1
|
Elfmann C, Zhu B, Stülke J, Halbedel S. ListiWiki: A database for the foodborne pathogen Listeria monocytogenes. Int J Med Microbiol 2023; 313:151591. [PMID: 38043216 DOI: 10.1016/j.ijmm.2023.151591] [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: 10/13/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023] Open
Abstract
Listeria monocytogenes is a Gram positive foodborne pathogen that regularly causes outbreaks of systemic infectious diseases. The bacterium maintains a facultative intracellular lifestyle; it thrives under a variety of environmental conditions and is able to infect human host cells. L. monocytogenes is genetically tractable and therefore has become an attractive model system to study the mechanisms employed by facultative intracellular bacteria to invade eukaryotic cells and to replicate in their cytoplasm. Besides its importance for basic research, L. monocytogenes also serves as a paradigmatic pathogen in genomic epidemiology, where the relative stability of its genome facilitates successful outbreak detection and elucidation of transmission chains in genomic pathogen surveillance systems. In both terms, it is necessary to keep the annotation of the L. monocytogenes genome up to date. Therefore, we have created the database ListiWiki (http://listiwiki.uni-goettingen.de/) which stores comprehensive information on the widely used L. monocytogenes reference strain EDG-e. ListiWiki is designed to collect information on genes, proteins and RNAs and their relevant functional characteristics, but also further information such as mutant phenotypes, available biological material, and publications. In its present form, ListiWiki combines the most recent annotation of the EDG-e genome with published data on gene essentiality, gene expression and subcellular protein localization. ListiWiki also predicts protein-protein interactions networks based on protein homology to Bacillus subtilis proteins, for which detailed interaction maps have been compiled in the sibling database SubtiWiki. Furthermore, crystallographic information of proteins is made accessible through integration of Protein Structure Database codes and AlphaFold structure predictions. ListiWiki is an easy-to-use web interface that has been developed with a focus on an intuitive access to all information. Use of ListiWiki is free of charge and its content can be edited by all members of the scientific community after registration. In our labs, ListiWiki has already become an important and easy to use tool to quickly access genome annotation details that we can keep updated with advancing knowledge. It also might be useful to promote the comprehensive understanding of the physiology and virulence of an important human pathogen.
Collapse
Affiliation(s)
- Christoph Elfmann
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Bingyao Zhu
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany.
| | - Sven Halbedel
- FG11 Division of Enteropathogenic bacteria and Legionella, Robert Koch Institute, Burgstrasse 37, 38855 Wernigerode, Germany; Institute for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany.
| |
Collapse
|
2
|
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: 10] [Impact Index Per Article: 10.0] [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.
Collapse
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
| |
Collapse
|
3
|
Wicke D, Meißner J, Warneke R, Elfmann C, Stülke J. Understudied proteins and understudied functions in the model bacterium Bacillus subtilis-A major challenge in current research. Mol Microbiol 2023. [PMID: 36882621 DOI: 10.1111/mmi.15053] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/28/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023]
Abstract
Model organisms such as the Gram-positive bacterium Bacillus subtilis have been studied intensively for decades. However, even for model organisms, no function has been identified for about one fourth of all proteins. It has recently been realized that such understudied proteins as well as poorly studied functions set a limitation to our understanding of the requirements for cellular life, and the Understudied Proteins Initiative has been launched. Of poorly studied proteins, those that are strongly expressed are likely to be important to the cell and should therefore be considered high priority in further studies. Since the functional analysis of unknown proteins can be extremely laborious, a minimal knowledge is required prior to targeted functional studies. In this review, we discuss strategies to obtain such a minimal annotation, for example, from global interaction, expression, or localization studies. We present a set of 41 highly expressed and poorly studied proteins of B. subtilis. Several of these proteins are thought or known to bind RNA and/or the ribosome, some may control the metabolism of B. subtilis, and another subset of particularly small proteins may act as regulatory elements to control the expression of downstream genes. Moreover, we discuss the challenges of poorly studied functions with a focus on RNA-binding proteins, amino acid transport, and the control of metabolic homeostasis. The identification of the functions of the selected proteins not only will strongly advance our knowledge on B. subtilis, but also on other organisms since many of the proteins are conserved in many groups of bacteria.
