiaoxuan Yu
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
- Sino‐German Joint Research Lab for Space Biomaterials and Translational TechnologySchool of Life SciencesNorthwestern Polytechnical UniversityXi'an710072China
| | - Hui Li
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
- Sino‐German Joint Research Lab for Space Biomaterials and Translational TechnologySchool of Life SciencesNorthwestern Polytechnical UniversityXi'an710072China
| | - Chengchen Xu
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
| | - Zhengwei Xu
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
| | - Shuheng Chen
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
| | - Wang Liu
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
| | - Tianlong Zhang
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
| | - Hongcheng Sun
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
| | - Yan Ge
- Sino‐German Joint Research Lab for Space Biomaterials and Translational TechnologySchool of Life SciencesNorthwestern Polytechnical UniversityXi'an710072China
| | - Zhenhui Qi
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
- Sino‐German Joint Research Lab for Space Biomaterials and Translational TechnologySchool of Life SciencesNorthwestern Polytechnical UniversityXi'an710072China
| | - Junqiu Liu
- Key Laboratory of Organosilicon Chemistry and Material TechnologyMinistry of EducationCollege of MaterialChemistry and Chemical EngineeringHangzhou Normal UniversityHangzhou311121China
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6
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Pulianmackal LT, Vecchiarelli AG. Positioning of cellular components by the ParA/MinD family of ATPases. Curr Opin Microbiol 2024; 79:102485. [PMID: 38723344 DOI: 10.1016/j.mib.2024.102485] [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: 01/23/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 06/11/2024]
Abstract
The ParA/MinD (A/D) family of ATPases spatially organize an array of genetic- and protein-based cellular cargos across the bacterial and archaeal domains of life. By far, the two best-studied members, and family namesake, are ParA and MinD, involved in bacterial DNA segregation and divisome positioning, respectively. ParA and MinD make protein waves on the nucleoid or membrane to segregate chromosomes and position the divisome. Less studied is the growing list of A/D ATPases widespread across bacteria and implicated in the subcellular organization of diverse protein-based complexes and organelles involved in myriad biological processes, from metabolism to pathogenesis. Here we describe mechanistic commonality, variation, and coordination among the most widespread family of positioning ATPases used in the subcellular organization of disparate cargos across bacteria and archaea.
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Affiliation(s)
- Lisa T Pulianmackal
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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7
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Wang R, Su Y, Yang W, Zhang H, Wang J, Gao W. Enhanced precision and efficiency in metabolic regulation: Compartmentalized metabolic engineering. BIORESOURCE TECHNOLOGY 2024; 402:130786. [PMID: 38703958 DOI: 10.1016/j.biortech.2024.130786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Metabolic engineering has witnessed remarkable advancements, enabling successful large-scale, cost-effective and efficient production of numerous compounds. However, the predominant expression of heterologous genes in the cytoplasm poses limitations, such as low substrate concentration, metabolic competition and product toxicity. To overcome these challenges, compartmentalized metabolic engineering allows the spatial separation of metabolic pathways for the efficient and precise production of target compounds. Compartmentalized metabolic engineering and its common strategies are comprehensively described in this study, where various membranous compartments and membraneless compartments have been used for compartmentalization and constructive progress has been made. Additionally, the challenges and future directions are discussed in depth. This review is dedicated to providing compartmentalized, precise and efficient methods for metabolic production, and provides valuable guidance for further development in the field of metabolic engineering.
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Affiliation(s)
- Rubing Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Huanyu Zhang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Faculty of Medicine, Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin 300072, China.
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8
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. Proc Natl Acad Sci U S A 2024; 121:e2321260121. [PMID: 38722807 PMCID: PMC11098114 DOI: 10.1073/pnas.2321260121] [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: 12/06/2023] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.
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Affiliation(s)
- Taylor N. Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
| | - Lohra M. Miller
- Chemistry Department, Indiana University, Bloomington, IN47405
| | | | - Farzad Fatehi
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
| | - Reidun Twarock
- Department of Mathematics, University of York, YorkYO10 5DD, United Kingdom
- York Cross-Disciplinary Centre for Systems Analysis, University of York, YorkYO10 5DD, United Kingdom
- Department of Biology, University of York, YorkYO10 5DD, United Kingdom
| | | | | | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI48109
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW2006, Australia
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Azuma Y, Gaweł S, Pasternak M, Woźnicka O, Pyza E, Heddle JG. Reengineering of an Artificial Protein Cage for Efficient Packaging of Active Enzymes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2312286. [PMID: 38738740 DOI: 10.1002/smll.202312286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/01/2024] [Indexed: 05/14/2024]
Abstract
Protein cages that readily encapsulate active enzymes of interest present useful nanotools for delivery and catalysis, wherein those with programmable disassembly characteristics serve as particularly attractive platforms. Here, a general guest packaging system based on an artificial protein cage, TRAP-cage, the disassembly of which can be induced by the addition of reducing agents, is established. In this system, TRAP-cage with SpyCatcher moieties in the lumen is prepared using genetic modification of the protein building block and assembled into a cage structure with either monovalent gold ions or molecular crosslinkers. The resulting protein cage can efficiently capture guest proteins equipped with a SpyTag by simply mixing them in an aqueous solution. This post-assembly loading system, which circumvents the exposure of guests to thiol-reactive crosslinkers, enables the packaging of enzymes possessing a catalytic cysteine or a metal cofactor while retaining their catalytic activity.
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Affiliation(s)
- Yusuke Azuma
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
| | - Szymon Gaweł
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, Krakow, 30-348, Poland
| | - Monika Pasternak
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, Krakow, 30-348, Poland
| | - Olga Woźnicka
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, Krakow, 30-387, Poland
| | - Elżbieta Pyza
- Institute of Zoology and Biomedical Research, Faculty of Biology, Jagiellonian University, Gronostajowa 9, Krakow, 30-387, Poland
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Krakow, 30-387, Poland
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Nitschke W, Farr O, Gaudu N, Truong C, Guyot F, Russell MJ, Duval S. The Winding Road from Origin to Emergence (of Life). Life (Basel) 2024; 14:607. [PMID: 38792628 PMCID: PMC11123232 DOI: 10.3390/life14050607] [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: 04/09/2024] [Revised: 05/02/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Humanity's strive to understand why and how life appeared on planet Earth dates back to prehistoric times. At the beginning of the 19th century, empirical biology started to tackle this question yielding both Charles Darwin's Theory of Evolution and the paradigm that the crucial trigger putting life on its tracks was the appearance of organic molecules. In parallel to these developments in the biological sciences, physics and physical chemistry saw the fundamental laws of thermodynamics being unraveled. Towards the end of the 19th century and during the first half of the 20th century, the tensions between thermodynamics and the "organic-molecules-paradigm" became increasingly difficult to ignore, culminating in Erwin Schrödinger's 1944 formulation of a thermodynamics-compliant vision of life and, consequently, the prerequisites for its appearance. We will first review the major milestones over the last 200 years in the biological and the physical sciences, relevant to making sense of life and its origins and then discuss the more recent reappraisal of the relative importance of metal ions vs. organic molecules in performing the essential processes of a living cell. Based on this reassessment and the modern understanding of biological free energy conversion (aka bioenergetics), we consider that scenarios wherein life emerges from an abiotic chemiosmotic process are both thermodynamics-compliant and the most parsimonious proposed so far.
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Affiliation(s)
- Wolfgang Nitschke
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
| | - Orion Farr
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
- CINaM, CNRS, Aix-Marseille-University, 13009 Marseille, France
| | - Nil Gaudu
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
| | - Chloé Truong
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
| | - François Guyot
- IMPMC (UMR 7590), CNRS, Sorbonne University, 75005 Paris, France;
| | - Michael J. Russell
- Dipartimento di Chimica, Università degli Studi di Torino, 10124 Torino, Italy;
| | - Simon Duval
- BIP (UMR 7281), CNRS, Aix-Marseille-University, 13009 Marseille, France; (O.F.); (N.G.); (C.T.); (S.D.)
