51
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Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2018. [DOI: 10.3390/jmse6010013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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52
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Kim KH, Jia B, Jeon CO. Identification of Trans-4-Hydroxy-L-Proline as a Compatible Solute and Its Biosynthesis and Molecular Characterization in Halobacillus halophilus. Front Microbiol 2017; 8:2054. [PMID: 29104571 PMCID: PMC5655121 DOI: 10.3389/fmicb.2017.02054] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/06/2017] [Indexed: 12/17/2022] Open
Abstract
Halobacillus halophilus, a moderately halophilic bacterium, accumulates a variety of compatible solutes including glycine betaine, glutamate, glutamine, proline, and ectoine to cope with osmotic stress. Non-targeted analysis of intracellular organic compounds using 1H-NMR showed that a large amount of trans-4-hydroxy-L-proline (Hyp), which has not been reported as a compatible solute in H. halophilus, was accumulated in response to high NaCl salinity, suggesting that Hyp may be an important compatible solute in H. halophilus. Candidate genes encoding proline 4-hydroxylase (PH-4), which hydroxylates L-proline to generate Hyp, were retrieved from the genome of H. halophilus through domain searches based on the sequences of known PH-4 proteins. A gene, HBHAL_RS11735, which was annotated as a multidrug DMT transporter permease in GenBank, was identified as the PH-4 gene through protein expression analysis in Escherichia coli. The PH-4 gene constituted a transcriptional unit with a promoter and a rho-independent terminator, and it was distantly located from the proline biosynthetic gene cluster (pro operon). Transcriptional analysis showed that PH-4 gene expression was NaCl concentration-dependent, and was specifically induced by chloride anion, similar to the pro operon. Accumulation of intracellular Hyp was also observed in other bacteria, suggesting that Hyp may be a widespread compatible solute in halophilic and halotolerant bacteria.
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Affiliation(s)
| | | | - Che Ok Jeon
- Department of Life Science, Chung-Ang University, Seoul, South Korea
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53
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Schott AS, Behr J, Geißler AJ, Kuster B, Hahne H, Vogel RF. Quantitative Proteomics for the Comprehensive Analysis of Stress Responses of Lactobacillus paracasei subsp. paracasei F19. J Proteome Res 2017; 16:3816-3829. [PMID: 28862000 DOI: 10.1021/acs.jproteome.7b00474] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lactic acid bacteria are broadly employed as starter cultures in the manufacture of foods. Upon technological preparation, they are confronted with drying stress that amalgamates numerous stress conditions resulting in losses of fitness and survival. To better understand and differentiate physiological stress responses, discover general and specific markers for the investigated stress conditions, and predict optimal preconditioning for starter cultures, we performed a comprehensive genomic and quantitative proteomic analysis of a commonly used model system, Lactobacillus paracasei subsp. paracasei TMW 1.1434 (isogenic with F19) under 11 typical stress conditions, including among others oxidative, osmotic, pH, and pressure stress. We identified and quantified >1900 proteins in triplicate analyses, representing 65% of all genes encoded in the genome. The identified genes were thoroughly annotated in terms of subcellular localization prediction and biological functions, suggesting unbiased and comprehensive proteome coverage. In total, 427 proteins were significantly differentially expressed in at least one condition. Most notably, our analysis suggests that optimal preconditioning toward drying was predicted to be alkaline and high-pressure stress preconditioning. Taken together, we believe the presented strategy may serve as a prototypic example for the analysis and utility of employing quantitative-mass-spectrometry-based proteomics to study bacterial physiology.
