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Warneke R, Herzberg C, Daniel R, Hormes B, Stülke J. Control of three-carbon amino acid homeostasis by promiscuous importers and exporters in Bacillus subtilis: role of the "sleeping beauty" amino acid exporters. mBio 2024; 15:e0345623. [PMID: 38470260 PMCID: PMC11005379 DOI: 10.1128/mbio.03456-23] [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: 12/19/2023] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
The Gram-positive model bacterium Bacillus subtilis can acquire amino acids by import, de novo biosynthesis, or degradation of proteins and peptides. The accumulation of several amino acids inhibits the growth of B. subtilis, probably due to misincorporation into cellular macromolecules such as proteins or peptidoglycan or due to interference with other amino acid biosynthetic pathways. Here, we studied the adaptation of B. subtilis to toxic concentrations of the three-carbon amino acids L-alanine, β-alanine, and 2,3-diaminopropionic acid, as well as the two-carbon amino acid glycine. Resistance to the non-proteinogenic amino acid β-alanine, which is a precursor for coenzyme A biosynthesis, is achieved by mutations that either activate a cryptic amino acid exporter, AexA (previously YdeD), or inactivate the amino acid importers AimA, AimB (previously YbxG), and BcaP. The aexA gene is very poorly expressed under most conditions studied. However, mutations affecting the transcription factor AerA (previously YdeC) can result in strong constitutive aexA expression. AexA is the first characterized member of a group of amino acid exporters in B. subtilis, which are all very poorly expressed. Therefore, we suggest to call this group "sleeping beauty amino acid exporters." 2,3-Diaminopropionic acid can also be exported by AexA, and this amino acid also seems to be a natural substrate of AerA/AexA, as it can cause a slight but significant induction of aexA expression, and AexA also provides some natural resistance toward 2,3-diaminopropionic acid. Moreover, our work shows how low-specificity amino acid transporters contribute to amino acid homeostasis in B. subtilis.IMPORTANCEEven though Bacillus subtilis is one of the most-studied bacteria, amino acid homeostasis in this organism is not fully understood. We have identified import and export systems for the C2 and C3 amino acids. Our work demonstrates that the responsible amino acid permeases contribute in a rather promiscuitive way to amino acid uptake. In addition, we have discovered AexA, the first member of a group of very poorly expressed amino acid exporters in B. subtilis that we call "sleeping beauty amino acid exporters." The expression of these transporters is typically triggered by mutations in corresponding regulator genes that are acquired upon exposure to toxic amino acids. These exporters are ubiquitous in all domains of life. It is tempting to speculate that many of them are not expressed until the cells experience selective pressure by toxic compounds, and they protect the cells from rare but potentially dangerous encounters with such compounds.
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Affiliation(s)
- Robert Warneke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University, Göttingen, Germany
| | - Christina Herzberg
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University, Göttingen, Germany
| | - Richard Daniel
- Center for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Björn Hormes
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University, Göttingen, Germany
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Öktem A, Pranoto DA, van Dijl JM. Post-translational secretion stress regulation in Bacillus subtilis is controlled by intra- and extracellular proteases. N Biotechnol 2024; 79:71-81. [PMID: 38158017 DOI: 10.1016/j.nbt.2023.12.009] [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: 10/26/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The Gram-positive bacterium Bacillus subtilis is a prolific producer of industrial enzymes that are effectively harvested from the fermentation broth. However, the high capacity of B. subtilis for protein secretion has so far not been exploited to the full due to particular bottlenecks, including product degradation by extracellular proteases and counterproductive secretion stress responses. To unlock the Bacillus secretion pathway for difficult-to-produce proteins, various cellular interventions have been explored, including genome engineering. Our previous research has shown a superior performance of genome-reduced B. subtilis strains in the production of staphylococcal antigens compared to the parental strain 168. This was attributed, at least in part, to redirected secretion stress responses, including the presentation of elevated levels of the quality control proteases HtrA and HtrB that also catalyse protein folding. Here we show that this relates to the elimination of two homologous serine proteases, namely the cytosolic protease AprX and the extracellular protease AprE. This unprecedented posttranslational regulation of secretion stress effectors, like HtrA and HtrB, by the concerted action of cytosolic and extracellular proteases has important implications for the biotechnological application of microbial cell factories. In B. subtilis, this conclusion is underscored by extracellular degradation of the staphylococcal antigen IsaA by both AprX and AprE. Extracellular activity of the cytosolic protease AprX is remarkable since it shows that not only extracellular, but also intracellular proteases impact extracellular product levels. We therefore conclude that intracellular proteases represent new targets for improved recombinant protein production in microbial cell factories like B. subtilis.
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Affiliation(s)
- Ayşegül Öktem
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Dicky A Pranoto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands.
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Put H, Gerstmans H, Vande Capelle H, Fauvart M, Michiels J, Masschelein J. Bacillus subtilis as a host for natural product discovery and engineering of biosynthetic gene clusters. Nat Prod Rep 2024. [PMID: 38465694 DOI: 10.1039/d3np00065f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Covering: up to October 2023Many bioactive natural products are synthesized by microorganisms that are either difficult or impossible to cultivate under laboratory conditions, or that produce only small amounts of the desired compound. By transferring biosynthetic gene clusters (BGCs) into alternative host organisms that are more easily cultured and engineered, larger quantities can be obtained and new analogues with potentially improved biological activity or other desirable properties can be generated. Moreover, expression of cryptic BGCs in a suitable host can facilitate the identification and characterization of novel natural products. Heterologous expression therefore represents a valuable tool for natural product discovery and engineering as it allows the study and manipulation of their biosynthetic pathways in a controlled setting, enabling innovative applications. Bacillus is a genus of Gram-positive bacteria that is widely used in industrial biotechnology as a host for the production of proteins from diverse origins, including enzymes and vaccines. However, despite numerous successful examples, Bacillus species remain underexploited as heterologous hosts for the expression of natural product BGCs. Here, we review important advantages that Bacillus species offer as expression hosts, such as high secretion capacity, natural competence for DNA uptake, and the increasing availability of a wide range of genetic tools for gene expression and strain engineering. We evaluate different strain optimization strategies and other critical factors that have improved the success and efficiency of heterologous natural product biosynthesis in B. subtilis. Finally, future perspectives for using B. subtilis as a heterologous host are discussed, identifying research gaps and promising areas that require further exploration.
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Affiliation(s)
- Hanne Put
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Hans Gerstmans
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
- Biosensors Group, KU Leuven, 3001 Leuven, Belgium
| | - Hanne Vande Capelle
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- imec, 3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven, 3001 Leuven, Belgium
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
| | - Joleen Masschelein
- VIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, 3001 Leuven, Belgium.