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11
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Waltmann C, Shrestha A, Olvera de la Cruz M. Patterning of multicomponent elastic shells by gaussian curvature. Phys Rev E 2024; 109:054409. [PMID: 38907410 DOI: 10.1103/physreve.109.054409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 04/19/2024] [Indexed: 06/24/2024]
Abstract
Recent findings suggest that shell protein distribution and the morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component patterning are coupled through the competition of mean and gaussian bending energies in multicomponent elastic shells that form three-component irregular polyhedra. We observe two softer components with lower bending rigidities allocated on the edges and vertices while the harder component occupies the faces. When subjected to a nonzero interfacial line tension, the two softer components further separate and pattern into subdomains that are mediated by the gaussian curvature. We find that this degree of fractionation is maximized when there is a weaker line tension and when the ratio of bending rigidities between the two softer domains ≈2. Our results reveal a patterning mechanism in multicomponent shells that can capture the observed morphologies of bacterial microcompartments, and moreover, can be realized in synthetic vesicles.
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Affiliation(s)
| | | | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
- Center for Computation and Theory of Soft Materials, Northwestern University, Evanston, Illinois 60208, USA
- Department of Physics and Astronomy, Northwestern University, Evanston, Illinois 60208, USA
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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12
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Duque CM, Hall DM, Tyukodi B, Hagan MF, Santangelo CD, Grason GM. Limits of economy and fidelity for programmable assembly of size-controlled triply periodic polyhedra. Proc Natl Acad Sci U S A 2024; 121:e2315648121. [PMID: 38669182 PMCID: PMC11067059 DOI: 10.1073/pnas.2315648121] [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: 09/08/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
We propose and investigate an extension of the Caspar-Klug symmetry principles for viral capsid assembly to the programmable assembly of size-controlled triply periodic polyhedra, discrete variants of the Primitive, Diamond, and Gyroid cubic minimal surfaces. Inspired by a recent class of programmable DNA origami colloids, we demonstrate that the economy of design in these crystalline assemblies-in terms of the growth of the number of distinct particle species required with the increased size-scale (e.g., periodicity)-is comparable to viral shells. We further test the role of geometric specificity in these assemblies via dynamical assembly simulations, which show that conditions for simultaneously efficient and high-fidelity assembly require an intermediate degree of flexibility of local angles and lengths in programmed assembly. Off-target misassembly occurs via incorporation of a variant of disclination defects, generalized to the case of hyperbolic crystals. The possibility of these topological defects is a direct consequence of the very same symmetry principles that underlie the economical design, exposing a basic tradeoff between design economy and fidelity of programmable, size controlled assembly.
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Affiliation(s)
- Carlos M. Duque
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden01307, Germany
- Center for Systems Biology Dresden, Dresden01307, Germany
- Department of Physics, University of Massachusetts, Amherst, MA01003
| | - Douglas M. Hall
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
| | - Botond Tyukodi
- Department of Physics, Babes-Bolyai University, Cluj-Napoca400084, Romania
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Michael F. Hagan
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Christian D. Santangelo
- Department of Physics, University of Massachusetts, Amherst, MA01003
- Department of Physics, Syracuse University, Syracuse, NY13210
| | - Gregory M. Grason
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, MA01003
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13
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Hori M, Steinauer A, Tetter S, Hälg J, Manz EM, Hilvert D. Stimulus-responsive assembly of nonviral nucleocapsids. Nat Commun 2024; 15:3576. [PMID: 38678040 PMCID: PMC11055949 DOI: 10.1038/s41467-024-47808-1] [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: 02/17/2023] [Accepted: 04/12/2024] [Indexed: 04/29/2024] Open
Abstract
Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fusing maltose binding protein to the subunits of NC-4, an engineered protein cage that encapsulates its own encoding mRNA, we successfully blocked spontaneous capsid assembly, allowing isolation of the individual monomers in soluble form. To initiate RNA-templated nucleocapsid formation, the steric block can be simply removed by selective proteolysis. Analyses by transmission and cryo-electron microscopy confirmed that the resulting assemblies are structurally identical to their RNA-containing counterparts produced in vivo. Enzymatically triggered cage formation broadens the range of RNA molecules that can be encapsulated by NC-4, provides unique opportunities to study the co-assembly of capsid and cargo, and could be useful for studying other nonviral and viral assemblies.
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Affiliation(s)
- Mao Hori
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda-ku, Tokyo, Japan
| | - Angela Steinauer
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- École Polytechnique Fédérale de Lausanne (EPFL), SB ISIC LIBN, Lausanne, Switzerland
| | - Stephan Tetter
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Jamiro Hälg
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Eva-Maria Manz
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, Zürich, Switzerland.
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14
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Dutcher CA, Andreas MP, Giessen TW. A two-component quasi-icosahedral protein nanocompartment with variable shell composition and irregular tiling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591138. [PMID: 38712103 PMCID: PMC11071501 DOI: 10.1101/2024.04.25.591138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Protein shells or capsids are a widespread form of compartmentalization in nature. Viruses use protein capsids to protect and transport their genomes while many cellular organisms use protein shells for varied metabolic purposes. These protein-based compartments often exhibit icosahedral symmetry and consist of a small number of structural components with defined roles. Encapsulins are a prevalent protein-based compartmentalization strategy in prokaryotes. All encapsulins studied thus far consist of a single shell protein that adopts the viral HK97-fold. Here, we report the characterization of a Family 2B two-component encapsulin from Streptomyces lydicus. We show the differential assembly behavior of the two shell components and demonstrate their ability to co-assemble into mixed shells with variable shell composition. We determined the structures of both shell proteins using cryo-electron microscopy. Using 3D-classification and crosslinking studies, we highlight the irregular tiling of mixed shells. Our work expands the known assembly modes of HK97-fold proteins and lays the foundation for future functional and engineering studies on two-component encapsulins.
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Affiliation(s)
- Cassandra A. Dutcher
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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15
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Structure of intact α-carboxysome specifies role of CsoS2 in shell assembly. NATURE PLANTS 2024; 10:535-536. [PMID: 38605241 DOI: 10.1038/s41477-024-01667-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
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16
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Zhou RQ, Jiang YL, Li H, Hou P, Kong WW, Deng JX, Chen Y, Zhou CZ, Zeng Q. Structure and assembly of the α-carboxysome in the marine cyanobacterium Prochlorococcus. NATURE PLANTS 2024; 10:661-672. [PMID: 38589484 DOI: 10.1038/s41477-024-01660-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/29/2024] [Indexed: 04/10/2024]
Abstract
Carboxysomes are bacterial microcompartments that encapsulate the enzymes RuBisCO and carbonic anhydrase in a proteinaceous shell to enhance the efficiency of photosynthetic carbon fixation. The self-assembly principles of the intact carboxysome remain elusive. Here we purified α-carboxysomes from Prochlorococcus and examined their intact structures using single-particle cryo-electron microscopy to solve the basic principles of their shell construction and internal RuBisCO organization. The 4.2 Å icosahedral-like shell structure reveals 24 CsoS1 hexamers on each facet and one CsoS4A pentamer at each vertex. RuBisCOs are organized into three concentric layers within the shell, consisting of 72, 32 and up to 4 RuBisCOs at the outer, middle and inner layers, respectively. We uniquely show how full-length and shorter forms of the scaffolding protein CsoS2 bind to the inner surface of the shell via repetitive motifs in the middle and C-terminal regions. Combined with previous reports, we propose a concomitant 'outside-in' assembly principle of α-carboxysomes: the inner surface of the self-assembled shell is reinforced by the middle and C-terminal motifs of the scaffolding protein, while the free N-terminal motifs cluster to recruit RuBisCO in concentric, three-layered spherical arrangements. These new insights into the coordinated assembly of α-carboxysomes may guide the rational design and repurposing of carboxysome structures for improving plant photosynthetic efficiency.
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Affiliation(s)
- Rui-Qian Zhou
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yong-Liang Jiang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Haofu Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Pu Hou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wen-Wen Kong
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Jia-Xin Deng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yuxing Chen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cong-Zhao Zhou
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Qinglu Zeng
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.