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Affiliation(s)
- Ann-Sophie Schott
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
| | - Jürgen Behr
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany.,Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising 85354, Germany
| | - Andreas J Geißler
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
| | - Bernhard Kuster
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising 85354, Germany.,Chair of Proteomics and Bioanalytics, Technische Universität München , Freising 85354, Germany.,Center for Integrated Protein Science Munich, Freising 85354, Germany
| | | | - Rudi F Vogel
- Chair of Technical Microbiology, Technische Universität München , Freising 85354, Germany
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Hoffmann T, Bleisteiner M, Sappa PK, Steil L, Mäder U, Völker U, Bremer E. Synthesis of the compatible solute proline by Bacillus subtilis: point mutations rendering the osmotically controlled proHJ promoter hyperactive. Environ Microbiol 2017; 19:3700-3720. [PMID: 28752945 DOI: 10.1111/1462-2920.13870] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/09/2017] [Accepted: 07/24/2017] [Indexed: 01/29/2023]
Abstract
The ProJ and ProH enzymes of Bacillus subtilis catalyse together with ProA (ProJ-ProA-ProH), osmostress-adaptive synthesis of the compatible solute proline. The proA-encoded gamma-glutamyl phosphate reductase is also used for anabolic proline synthesis (ProB-ProA-ProI). Transcription of the proHJ operon is osmotically inducible whereas that of the proBA operon is not. Targeted and quantitative proteome analysis revealed that the amount of ProA is not limiting for the interconnected anabolic and osmostress-responsive proline production routes. A key player for enhanced osmostress-adaptive proline production is the osmotically regulated proHJ promoter. We used site-directed mutagenesis to study the salient features of this stress-responsive promoter. Two important features were identified: (i) deviations of the proHJ promoter from the consensus sequence of SigA-type promoters serve to keep transcription low under non-inducing growth conditions, while still allowing a finely tuned induction of transcriptional activity when the external osmolarity is increased and (ii) a suboptimal spacer length for SigA-type promoters of either 16-bp (the natural proHJ promoter), or 18-bp (a synthetic promoter variant) is strictly required to allow regulation of promoter activity in proportion to the external salinity. Collectively, our data suggest that changes in the local DNA structure at the proHJ promoter are important determinants for osmostress-inducibility of transcription.
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Affiliation(s)
- Tamara Hoffmann
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
| | - Monika Bleisteiner
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
| | - Praveen Kumar Sappa
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Leif Steil
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Ulrike Mäder
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, Department Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15, Greifswald D-17475, Germany
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Karl-von-Frisch-Str. 8, Marburg D-35043, Germany
- LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerweinstr. 6, Marburg D-35043, Germany
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55
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Hoffmann T, Bremer E. Guardians in a stressful world: the Opu family of compatible solute transporters from Bacillus subtilis. Biol Chem 2017; 398:193-214. [PMID: 27935846 DOI: 10.1515/hsz-2016-0265] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 08/29/2016] [Indexed: 01/09/2023]
Abstract
The development of a semi-permeable cytoplasmic membrane was a key event in the evolution of microbial proto-cells. As a result, changes in the external osmolarity will inevitably trigger water fluxes along the osmotic gradient. The ensuing osmotic stress has consequences for the magnitude of turgor and will negatively impact cell growth and integrity. No microorganism can actively pump water across the cytoplasmic membrane; hence, microorganisms have to actively adjust the osmotic potential of their cytoplasm to scale and direct water fluxes in order to prevent dehydration or rupture. They will accumulate ions and physiologically compliant organic osmolytes, the compatible solutes, when they face hyperosmotic conditions to retain cell water, and they rapidly expel these compounds through the transient opening of mechanosensitive channels to curb water efflux when exposed to hypo-osmotic circumstances. Here, we provide an overview on the salient features of the osmostress response systems of the ubiquitously distributed bacterium Bacillus subtilis with a special emphasis on the transport systems and channels mediating regulation of cellular hydration and turgor under fluctuating osmotic conditions. The uptake of osmostress protectants via the Opu family of transporters, systems of central importance for the management of osmotic stress by B. subtilis, will be particularly highlighted.
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56
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Lakowitz A, Godard T, Biedendieck R, Krull R. Mini review: Recombinant production of tailored bio-pharmaceuticals in different Bacillus strains and future perspectives. Eur J Pharm Biopharm 2017; 126:27-39. [PMID: 28606596 DOI: 10.1016/j.ejpb.2017.06.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/30/2017] [Accepted: 06/07/2017] [Indexed: 01/06/2023]
Abstract
Bio-pharmaceuticals like antibodies, hormones and growth factors represent about one-fifth of commercial pharmaceuticals. Host candidates of growing interest for recombinant production of these proteins are strains of the genus Bacillus, long being established for biotechnological production of homologous and heterologous proteins. Bacillus strains benefit from development of efficient expression systems in the last decades and emerge as major industrial workhorses for recombinant proteins due to easy cultivation, non-pathogenicity and their ability to secrete recombinant proteins directly into extracellular medium allowing cost-effective downstream processing. Their broad product portfolio of pharmaceutically relevant recombinant proteins described in research include antibody fragments, growth factors, interferons and interleukins, insulin, penicillin G acylase, streptavidin and different kinases produced in various cultivation systems like microtiter plates, shake flasks and bioreactor systems in batch, fed-batch and continuous mode. To further improve production and secretion performance of Bacillus, bottlenecks and limiting factors concerning proteases, chaperones, secretion machinery or feedback mechanisms can be identified on different cell levels from genomics and transcriptomics via proteomics to metabolomics and fluxomics. For systematical identification of recurring patterns characteristic of given regulatory systems and key genetic targets, systems biology and omics-technology provide suitable and promising approaches, pushing Bacillus further towards industrial application for recombinant pharmaceutical protein production.