- Laboratory for Biomolecular Discovery & Engineering, KU Leuven, 3001 Leuven, Belgium
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Meißner J, Königshof M, Wrede K, Warneke R, Mardoukhi MSY, Commichau FM, Stülke J. Control of asparagine homeostasis in Bacillus subtilis: identification of promiscuous amino acid importers and exporters. J Bacteriol 2024; 206:e0042023. [PMID: 38193659 PMCID: PMC10882977 DOI: 10.1128/jb.00420-23] [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: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
The Gram-positive model bacterium B. subtilis is able to import all proteinogenic amino acids from the environment as well as to synthesize them. However, the players involved in the acquisition of asparagine have not yet been identified for this bacterium. In this work, we used d-asparagine as a toxic analog of l-asparagine to identify asparagine transporters. This revealed that d- but not l-asparagine is taken up by the malate/lactate antiporter MleN. Specific strains that are sensitive to the presence of l-asparagine due to the lack of the second messenger cyclic di-AMP or due to the intracellular accumulation of this amino acid were used to isolate and characterize suppressor mutants that were resistant to the presence of otherwise growth-inhibiting concentrations of l-asparagine. These screens identified the broad-spectrum amino acid importers AimA and BcaP as responsible for the acquisition of l-asparagine. The amino acid exporter AzlCD allows detoxification of l-asparagine in addition to 4-azaleucine and histidine. This work supports the idea that amino acids are often transported by promiscuous importers and exporters. However, our work also shows that even stereo-enantiomeric amino acids do not necessarily use the same transport systems.IMPORTANCETransport of amino acid is a poorly studied function in many bacteria, including the model organism Bacillus subtilis. The identification of transporters is hampered by the redundancy of transport systems for most amino acids as well as by the poor specificity of the transporters. Here, we apply several strategies to use the growth-inhibitive effect of many amino acids under defined conditions to isolate suppressor mutants that exhibit either reduced uptake or enhanced export of asparagine, resulting in the identification of uptake and export systems for l-asparagine. The approaches used here may be useful for the identification of transporters for other amino acids both in B. subtilis and in other bacteria.
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Affiliation(s)
- Janek Meißner
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Manuel Königshof
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Katrin Wrede
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Robert Warneke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Fabian M. Commichau
- FG Molecular Microbiology, Institute for Biology, University of Hohenheim, Stuttgart, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology & Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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Stülke J, Grüppen A, Bramkamp M, Pelzer S. Bacillus subtilis, a Swiss Army Knife in Science and Biotechnology. J Bacteriol 2023; 205:e0010223. [PMID: 37140386 PMCID: PMC10210981 DOI: 10.1128/jb.00102-23] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Next to Escherichia coli, Bacillus subtilis is the most studied and best understood organism that also serves as a model for many important pathogens. Due to its ability to form heat-resistant spores that can germinate even after very long periods of time, B. subtilis has attracted much scientific interest. Another feature of B. subtilis is its genetic competence, a developmental state in which B. subtilis actively takes up exogenous DNA. This makes B. subtilis amenable to genetic manipulation and investigation. The bacterium was one of the first with a fully sequenced genome, and it has been subject to a wide variety of genome- and proteome-wide studies that give important insights into many aspects of the biology of B. subtilis. Due to its ability to secrete large amounts of proteins and to produce a wide range of commercially interesting compounds, B. subtilis has become a major workhorse in biotechnology. Here, we review the development of important aspects of the research on B. subtilis with a specific focus on its cell biology and biotechnological and practical applications from vitamin production to concrete healing. The intriguing complexity of the developmental programs of B. subtilis, paired with the availability of sophisticated tools for genetic manipulation, positions it at the leading edge for discovering new biological concepts and deepening our understanding of the organization of bacterial cells.
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Affiliation(s)
- Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | | | - Marc Bramkamp
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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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.
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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
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Abstract
Living systems are built from a small subset of the atomic elements, including the bulk macronutrients (C,H,N,O,P,S) and ions (Mg,K,Na,Ca) together with a small but variable set of trace elements (micronutrients). Here, we provide a global survey of how chemical elements contribute to life. We define five classes of elements: those that are (i) essential for all life, (ii) essential for many organisms in all three domains of life, (iii) essential or beneficial for many organisms in at least one domain, (iv) beneficial to at least some species, and (v) of no known beneficial use. The ability of cells to sustain life when individual elements are absent or limiting relies on complex physiological and evolutionary mechanisms (elemental economy). This survey of elemental use across the tree of life is encapsulated in a web-based, interactive periodic table that summarizes the roles chemical elements in biology and highlights corresponding mechanisms of elemental economy.
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Affiliation(s)
- Kaleigh A Remick
- Department of Microbiology, Cornell University, New York, NY, United States
| | - John D Helmann
- Department of Microbiology, Cornell University, New York, NY, United States.
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How To Deal with Toxic Amino Acids: the Bipartite AzlCD Complex Exports Histidine in Bacillus subtilis. J Bacteriol 2022; 204:e0035322. [PMID: 36377869 PMCID: PMC9765041 DOI: 10.1128/jb.00353-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The Gram-positive model bacterium Bacillus subtilis can use several amino acids as sources of carbon and nitrogen. However, some amino acids inhibit the growth of this bacterium. This amino acid toxicity is often enhanced in strains lacking the second messenger cyclic dimeric adenosine 3',5'-monophosphate (c-di-AMP). We observed that the presence of histidine is also toxic for a B. subtilis strain that lacks all three c-di-AMP synthesizing enzymes. However, suppressor mutants emerged, and whole-genome sequencing revealed mutations in the azlB gene that encode the repressor of the azl operon. This operon encodes an exporter and an importer for branched-chain amino acids. The suppressor mutations result in an overexpression of the azl operon. Deletion of the azlCD genes encoding the branched-chain amino acid exporter restored the toxicity of histidine, indicating that this exporter is required for histidine export and for resistance to otherwise toxic levels of the amino acid. The higher abundance of the amino acid exporter AzlCD increased the extracellular concentration of histidine, thus confirming the new function of AzlCD as a histidine exporter. Unexpectedly, the AzlB-mediated repression of the operon remains active even in the presence of amino acids, suggesting that the expression of the azl operon requires the mutational inactivation of AzlB. IMPORTANCE Amino acids are building blocks for protein biosynthesis in each living cell. However, due to their reactivity and the similarity between several amino acids, they may also be involved in harmful reactions or in noncognate interactions and thus may be toxic. Bacillus subtilis can deal with otherwise toxic histidine by overexpressing the bipartite amino acid exporter AzlCD. Although encoded in an operon that also contains a gene for an amino acid importer, the corresponding genes are not expressed, irrespective of the availability of amino acids in the medium. This suggests that the azl operon is a last resort by which to deal with histidine stress that can be expressed due to the mutational inactivation of the cognate repressor AzlB.
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Sakai A, Deich CR, Nelissen FHT, Jonker AJ, Bittencourt DMDC, Kempes CP, Wise KS, Heus HA, Huck WTS, Adamala KP, Glass JI. Traditional Protocols and Optimization Methods Lead to Absent Expression in a Mycoplasma Cell-Free Gene Expression Platform. Synth Biol (Oxf) 2022; 7:ysac008. [PMID: 35774105 PMCID: PMC9239315 DOI: 10.1093/synbio/ysac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 04/11/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Cell-free expression (CFE) systems are one of the main platforms for building synthetic cells. A major drawback is the orthogonality of cell-free systems across species. To generate a CFE system compatible with recently established minimal cell constructs, we attempted to optimize a Mycoplasma bacterium-based CFE system using lysates of the genome-minimized cell JCVI-syn3A (Syn3A) and its close phylogenetic relative Mycoplasma capricolum (Mcap). To produce mycoplasma-derived crude lysates, we systematically tested methods commonly used for bacteria, based on the S30 protocol of Escherichia coli. Unexpectedly, after numerous attempts to optimize lysate production methods or composition of feeding buffer, none of the Mcap or Syn3A lysates supported cell-free gene expression. Only modest levels of in vitro transcription of RNA aptamers were observed. While our experimental systems were intended to perform transcription and translation, our assays focused on RNA. Further investigations identified persistently high ribonuclease (RNase) activity in all lysates, despite removal of recognizable nucleases from the respective genomes and attempts to inhibit nuclease activities in assorted CFE preparations. An alternative method using digitonin to permeabilize the mycoplasma cell membrane produced a lysate with diminished RNase activity yet still was unable to support cell-free gene expression. We found that intact mycoplasma cells poisoned E. coli cell-free extracts by degrading ribosomal RNAs, indicating that the mycoplasma cells, even the minimal cell, have a surface-associated RNase activity. However, it is not clear which gene encodes the RNase. This work summarizes attempts to produce mycoplasma-based CFE and serves as a cautionary tale for researchers entering this field.