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17
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Abeysinghe AADT, Young EJ, Rowland AT, Dunshee LC, Urandur S, Sullivan MO, Kerfeld CA, Keating CD. Interfacial Assembly of Bacterial Microcompartment Shell Proteins in Aqueous Multiphase Systems. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308390. [PMID: 38037673 DOI: 10.1002/smll.202308390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/13/2023] [Indexed: 12/02/2023]
Abstract
Compartments are a fundamental feature of life, based variously on lipid membranes, protein shells, or biopolymer phase separation. Here, this combines self-assembling bacterial microcompartment (BMC) shell proteins and liquid-liquid phase separation (LLPS) to develop new forms of compartmentalization. It is found that BMC shell proteins assemble at the liquid-liquid interfaces between either 1) the dextran-rich droplets and PEG-rich continuous phase of a poly(ethyleneglycol)(PEG)/dextran aqueous two-phase system, or 2) the polypeptide-rich coacervate droplets and continuous dilute phase of a polylysine/polyaspartate complex coacervate system. Interfacial protein assemblies in the coacervate system are sensitive to the ratio of cationic to anionic polypeptides, consistent with electrostatically-driven assembly. In both systems, interfacial protein assembly competes with aggregation, with protein concentration and polycation availability impacting coating. These two LLPS systems are then combined to form a three-phase system wherein coacervate droplets are contained within dextran-rich phase droplets. Interfacial localization of BMC hexameric shell proteins is tunable in a three-phase system by changing the polyelectrolyte charge ratio. The tens-of-micron scale BMC shell protein-coated droplets introduced here can accommodate bioactive cargo such as enzymes or RNA and represent a new synthetic cell strategy for organizing biomimetic functionality.
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Affiliation(s)
| | - Eric J Young
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Andrew T Rowland
- Department of Chemistry, Pennsylvania State University, State College, PA, 16801, USA
| | - Lucas C Dunshee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Sandeep Urandur
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Millicent O Sullivan
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
- Department of Biomedical Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Cheryl A Kerfeld
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Christine D Keating
- Department of Chemistry, Pennsylvania State University, State College, PA, 16801, USA
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18
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Xiao H, Zou Y, Wang J, Wan S. A Review for Artificial Intelligence Based Protein Subcellular Localization. Biomolecules 2024; 14:409. [PMID: 38672426 PMCID: PMC11048326 DOI: 10.3390/biom14040409] [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: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Proteins need to be located in appropriate spatiotemporal contexts to carry out their diverse biological functions. Mislocalized proteins may lead to a broad range of diseases, such as cancer and Alzheimer's disease. Knowing where a target protein resides within a cell will give insights into tailored drug design for a disease. As the gold validation standard, the conventional wet lab uses fluorescent microscopy imaging, immunoelectron microscopy, and fluorescent biomarker tags for protein subcellular location identification. However, the booming era of proteomics and high-throughput sequencing generates tons of newly discovered proteins, making protein subcellular localization by wet-lab experiments a mission impossible. To tackle this concern, in the past decades, artificial intelligence (AI) and machine learning (ML), especially deep learning methods, have made significant progress in this research area. In this article, we review the latest advances in AI-based method development in three typical types of approaches, including sequence-based, knowledge-based, and image-based methods. We also elaborately discuss existing challenges and future directions in AI-based method development in this research field.
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Affiliation(s)
- Hanyu Xiao
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Yijin Zou
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China;
| | - Jieqiong Wang
- Department of Neurological Sciences, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Shibiao Wan
- Department of Genetics, Cell Biology and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
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19
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Li T, Chang P, Chen W, Shi Z, Xue C, Dykes GF, Huang F, Wang Q, Liu LN. Nanoengineering Carboxysome Shells for Protein Cages with Programmable Cargo Targeting. ACS NANO 2024; 18:7473-7484. [PMID: 38326220 PMCID: PMC10938918 DOI: 10.1021/acsnano.3c11559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Protein nanocages have emerged as promising candidates for enzyme immobilization and cargo delivery in biotechnology and nanotechnology. Carboxysomes are natural proteinaceous organelles in cyanobacteria and proteobacteria and have exhibited great potential in creating versatile nanocages for a wide range of applications given their intrinsic characteristics of self-assembly, cargo encapsulation, permeability, and modularity. However, how to program intact carboxysome shells with specific docking sites for tunable and efficient cargo loading is a key question in the rational design and engineering of carboxysome-based nanostructures. Here, we generate a range of synthetically engineered nanocages with site-directed cargo loading based on an α-carboxysome shell in conjunction with SpyTag/SpyCatcher and Coiled-coil protein coupling systems. The systematic analysis demonstrates that the cargo-docking sites and capacities of the carboxysome shell-based protein nanocages could be precisely modulated by selecting specific anchoring systems and shell protein domains. Our study provides insights into the encapsulation principles of the α-carboxysome and establishes a solid foundation for the bioengineering and manipulation of nanostructures capable of capturing cargos and molecules with exceptional efficiency and programmability, thereby enabling applications in catalysis, delivery, and medicine.
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Affiliation(s)
- Tianpei Li
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Ping Chang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Weixian Chen
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Zhaoyang Shi
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Chunling Xue
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Gregory F. Dykes
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Fang Huang
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
| | - Qiang Wang
- State
Key Laboratory of Crop Stress Adaptation and Improvement, School of
Life Sciences, Henan University, Kaifeng 475004, China
| | - Lu-Ning Liu
- Institute
of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United
Kingdom
- MOE
Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science
Center for Deep Ocean Multispheres and Earth System & College
of Marine Life Sciences, Ocean University
of China, Qingdao 266003, China
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20
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Raza S, Sarkar D, Chan LJG, Mae J, Sutter M, Petzold CJ, Kerfeld CA, Ralston CY, Gupta S, Vermaas JV. Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584231. [PMID: 38559214 PMCID: PMC10980050 DOI: 10.1101/2024.03.12.584231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo, the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We use molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo. Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceum model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.
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Affiliation(s)
- Saad Raza
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Daipayan Sarkar
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Leanne Jade G Chan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Current address: Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Joshua Mae
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Department Of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Corie Y Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Department Of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824
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21
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Scott KM, Payne RR, Gahramanova A. Widespread dissolved inorganic carbon-modifying toolkits in genomes of autotrophic Bacteria and Archaea and how they are likely to bridge supply from the environment to demand by autotrophic pathways. Appl Environ Microbiol 2024; 90:e0155723. [PMID: 38299815 PMCID: PMC10880623 DOI: 10.1128/aem.01557-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
Using dissolved inorganic carbon (DIC) as a major carbon source, as autotrophs do, is complicated by the bedeviling nature of this substance. Autotrophs using the Calvin-Benson-Bassham cycle (CBB) are known to make use of a toolkit comprised of DIC transporters and carbonic anhydrase enzymes (CA) to facilitate DIC fixation. This minireview provides a brief overview of the current understanding of how toolkit function facilitates DIC fixation in Cyanobacteria and some Proteobacteria using the CBB and continues with a survey of the DIC toolkit gene presence in organisms using different versions of the CBB and other autotrophic pathways (reductive citric acid cycle, Wood-Ljungdahl pathway, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate cycle, and dicarboxylate-hydroxybutyrate cycle). The potential function of toolkit gene products in these organisms is discussed in terms of CO2 and HCO3- supply from the environment and demand by the autotrophic pathway. The presence of DIC toolkit genes in autotrophic organisms beyond those using the CBB suggests the relevance of DIC metabolism to these organisms and provides a basis for better engineering of these organisms for industrial and agricultural purposes.
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Affiliation(s)
- Kathleen M. Scott
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Ren R. Payne
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
| | - Arin Gahramanova
- Integrative Biology Department, University of South Florida, Tampa, Florida, USA
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22
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Trettel DS, Pacheco SL, Laskie AK, Gonzalez-Esquer CR. Modeling bacterial microcompartment architectures for enhanced cyanobacterial carbon fixation. FRONTIERS IN PLANT SCIENCE 2024; 15:1346759. [PMID: 38425792 PMCID: PMC10902431 DOI: 10.3389/fpls.2024.1346759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
The carboxysome is a bacterial microcompartment (BMC) which plays a central role in the cyanobacterial CO2-concentrating mechanism. These proteinaceous structures consist of an outer protein shell that partitions Rubisco and carbonic anhydrase from the rest of the cytosol, thereby providing a favorable microenvironment that enhances carbon fixation. The modular nature of carboxysomal architectures makes them attractive for a variety of biotechnological applications such as carbon capture and utilization. In silico approaches, such as molecular dynamics (MD) simulations, can support future carboxysome redesign efforts by providing new spatio-temporal insights on their structure and function beyond in vivo experimental limitations. However, specific computational studies on carboxysomes are limited. Fortunately, all BMC (including the carboxysome) are highly structurally conserved which allows for practical inferences to be made between classes. Here, we review simulations on BMC architectures which shed light on (1) permeation events through the shell and (2) assembly pathways. These models predict the biophysical properties surrounding the central pore in BMC-H shell subunits, which in turn dictate the efficiency of substrate diffusion. Meanwhile, simulations on BMC assembly demonstrate that assembly pathway is largely dictated kinetically by cargo interactions while final morphology is dependent on shell factors. Overall, these findings are contextualized within the wider experimental BMC literature and framed within the opportunities for carboxysome redesign for biomanufacturing and enhanced carbon fixation.