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Affiliation(s)
- Antonia Lakowitz
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-List-Straβe 35a, 38106 Braunschweig, Germany; Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Thibault Godard
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-List-Straβe 35a, 38106 Braunschweig, Germany; Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Rebekka Biedendieck
- Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; Institute of Microbiology, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany
| | - Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany; Center of Pharmaceutical Engineering (PVZ), Technische Universität Braunschweig, Franz-List-Straβe 35a, 38106 Braunschweig, Germany; Braunschweig Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106 Braunschweig, Germany.
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57
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Noda-Garcia L, Romero Romero ML, Longo LM, Kolodkin-Gal I, Tawfik DS. Bacilli glutamate dehydrogenases diverged via coevolution of transcription and enzyme regulation. EMBO Rep 2017; 18:1139-1149. [PMID: 28468957 DOI: 10.15252/embr.201743990] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/29/2022] Open
Abstract
The linkage between regulatory elements of transcription, such as promoters, and their protein products is central to gene function. Promoter-protein coevolution is therefore expected, but rarely observed, and the manner by which these two regulatory levels are linked remains largely unknown. We study glutamate dehydrogenase-a hub of carbon and nitrogen metabolism. In Bacillus subtilis, two paralogues exist: GudB is constitutively transcribed whereas RocG is tightly regulated. In their active, oligomeric states, both enzymes show similar enzymatic rates. However, swaps of enzymes and promoters cause severe fitness losses, thus indicating promoter-enzyme coevolution. Characterization of the proteins shows that, compared to RocG, GudB's enzymatic activity is highly dependent on glutamate and pH Promoter-enzyme swaps therefore result in excessive glutamate degradation when expressing a constitutive enzyme under a constitutive promoter, or insufficient activity when both the enzyme and its promoter are tightly regulated. Coevolution of transcriptional and enzymatic regulation therefore underlies paralogue-specific spatio-temporal control, especially under diverse growth conditions.
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Affiliation(s)
- Lianet Noda-Garcia
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Liam M Longo
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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58
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Complete Genome Sequence of Bacillus subtilis Strain 29R7-12, a Piezophilic Bacterium Isolated from Coal-Bearing Sediment 2.4 Kilometers below the Seafloor. GENOME ANNOUNCEMENTS 2017; 5:5/8/e01621-16. [PMID: 28232436 PMCID: PMC5323615 DOI: 10.1128/genomea.01621-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here, we report the genome sequence of Bacillus subtilis strain 29R7-12, a piezophilic bacterium isolated from coal-bearing sediment down to ~2.4 km below the ocean floor in the northwestern Pacific. The strain is a Gram-positive spore-forming bacterium, closely related to Bacillus subtilis within the phylum Firmicutes. This is the first complete genome sequence of a Bacillus subtilis strain from the deep biosphere. The genome sequence will provide a valuable resource for comparative studies of microorganisms from the surface and subsurface environments.
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59
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Liu Y, Li J, Du G, Chen J, Liu L. Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions. Biotechnol Adv 2017; 35:20-30. [DOI: 10.1016/j.biotechadv.2016.11.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/21/2016] [Accepted: 11/16/2016] [Indexed: 12/25/2022]
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60
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Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
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61
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Poblete-Castro I, Borrero-de Acuña JM, Nikel PI, Kohlstedt M, Wittmann C. Host Organism: Pseudomonas putida. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ignacio Poblete-Castro
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - José M. Borrero-de Acuña
- Universidad Andrés Bello; Center for Bioinformatics and Integrative Biology, Biosystems Engineering Laboratory, Faculty of Biological Sciences; Av. República 239 8340176 Santiago de Chile Chile
| | - Pablo I. Nikel
- Systems and Synthetic Biology Program; National Spanish Center for Biotechnology (CNB-CSIC); Calle Darwin, 3 28049 Madrid, Spain
| | - Michael Kohlstedt
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biology, Biosciences; Campus A1.5 66123 Saarbrücken, Germany
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62
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Becker J, Wittmann C. Industrial Microorganisms: Corynebacterium glutamicum. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Judith Becker
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
| | - Christoph Wittmann
- Saarland University; Institute of Systems Biotechnology; Campus A 15 66123 Saarbrücken Germany
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63