Graphical Abstract
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Affiliation(s)
- Andrei Sakai
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Christopher R Deich
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Aafke J Jonker
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Daniela M de C Bittencourt
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
- Embrapa Genetic Resources and Biotechnology/National Institute of Science and Technology - Synthetic Biology, Parque Estação Biológica, PqEB, Av. W5 Norte (final), Brasília, DF, 70770-917, Brazil, Norte (final), Brasília, DF, 70770-917, Brazil
| | | | - Kim S Wise
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - John I Glass
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
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Redirected Stress Responses in a Genome-Minimized 'midi Bacillus' Strain with Enhanced Capacity for Protein Secretion. mSystems 2021; 6:e0065521. [PMID: 34904864 PMCID: PMC8670375 DOI: 10.1128/msystems.00655-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Genome engineering offers the possibility to create completely novel cell factories with enhanced properties for biotechnological applications. In recent years, genome minimization was extensively explored in the Gram-positive bacterial cell factory Bacillus subtilis, where up to 42% of the genome encoding dispensable functions was removed. Such studies showed that some strains with minimized genomes gained beneficial features, especially for secretory protein production. However, strains with the most minimal genomes displayed growth defects. This focused our attention on strains with less extensive genomic deletions that display close-to-wild-type growth properties while retaining the acquired beneficial traits in secretory protein production. A strain of this category is B. subtilis IIG-Bs27-47-24, here referred to as midiBacillus, which lacks 30.95% of the parental genome. To date, it was unknown how the altered genomic configuration of midiBacillus impacts cell physiology in general, and protein secretion in particular. The present study bridges this knowledge gap through comparative quantitative proteome analyses with focus on protein secretion. Interestingly, the results show that the secretion stress responses of midiBacillus, as elicited by high-level expression of the immunodominant staphylococcal antigen A, are completely different from secretion stress responses that occur in the parental strain 168. We further show that midiBacillus has an increased capacity for translation and that a variety of critical Sec secretion machinery components is present at elevated levels. Altogether, our observations demonstrate that high-level protein secretion has different consequences for wild-type and genome-engineered Bacillus strains, dictated by the altered genomic and proteomic configurations. IMPORTANCE Our present study showcases a genome-minimized nonpathogenic bacterium, the so-called midiBacillus, as a chassis for the development of future industrial strains that serve in the production of high-value difficult-to-produce proteins. In particular, we explain how midiBacillus, which lacks about one-third of the original genome, effectively secretes a protein of the major human pathogen Staphylococcus aureus that cannot be produced by the parental Bacillus subtilis strain. This is important, because the secreted S. aureus protein is exemplary for a range of targets that can be implemented in future antistaphylococcal immunotherapies. Accordingly, we anticipate that midiBacillus chassis will contribute to the development of vaccines that protect both humans and livestock against diseases caused by S. aureus, a bacterial pathogen that is increasingly difficult to fight with antibiotics, because it has accumulated resistances to essentially all antibiotics that are currently in clinical practice.
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Pedreira T, Elfmann C, Stülke J. The current state of SubtiWiki, the database for the model organism Bacillus subtilis. Nucleic Acids Res 2021; 50:D875-D882. [PMID: 34664671 PMCID: PMC8728116 DOI: 10.1093/nar/gkab943] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 11/16/2022] Open
Abstract
Bacillus subtilis is a Gram-positive model bacterium with extensive documented annotation. However, with the rise of high-throughput techniques, the amount of complex data being generated every year has been increasing at a fast pace. Thus, having platforms ready to integrate and give a representation to these data becomes a priority. To address it, SubtiWiki (http://subtiwiki.uni-goettingen.de/) was created in 2008 and has been growing in data and viewership ever since. With millions of requests every year, it is the most visited B. subtilis database, providing scientists all over the world with curated information about its genes and proteins, as well as intricate protein–protein interactions, regulatory elements, expression data and metabolic pathways. However, there is still a large portion of annotation to be unveiled for some biological elements. Thus, to facilitate the development of new hypotheses for research, we have added a Homology section covering potential protein homologs in other organisms. Here, we present the recent developments of SubtiWiki and give a guided tour of our database and the current state of the data for this organism.
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Affiliation(s)
- Tiago Pedreira
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg August University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Christoph Elfmann
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg August University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Jörg Stülke
- To whom correspondence should be addressed. Tel: +49 551 3933781; Fax: +49 551 3933808;
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12
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Michalik S, Reder A, Richts B, Faßhauer P, Mäder U, Pedreira T, Poehlein A, van Heel AJ, van Tilburg AY, Altenbuchner J, Klewing A, Reuß DR, Daniel R, Commichau FM, Kuipers OP, Hamoen LW, Völker U, Stülke J. The Bacillus subtilis Minimal Genome Compendium. ACS Synth Biol 2021; 10:2767-2771. [PMID: 34587446 DOI: 10.1021/acssynbio.1c00339] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To better understand cellular life, it is essential to decipher the contribution of individual components and their interactions. Minimal genomes are an important tool to investigate these interactions. Here, we provide a database of 105 fully annotated genomes of a series of strains with sequential deletion steps of the industrially relevant model bacterium Bacillus subtilis starting with the laboratory wild type strain B. subtilis 168 and ending with B. subtilis PG38, which lacks approximately 40% of the original genome. The annotation is supported by sequencing of key intermediate strains as well as integration of literature knowledge for the annotation of the deletion scars and their potential effects. The strain compendium presented here represents a comprehensive genome library of the entire MiniBacillus project. This resource will facilitate the more effective application of the different strains in basic science as well as in biotechnology.
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Affiliation(s)
- Stephan Michalik
- C_FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Alexander Reder
- C_FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Björn Richts
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Patrick Faßhauer
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Ulrike Mäder
- C_FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Tiago Pedreira
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Auke J. van Heel
- Department of Molecular Genetics, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Amanda Y. van Tilburg
- Department of Molecular Genetics, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Josef Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, 70569 Stuttgart, Germany
| | - Anika Klewing
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Daniel R. Reuß
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Fabian M. Commichau
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
- FG Synthetic Microbiology, Brandenburg University of Technology, 01958 Senftenberg, Germany
| | - Oscar P. Kuipers
- Department of Molecular Genetics, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Leendert W. Hamoen
- Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
| | - Uwe Völker
- C_FunGene, Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Jörg Stülke
- Institute of Microbiology and Genetics, GZMB, Georg-August University Göttingen, 37077 Göttingen, Germany
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13
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Sutton G, Fogel GB, Abramson B, Brinkac L, Michael T, Liu ES, Thomas S. A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes. F1000Res 2021; 10:286. [PMID: 34113437 PMCID: PMC8156514 DOI: 10.12688/f1000research.51873.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/17/2021] [Indexed: 11/22/2022] Open
Abstract
Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.