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Affiliation(s)
- Daniel S. Trettel
- Los Alamos National Laboratory, Bioscience Division, Microbial and Biome Sciences Group, Los Alamos, NM, United States
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23
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Christians LF, Halingstad EV, Kram E, Okolovitch EM, Pak AJ. Formalizing Coarse-Grained Representations of Anisotropic Interactions at Multimeric Protein Interfaces Using Virtual Sites. J Phys Chem B 2024; 128:1394-1406. [PMID: 38316012 DOI: 10.1021/acs.jpcb.3c07023] [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: 02/07/2024]
Abstract
Molecular simulations of biomacromolecules that assemble into multimeric complexes remain a challenge due to computationally inaccessible length and time scales. Low-resolution and implicit-solvent coarse-grained modeling approaches using traditional nonbonded interactions (both pairwise and spherically isotropic) have been able to partially address this gap. However, these models may fail to capture the complex anisotropic interactions present at macromolecular interfaces unless higher-order interaction potentials are incorporated at the expense of the computational cost. In this work, we introduce an alternate and systematic approach to represent directional interactions at protein-protein interfaces by using virtual sites restricted to pairwise interactions. We show that virtual site interaction parameters can be optimized within a relative entropy minimization framework by using only information from known statistics between coarse-grained sites. We compare our virtual site models to traditional coarse-grained models using two case studies of multimeric protein assemblies and find that the virtual site models predict pairwise correlations with higher fidelity and, more importantly, assembly behavior that is morphologically consistent with experiments. Our study underscores the importance of anisotropic interaction representations and paves the way for more accurate yet computationally efficient coarse-grained simulations of macromolecular assembly in future research.
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Affiliation(s)
- Luc F Christians
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Ethan V Halingstad
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Emiel Kram
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Evan M Okolovitch
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Alexander J Pak
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado 80401, United States
- Quantitative Biosciences and Engineering Program, Colorado School of Mines, Golden, Colorado 80401, United States
- Materials Science Program, Colorado School of Mines, Golden, Colorado 80401, United States
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24
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Szyszka TN, Andreas MP, Lie F, Miller LM, Adamson LSR, Fatehi F, Twarock R, Draper BE, Jarrold MF, Giessen TW, Lau YH. Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.579038. [PMID: 38370832 PMCID: PMC10871247 DOI: 10.1101/2024.02.05.579038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Protein capsids are a widespread form of compartmentalisation in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximises the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of novel symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryo-EM, we determine the structures of a precedented 60-mer icosahedral assembly and an unprecedented 36-mer tetrahedron that features significant geometric rearrangements around a novel interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple point mutation to various amino acids, and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent the first example of tetrahedral geometry across all characterised encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in protein sequence.
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Affiliation(s)
- Taylor N Szyszka
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Felicia Lie
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Lohra M Miller
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Lachlan S R Adamson
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Farzad Fatehi
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
| | - Reidun Twarock
- Department of Mathematics, University of York, York, UK
- York Cross-Disciplinary Centre for Systems Analysis, University of York, York, UK
- Department of Biology, University of York, York, UK
| | - Benjamin E Draper
- Megadalton Solutions Inc., 3750 E Bluebird Ln, Bloomington, IN 47401, USA
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E. Kirkwood Avenue, Bloomington, IN 47405, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia
- The University of Sydney Nano Institute, The University of Sydney, Camperdown, NSW 2006, Australia
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25
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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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26
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Kalnins G, Bertins M, Viksna A, Tars K. Functionalization of bacterial microcompartment shell interior with cysteine containing peptides enhances the iron and cobalt loading capacity. Biometals 2024; 37:267-274. [PMID: 37728832 DOI: 10.1007/s10534-023-00538-1] [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: 05/15/2023] [Accepted: 09/11/2023] [Indexed: 09/21/2023]
Abstract
Bacterial microcompartments (BMCs) are prokaryotic organelles involved in several biochemical processes in bacterial cells. These cellular substructures consist of an icosahedral shell and an encapsulated enzymatic core. The outer shells of BMCs have been proposed as an attractive platform for the creation of novel nanomaterials, nanocages, and nanoreactors. In this study, we present a method for functionalizing recombinant GRM2-type BMC shell lumens with short cysteine-containing sequences and demonstrate that the iron and cobalt loading capacity of such modified shells is markedly increased. These results also imply that a passive flow of cobalt and iron atoms across the BMC shell could be possible.
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Affiliation(s)
- Gints Kalnins
- Latvian Biomedical Research and Study Centre, Ratsupites street 1, Riga, 1067, Latvia.
| | - Maris Bertins
- University of Latvia, Jelgavas street 1, Riga, 1004, Latvia
| | - Arturs Viksna
- University of Latvia, Jelgavas street 1, Riga, 1004, Latvia
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, Ratsupites street 1, Riga, 1067, Latvia
- University of Latvia, Jelgavas street 1, Riga, 1004, Latvia
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27
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Zeng Z, Wijnands LM, Boeren S, Smid EJ, Notebaart RA, Abee T. Impact of vitamin B 12 on rhamnose metabolism, stress defense and in-vitro virulence of Listeria monocytogenes. Int J Food Microbiol 2024; 410:110486. [PMID: 37992553 DOI: 10.1016/j.ijfoodmicro.2023.110486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/05/2023] [Accepted: 11/11/2023] [Indexed: 11/24/2023]
Abstract
Listeria monocytogenes is a facultative anaerobe which can cause a severe food-borne infection known as listeriosis. L. monocytogenes is capable of utilizing various nutrient sources including rhamnose, a naturally occurring deoxy sugar abundant in foods. L. monocytogenes can degrade rhamnose into lactate, acetate and 1,2-propanediol. Our previous study showed that addition of vitamin B12 stimulated anaerobic growth of L. monocytogenes on rhamnose due to the activation of bacterial microcompartments for 1,2-propanediol utilization (pdu BMC) with concomitant production of propionate and propanol. Notably, anaerobic 1,2-propanediol metabolism has been linked to virulence of enteric pathogens including Salmonella spp. and L. monocytogenes. In this study we investigated the impact of B12 and BMC activation on i) aerobic and anerobic growth of L. monocytogenes on rhamnose and ii) the level of virulence. We observed B12-induced pdu BMC activation and growth stimulation only in anaerobically grown cells. Comparative Caco-2 virulence assays showed that these pdu BMC-induced cells have significantly higher translocation efficiency compared to non-induced cells (anaerobic growth without B12; aerobic growth with or without B12), while adhesion and invasion capacity is similar for all cells. Comparative proteome analysis showed specific and overlapping responses linked to metabolic shifts, activation of stress defense proteins and virulence factors, with RNA polymerase sigma factor SigL, teichoic acid export ATP-binding protein TagH, DNA repair and protection proteins, RadA and DPS, and glutathione synthase GshAB, previously linked to activation of virulence response in L. monocytogenes, uniquely upregulated in anaerobically rhamnose grown pdu-induced cells. Our results shed light on possible effects of B12 on L. monocytogenes competitive fitness and virulence activation when utilizing rhamnose in anaerobic conditions encountered during transmission and the human intestine.
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Affiliation(s)
- Zhe Zeng
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Lucas M Wijnands
- National Institute of Public Health and the Environment, Bilthoven, the Netherlands
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands
| | - Eddy J Smid
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Richard A Notebaart
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands
| | - Tjakko Abee
- Food Microbiology, Wageningen University and Research, Wageningen, the Netherlands.
