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Justice I, Kiesel P, Safronova N, von Appen A, Saenz JP. A tuneable minimal cell membrane reveals that two lipid species suffice for life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.24.563757. [PMID: 39464110 PMCID: PMC11507672 DOI: 10.1101/2023.10.24.563757] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
All cells are encapsulated by a lipid membrane which facilitates the interaction between life and its environment. How life exploits the diverse mixtures of lipids that dictate membrane property and function has been experimentally challenging to address. We introduce an approach to tune and minimize lipidomes in Mycoplasma mycoides and the Minimal Cell (JCVI-Syn3A) revealing that a 2-component lipidome can support life. Systematically reintroducing phospholipid features demonstrated that acyl chain diversity is more critical for growth than head group diversity. By tuning lipid chirality, we explored the lipid divide between Archaea and the rest of life, showing that ancestral lipidomes could have been heterochiral. Our approach offers a tunable minimal membrane system to explore the fundamental lipidomic requirements for life, thereby extending the concept of minimal life from the genome to the lipidome.
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Affiliation(s)
- Isaac Justice
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | - Petra Kiesel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 107, 01307 Dresden
| | - Nataliya Safronova
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
| | - Alexander von Appen
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 107, 01307 Dresden
| | - James P. Saenz
- Technische Universität Dresden, B CUBE Center for Molecular Bioengineering, 01307 Dresden, Germany
- Technische Universität Dresden, Faculty of Medicine, Dresden 01307, Germany
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2
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Safronova N, Junghans L, Saenz JP. Temperature change elicits lipidome adaptation in the simple organisms Mycoplasma mycoides and JCVI-syn3B. Cell Rep 2024; 43:114435. [PMID: 38985673 DOI: 10.1016/j.celrep.2024.114435] [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: 11/27/2023] [Revised: 04/05/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
Cell membranes mediate interactions between life and its environment, with lipids determining their properties. Understanding how cells adjust their lipidomes to tune membrane properties is crucial yet poorly defined due to the complexity of most organisms. We used quantitative shotgun lipidomics to study temperature adaptation in the simple organism Mycoplasma mycoides and the minimal cell JCVI-syn3B. We show that lipid abundances follow a universal logarithmic distribution across eukaryotes and bacteria, with comparable degrees of lipid remodeling for adaptation regardless of lipidomic or organismal complexity. Lipid features analysis demonstrates head-group-specific acyl chain remodeling as characteristic of lipidome adaptation; its deficiency in Syn3B is associated with impaired homeoviscous adaptation. Temporal analysis reveals a two-stage cold adaptation process: swift cholesterol and cardiolipin shifts followed by gradual acyl chain modifications. This work provides an in-depth analysis of lipidome adaptation in minimal cells, laying a foundation to probe the design principles of living membranes.
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Affiliation(s)
- Nataliya Safronova
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - Lisa Junghans
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany
| | - James P Saenz
- B CUBE Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany; Faculty of Medicine, Technische Universität Dresden, 01062 Dresden, Germany.
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3
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Autin L, Goodsell DS, Viola I, Olson A. CellVis2: a conference on visualizing the molecular cell. Trends Biochem Sci 2024; 49:559-563. [PMID: 38670884 DOI: 10.1016/j.tibs.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024]
Abstract
In January 2024, a targeted conference, 'CellVis2', was held at Scripps Research in La Jolla, USA, the second in a series designed to explore the promise, practices, roadblocks, and prospects of creating, visualizing, sharing, and communicating physical representations of entire biological cells at scales down to the atom.
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Affiliation(s)
| | | | - Ivan Viola
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Arthur Olson
- The Scripps Research Institute, La Jolla, CA, USA.
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4
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Jouan R, Lextrait G, Lachat J, Yokota A, Cossard R, Naquin D, Timchenko T, Kikuchi Y, Ohbayashi T, Mergaert P. Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont Caballeronia insecticola. ISME COMMUNICATIONS 2024; 4:ycad001. [PMID: 38282642 PMCID: PMC10809759 DOI: 10.1093/ismeco/ycad001] [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: 09/06/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/30/2024]
Abstract
Caballeronia insecticola is a bacterium belonging to the Burkholderia genus sensu lato, which is able to colonize multiple environments like soils and the gut of the bean bug Riptortus pedestris. We constructed a saturated Himar1 mariner transposon library and revealed by transposon-sequencing that 498 protein-coding genes constitute the essential genome of Caballeronia insecticola for growth in free-living conditions. By comparing essential gene sets of Caballeronia insecticola and seven related Burkholderia s.l. strains, only 120 common genes were identified, indicating that a large part of the essential genome is strain-specific. In order to reproduce specific nutritional conditions that are present in the gut of Riptortus pedestris, we grew the mutant library in minimal media supplemented with candidate gut nutrients and identified several condition-dependent fitness-defect genes by transposon-sequencing. To validate the robustness of the approach, insertion mutants in six fitness genes were constructed and their growth deficiency in media supplemented with the corresponding nutrient was confirmed. The mutants were further tested for their efficiency in Riptortus pedestris gut colonization, confirming that gluconeogenic carbon sources, taurine and inositol, are nutrients consumed by the symbiont in the gut. Thus, our study provides insights about specific contributions provided by the insect host to the bacterial symbiont.