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Affiliation(s)
- Granger Sutton
- J. Craig Venter Institute, Rockville, Maryland, 20850, USA
| | - Gary B Fogel
- Natural Selection, Inc., San Diego, CA, 92121, USA
| | | | | | - Todd Michael
- J. Craig Venter Institute, Rockville, Maryland, 20850, USA
| | - Enoch S Liu
- Natural Selection, Inc., San Diego, CA, 92121, USA
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14
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Pedreira T, Elfmann C, Singh N, Stülke J. SynWiki: Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A. Protein Sci 2021; 31:54-62. [PMID: 34515387 PMCID: PMC8740822 DOI: 10.1002/pro.4179] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/02/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022]
Abstract
The new field of synthetic biology aims at the creation of artificially designed organisms. A major breakthrough in the field was the generation of the artificial synthetic organism Mycoplasma mycoides JCVI-syn3A. This bacterium possesses only 452 protein-coding genes, the smallest number for any organism that is viable independent of a host cell. However, about one third of the proteins have no known function indicating major gaps in our understanding of simple living cells. To facilitate the investigation of the components of this minimal bacterium, we have generated the database SynWiki (http://synwiki.uni-goettingen.de/). SynWiki is based on a relational database and gives access to published information about the genes and proteins of M. mycoides JCVI-syn3A. To gain a better understanding of the functions of the genes and proteins of the artificial bacteria, protein-protein interactions that may provide clues for the protein functions are included in an interactive manner. SynWiki is an important tool for the synthetic biology community that will support the comprehensive understanding of a minimal cell as well as the functional annotation of so far uncharacterized proteins.
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Affiliation(s)
- Tiago Pedreira
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Christoph Elfmann
- Department of General Microbiology, Göttingen Center for Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
| | - Neil Singh
- 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
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15
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Unchaining mini Bacillus Strain PG10: Relief of FlgM-Mediated Repression of Autolysin Genes. Appl Environ Microbiol 2021; 87:e0112321. [PMID: 34232062 DOI: 10.1128/aem.01123-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cell chaining in Bacillus subtilis is naturally observed in a subset of cells during exponential growth and during biofilm formation. However, the recently constructed large-scale genome-minimized B. subtilis strain PG10 displays a severe and permanent defect in cell separation, as it exclusively grows in the form of long filaments of nonseparated cells. In this study, we investigated the underlying mechanisms responsible for the incomplete cell division of PG10 by genomic and transcriptomic analyses. Repression of the SigD regulon, including the major autolysin gene lytF, was identified as the cause for the cell separation problem of PG10. It appeared that SigD-regulated genes are downregulated in PG10 due to the absence of the flagellar export apparatus, which normally is responsible for secretion of FlgM, the anti-sigma factor of SigD. Although mild negative effects on growth and cell morphology were observed, deletion of flgM could revert the aberrant cell-chaining phenotype and increased transformation efficiency. Interestingly, our work also demonstrates the occurrence of increased antisense transcription of slrR, a transcriptional repressor of autolysin genes, in PG10 and provides further understanding for this observation. In addition to revealing the molecular basis of the cell separation defect in PG10, our work provides novel targets for subsequent genome reduction efforts and future directions for further optimization of miniBacillus PG10. IMPORTANCE Reduction of the size of bacterial genomes is relevant for understanding the minimal requirements for cellular life as well as from a biotechnological point of view. Although the genome-minimized Bacillus subtilis strain PG10 displays several beneficial traits as a microbial cell factory compared to its parental strain, a defect at the final stage of cell division was introduced during the genome reduction process. By genetic and transcriptomic analyses, we identified the underlying reasons for the cell separation problem of PG10. In addition to enabling PG10 to grow in a way similar to that of B. subtilis wild-type strains, our work points toward subsequent targets for fine-tuning and further reduction of the genome of PG10. Moreover, solving the cell separation defect facilitates laboratory handling of PG10 by increasing the transformation efficiency, among other means. Overall, our work contributes to understanding and improving biotechnologically attractive minimal bacterial cell factories.
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16
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Benda M, Woelfel S, Faßhauer P, Gunka K, Klumpp S, Poehlein A, Kálalová D, Šanderová H, Daniel R, Krásný L, Stülke J. Quasi-essentiality of RNase Y in Bacillus subtilis is caused by its critical role in the control of mRNA homeostasis. Nucleic Acids Res 2021; 49:7088-7102. [PMID: 34157109 PMCID: PMC8266666 DOI: 10.1093/nar/gkab528] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 05/28/2021] [Accepted: 06/08/2021] [Indexed: 01/18/2023] Open
Abstract
RNA turnover is essential in all domains of life. The endonuclease RNase Y (rny) is one of the key components involved in RNA metabolism of the model organism Bacillus subtilis. Essentiality of RNase Y has been a matter of discussion, since deletion of the rny gene is possible, but leads to severe phenotypic effects. In this work, we demonstrate that the rny mutant strain rapidly evolves suppressor mutations to at least partially alleviate these defects. All suppressor mutants had acquired a duplication of an about 60 kb long genomic region encompassing genes for all three core subunits of the RNA polymerase—α, β, β′. When the duplication of the RNA polymerase genes was prevented by relocation of the rpoA gene in the B. subtilis genome, all suppressor mutants carried distinct single point mutations in evolutionary conserved regions of genes coding either for the β or β’ subunits of the RNA polymerase that were not tolerated by wild type bacteria. In vitro transcription assays with the mutated polymerase variants showed a severe decrease in transcription efficiency. Altogether, our results suggest a tight cooperation between RNase Y and the RNA polymerase to establish an optimal RNA homeostasis in B. subtilis cells.
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Affiliation(s)
- Martin Benda
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Simon Woelfel
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Patrick Faßhauer
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Katrin Gunka
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Stefan Klumpp
- Institute for the Dynamics of Complex Systems, Georg-August-University Göttingen, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Debora Kálalová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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17
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Appelbaum M, Schweder T. Metabolic Engineering of
Bacillus
– New Tools, Strains, and Concepts. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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18
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Faßhauer P, Busche T, Kalinowski J, Mäder U, Poehlein A, Daniel R, Stülke J. Functional Redundancy and Specialization of the Conserved Cold Shock Proteins in Bacillus subtilis. Microorganisms 2021; 9:1434. [PMID: 34361870 PMCID: PMC8307031 DOI: 10.3390/microorganisms9071434] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 12/26/2022] Open
Abstract
Many bacteria encode so-called cold shock proteins. These proteins are characterized by a conserved protein domain. Often, the bacteria have multiple cold shock proteins that are expressed either constitutively or at low temperatures. In the Gram-positive model bacterium Bacillussubtilis, two of three cold shock proteins, CspB and CspD, belong to the most abundant proteins suggesting a very important function. To get insights into the role of these highly abundant proteins, we analyzed the phenotypes of single and double mutants, tested the expression of the csp genes and the impact of CspB and CspD on global gene expression in B. subtilis. We demonstrate that the simultaneous loss of both CspB and CspD results in a severe growth defect, in the loss of genetic competence, and the appearance of suppressor mutations. Overexpression of the third cold shock protein CspC could compensate for the loss of CspB and CspD. The transcriptome analysis revealed that the lack of CspB and CspD affects the expression of about 20% of all genes. In several cases, the lack of the cold shock proteins results in an increased read-through at transcription terminators suggesting that CspB and CspD might be involved in the control of transcription termination.