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28
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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29
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Liu N, Dong W, Yang H, Li JH, Chiu TY. Application of artificial scaffold systems in microbial metabolic engineering. Front Bioeng Biotechnol 2023; 11:1328141. [PMID: 38188488 PMCID: PMC10771841 DOI: 10.3389/fbioe.2023.1328141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024] Open
Abstract
In nature, metabolic pathways are often organized into complex structures such as multienzyme complexes, enzyme molecular scaffolds, or reaction microcompartments. These structures help facilitate multi-step metabolic reactions. However, engineered metabolic pathways in microbial cell factories do not possess inherent metabolic regulatory mechanisms, which can result in metabolic imbalance. Taking inspiration from nature, scientists have successfully developed synthetic scaffolds to enhance the performance of engineered metabolic pathways in microbial cell factories. By recruiting enzymes, synthetic scaffolds facilitate the formation of multi-enzyme complexes, leading to the modulation of enzyme spatial distribution, increased enzyme activity, and a reduction in the loss of intermediate products and the toxicity associated with harmful intermediates within cells. In recent years, scaffolds based on proteins, nucleic acids, and various organelles have been developed and employed to facilitate multiple metabolic pathways. Despite varying degrees of success, synthetic scaffolds still encounter numerous challenges. The objective of this review is to provide a comprehensive introduction to these synthetic scaffolds and discuss their latest research advancements and challenges.
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Affiliation(s)
- Nana Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Wei Dong
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Huanming Yang
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Jing-Hua Li
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Tsan-Yu Chiu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
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30
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Yao L, Wu X, Jiang X, Shan M, Zhang Z, Li Y, Yang A, Li Y, Yang C. Subcellular compartmentalization in the biosynthesis and engineering of plant natural products. Biotechnol Adv 2023; 69:108258. [PMID: 37722606 DOI: 10.1016/j.biotechadv.2023.108258] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.
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Affiliation(s)
- Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xun Jiang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Zhuoxiang Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yiting Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Changqing Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China.
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31
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Česle EEL, Ta Rs K, Jansons J, Kalniņš G. Modulation of Hybrid GRM2-type Bacterial Microcompartment Shells through BMC-H Shell Protein Fusion and Incorporation of Non-native BMC-T Shell Proteins. ACS Synth Biol 2023; 12:3275-3286. [PMID: 37937366 DOI: 10.1021/acssynbio.3c00281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Bacterial microcompartments (BMCs) are organelle-like structures in bacteria that facilitate a wide range of enzymatic reactions. The microcompartment shell contains an encapsulated enzymatic core and, in contrast to phospholipid-based eukaryotic organelle membranes, has a pseudoicosahedral shape composed of BMC-H, BMC-T, and BMC-P proteins with conserved structures. This semipermeable microcompartment shell delineates the enzymatic core assemblies and the intermediates from the rest of the cell. It is also thought to function as a barrier against toxic intermediates as well as to increase the reaction rate. These properties of BMCs have made them intriguing candidates for biotechnological applications, for which it is important to explore the potential scope of the BMC shell modulation possibilities. In this work, we explore two BMC shell modulation mechanisms: first, confirming the incorporation of three trimeric BMC-T shell proteins and two truncated BMC-T shell proteins into Klebsiella pneumoniae GRM2-type BMC protein shells containing no representatives of this group, and second, producing BMC particles from double- and triple-fused hexameric BMC-H shell proteins. These results reveal the potential for "mix and match" synthetic BMC shell formation to ensure shell properties specifically suited to the encapsulated cargo and show for the first time the involvement of an essentially dimeric pseudohexameric shell protein in BMC shell formation.
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Affiliation(s)
- Eva Emi Lija Česle
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
| | - Kaspars Ta Rs
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
- University of Latvia, Jelgavas 1, Riga 1004, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga LV-1067, Latvia
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32
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Kaltbeitzel J, Wich PR. Protein-based Nanoparticles: From Drug Delivery to Imaging, Nanocatalysis and Protein Therapy. Angew Chem Int Ed Engl 2023; 62:e202216097. [PMID: 36917017 DOI: 10.1002/anie.202216097] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/16/2023]
Abstract
Proteins and enzymes are versatile biomaterials for a wide range of medical applications due to their high specificity for receptors and substrates, high degradability, low toxicity, and overall good biocompatibility. Protein nanoparticles are formed by the arrangement of several native or modified proteins into nanometer-sized assemblies. In this review, we will focus on artificial nanoparticle systems, where proteins are the main structural element and not just an encapsulated payload. While under natural conditions, only certain proteins form defined aggregates and nanoparticles, chemical modifications or a change in the physical environment can further extend the pool of available building blocks. This allows the assembly of many globular proteins and even enzymes. These advances in preparation methods led to the emergence of new generations of nanosystems that extend beyond transport vehicles to diverse applications, from multifunctional drug delivery to imaging, nanocatalysis and protein therapy.
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Affiliation(s)
- Jonas Kaltbeitzel
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Peter R Wich
- School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052, Australia
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33
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Quinton AR, McDowell HB, Hoiczyk E. Encapsulins: Nanotechnology's future in a shell. ADVANCES IN APPLIED MICROBIOLOGY 2023; 125:1-48. [PMID: 38783722 DOI: 10.1016/bs.aambs.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Encapsulins, virus capsid-like bacterial nanocompartments have emerged as promising tools in medicine, imaging, and material sciences. Recent work has shown that these protein-bound icosahedral 'organelles' possess distinct properties that make them exceptionally usable for nanotechnology applications. A key factor contributing to their appeal is their ability to self-assemble, coupled with their capacity to encapsulate a wide range of cargos. Their genetic manipulability, stability, biocompatibility, and nano-size further enhance their utility, offering outstanding possibilities for practical biotechnology applications. In particular, their amenability to engineering has led to their extensive modification, including the packaging of non-native cargos and the utilization of the shell surface for displaying immunogenic or targeting proteins and peptides. This inherent versatility, combined with the ease of expressing encapsulins in heterologous hosts, promises to provide broad usability. Although mostly not yet commercialized, encapsulins have started to demonstrate their vast potential for biotechnology, from drug delivery to biofuel production and the synthesis of valuable inorganic materials. In this review, we will initially discuss the structure, function and diversity of encapsulins, which form the basis for these emerging applications, before reviewing ongoing practical uses and highlighting promising applications in medicine, engineering and environmental sciences.
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Affiliation(s)
- Amy Ruth Quinton
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Harry Benjamin McDowell
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom
| | - Egbert Hoiczyk
- School of Biosciences, The Krebs Institute, The University of Sheffield, Sheffield, United Kingdom.
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34
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Kumar G, Hazra JP, Sinha S. Disordered regions endow structural flexibility to shell proteins and function towards shell-enzyme interactions in 1,2-propanediol utilization microcompartment. J Biomol Struct Dyn 2023; 41:8891-8901. [PMID: 36318590 DOI: 10.1080/07391102.2022.2138552] [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: 07/12/2022] [Accepted: 10/16/2022] [Indexed: 11/07/2022]
Abstract
Intrinsically disordered regions in proteins have been functionally linked to the protein-protein interactions and genesis of several membraneless organelles. Depending on their residual makeup, hydrophobicity or charge distribution they may remain in extended form or may assume certain conformations upon biding to a partner protein or peptide. The present work investigates the distribution and potential roles of disordered regions in the integral proteins of 1,2-propanediol utilization microcompartments. We use bioinformatics tools to identify the probable disordered regions in the shell proteins and enzyme of the 1,2-propanediol utilization microcompartment. Using a combination of computational modelling and biochemical techniques we elucidate the role of disordered terminal regions of a major shell protein and enzyme. Our findings throw light on the importance of disordered regions in the self-assembly, providing flexibility to shell protein and mediating its interaction with a native enzyme.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gaurav Kumar
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Sharmistha Sinha
- Chemical Biology Unit, Institute of Nano Science and Technology, Mohali, India
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35
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Ouazan-Reboul V, Golestanian R, Agudo-Canalejo J. Network Effects Lead to Self-Organization in Metabolic Cycles of Self-Repelling Catalysts. PHYSICAL REVIEW LETTERS 2023; 131:128301. [PMID: 37802958 DOI: 10.1103/physrevlett.131.128301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/27/2023] [Indexed: 10/08/2023]
Abstract
Mixtures of particles that interact through phoretic effects are known to aggregate if they belong to species that exhibit attractive self-interactions. We study self-organization in a model metabolic cycle composed of three species of catalytically active particles that are chemotactic toward the chemicals that define their connectivity network. We find that the self-organization can be controlled by the network properties, as exemplified by a case where a collapse instability is achieved by design for self-repelling species. Our findings highlight a possibility for controlling the intricate functions of metabolic networks by taking advantage of the physics of phoretic active matter.