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Gallegos-Monterrosa R, Mhatre E, Kovács ÁT. Specific Bacillus subtilis 168 variants form biofilms on nutrient-rich medium. MICROBIOLOGY-SGM 2016; 162:1922-1932. [PMID: 27655338 DOI: 10.1099/mic.0.000371] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bacillus subtilis is an intensively studied Gram-positive bacterium that has become one of the models for biofilm development. B. subtilis 168 is a well-known domesticated strain that has been suggested to be deficient in robust biofilm formation. Moreover, the diversity of available B. subtilis laboratory strains and their derivatives have made it difficult to compare independent studies related to biofilm formation. Here, we analysed numerous 168 stocks from multiple laboratories for their ability to develop biofilms in different set-ups and media. We report a wide variation among the biofilm-forming capabilities of diverse stocks of B. subtilis 168, both in architecturally complex colonies and liquid-air interface pellicles, as well as during plant root colonization. Some 168 variants are indeed unable to develop robust biofilm structures, while others do so as efficiently as the non-domesticated NCIB 3610 strain. In all cases studied, the addition of glucose to the medium dramatically improved biofilm development of the laboratory strains. Furthermore, the expression of biofilm matrix component operons, epsA-O and tapA-sipW-tasA, was monitored during colony biofilm formation. We found a lack of direct correlation between the expression of these genes and the complexity of wrinkles in colony biofilms. However, the presence of a single mutation in the exopolysaccharide-related gene epsC correlates with the ability of the stocks tested to form architecturally complex colonies and pellicles, and to colonize plant roots.
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Affiliation(s)
- Ramses Gallegos-Monterrosa
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Eisha Mhatre
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Ákos T Kovács
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
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64
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Song Y, Nikoloff JM, Fu G, Chen J, Li Q, Xie N, Zheng P, Sun J, Zhang D. Promoter Screening from Bacillus subtilis in Various Conditions Hunting for Synthetic Biology and Industrial Applications. PLoS One 2016; 11:e0158447. [PMID: 27380260 PMCID: PMC4933340 DOI: 10.1371/journal.pone.0158447] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/16/2016] [Indexed: 11/24/2022] Open
Abstract
The use of Bacillus subtilis in synthetic biology and metabolic engineering is highly desirable to take advantage of the unique metabolic pathways present in this organism. To do this, an evaluation of B. subtilis’ intrinsic biological parts is required to determine the best strategies to accurately regulate metabolic circuits and expression of target proteins. The strengths of promoter candidates were evaluated by measuring relative fluorescence units of a green fluorescent protein reporter, integrated into B. subtilis’ chromosome. A total of 84 predicted promoter sequences located upstream of different classes of proteins including heat shock proteins, cell-envelope proteins, and proteins resistant against toxic metals (based on similarity) and other kinds of genes were tested. The expression levels measured ranged from 0.0023 to 4.53-fold of the activity of the well-characterized strong promoter P43. No significant shifts were observed when strains, carrying different promoter candidates, were cultured at high temperature or in media with ethanol, but some strains showed increased activity when cultured under high osmotic pressure. Randomly selected promoter candidates were tested and found to activate transcription of thermostable β-galactosidase (bgaB) at a similar level, implying the ability of these sequences to function as promoter elements in multiple genetic contexts. In addition, selected promoters elevated the final production of both cytoplasmic bgaB and secreted protein α-amylase to about fourfold and twofold, respectively. The generated data allows a deeper understanding of B. subtilis’ metabolism and will facilitate future work to develop this organism for synthetic biology.
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Affiliation(s)
- Yafeng Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jonas M Nikoloff
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jingqi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Qinggang Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Nengzhong Xie
- National Engineering Research Center for Non-food Biorefinery, State Key Laboratory of Non-food Biomass Energy and Enzyme Technology, Nanning 5300074, P. R. China
- Guangxi Biomass Industrialization Engineering Institute, Guangxi Academy of Sciences, Nanning 530007, P. R. China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
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65
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Mwita L, Chan WY, Pretorius T, Lyantagaye SL, Lapa SV, Avdeeva LV, Reva ON. Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates. Gene 2016; 590:18-28. [PMID: 27259668 DOI: 10.1016/j.gene.2016.05.045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/04/2016] [Accepted: 05/31/2016] [Indexed: 12/17/2022]
Abstract
Despite successful use of Plant Growth Promoting Rhizobacteria (PGPR) in agriculture, little is known about specific mechanisms of gene regulation facilitating the effective communication between bacteria and plants during plant colonization. Active PGPR strain Bacillus atrophaeus UCMB-5137 was studied in this research. RNA sequencing profiles were generated in experiments where root exudate stimulations were used to mimic interactions between bacteria and plants. It was found that the gene regulation in B. atrophaeus UCMB-5137 in response to the root exudate stimuli differed from the reported gene regulation at similar conditions in B. amyloliquefaciens FZB42, which was considered as a paradigm PGPR. This difference was explained by hypersensitivity of UCMB-5137 to the root exudate stimuli impelling it to a sessile root colonization behavior through the CcpA-CodY-AbrB regulation. It was found that the transcriptional factor DegU also could play an important role in gene regulations during plant colonization. A significant stress caused by the root exudates on in vitro cultivated B. atrophaeus UCMB-5137 was noticed and discussed. Multiple cases of conflicted gene regulations showed scantiness of our knowledge on the regulatory network in Bacillus. Some of these conflicted regulations could be explained by interference of non-coding RNA (ncRNA). Search through differential expressed intergenic regions revealed 49 putative loci of ncRNA regulated by the root exudate stimuli. Possible target mRNA were predicted and a general regulatory network of B. atrophaeus UCMB-5137 genome was designed.