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Grants
- JSPS Research Fellowship for Young Scientists, Japan
- Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan
- Ministry of Higher Education, Research, and Innovation, France
- CNRS International Research Project, France
- JSPS-CNRS Bilateral Open Partnership Joint Research Project, France-Japan
- Agence Nationale de la Recherche, France
- Saclay Plant Sciences-SPS
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Affiliation(s)
- Romain Jouan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Gaëlle Lextrait
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Joy Lachat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Aya Yokota
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Raynald Cossard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Tatiana Timchenko
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, Sapporo 062-8517, Japan
| | - Tsubasa Ohbayashi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8604, Japan
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
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5
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Moger-Reischer RZ, Glass JI, Wise KS, Sun L, Bittencourt DMC, Lehmkuhl BK, Schoolmaster DR, Lynch M, Lennon JT. Evolution of a minimal cell. Nature 2023; 620:122-127. [PMID: 37407813 PMCID: PMC10396959 DOI: 10.1038/s41586-023-06288-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/06/2023] [Indexed: 07/07/2023]
Abstract
Possessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life1,2. Here we report on how an engineered minimal cell3,4 contends with the forces of evolution compared with the Mycoplasma mycoides non-minimal cell from which it was synthetically derived. Mutation rates were the highest among all reported bacteria, but were not affected by genome minimization. Genome streamlining was costly, leading to a decrease in fitness of greater than 50%, but this deficit was regained during 2,000 generations of evolution. Despite selection acting on distinct genetic targets, increases in the maximum growth rate of the synthetic cells were comparable. Moreover, when performance was assessed by relative fitness, the minimal cell evolved 39% faster than the non-minimal cell. The only apparent constraint involved the evolution of cell size. The size of the non-minimal cell increased by 80%, whereas the minimal cell remained the same. This pattern reflected epistatic effects of mutations in ftsZ, which encodes a tubulin-homologue protein that regulates cell division and morphology5,6. Our findings demonstrate that natural selection can rapidly increase the fitness of one of the simplest autonomously growing organisms. Understanding how species with small genomes overcome evolutionary challenges provides critical insights into the persistence of host-associated endosymbionts, the stability of streamlined chassis for biotechnology and the targeted refinement of synthetically engineered cells2,7-9.
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Affiliation(s)
| | - J I Glass
- J. Craig Venter Institute, La Jolla, CA, USA
| | - K S Wise
- J. Craig Venter Institute, La Jolla, CA, USA
| | - L Sun
- J. Craig Venter Institute, La Jolla, CA, USA
- Novartis Gene Therapy, San Diego, CA, USA
| | - D M C Bittencourt
- J. Craig Venter Institute, La Jolla, CA, USA
- Embrapa Genetic Resources and Biotechnology, National Institute of Science and Technology in Synthetic Biology, Brasília, Brazil
| | - B K Lehmkuhl
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - D R Schoolmaster
- US Geological Survey, Wetland and Aquatic Research Center, Lafayette, LA, USA
| | - M Lynch
- Arizona State University, Tempe, AZ, USA
| | - J T Lennon
- Department of Biology, Indiana University, Bloomington, IN, USA.
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6
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Sakai A, Jonker AJ, Nelissen FHT, Kalb EM, van Sluijs B, Heus HA, Adamala KP, Glass JI, Huck WTS. Cell-Free Expression System Derived from a Near-Minimal Synthetic Bacterium. ACS Synth Biol 2023; 12:1616-1623. [PMID: 37278603 PMCID: PMC10278164 DOI: 10.1021/acssynbio.3c00114] [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: 02/22/2023] [Indexed: 06/07/2023]
Abstract
Cell-free expression (CFE) systems are fundamental to reconstituting metabolic pathways in vitro toward the construction of a synthetic cell. Although an Escherichia coli-based CFE system is well-established, simpler model organisms are necessary to understand the principles behind life-like behavior. Here, we report the successful creation of a CFE system derived from JCVI-syn3A (Syn3A), the minimal synthetic bacterium. Previously, high ribonuclease activity in Syn3A lysates impeded the establishment of functional CFE systems. Now, we describe how an unusual cell lysis method (nitrogen decompression) yielded Syn3A lysates with reduced ribonuclease activity that supported in vitro expression. To improve the protein yields in the Syn3A CFE system, we optimized the Syn3A CFE reaction mixture using an active machine learning tool. The optimized reaction mixture improved the CFE 3.2-fold compared to the preoptimized condition. This is the first report of a functional CFE system derived from a minimal synthetic bacterium, enabling further advances in bottom-up synthetic biology.