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Affiliation(s)
- Vincent Ouazan-Reboul
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, D-37077 Göttingen, Germany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, D-37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Jaime Agudo-Canalejo
- Max Planck Institute for Dynamics and Self-Organization, Am Fassberg 17, D-37077 Göttingen, Germany
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36
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Trettel DS, Neale C, Zhao M, Gnanakaran S, Gonzalez-Esquer CR. Monatomic ions influence substrate permeation across bacterial microcompartment shells. Sci Rep 2023; 13:15738. [PMID: 37735196 PMCID: PMC10514305 DOI: 10.1038/s41598-023-42688-9] [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: 03/20/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications.
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Affiliation(s)
- Daniel S Trettel
- Biosciences Division, Microbial and Biome Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Chris Neale
- Theoretical Division, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Mingfei Zhao
- Theoretical Division, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - S Gnanakaran
- Theoretical Division, Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
| | - C Raul Gonzalez-Esquer
- Biosciences Division, Microbial and Biome Sciences Group, Los Alamos National Laboratory, Los Alamos, NM, USA.
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37
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Tong Y, Wei Y, Ju Y, Li P, Zhang Y, Li L, Gao L, Liu S, Liu D, Hu Y, Li Z, Yu H, Luo Y, Wang J, Wang Y, Zhang Y. Anaerobic purinolytic enzymes enable dietary purine clearance by engineered gut bacteria. Cell Chem Biol 2023; 30:1104-1114.e7. [PMID: 37164019 DOI: 10.1016/j.chembiol.2023.04.008] [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: 01/06/2023] [Revised: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/12/2023]
Abstract
Uric acid, the end product of purine degradation, causes hyperuricemia and gout, afflicting hundreds of millions of people. The debilitating effects of gout are exacerbated by dietary purine intake, and thus a potential therapeutic strategy is to enhance purine degradation in the gut microbiome. Aerobic purine degradation involves oxidative dearomatization of uric acid catalyzed by the O2-dependent uricase. The enzymes involved in purine degradation in strictly anaerobic bacteria remain unknown. Here we report the identification and characterization of these enzymes, which include four hydrolases belonging to different enzyme families, and a prenyl-flavin mononucleotide-dependent decarboxylase. Introduction of the first two hydrolases to Escherichia coli Nissle 1917 enabled its anaerobic growth on xanthine as the sole nitrogen source. Oral supplementation of these engineered probiotics ameliorated hyperuricemia in a Drosophila melanogaster model, including the formation of renal uric acid stones and a shortened lifespan, providing a route toward the development of purinolytic probiotics.
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Affiliation(s)
- Yang Tong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China
| | - Yifeng Wei
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A∗STAR), Singapore 138669, Singapore
| | - Yingjie Ju
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Peishan Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yumin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300192, P.R. China
| | - Liqin Li
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Lujuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Shengnan Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Dazhi Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Meining Pharma Inc, 2-401-1, Bldg 8, Huiying Industrial Park, No. 86 West Zhonghuan Road, Tianjin Pilot Free Trade Zone, Tianjin 300308, China
| | - Yiling Hu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Zhi Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Hongbin Yu
- Department of Hematology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yunzi Luo
- Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Jian Wang
- Tianjin Speerise Challenge Biotechnology Co., Ltd., Zhangjiawo Industrial Park, No. 16 Huiyuan Road, Zhangjiawo Town, Xiqing District, Tianjin 300380, China
| | - Yiwen Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300072, China; Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Department of Chemistry, Tianjin University, Tianjin 300072, P.R. China.
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38
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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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39
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Basalla JL, Mak CA, Byrne JA, Ghalmi M, Hoang Y, Vecchiarelli AG. Dissecting the phase separation and oligomerization activities of the carboxysome positioning protein McdB. eLife 2023; 12:e81362. [PMID: 37668016 PMCID: PMC10554743 DOI: 10.7554/elife.81362] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/01/2023] [Indexed: 09/06/2023] Open
Abstract
Across bacteria, protein-based organelles called bacterial microcompartments (BMCs) encapsulate key enzymes to regulate their activities. The model BMC is the carboxysome that encapsulates enzymes for CO2 fixation to increase efficiency and is found in many autotrophic bacteria, such as cyanobacteria. Despite their importance in the global carbon cycle, little is known about how carboxysomes are spatially regulated. We recently identified the two-factor system required for the maintenance of carboxysome distribution (McdAB). McdA drives the equal spacing of carboxysomes via interactions with McdB, which associates with carboxysomes. McdA is a ParA/MinD ATPase, a protein family well studied in positioning diverse cellular structures in bacteria. However, the adaptor proteins like McdB that connect these ATPases to their cargos are extremely diverse. In fact, McdB represents a completely unstudied class of proteins. Despite the diversity, many adaptor proteins undergo phase separation, but functional roles remain unclear. Here, we define the domain architecture of McdB from the model cyanobacterium Synechococcus elongatus PCC 7942, and dissect its mode of biomolecular condensate formation. We identify an N-terminal intrinsically disordered region (IDR) that modulates condensate solubility, a central coiled-coil dimerizing domain that drives condensate formation, and a C-terminal domain that trimerizes McdB dimers and provides increased valency for condensate formation. We then identify critical basic residues in the IDR, which we mutate to glutamines to solubilize condensates. Finally, we find that a condensate-defective mutant of McdB has altered association with carboxysomes and influences carboxysome enzyme content. The results have broad implications for understanding spatial organization of BMCs and the molecular grammar of protein condensates.
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Affiliation(s)
- Joseph L Basalla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Claudia A Mak
- Department of Biological Chemistry, University of Michigan-Ann ArborAnn ArborUnited States
| | - Jordan A Byrne
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Y Hoang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann ArborAnn ArborUnited States
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40
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Dedysh SN. Describing difficult-to-culture bacteria: Taking a shortcut or investing time to discover something new? Syst Appl Microbiol 2023; 46:126439. [PMID: 37413783 DOI: 10.1016/j.syapm.2023.126439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/17/2023] [Accepted: 06/29/2023] [Indexed: 07/08/2023]
Abstract
Despite the growing interest in isolating representatives of poorly studied and as-yet-uncultivated bacterial phylogenetic groups, these microorganisms remain difficult objects for taxonomic studies. The time required for describing one of these fastidious bacteria is commonly measured in several years. What is even more problematic, many routine laboratory tests, which were originally developed for fast-growing and fast-responding microorganisms, are not fully suitable for many environmentally relevant, slow-growing bacteria. Standard techniques used in chemotaxonomic analyses do not identify unique lipids produced by these bacteria. A common practice of preparing taxonomic descriptions that report a minimal set of features to name a newly isolated organism deepens a gap between microbial ecologists and taxonomists. By contrast, investing time in detailed analysis of cell biology and experimental verification of genome-encoded capabilities of newly isolated microorganisms opens a window for novel, unexpected findings, which may shape our ideas about the functional role of these microbes in the environment.
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Affiliation(s)
- Svetlana N Dedysh
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.
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41
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Solis-Miranda J, Chodasiewicz M, Skirycz A, Fernie AR, Moschou PN, Bozhkov PV, Gutierrez-Beltran E. Stress-related biomolecular condensates in plants. THE PLANT CELL 2023; 35:3187-3204. [PMID: 37162152 PMCID: PMC10473214 DOI: 10.1093/plcell/koad127] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Biomolecular condensates are membraneless organelle-like structures that can concentrate molecules and often form through liquid-liquid phase separation. Biomolecular condensate assembly is tightly regulated by developmental and environmental cues. Although research on biomolecular condensates has intensified in the past 10 years, our current understanding of the molecular mechanisms and components underlying their formation remains in its infancy, especially in plants. However, recent studies have shown that the formation of biomolecular condensates may be central to plant acclimation to stress conditions. Here, we describe the mechanism, regulation, and properties of stress-related condensates in plants, focusing on stress granules and processing bodies, 2 of the most well-characterized biomolecular condensates. In this regard, we showcase the proteomes of stress granules and processing bodies in an attempt to suggest methods for elucidating the composition and function of biomolecular condensates. Finally, we discuss how biomolecular condensates modulate stress responses and how they might be used as targets for biotechnological efforts to improve stress tolerance.