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Affiliation(s)
- Liberata Mwita
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Wai Yin Chan
- Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Theresa Pretorius
- Department of Microbiology and Plant Pathology, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa
| | - Sylvester L Lyantagaye
- Department of Molecular Biology and Biotechnology, College of Natural and Applied Sciences, University of Dar es Salaam, P.O. Box 35179, Dar es Salaam, Tanzania
| | - Svitlana V Lapa
- Dep. Antibiotics, D. K. Zabolotnogo Institute of Microbiology and Virology, 154 Zabolotnogo Str., Kiev, Ukraine
| | - Lilia V Avdeeva
- Dep. Antibiotics, D. K. Zabolotnogo Institute of Microbiology and Virology, 154 Zabolotnogo Str., Kiev, Ukraine
| | - Oleg N Reva
- Centre for Bioinformatics and Computational Biology, Dep. Biochemistry, University of Pretoria, Lynnwood Rd, Hillcrest, Pretoria 0002, South Africa.
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Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol. Microb Cell Fact 2016; 15:73. [PMID: 27142075 PMCID: PMC4855977 DOI: 10.1186/s12934-016-0470-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/24/2016] [Indexed: 02/02/2023] Open
Abstract
Background Given its high surplus and low cost, glycerol has emerged as interesting carbon substrate for the synthesis of value-added chemicals. The soil bacterium Pseudomonas putida KT2440 can use glycerol to synthesize medium-chain-length poly(3-hydroxyalkanoates) (mcl-PHA), a class of biopolymers of industrial interest. Here, glycerol metabolism in P. putida KT2440 was studied on the level of gene expression (transcriptome) and metabolic fluxes (fluxome), using precisely adjusted chemostat cultures, growth kinetics and stoichiometry, to gain a systematic understanding of the underlying metabolic and regulatory network. Results Glycerol-grown P. putida KT2440 has a maintenance energy requirement [0.039 (mmolglycerol (gCDW h)−1)] that is about sixteen times lower than that of other bacteria, such as Escherichia coli, which provides a great advantage to use this substrate commercially. The shift from carbon (glycerol) to nitrogen (ammonium) limitation drives the modulation of specific genes involved in glycerol metabolism, transport electron chain, sensors to assess the energy level of the cell, and PHA synthesis, as well as changes in flux distribution to increase the precursor availability for PHA synthesis (Entner–Doudoroff pathway and pyruvate metabolism) and to reduce respiration (glyoxylate shunt). Under PHA-producing conditions (N-limitation), a higher PHA yield was achieved at low dilution rate (29.7 wt% of CDW) as compared to a high rate (12.8 wt% of CDW). By-product formation (succinate, malate) was specifically modulated under these regimes. On top of experimental data, elementary flux mode analysis revealed the metabolic potential of P. putida KT2440 to synthesize PHA and identified metabolic engineering targets towards improved production performance on glycerol. Conclusion This study revealed the complex interplay of gene expression levels and metabolic fluxes under PHA- and non-PHA producing conditions using the attractive raw material glycerol as carbon substrate. This knowledge will form the basis for the development of future metabolically engineered hyper-PHA-producing strains derived from the versatile bacterium P. putida KT2440.