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Affiliation(s)
- Patrick Faßhauer
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany;
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (T.B.); (J.K.)
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany; (T.B.); (J.K.)
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany;
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany; (A.P.); (R.D.)
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany; (A.P.); (R.D.)
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany;
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19
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Abstract
Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 16 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.
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20
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Sutton G, Fogel GB, Abramson B, Brinkac L, Michael T, Liu ES, Thomas S. A pan-genome method to determine core regions of the Bacillus subtilis and Escherichia coli genomes. F1000Res 2021; 10:286. [DOI: 10.12688/f1000research.51873.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/31/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Synthetic engineering of bacteria to produce industrial products is a burgeoning field of research and application. In order to optimize genome design, designers need to understand which genes are essential, which are optimal for growth, and locations in the genome that will be tolerated by the organism when inserting engineered cassettes. Methods: We present a pan-genome based method for the identification of core regions in a genome that are strongly conserved at the species level. Results: We show that the core regions determined by our method contain all or almost all essential genes. This demonstrates the accuracy of our method as essential genes should be core genes. We show that we outperform previous methods by this measure. We also explain why there are exceptions to this rule for our method. Conclusions: We assert that synthetic engineers should avoid deleting or inserting into these core regions unless they understand and are manipulating the function of the genes in that region. Similarly, if the designer wishes to streamline the genome, non-core regions and in particular low penetrance genes would be good targets for deletion. Care should be taken to remove entire cassettes with similar penetrance of the genes within cassettes as they may harbor toxin/antitoxin genes which need to be removed in tandem. The bioinformatic approach introduced here saves considerable time and effort relative to knockout studies on single isolates of a given species and captures a broad understanding of the conservation of genes that are core to a species.
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21
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Richts B, Lentes S, Poehlein A, Daniel R, Commichau FM. A Bacillus subtilis ΔpdxT mutant suppresses vitamin B6 limitation by acquiring mutations enhancing pdxS gene dosage and ammonium assimilation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:218-233. [PMID: 33559288 DOI: 10.1111/1758-2229.12936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
Pyridoxal-5'-phosphate (PLP), the biologically active form of vitamin B6, serves as a cofactor for many enzymes. The Gram-positive model bacterium Bacillus subtilis synthesizes PLP via the PdxST enzyme complex, consisting of the PdxT glutaminase and the PdxS PLP synthase subunits, respectively. PdxT converts glutamine to glutamate and ammonia of which the latter is channelled to PdxS. At high extracellular ammonium concentrations, the PdxS PLP synthase subunit does not depend on PdxT. Here, we assessed the potential of a B. subtilis ΔpdxT mutant to adapt to PLP limitation at the genome level. The majority of ΔpdxT suppressors had amplified a genomic region containing the pdxS gene. We also identified mutants having acquired as yet undescribed mutations in ammonium assimilation genes, indicating that the overproduction of PdxS and the NrgA ammonium transporter partially relieve vitamin B6 limitation in a ΔpdxT mutant when extracellular ammonium is scarce. Furthermore, we found that PdxS positively affects complex colony formation in B. subtilis. The catalytic mechanism of the PdxS PLP synthase subunit could be the reason for the limited evolution of the enzyme and why we could not identify a PdxS variant producing PLP independently of PdxT at low ammonium concentrations.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Sabine Lentes
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, Göttingen, 37077, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, Senftenberg, 01968, Germany
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22
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Zwiener T, Dziuba M, Mickoleit F, Rückert C, Busche T, Kalinowski J, Uebe R, Schüler D. Towards a 'chassis' for bacterial magnetosome biosynthesis: genome streamlining of Magnetospirillum gryphiswaldense by multiple deletions. Microb Cell Fact 2021; 20:35. [PMID: 33541381 PMCID: PMC7860042 DOI: 10.1186/s12934-021-01517-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/12/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Because of its tractability and straightforward cultivation, the magnetic bacterium Magnetospirillum gryphiswaldense has emerged as a model for the analysis of magnetosome biosynthesis and bioproduction. However, its future use as platform for synthetic biology and biotechnology will require methods for large-scale genome editing and streamlining. RESULTS We established an approach for combinatory genome reduction and generated a library of strains in which up to 16 regions including large gene clusters, mobile genetic elements and phage-related genes were sequentially removed, equivalent to ~ 227.6 kb and nearly 5.5% of the genome. Finally, the fragmented genomic magnetosome island was replaced by a compact cassette comprising all key magnetosome biosynthetic gene clusters. The prospective 'chassis' revealed wild type-like cell growth and magnetosome biosynthesis under optimal conditions, as well as slightly improved resilience and increased genetic stability. CONCLUSION We provide first proof-of-principle for the feasibility of multiple genome reduction and large-scale engineering of magnetotactic bacteria. The library of deletions will be valuable for turning M. gryphiswaldense into a microbial cell factory for synthetic biology and production of magnetic nanoparticles.
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Affiliation(s)
- Theresa Zwiener
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Marina Dziuba
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Frank Mickoleit
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Christian Rückert
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
| | - René Uebe
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, Germany.
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23
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Bonfio C. The curious case of peptide-coordinated iron-sulfur clusters: prebiotic and biomimetic insights. Dalton Trans 2021; 50:801-807. [PMID: 33351009 DOI: 10.1039/d0dt03947k] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-sulfur clusters are among the most ancient biological cofactors and are thought to have had an ancient role in mediating the chemical reactions that led to life. Two different, yet complementary approaches, based on bioinorganic chemistry and prebiotic chemistry, have already provided important clues for the formation and activity of biomimetic iron-sulfur analogues in aqueous solution. This frontier article discusses the efforts spent in the last 50 years in the context of peptide-coordinated iron-sulfur clusters, with a particular emphasis on insightful contributions from recent prebiotic chemistry research.
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Affiliation(s)
- Claudia Bonfio
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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24
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Kurasawa H, Ohno T, Arai R, Aizawa Y. A guideline and challenges toward the minimization of bacterial and eukaryotic genomes. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.coisb.2020.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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25
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Klewing A, Koo BM, Krüger L, Poehlein A, Reuß D, Daniel R, Gross CA, Stülke J. Resistance to serine in Bacillus subtilis: identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism. Environ Microbiol 2020; 22:3937-3949. [PMID: 32743959 PMCID: PMC8226366 DOI: 10.1111/1462-2920.15179] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/27/2020] [Indexed: 01/10/2023]
Abstract
The Gram‐positive bacterium Bacillus subtilis uses serine not only as a building block for proteins but also as an important precursor in many anabolic reactions. Moreover, a lack of serine results in the initiation of biofilm formation. However, excess serine inhibits the growth of B. subtilis. To unravel the underlying mechanisms, we isolated suppressor mutants that can tolerate toxic serine concentrations by three targeted and non‐targeted genome‐wide screens. All screens as well as genetic complementation in Escherichia coli identified the so far uncharacterized permease YbeC as the major serine transporter of B. subtilis. In addition to YbeC, the threonine transporters BcaP and YbxG make minor contributions to serine uptake. A strain lacking these three transporters was able to tolerate 100 mM serine whereas the wild type strain was already inhibited by 1 mM of the amino acid. The screen for serine‐resistant mutants also identified mutations that result in increased serine degradation and in increased expression of threonine biosynthetic enzymes suggesting that serine toxicity results from interference with threonine biosynthesis.