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Affiliation(s)
- Jorge Solis-Miranda
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Monika Chodasiewicz
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Department of Biology, University of Crete, Heraklion 71409, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Emilio Gutierrez-Beltran
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
- Departamento de Bioquimica Vegetal y Biologia Molecular, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
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42
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Doron L, Sutter M, Kerfeld CA. Characterization of a novel aromatic substrate-processing microcompartment in Actinobacteria. mBio 2023; 14:e0121623. [PMID: 37462359 PMCID: PMC10470539 DOI: 10.1128/mbio.01216-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/07/2023] [Indexed: 09/02/2023] Open
Abstract
We have discovered a new cluster of genes that is found exclusively in the Actinobacteria phylum. This locus includes genes for the 2-aminophenol meta-cleavage pathway and the shell proteins of a bacterial microcompartment (BMC) and has been named aromatics (ARO) for its putative role in the breakdown of aromatic compounds. In this study, we provide details about the distribution and composition of the ARO BMC locus and conduct phylogenetic, structural, and functional analyses of the first two enzymes in the catabolic pathway: a unique 2-aminophenol dioxygenase, which is exclusively found alongside BMC shell genes in Actinobacteria, and a semialdehyde dehydrogenase, which works downstream of the dioxygenase. Genomic analysis reveals variations in the complexity of the ARO loci across different orders. Some loci are simple, containing shell proteins and enzymes for the initial steps of the catabolic pathway, while others are extensive, encompassing all the necessary genes for the complete breakdown of 2-aminophenol into pyruvate and acetyl-CoA. Furthermore, our analysis uncovers two subtypes of ARO BMC that likely degrade either 2-aminophenol or catechol, depending on the presence of a pathway-specific gene within the ARO locus. The precise precursor of 2-aminophenol, which serves as the initial substrate and/or inducer for the ARO pathway, remains unknown, as our model organism Micromonospora rosaria cannot utilize 2-aminophenol as its sole energy source. However, using enzymatic assays, we demonstrate the dioxygenase's ability to cleave both 2-aminophenol and catechol in vitro, in collaboration with the aldehyde dehydrogenase, to facilitate the rapid conversion of these unstable and toxic intermediates. IMPORTANCE Bacterial microcompartments (BMCs) are proteinaceous organelles that are widespread among bacteria and provide a competitive advantage in specific environmental niches. Studies have shown that the genetic information necessary to form functional BMCs is encoded in loci that contain genes encoding shell proteins and the enzymatic core. This allows the bioinformatic discovery of BMCs with novel functions and expands our understanding of the metabolic diversity of BMCs. ARO loci, found only in Actinobacteria, contain genes encoding for phylogenetically remote shell proteins and homologs of the meta-cleavage degradation pathway enzymes that were shown to convert central aromatic intermediates into pyruvate and acetyl-CoA in gamma Proteobacteria. By analyzing the gene composition of ARO BMC loci and characterizing two core enzymes phylogenetically, structurally, and functionally, we provide an initial functional characterization of the ARO BMC, the most unusual BMC identified to date, distinctive among the repertoire of studied BMCs.
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Affiliation(s)
- Lior Doron
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
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43
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Waltmann C, Kennedy NW, Mills CE, Roth EW, Ikonomova SP, Tullman-Ercek D, Olvera de la Cruz M. Kinetic Growth of Multicomponent Microcompartment Shells. ACS NANO 2023; 17:15751-15762. [PMID: 37552700 DOI: 10.1021/acsnano.3c03353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Overall, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.
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Affiliation(s)
- Curt Waltmann
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Nolan W Kennedy
- Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Carolyn E Mills
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Eric W Roth
- Northwestern University Atomic and Nanoscale Characterization Experimentation Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Svetlana P Ikonomova
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Danielle Tullman-Ercek
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Monica Olvera de la Cruz
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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44
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Zakaszewski D, Koziej L, Pankowski J, Malolan VV, Gämperli N, Heddle JG, Hilvert D, Azuma Y. Complementary charge-driven encapsulation of functional protein by engineered protein cages in cellulo. J Mater Chem B 2023; 11:6540-6546. [PMID: 37427706 DOI: 10.1039/d3tb00754e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Charge-driven inclusion complex formation in live cells was examined using a degradation-prone fluorescent protein and a series of protein cages. The results show that sufficiently strong host-guest ionic interaction and an intact shell-like structure are crucial for the protective guest encapsulation.
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Affiliation(s)
- Daniel Zakaszewski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa 7A, 30387 Krakow, Poland.
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, 30348 Krakow, Poland
| | - Lukasz Koziej
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa 7A, 30387 Krakow, Poland.
| | - Jędrzej Pankowski
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa 7A, 30387 Krakow, Poland.
- Faculty of Biochemistry, Biophysics, sand Biotechnology, Jagiellonian University, Gronostajowa 7, 30387 Krakow, Poland
| | - V Vishal Malolan
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa 7A, 30387 Krakow, Poland.
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. S. Łojasiewicza 11, 30348 Krakow, Poland
| | - Nina Gämperli
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Jonathan G Heddle
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa 7A, 30387 Krakow, Poland.
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Yusuke Azuma
- Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Gronostajowa 7A, 30387 Krakow, Poland.
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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45
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Beal DM, Liang M, Brown I, Budge JD, Burrows ER, Howland K, Lee P, Martin S, Morrell A, Nemoto-Smith E, Roobol J, Stanley M, Smales CM, Warren MJ. Modification of bacterial microcompartments with target biomolecules via post-translational SpyTagging. MATERIALS ADVANCES 2023; 4:2963-2970. [PMID: 37465645 PMCID: PMC10350929 DOI: 10.1039/d3ma00071k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/31/2023] [Indexed: 07/20/2023]
Abstract
Bacterial microcompartments (BMCs) are proteinaceous organelle-like structures formed within bacteria, often encapsulating enzymes and cellular processes, in particular, allowing toxic intermediates to be shielded from the general cellular environment. Outside of their biological role they are of interest, through surface modification, as potential drug carriers and polyvalent antigen display scaffolds. Here we use a post-translational modification approach, using copper free click chemistry, to attach a SpyTag to a target protein molecule for attachment to a specific SpyCatcher modified BMC shell protein. We demonstrate that a post-translationally SpyTagged material can react with a SpyCatcher modified BMC and show its presence on the surface of BMCs, enabling future investigation of these structures as polyvalent antigen display scaffolds for vaccine development. This post-translational 'click' methodology overcomes the necessity to genetically encode the SpyTag, avoids any potential reduction in expression yield and expands the scope of SpyTag/SpyCatcher vaccine scaffolds to form peptide epitope vaccines and small molecule delivery agents.
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Affiliation(s)
- David M Beal
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Mingzhi Liang
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Ian Brown
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - James D Budge
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Kevin Howland
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Phoebe Lee
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Andrew Morrell
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | | | - Joanne Roobol
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - Maria Stanley
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
| | - C Mark Smales
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co Dublin A94 X099 Ireland
| | - Martin J Warren
- School of Biosciences, Division of Natural Sciences, University of Kent Canterbury UK
- Quadram Institute Bioscience Norwich UK
- Norwich Medical School, University of East Anglia Norwich UK
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46
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Pulianmackal LT, Limcaoco JMI, Ravi K, Yang S, Zhang J, Tran MK, Ghalmi M, O'Meara MJ, Vecchiarelli AG. Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell. Nat Commun 2023; 14:3255. [PMID: 37277398 DOI: 10.1038/s41467-023-39019-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
In eukaryotes, linear motor proteins govern intracellular transport and organization. In bacteria, where linear motors involved in spatial regulation are absent, the ParA/MinD family of ATPases organize an array of genetic- and protein-based cellular cargos. The positioning of these cargos has been independently investigated to varying degrees in several bacterial species. However, it remains unclear how multiple ParA/MinD ATPases can coordinate the positioning of diverse cargos in the same cell. Here, we find that over a third of sequenced bacterial genomes encode multiple ParA/MinD ATPases. We identify an organism (Halothiobacillus neapolitanus) with seven ParA/MinD ATPases, demonstrate that five of these are each dedicated to the spatial regulation of a single cellular cargo, and define potential specificity determinants for each system. Furthermore, we show how these positioning reactions can influence each other, stressing the importance of understanding how organelle trafficking, chromosome segregation, and cell division are coordinated in bacterial cells. Together, our data show how multiple ParA/MinD ATPases coexist and function to position a diverse set of fundamental cargos in the same bacterial cell.