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Lassek C, Berger A, Zühlke D, Wittmann C, Riedel K. Proteome and carbon flux analysis of Pseudomonas aeruginosa clinical isolates from different infection sites. Proteomics 2016; 16:1381-5. [PMID: 26959854 DOI: 10.1002/pmic.201500228] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 01/31/2016] [Accepted: 03/03/2016] [Indexed: 11/11/2022]
Abstract
Pseudomonas aeruginosa is known as opportunistic pathogen frequently isolated from different infection sites. To investigate the expression rates of P. aeruginosa proteins commonly expressed by different clinical isolates, absolute protein quantities were determined employing a gel-free and data-independent LC-IMS(E) approach. Moreover, the metabolic diversity of these isolates was investigated by (13) C-metabolic flux analyses. 812 proteins were reproducibly identified and absolutely quantified for the reference strain P. aeruginosa PAO1, 363 of which were also identified and relatively quantified in all isolates. Whilst the majority of these proteins were expressed in constant amounts, expression rates of 42 proteins were highly variable between the isolates. Notably, the outer membrane protein OprH and the response regulator PhoP were strongly expressed in burned wounds isolates compared to lung/urinary tract isolates. Moreover, proteins involved in iron/amino acids uptake were found to be highly abundant in urinary tract isolates. The fluxome data revealed a conserved glycolysis, and a niche-specific divergence in fluxes through the glyoxylate shunt and the TCA cycle among the isolates. The integrated proteome/fluxome analysis did not indicate straightforward correlation between the protein amount and flux, but rather points to additional layers of regulation that mediate metabolic adaption of P. aeruginosa to different host environments. All MS data have been deposited in the ProteomeXchange with identifier PXD002373 (http://proteomecentral.proteomexchange.org/dataset/PXD002373).
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Affiliation(s)
- Christian Lassek
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Antje Berger
- Institute of Biochemical Engineering, TU Braunschweig, Braunschweig, Germany
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Saarbrücken, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.,Helmholtz Centre for Infection Research, Braunschweig, Germany
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68
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Dersch LM, Beckers V, Wittmann C. Green pathways: Metabolic network analysis of plant systems. Metab Eng 2016; 34:1-24. [DOI: 10.1016/j.ymben.2015.12.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/30/2015] [Accepted: 12/01/2015] [Indexed: 12/18/2022]
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69
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Becker J, Wittmann C. Advanced Biotechnology: Metabolically Engineered Cells for the Bio-Based Production of Chemicals and Fuels, Materials, and Health-Care Products. Angew Chem Int Ed Engl 2015; 54:3328-50. [DOI: 10.1002/anie.201409033] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 12/16/2022]
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70
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Biotechnologie von Morgen: metabolisch optimierte Zellen für die bio-basierte Produktion von Chemikalien und Treibstoffen, Materialien und Gesundheitsprodukten. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201409033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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71
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Kerkhoven EJ, Lahtvee PJ, Nielsen J. Applications of computational modeling in metabolic engineering of yeast. FEMS Yeast Res 2015; 15:1-13. [PMID: 25156867 DOI: 10.1111/1567-1364.12199] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/28/2014] [Accepted: 08/19/2014] [Indexed: 12/13/2022] Open
Abstract
Generally, a microorganism's phenotype can be described by its pattern of metabolic fluxes. Although fluxes cannot be measured directly, inference of fluxes is well established. In biotechnology the aim is often to increase the capacity of specific fluxes. For this, metabolic engineering methods have been developed and applied extensively. Many of these rely on balancing of intracellular metabolites, redox, and energy fluxes, using genome-scale models (GEMs) that in combination with appropriate objective functions and constraints can be used to predict potential gene targets for obtaining a preferred flux distribution. These methods point to strategies for altering gene expression; however, fluxes are often controlled by post-transcriptional events. Moreover, GEMs are usually not taking into account metabolic regulation, thermodynamics and enzyme kinetics. To facilitate metabolic engineering, tools from synthetic biology have emerged, enabling integration and assembly of naturally nonexistent, but well-characterized components into a living organism. To describe these systems kinetic models are often used and to integrate these systems with the standard metabolic engineering approach, it is necessary to expand the modeling of metabolism to consider kinetics of individual processes. This review will give an overview about models available for metabolic engineering of yeast and discusses their applications.