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Affiliation(s)
- Anika Klewing
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Larissa Krüger
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Daniel Reuß
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Grisebachstr. 8, Göttingen, D-37077, Germany
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26
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Yang H, Liu Y, Li J, Liu L, Du G, Chen J. Systems metabolic engineering of
Bacillus subtilis
for efficient biosynthesis of 5‐methyltetrahydrofolate. Biotechnol Bioeng 2020; 117:2116-2130. [DOI: 10.1002/bit.27332] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/11/2020] [Accepted: 03/12/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Han Yang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of EducationJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of EducationJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of EducationJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of EducationJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of EducationJiangnan University Wuxi China
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of EducationJiangnan University Wuxi China
- National Engineering Laboratory for Cereal Fermentation TechnologyJiangnan University Wuxi China
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27
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Wu H, Wang D, Gao F. Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains. Brief Bioinform 2020; 22:1951-1971. [PMID: 32065216 DOI: 10.1093/bib/bbaa013] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 02/05/2023] Open
Abstract
Pan-genome analysis is widely used to study the evolution and genetic diversity of species, particularly in bacteria. However, the impact of strain selection on the outcome of pan-genome analysis is poorly understood. Furthermore, a standard protocol to ensure high-quality pan-genome results is lacking. In this study, we carried out a series of pan-genome analyses of different strain sets of Bacillus subtilis to understand the impact of various strains on the performance and output quality of pan-genome analyses. Consequently, we found that the results obtained by pan-genome analyses of B. subtilis can be influenced by the inclusion of incorrectly classified Bacillus subspecies strains, phylogenetically distinct strains, engineered genome-reduced strains, chimeric strains, strains with a large number of unique genes or a large proportion of pseudogenes, and multiple clonal strains. Since the presence of these confounding strains can seriously affect the quality and true landscape of the pan-genome, we should remove these deviations in the process of pan-genome analyses. Our study provides new insights into the removal of biases from confounding strains in pan-genome analyses at the beginning of data processing, which enables the achievement of a closer representation of a high-quality pan-genome landscape of B. subtilis that better reflects the performance and credibility of the B. subtilis pan-genome. This procedure could be added as an important quality control step in pan-genome analyses for improving the efficiency of analyses, and ultimately contributing to a better understanding of genome function, evolution and genome-reduction strategies for B. subtilis in the future.
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Affiliation(s)
- Hao Wu
- Department of Physics, School of Science, Tianjin University
| | - Dan Wang
- Department of Physics, School of Science, Tianjin University
| | - Feng Gao
- Department of Physics, School of Science, and the Frontier Science Center of Synthetic Biology (MOE), Key Laboratory of Systems Bioengineering (MOE), Tianjin University
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28
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Baby V, Labroussaa F, Lartigue C, Rodrigue S. [Synthetic chromosomes: rewriting the code of life]. Med Sci (Paris) 2019; 35:753-760. [PMID: 31625897 DOI: 10.1051/medsci/2019153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The past decade has seen vast improvements in DNA synthesis and assembly methods. The creation of synthetic DNA molecules is becoming easier and more affordable, such that entire chromosomes can now be synthesized. These advances mark the beginning of synthetic genomics, a new discipline interested in the construction of complete genomes tailored for the study and application of biological systems. From viral genome synthesis to the reconstruction of the yeast 16 chromosomes, we discuss the main discoveries, the regulations and ethical considerations along with the potential of this emerging discipline for the future.
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Affiliation(s)
- Vincent Baby
- INRA, UMR 1332 de biologie du fruit et pathologie, 71 avenue E. Bourlaux, 33140 Villenave d'Ornon, France - Univ. Bordeaux, UMR 1332 de biologie du fruit et pathologie, 71 avenue E. Bourlaux 33140 Villenave d'Ornon, France
| | - Fabien Labroussaa
- Institute of veterinary bacteriology of Bern, Vetsuisse Faculty, University of Bern, 3001 Berne, Suisse
| | - Carole Lartigue
- INRA, UMR 1332 de biologie du fruit et pathologie, 71 avenue E. Bourlaux, 33140 Villenave d'Ornon, France - Univ. Bordeaux, UMR 1332 de biologie du fruit et pathologie, 71 avenue E. Bourlaux 33140 Villenave d'Ornon, France
| | - Sébastien Rodrigue
- Département de biologie, Université de Sherbrooke, 2500 boulevard de l'Université, J1K 2R1 Sherbrooke, Québec, Canada
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29
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Garcia PS, Gribaldo S, Py B, Barras F. The SUF system: an ABC ATPase-dependent protein complex with a role in Fe-S cluster biogenesis. Res Microbiol 2019; 170:426-434. [PMID: 31419582 DOI: 10.1016/j.resmic.2019.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022]
Abstract
Iron-sulfur (Fe-S) clusters are considered one of the most ancient and versatile inorganic cofactors present in the three domains of life. Fe-S clusters can act as redox sensors or catalysts and are found to be used by a large number of functional and structurally diverse proteins. Here, we cover current knowledge of the SUF multiprotein machinery that synthesizes and inserts Fe-S clusters into proteins. Specific focus is put on the ABC ATPase SufC, which contributes to building Fe-S clusters, and appeared early on during evolution.
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Affiliation(s)
- Pierre Simon Garcia
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, ERL CNRS 6002, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France; Department of Microbiology, Evolutionary Biology of the Microbial Cell Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Simonetta Gribaldo
- Department of Microbiology, Evolutionary Biology of the Microbial Cell Unit, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France
| | - Béatrice Py
- Laboratoire de Chimie Bactérienne, UMR7243 Aix-Marseille Université CNRS, 31 Chemin Joseph Aiguier, 13009, Marseille, France.
| | - Frédéric Barras
- Department of Microbiology, Stress Adaptation and Metabolism in Enterobacteria Unit, ERL CNRS 6002, Institut Pasteur, 25-28 Rue du Dr Roux, 75015, Paris, France.