Collapse
Affiliation(s)
- Dennis Wicke
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| | - Janek Meißner
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| | - Robert Warneke
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| | - Christoph Elfmann
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg-August-University Göttingen, GZMB, Göttingen, Germany
| |
Collapse
|
4
|
Pelletier JF, Glass JI, Strychalski EA. Cellular mechanics during division of a genomically minimal cell. Trends Cell Biol 2022; 32:900-907. [PMID: 35907702 DOI: 10.1016/j.tcb.2022.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 01/21/2023]
Abstract
Genomically minimal cells, such as JCVI-syn3.0 and JCVI-syn3A, offer an empowering framework to study relationships between genotype and phenotype. With a polygenic basis, the fundamental physiological process of cell division depends on multiple genes of known and unknown function in JCVI-syn3A. A physical description of cellular mechanics can further understanding of the contributions of genes to cell division in this genomically minimal context. We review current knowledge on genes in JCVI-syn3A contributing to two physical parameters relevant to cell division, namely, the surface-area-to-volume ratio and membrane curvature. This physical view of JCVI-syn3A may inform the attribution of gene functions and conserved processes in bacterial physiology, as well as whole-cell models and the engineering of synthetic cells.
Collapse
Affiliation(s)
- James F Pelletier
- Centro Nacional de Biotecnología, 28049 Madrid, Spain; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John I Glass
- J. Craig Venter Institute, La Jolla, CA 92037, USA
| | | |
Collapse
|
5
|
Bianchi D, Pelletier JF, Hutchison CA, Glass JI, Luthey-Schulten Z. Toward the Complete Functional Characterization of a Minimal Bacterial Proteome. J Phys Chem B 2022; 126:6820-6834. [PMID: 36048731 PMCID: PMC9483919 DOI: 10.1021/acs.jpcb.2c04188] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/10/2022] [Indexed: 11/29/2022]
Abstract
Recently, we presented a whole-cell kinetic model of the genetically minimal bacterium JCVI-syn3A that described the coupled metabolic and genetic information processes and predicted behaviors emerging from the interactions among these networks. JCVI-syn3A is a genetically reduced bacterial cell that has the fewest number and smallest fraction of genes of unclear function, with approximately 90 of its 452 protein-coding genes (that is less than 20%) unannotated. Further characterization of unclear JCVI-syn3A genes strengthens the robustness and predictive power of cell modeling efforts and can lead to a deeper understanding of biophysical processes and pathways at the cell scale. Here, we apply computational analyses to elucidate the functions of the products of several essential but previously uncharacterized genes involved in integral cellular processes, particularly those directly affecting cell growth, division, and morphology. We also suggest directed wet-lab experiments informed by our analyses to further understand these "missing puzzle pieces" that are an essential part of the mosaic of biological interactions present in JCVI-syn3A. Our workflow leverages evolutionary sequence analysis, protein structure prediction, interactomics, and genome architecture to determine upgraded annotations. Additionally, we apply the structure prediction analysis component of our work to all 452 protein coding genes in JCVI-syn3A to expedite future functional annotation studies as well as the inverse mapping of the cell state to more physical models requiring all-atom or coarse-grained representations for all JCVI-syn3A proteins.
Collapse
Affiliation(s)
- David
M. Bianchi
- Department
of Chemistry, University of Illinois Urbana−Champaign, 600 S Mathews Ave, Urbana, Illinois 61801, United States
| | - James F. Pelletier
- Centro
Nacional de Biotecnologia, Calle Darwin no. 3, 28049 Madrid, Spain
| | - Clyde A. Hutchison
- J.
Craig Venter Institute, 4120 Capricorn Ln. La Jolla, California 92037, United States
| | - John I. Glass
- J.