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Affiliation(s)
- Lisa T Pulianmackal
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jose Miguel I Limcaoco
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Keerthikka Ravi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sinyu Yang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Zhang
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mimi K Tran
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Maria Ghalmi
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew J O'Meara
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anthony G Vecchiarelli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
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Evans SL, Al-Hazeem MMJ, Mann D, Smetacek N, Beavil AJ, Sun Y, Chen T, Dykes GF, Liu LN, Bergeron JRC. Single-particle cryo-EM analysis of the shell architecture and internal organization of an intact α-carboxysome. Structure 2023; 31:677-688.e4. [PMID: 37015227 PMCID: PMC10689251 DOI: 10.1016/j.str.2023.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/19/2023] [Accepted: 03/09/2023] [Indexed: 04/05/2023]
Abstract
Carboxysomes are proteinaceous bacterial microcompartments that sequester the key enzymes for carbon fixation in cyanobacteria and some proteobacteria. They consist of a virus-like icosahedral shell, encapsulating several enzymes, including ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for the first step of the Calvin-Benson-Bassham cycle. Despite their significance in carbon fixation and great bioengineering potentials, the structural understanding of native carboxysomes is currently limited to low-resolution studies. Here, we report the characterization of a native α-carboxysome from a marine cyanobacterium by single-particle cryoelectron microscopy (cryo-EM). We have determined the structure of its RuBisCO enzyme, and obtained low-resolution maps of its icosahedral shell, and of its concentric interior organization. Using integrative modeling approaches, we have proposed a complete atomic model of an intact carboxysome, providing insight into its organization and assembly. This is critical for a better understanding of the carbon fixation mechanism and toward repurposing carboxysomes in synthetic biology for biotechnological applications.
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Affiliation(s)
- Sasha L Evans
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Monsour M J Al-Hazeem
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daniel Mann
- Ernst-Ruska Centre 3, Forschungszentrum Jülich, Jülich, Germany
| | - Nicolas Smetacek
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Andrew J Beavil
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, 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, Shandong, China.
| | - Julien R C Bergeron
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK; Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK.
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48
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Ferlez BH, Kirst H, Greber BJ, Nogales E, Sutter M, Kerfeld CA. Heterologous Assembly of Pleomorphic Bacterial Microcompartment Shell Architectures Spanning the Nano- to Microscale. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2212065. [PMID: 36932732 PMCID: PMC10330516 DOI: 10.1002/adma.202212065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/09/2023] [Indexed: 06/09/2023]
Abstract
Many bacteria use protein-based organelles known as bacterial microcompartments (BMCs) to organize and sequester sequential enzymatic reactions. Regardless of their specialized metabolic function, all BMCs are delimited by a shell made of multiple structurally redundant, yet functionally diverse, hexameric (BMC-H), pseudohexameric/trimeric (BMC-T), or pentameric (BMC-P) shell protein paralogs. When expressed without their native cargo, shell proteins have been shown to self-assemble into 2D sheets, open-ended nanotubes, and closed shells of ≈40 nm diameter that are being developed as scaffolds and nanocontainers for applications in biotechnology. Here, by leveraging a strategy for affinity-based purification, it is demonstrated that a wide range of empty synthetic shells, many differing in end-cap structures, can be derived from a glycyl radical enzyme-associated microcompartment. The range of pleomorphic shells observed, which span ≈2 orders of magnitude in size from ≈25 nm to ≈1.8 µm, reveal the remarkable plasticity of BMC-based biomaterials. In addition, new capped nanotube and nanocone morphologies are observed that are consistent with a multicomponent geometric model in which architectural principles are shared among asymmetric carbon, viral protein, and BMC-based structures.
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Affiliation(s)
- Bryan H. Ferlez
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Henning Kirst
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Basil J. Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720, USA; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Markus Sutter
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Cheryl A. Kerfeld
- Environmental Genomics and Systems Biology and Molecular Biophysics and Integrative Bioimaging Divisions, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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49
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Occhialini A, Lenaghan SC. Plastid engineering using episomal DNA. PLANT CELL REPORTS 2023:10.1007/s00299-023-03020-x. [PMID: 37127835 DOI: 10.1007/s00299-023-03020-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/11/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Novel episomal systems have the potential to accelerate plastid genetic engineering for application in plant synthetic biology. Plastids represent valuable subcellular compartments for genetic engineering of plants with intrinsic advantages to engineering the nucleus. The ability to perform site-specific transgene integration by homologous recombination (HR), coordination of transgene expression in operons, and high production of heterologous proteins, all make plastids an attractive target for synthetic biology. Typically, plastid engineering is performed by homologous recombination; however, episomal-replicating vectors have the potential to accelerate the design/build/test cycles for plastid engineering. By accelerating the timeline from design to validation, it will be possible to generate translational breakthroughs in fields ranging from agriculture to biopharmaceuticals. Episomal-based plastid engineering will allow precise single step metabolic engineering in plants enabling the installation of complex synthetic circuits with the ambitious goal of reaching similar efficiency and flexibility of to the state-of-the-art genetic engineering of prokaryotic systems. The prospect to design novel episomal systems for production of transplastomic marker-free plants will also improve biosafety for eventual release in agriculture.
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Affiliation(s)
- Alessandro Occhialini
- Department of Plant Sciences, University of Tennessee, 112 Plant Biotechnology Building 2505 E J Chapman Drive, Knoxville, TN, 37996, USA.
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, 2640 Morgan Circle Drive, Knoxville, TN, 37996, USA.
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology (CASB), University of Tennessee, 2640 Morgan Circle Drive, Knoxville, TN, 37996, USA.
- Department of Food Science, University of Tennessee, 102 Food Safety and Processing Building 2600 River Dr., Knoxville, TN, 37996, USA.
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50
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Chen T, Hojka M, Davey P, Sun Y, Dykes GF, Zhou F, Lawson T, Nixon PJ, Lin Y, Liu LN. Engineering α-carboxysomes into plant chloroplasts to support autotrophic photosynthesis. Nat Commun 2023; 14:2118. [PMID: 37185249 PMCID: PMC10130085 DOI: 10.1038/s41467-023-37490-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 03/17/2023] [Indexed: 05/17/2023] Open
Abstract
The growth in world population, climate change, and resource scarcity necessitate a sustainable increase in crop productivity. Photosynthesis in major crops is limited by the inefficiency of the key CO2-fixing enzyme Rubisco, owing to its low carboxylation rate and poor ability to discriminate between CO2 and O2. In cyanobacteria and proteobacteria, carboxysomes function as the central CO2-fixing organelles that elevate CO2 levels around encapsulated Rubisco to enhance carboxylation. There is growing interest in engineering carboxysomes into crop chloroplasts as a potential route for improving photosynthesis and crop yields. Here, we generate morphologically correct carboxysomes in tobacco chloroplasts by transforming nine carboxysome genetic components derived from a proteobacterium. The chloroplast-expressed carboxysomes display a structural and functional integrity comparable to native carboxysomes and support autotrophic growth and photosynthesis of the transplastomic plants at elevated CO2. Our study provides proof-of-concept for a route to engineering fully functional CO2-fixing modules and entire CO2-concentrating mechanisms into chloroplasts to improve crop photosynthesis and productivity.
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Affiliation(s)
- Taiyu Chen
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Marta Hojka
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Philip Davey
- School of Life Sciences, University of Essex, Colchester, CO4 4SQ, UK
| | - Yaqi Sun
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Gregory F Dykes
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China
| | - Tracy Lawson
- School of Life Sciences, University of Essex, Colchester, CO4 4SQ, UK
| | - Peter J Nixon
- Department of Life Sciences, Sir Ernst Chain Building-Wolfson Laboratories, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China.
| | - 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, 266003, Qingdao, China.
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