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30
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Zhu B, Stülke J. SubtiWiki in 2018: from genes and proteins to functional network annotation of the model organism Bacillus subtilis. Nucleic Acids Res 2019; 46:D743-D748. [PMID: 29788229 PMCID: PMC5753275 DOI: 10.1093/nar/gkx908] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/26/2017] [Indexed: 01/20/2023] Open
Abstract
Living cells are made up of individual parts, i.e. the genome, the proteins, the RNA and lipid molecules as well as the metabolites and ions. However, life depends on the functional interaction among these components which is often organized in networks. Here, we present the recent development of SubtiWiki, the integrated database for the model bacterium Bacillus subtilis (http://subtiwiki.uni-goettingen.de/). SubtiWiki is based on a relational database and provides access to published information about the genes and proteins of B. subtilis and about metabolic and regulatory pathways. We have included a network visualization tool that can be used to visualize regulatory as well as protein-protein interaction networks. The resulting interactive graphical presentations allow the user to detect novel associations and thus to develop novel hypotheses that can then be tested experimentally. To facilitate the mobile use of SubtiWiki, we provide enhanced versions of the SubtiWiki App that are available for iOS and Android devices. Importantly, the App allows to link private notes and pictures to the gene/protein pages that can be synchronized on multiple devices. SubtiWiki has become one of the most complete resources of knowledge on a living organism.
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Affiliation(s)
- Bingyao Zhu
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
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31
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Reuß DR, Faßhauer P, Mroch PJ, Ul-Haq I, Koo BM, Pöhlein A, Gross CA, Daniel R, Brantl S, Stülke J. Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis. Nucleic Acids Res 2019; 47:5231-5242. [PMID: 30957856 PMCID: PMC6547408 DOI: 10.1093/nar/gkz260] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 03/30/2019] [Accepted: 04/01/2019] [Indexed: 12/22/2022] Open
Abstract
DNA topoisomerases play essential roles in chromosome organization and replication. Most bacteria possess multiple topoisomerases which have specialized functions in the control of DNA supercoiling or in DNA catenation/decatenation during recombination and chromosome segregation. DNA topoisomerase I is required for the relaxation of negatively supercoiled DNA behind the transcribing RNA polymerase. Conflicting results have been reported on the essentiality of the topA gene encoding topoisomerase I in the model bacterium Bacillus subtilis. In this work, we have studied the requirement for topoisomerase I in B. subtilis. All stable topA mutants carried different chromosomal amplifications of the genomic region encompassing the parEC operon encoding topoisomerase IV. Using a fluorescent amplification reporter system we observed that each individual topA mutant had acquired such an amplification. Eventually, the amplifications were replaced by a point mutation in the parEC promoter region which resulted in a fivefold increase of parEC expression. In this strain both type I topoisomerases, encoded by topA and topB, were dispensable. Our results demonstrate that topoisomerase IV at increased expression is necessary and sufficient to take over the function of type 1A topoisomerases.
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Affiliation(s)
- Daniel R Reuß
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Patrick Faßhauer
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Philipp Joel Mroch
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Inam Ul-Haq
- Matthias-Schleiden-Institut, AG Bakteriengenetik, Friedrich-Schiller-University Jena, Jena, Germany
| | - Byoung-Mo Koo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Anja Pöhlein
- Department of Genomic and Applied Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Carol A Gross
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
| | - Sabine Brantl
- Matthias-Schleiden-Institut, AG Bakteriengenetik, Friedrich-Schiller-University Jena, Jena, Germany
| | - Jörg Stülke
- Department of General Microbiology, GZMB, Georg-August-University Göttingen, Göttingen, Germany
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32
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Richts B, Rosenberg J, Commichau FM. A Survey of Pyridoxal 5'-Phosphate-Dependent Proteins in the Gram-Positive Model Bacterium Bacillus subtilis. Front Mol Biosci 2019; 6:32. [PMID: 31134210 PMCID: PMC6522883 DOI: 10.3389/fmolb.2019.00032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/18/2019] [Indexed: 11/13/2022] Open
Abstract
The B6 vitamer pyridoxal 5′-phosphate (PLP) is a co-factor for proteins and enzymes that are involved in diverse cellular processes. Therefore, PLP is essential for organisms from all kingdoms of life. Here we provide an overview about the PLP-dependent proteins from the Gram-positive soil bacterium Bacillus subtilis. Since B. subtilis serves as a model system in basic research and as a production host in industry, knowledge about the PLP-dependent proteins could facilitate engineering the bacteria for biotechnological applications. The survey revealed that the majority of the PLP-dependent proteins are involved in metabolic pathways like amino acid biosynthesis and degradation, biosynthesis of antibacterial compounds, utilization of nucleotides as well as in iron and carbon metabolism. Many PLP-dependent proteins participate in de novo synthesis of the co-factors biotin, folate, heme, and NAD+ as well as in cell wall metabolism, tRNA modification, regulation of gene expression, sporulation, and biofilm formation. A surprisingly large group of PLP-dependent proteins (29%) belong to the group of poorly characterized proteins. This review underpins the need to characterize the PLP-dependent proteins of unknown function to fully understand the “PLP-ome” of B. subtilis.
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Affiliation(s)
- Björn Richts
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, University of Goettingen, Göttingen, Germany
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33
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Noack S, Baumgart M. Communities of Niche-Optimized Strains: Small-Genome Organism Consortia in Bioproduction. Trends Biotechnol 2019; 37:126-139. [DOI: 10.1016/j.tibtech.2018.07.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/30/2022]
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34
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Aguilar Suárez R, Stülke J, van Dijl JM. Less Is More: Toward a Genome-Reduced Bacillus Cell Factory for "Difficult Proteins". ACS Synth Biol 2019; 8:99-108. [PMID: 30540431 PMCID: PMC6343112 DOI: 10.1021/acssynbio.8b00342] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The availability of complete genome
sequences and the definition
of essential gene sets were fundamental in the start of the genome
engineering era. In a recent study, redundant and unnecessary genes
were systematically deleted from the Gram-positive bacterium Bacillus subtilis, an industrial production host of high-value
secreted proteins. This culminated in strain PG10, which lacks about
36% of the genome, thus representing the most minimal Bacillus chassis currently available. Here, we show that this “miniBacillus” strain has synthetic traits that are favorable
for producing “difficult-to-produce proteins”. As exemplified
with different staphylococcal antigens, PG10 overcomes several bottlenecks
in protein production related to the secretion process and instability
of the secreted product. These findings show for the first time that
massive genome reduction can substantially improve secretory protein
production by a bacterial expression host, and underpin the high potential
of genome-engineered strains as future cell factories.
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Affiliation(s)
- Rocío Aguilar Suárez
- University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands
| | - Jörg Stülke
- Institute of Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Jan Maarten van Dijl
- University Medical Center Groningen, University of Groningen, 9712 CP Groningen, The Netherlands
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35
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Harnessing Underground Metabolism for Pathway Development. Trends Biotechnol 2019; 37:29-37. [DOI: 10.1016/j.tibtech.2018.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 07/17/2018] [Accepted: 08/06/2018] [Indexed: 01/13/2023]
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36
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Making and Breaking of an Essential Poison: the Cyclases and Phosphodiesterases That Produce and Degrade the Essential Second Messenger Cyclic di-AMP in Bacteria. J Bacteriol 2018; 201:JB.00462-18. [PMID: 30224435 DOI: 10.1128/jb.00462-18] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cyclic di-AMP is a second-messenger nucleotide that is produced by many bacteria and some archaea. Recent work has shown that c-di-AMP is unique among the signaling nucleotides, as this molecule is in many bacteria both essential on one hand and toxic upon accumulation on the other. Moreover, in bacteria, like Bacillus subtilis, c-di-AMP controls a biological process, potassium homeostasis, by binding both potassium transporters and riboswitch molecules in the mRNAs that encode the potassium transporters. In addition to the control of potassium homeostasis, c-di-AMP has been implicated in many cellular activities, including DNA repair, cell wall homeostasis, osmotic adaptation, biofilm formation, central metabolism, and virulence. c-di-AMP is synthesized and degraded by diadenylate cyclases and phosphodiesterases, respectively. In the diadenylate cyclases, one type of catalytic domain, the diadenylate cyclase (DAC) domain, is coupled to various other domains that control the localization, the protein-protein interactions, and the regulation of the enzymes. The phosphodiesterases have a catalytic core that consists either of a DHH/DHHA1 or of an HD domain. Recent findings on the occurrence, domain organization, activity control, and structural features of diadenylate cyclases and phosphodiesterases are discussed in this review.