Craig Venter Institute, 4120 Capricorn Ln. La Jolla, California 92037, United States
| | - Zaida Luthey-Schulten
- Department
of Chemistry, University of Illinois Urbana−Champaign, 600 S Mathews Ave, Urbana, Illinois 61801, United States
| |
Collapse
|
6
|
Elfmann C, Zhu B, Pedreira T, Hoßbach B, Lluch-Senar M, Serrano L, Stülke J. MycoWiki: Functional annotation of the minimal model organism Mycoplasma pneumoniae. Front Microbiol 2022; 13:935066. [PMID: 35958127 PMCID: PMC9358437 DOI: 10.3389/fmicb.2022.935066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
The human pathogen Mycoplasma pneumoniae is viable independently from host cells or organisms, despite its strongly reduced genome with only about 700 protein-coding genes. The investigation of M. pneumoniae can therefore help to obtain general insights concerning the basic requirements for cellular life. Accordingly, M. pneumoniae has become a model organism for systems biology in the past decade. To support the investigation of the components of this minimal bacterium, we have generated the database MycoWiki. (http://mycowiki.uni-goettingen.de) MycoWiki organizes data under a relational database and provides access to curated and state-of-the-art information on the genes and proteins of M. pneumoniae. Interestingly, M. pneumoniae has undergone an evolution that resulted in the limited similarity of many proteins to proteins of model organisms. To facilitate the analysis of the functions of M. pneumoniae proteins, we have integrated structure predictions from the AlphaFold Protein Structure Database for most proteins, structural information resulting from in vivo cross-linking, and protein-protein interactions based on a global in vivo study. MycoWiki is an important tool for the systems and synthetic biology community that will support the comprehensive understanding of a minimal organism and the functional annotation of so far uncharacterized proteins.
Collapse
Affiliation(s)
- Christoph Elfmann
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Bingyao Zhu
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Tiago Pedreira
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Ben Hoßbach
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Maria Lluch-Senar
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Luis Serrano
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jörg Stülke
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| |
Collapse
|
7
|
Hill V, Akarsu H, Barbarroja RS, Cippà VL, Kuhnert P, Heller M, Falquet L, Heller M, Stoffel MH, Labroussaa F, Jores J. Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems. PLoS Genet 2021; 17:e1009365. [PMID: 34673769 PMCID: PMC8562856 DOI: 10.1371/journal.pgen.1009365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 11/02/2021] [Accepted: 09/29/2021] [Indexed: 11/19/2022] Open
Abstract
Mycoplasmas are minute bacteria controlled by very small genomes ranging from 0.6 to 1.4 Mbp. They encompass several important medical and veterinary pathogens that are often associated with a wide range of chronic diseases. The long persistence of mycoplasma cells in their hosts can exacerbate the spread of antimicrobial resistance observed for many species. However, the nature of the virulence factors driving this phenomenon in mycoplasmas is still unclear. Toxin-antitoxin systems (TA systems) are genetic elements widespread in many bacteria that were historically associated with bacterial persistence. Their presence on mycoplasma genomes has never been carefully assessed, especially for pathogenic species. Here we investigated three candidate TA systems in M. mycoides subsp. capri encoding a (i) novel AAA-ATPase/subtilisin-like serine protease module, (ii) a putative AbiEii/AbiEi pair and (iii) a putative Fic/RelB pair. We sequence analyzed fourteen genomes of M. mycoides subsp. capri and confirmed the presence of at least one TA module in each of them. Interestingly, horizontal gene transfer signatures were also found in several genomic loci containing TA systems for several mycoplasma species. Transcriptomic and proteomic data confirmed differential expression profiles of these TA systems during mycoplasma growth in vitro. While the use of heterologous expression systems based on E. coli and B. subtilis showed clear limitations, the functionality and neutralization capacities of all three candidate TA systems were successfully confirmed using M. capricolum subsp. capricolum as a host. Additionally, M. capricolum subsp. capricolum was used to confirm the presence of functional TA system homologs in mycoplasmas of the Hominis and Pneumoniae phylogenetic groups. Finally, we showed that several of these M. mycoides subsp. capri toxins tested in this study, and particularly the subtilisin-like serine protease, could be used to establish a kill switch in mycoplasmas for industrial applications.
Collapse
Affiliation(s)
- Virginia Hill
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Hatice Akarsu
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | | | - Valentina L. Cippà
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Martin Heller
- Friedrich-Loeffler-Institute—Federal Research Institute for Animal Health, Jena, Germany
| | - Laurent Falquet
- Biochemistry Unit, University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michael H. Stoffel
- Division of Veterinary Anatomy, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland
- * E-mail:
| |
Collapse
|