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Affiliation(s)
- Andrei Sakai
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Aafke J. Jonker
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Frank H. T. Nelissen
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Evan M. Kalb
- Department
of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Bob van Sluijs
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Hans A. Heus
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - John I. Glass
- Synthetic
Biology & Bioenergy, J. Craig Venter
Institute, La Jolla, California 92037, United States
| | - Wilhelm T. S. Huck
- Institute
for Molecules and Materials, Radboud University, Nijmegen 6525AJ, The Netherlands
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7
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Bailoni E, Partipilo M, Coenradij J, Grundel DAJ, Slotboom DJ, Poolman B. Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective. ACS Synth Biol 2023; 12:922-946. [PMID: 37027340 PMCID: PMC10127287 DOI: 10.1021/acssynbio.3c00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 04/08/2023]
Abstract
Life-like systems need to maintain a basal metabolism, which includes importing a variety of building blocks required for macromolecule synthesis, exporting dead-end products, and recycling cofactors and metabolic intermediates, while maintaining steady internal physical and chemical conditions (physicochemical homeostasis). A compartment, such as a unilamellar vesicle, functionalized with membrane-embedded transport proteins and metabolic enzymes encapsulated in the lumen meets these requirements. Here, we identify four modules designed for a minimal metabolism in a synthetic cell with a lipid bilayer boundary: energy provision and conversion, physicochemical homeostasis, metabolite transport, and membrane expansion. We review design strategies that can be used to fulfill these functions with a focus on the lipid and membrane protein composition of a cell. We compare our bottom-up design with the equivalent essential modules of JCVI-syn3a, a top-down genome-minimized living cell with a size comparable to that of large unilamellar vesicles. Finally, we discuss the bottlenecks related to the insertion of a complex mixture of membrane proteins into lipid bilayers and provide a semiquantitative estimate of the relative surface area and lipid-to-protein mass ratios (i.e., the minimal number of membrane proteins) that are required for the construction of a synthetic cell.
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Affiliation(s)
- Eleonora Bailoni
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Michele Partipilo
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Jelmer Coenradij
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Douwe A. J. Grundel
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Dirk J. Slotboom
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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8
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Zhang H, Xiong Y, Xiao W, Wu Y. Investigation of Genome Biology by Synthetic Genome Engineering. Bioengineering (Basel) 2023; 10:271. [PMID: 36829765 PMCID: PMC9952402 DOI: 10.3390/bioengineering10020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Synthetic genomes were designed based on an understanding of natural genomic information, offering an opportunity to engineer and investigate biological systems on a genome-wide scale. Currently, the designer version of the M. mycoides genome and the E. coli genome, as well as most of the S. cerevisiae genome, have been synthesized, and through the cycles of design-build-test and the following engineering of synthetic genomes, many fundamental questions of genome biology have been investigated. In this review, we summarize the use of synthetic genome engineering to explore the structure and function of genomes, and highlight the unique values of synthetic genomics.
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Affiliation(s)
- Hui Zhang
- 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
| | - Yao Xiong
- 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
| | - Wenhai Xiao
- 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
| | - Yi Wu
- 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
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Stevens JA, Grünewald F, van Tilburg PAM, König M, Gilbert BR, Brier TA, Thornburg ZR, Luthey-Schulten Z, Marrink SJ. Molecular dynamics simulation of an entire cell. Front Chem 2023; 11:1106495. [PMID: 36742032 PMCID: PMC9889929 DOI: 10.3389/fchem.2023.1106495] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell's components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge. In this perspective, we show how an integrative approach can be employed to model an entire cell, the minimal cell, JCVI-syn3A, at full complexity. This step opens the way to interrogate the cell's spatio-temporal evolution with molecular dynamics simulations, an approach that can be extended to other cell types in the near future.
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Affiliation(s)
- Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - P. A. Marco van Tilburg
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Melanie König
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Champaign, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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