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37
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Baumgart M, Unthan S, Kloß R, Radek A, Polen T, Tenhaef N, Müller MF, Küberl A, Siebert D, Brühl N, Marin K, Hans S, Krämer R, Bott M, Kalinowski J, Wiechert W, Seibold G, Frunzke J, Rückert C, Wendisch VF, Noack S. Corynebacterium glutamicum Chassis C1*: Building and Testing a Novel Platform Host for Synthetic Biology and Industrial Biotechnology. ACS Synth Biol 2018; 7:132-144. [PMID: 28803482 DOI: 10.1021/acssynbio.7b00261] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Targeted top-down strategies for genome reduction are considered to have a high potential for providing robust basic strains for synthetic biology and industrial biotechnology. Recently, we created a library of 26 genome-reduced strains of Corynebacterium glutamicum carrying broad deletions in single gene clusters and showing wild-type-like biological fitness. Here, we proceeded with combinatorial deletions of these irrelevant gene clusters in two parallel orders, and the resulting library of 28 strains was characterized under various environmental conditions. The final chassis strain C1* carries a genome reduction of 13.4% (412 deleted genes) and shows wild-type-like growth behavior in defined medium with d-glucose as carbon and energy source. Moreover, C1* proves to be robust against several stresses (including oxygen limitation) and shows long-term growth stability under defined and complex medium conditions. In addition to providing a novel prokaryotic chassis strain, our results comprise a large strain library and a revised genome annotation list, which will be valuable sources for future systemic studies of C. glutamicum.
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Affiliation(s)
- Meike Baumgart
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Simon Unthan
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Ramona Kloß
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Andreas Radek
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Tino Polen
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Niklas Tenhaef
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Moritz Fabian Müller
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Andreas Küberl
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Daniel Siebert
- Institute
for Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Natalie Brühl
- Institute
of Biochemistry, University of Cologne, 50923 Cologne, Germany
| | - Kay Marin
- Evonik Nutrition & Care GmbH, 45128 Essen, Germany
| | - Stephan Hans
- Evonik Nutrition & Care GmbH, 45128 Essen, Germany
| | - Reinhard Krämer
- Institute
of Biochemistry, University of Cologne, 50923 Cologne, Germany
| | - Michael Bott
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Jörn Kalinowski
- Microbial
Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Wolfgang Wiechert
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
- Computational
Systems Biotechnology, RWTH Aachen University, 52062 Aachen, Germany
| | - Gerd Seibold
- Institute
for Microbiology and Biotechnology, Ulm University, 89081 Ulm, Germany
| | - Julia Frunzke
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systemic
Microbiology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Christian Rückert
- Microbial
Genomics and Biotechnology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Volker F. Wendisch
- Chair
of Genetics of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Stephan Noack
- Institute
of Bio- and Geosciences, IBG-1: Biotechnology, Systems Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
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38
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Tödter D, Gunka K, Stülke J. The Highly Conserved Asp23 Family Protein YqhY Plays a Role in Lipid Biosynthesis in Bacillus subtilis. Front Microbiol 2017; 8:883. [PMID: 28579978 PMCID: PMC5437119 DOI: 10.3389/fmicb.2017.00883] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/02/2017] [Indexed: 01/22/2023] Open
Abstract
In most bacteria, fatty acid biosynthesis is an essential process that must be controlled by the availability of precursors and by the needs of cell division. So far, no mechanisms controlling synthesis of malonyl-coenzyme A (CoA), the committed step in fatty acid synthesis, have been identified in the Gram-positive model bacterium Bacillus subtilis. We have studied the localization and function of two highly expressed proteins of unknown function, YqhY and YloU. Both proteins are members of the conserved and widespread Asp23 family. While the deletion of yloU had no effect, loss of the yqhY gene induced the rapid acquisition of suppressor mutations. The vast majority of these mutations affect subunits of the acetyl-CoA carboxylase (ACCase) complex, the enzyme that catalyzes the formation of malonyl-CoA. Moreover, lack of yqhY is accompanied by the formation of lipophilic clusters in the polar regions of the cells indicating an increased activity of ACCase. Our results suggest that YqhY controls the activity of ACCase and that this control results in inhibition of ACCase activity. Hyperactivity of the enzyme complex in the absence of YqhY does then provoke mutations that cause reduced ACCase activity.
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Affiliation(s)
- Dominik Tödter
- Department of General Microbiology, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
| | - Katrin Gunka
- Department of General Microbiology, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, University of GöttingenGöttingen, Germany
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39
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40
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Reuß DR, Altenbuchner J, Mäder U, Rath H, Ischebeck T, Sappa PK, Thürmer A, Guérin C, Nicolas P, Steil L, Zhu B, Feussner I, Klumpp S, Daniel R, Commichau FM, Völker U, Stülke J. Large-scale reduction of the Bacillus subtilis genome: consequences for the transcriptional network, resource allocation, and metabolism. Genome Res 2016; 27:289-299. [PMID: 27965289 PMCID: PMC5287234 DOI: 10.1101/gr.215293.116] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/01/2016] [Indexed: 11/24/2022]
Abstract
Understanding cellular life requires a comprehensive knowledge of the essential cellular functions, the components involved, and their interactions. Minimized genomes are an important tool to gain this knowledge. We have constructed strains of the model bacterium, Bacillus subtilis, whose genomes have been reduced by ∼36%. These strains are fully viable, and their growth rates in complex medium are comparable to those of wild type strains. An in-depth multi-omics analysis of the genome reduced strains revealed how the deletions affect the transcription regulatory network of the cell, translation resource allocation, and metabolism. A comparison of gene counts and resource allocation demonstrates drastic differences in the two parameters, with 50% of the genes using as little as 10% of translation capacity, whereas the 6% essential genes require 57% of the translation resources. Taken together, the results are a valuable resource on gene dispensability in B. subtilis, and they suggest the roads to further genome reduction to approach the final aim of a minimal cell in which all functions are understood.
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Affiliation(s)
- Daniel R Reuß
- Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Josef Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Praveen Kumar Sappa
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Cyprien Guérin
- MaIAGE, INRA Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Pierre Nicolas
- MaIAGE, INRA Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Leif Steil
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Bingyao Zhu
- Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Georg-August-University Göttingen, 37077 Göttingen, Germany.,Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany
| | - Stefan Klumpp
- Institute for Nonlinear Dynamics, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Georg-August-University Göttingen, 37077 Göttingen, Germany.,Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany.,Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg-August-University Göttingen, 37077 Göttingen, Germany.,Georg-August-University, Göttingen Center for Molecular Biosciences (GZMB), 37077 Göttingen, Germany
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