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Affiliation(s)
- Eduard J Kerkhoven
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Petri-Jaan Lahtvee
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
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72
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Broy S, Chen C, Hoffmann T, Brock NL, Nau-Wagner G, Jebbar M, Smits SHJ, Dickschat JS, Bremer E. Abiotic stress protection by ecologically abundant dimethylsulfoniopropionate and its natural and synthetic derivatives: insights from Bacillus subtilis. Environ Microbiol 2014; 17:2362-78. [PMID: 25384455 DOI: 10.1111/1462-2920.12698] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/22/2014] [Accepted: 10/28/2014] [Indexed: 12/01/2022]
Abstract
Dimethylsulfoniopropionate (DMSP) is an abundant osmolyte and anti-stress compound produced primarily in marine ecosystems. After its release into the environment, microorganisms can exploit DMSP as a source of sulfur and carbon, or accumulate it as an osmoprotectant. However, import systems for this ecophysiologically important compatible solute, and its stress-protective properties for microorganisms that do not produce it are insufficiently understood. Here we address these questions using a well-characterized set of Bacillus subtilis mutants to chemically profile the influence of DMSP import on stress resistance, the osmostress-adaptive proline pool and on osmotically controlled gene expression. We included in this study the naturally occurring selenium analogue of DMSP, dimethylseleniopropionate (DMSeP), as well as a set of synthetic DMSP derivatives. We found that DMSP is not a nutrient for B. subtilis, but it serves as an excellent stress protectant against challenges conferred by sustained high salinity or lasting extremes in both low and high growth temperatures. DMSeP and synthetic DMSP derivatives retain part of these stress protective attributes, but DMSP is clearly the more effective stress protectant. We identified the promiscuous and widely distributed ABC transporter OpuC as a high-affinity uptake system not only for DMSP, but also for its natural and synthetic derivatives.
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Affiliation(s)
- Sebastian Broy
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Chiliang Chen
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
| | - Nelson L Brock
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany
| | - Gabriele Nau-Wagner
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany
| | - Mohamed Jebbar
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,Laboratory of Microbiology of Extreme Environments, UMR 6197 (CNRS - Ifremer - UBO), European Institute of Marine Studies, University of West Brittany (Brest), Technopole Brest-Iroise, F-29280, Plouzané, France
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitäts Str. 1, D-40225, Düsseldorf, Germany
| | - Jeroen S Dickschat
- Institute of Organic Chemistry, Technical University of Braunschweig, Hagenring 30, D-38106, Braunschweig, Germany.,Kekule-Institute for Organic Chemistry and Biochemistry, Friedrich Wilhelms-University Bonn, Gerhard-Domagk-Str. 1, D-53121, Bonn, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Karl-von-Frisch Str. 8, D-35043, Marburg, Germany.,LOEWE-Center for Synthetic Microbiology, Philipps-University Marburg, Hans-Meerwein Str., D-35043, Marburg, Germany
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73
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Voigt B, Schroeter R, Schweder T, Jürgen B, Albrecht D, van Dijl JM, Maurer KH, Hecker M. A proteomic view of cell physiology of the industrial workhorse Bacillus licheniformis. J Biotechnol 2014; 191:139-49. [DOI: 10.1016/j.jbiotec.2014.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/26/2014] [Accepted: 06/03/2014] [Indexed: 11/16/2022]
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74
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Juhas M, Reuß DR, Zhu B, Commichau FM. Bacillus subtilis and Escherichia coli essential genes and minimal cell factories after one decade of genome engineering. Microbiology (Reading) 2014; 160:2341-2351. [DOI: 10.1099/mic.0.079376-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Investigation of essential genes, besides contributing to understanding the fundamental principles of life, has numerous practical applications. Essential genes can be exploited as building blocks of a tightly controlled cell ‘chassis’. Bacillus subtilis and Escherichia coli K-12 are both well-characterized model bacteria used as hosts for a plethora of biotechnological applications. Determination of the essential genes that constitute the B. subtilis and E. coli minimal genomes is therefore of the highest importance. Recent advances have led to the modification of the original B. subtilis and E. coli essential gene sets identified 10 years ago. Furthermore, significant progress has been made in the area of genome minimization of both model bacteria. This review provides an update, with particular emphasis on the current essential gene sets and their comparison with the original gene sets identified 10 years ago. Special attention is focused on the genome reduction analyses in B. subtilis and E. coli and the construction of minimal cell factories for industrial applications.
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Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Daniel R. Reuß
- Department of General Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Bingyao Zhu
- Department of General Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Fabian M. Commichau
- Department of General Microbiology, Georg-August-University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
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75
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Uptake of amino acids and their metabolic conversion into the compatible solute proline confers osmoprotection to Bacillus subtilis. Appl Environ Microbiol 2014; 81:250-9. [PMID: 25344233 DOI: 10.1128/aem.02797-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The data presented here reveal a new facet of the physiological adjustment processes through which Bacillus subtilis can derive osmostress protection. We found that the import of proteogenic (Glu, Gln, Asp, Asn, and Arg) and of nonproteogenic (Orn and Cit) amino acids and their metabolic conversion into proline enhances growth under otherwise osmotically unfavorable conditions. Osmoprotection by amino acids depends on the functioning of the ProJ-ProA-ProH enzymes, but different entry points into this biosynthetic route are used by different amino acids to finally yield the compatible solute proline. Glu, Gln, Asp, and Asn are used to replenish the cellular pool of glutamate, the precursor for proline production, whereas Arg, Orn, and Cit are converted into γ-glutamic semialdehyde/Δ(1)-pyrroline-5-carboxylate, an intermediate in proline biosynthesis. The import of Glu, Gln, Asp, Asn, Arg, Orn, and Cit did not lead to a further increase in the size of the proline pool that is already present in osmotically stressed cells. Hence, our data suggest that osmoprotection of B. subtilis by this group of amino acids rests on the savings in biosynthetic building blocks and energy that would otherwise have to be devoted either to the synthesis of the proline precursor glutamate or of proline itself. Since glutamate is the direct biosynthetic precursor for proline, we studied its uptake and found that GltT, an Na(+)-coupled symporter, is the main uptake system for both glutamate and aspartate in B. subtilis. Collectively, our data show how effectively B. subtilis can exploit environmental resources to derive osmotic-stress protection through physiological means.
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76
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Bashir A, Hoffmann T, Kempf B, Xie X, Smits SHJ, Bremer E. Plant-derived compatible solutes proline betaine and betonicine confer enhanced osmotic and temperature stress tolerance to Bacillus subtilis. MICROBIOLOGY-SGM 2014; 160:2283-2294. [PMID: 25012968 DOI: 10.1099/mic.0.079665-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
L-Proline is a widely used compatible solute and is employed by Bacillus subtilis, through both synthesis and uptake, as an osmostress protectant. Here, we assessed the stress-protective potential of the plant-derived L-proline derivatives N-methyl-L-proline, L-proline betaine (stachydrine), trans-4-L-hydroxproline and trans-4-hydroxy-L-proline betaine (betonicine) for cells challenged by high salinity or extremes in growth temperature. l-Proline betaine and betonicine conferred salt stress protection, but trans-4-L-hydroxyproline and N-methyl-L-proline was unable to do so. Except for L-proline, none of these compounds served as a nutrient for B. subtilis. L-Proline betaine was a considerably better osmostress protectant than betonicine, and its import strongly reduced the l-proline pool produced by B. subtilis under osmotic stress conditions, whereas a supply of betonicine affected the L-proline pool only modestly. Both compounds downregulated the transcription of the osmotically inducible opuA operon, albeit to different extents. Mutant studies revealed that L-proline betaine was taken up via the ATP-binding cassette transporters OpuA and OpuC, and the betaine-choline-carnitine-transporter-type carrier OpuD; betonicine was imported only through OpuA and OpuC. L-Proline betaine and betonicine also served as temperature stress protectants. A striking difference between these chemically closely related compounds was observed: L-proline betaine was an excellent cold stress protectant, but did not provide heat stress protection, whereas the reverse was true for betonicine. Both compounds were primarily imported in temperature-challenged cells via the high-capacity OpuA transporter. We developed an in silico model for the OpuAC-betonicine complex based on the crystal structure of the OpuAC solute receptor complexed with L-proline betaine.
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Affiliation(s)
- Abdallah Bashir
- Max Planck Institute for Terrestrial Microbiology, Emeritus Group R. K. Thauer, Karl-von-Frisch Strasse 10, 35043 Marburg, Germany.,Al-Azhar University Gaza, Faculty of Science, Biology Department, PO Box 1277, Gaza, Palestine.,Laboratory for Microbiology, Department of Biology, Philipps University Marburg, Karl-von-Frisch Strasse 8, 35043 Marburg, Germany
| | - Tamara Hoffmann
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Strasse, 35043 Marburg, Germany.,Laboratory for Microbiology, Department of Biology, Philipps University Marburg, Karl-von-Frisch Strasse 8, 35043 Marburg, Germany
| | - Bettina Kempf
- Laboratory for Microbiology, Department of Biology, Philipps University Marburg, Karl-von-Frisch Strasse 8, 35043 Marburg, Germany
| | - Xiulan Xie
- NMR Facility, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse 8, 35043 Marburg, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstrasse 1, 40225 Düsseldorf, Germany
| | - Erhard Bremer
- LOEWE Center for Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Strasse, 35043 Marburg, Germany.,Laboratory for Microbiology, Department of Biology, Philipps University Marburg, Karl-von-Frisch Strasse 8, 35043 Marburg, Germany
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