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Mardoukhi MSY, Rapp J, Irisarri I, Gunka K, Link H, Marienhagen J, de Vries J, Stülke J, Commichau FM. Metabolic rewiring enables ammonium assimilation via a non-canonical fumarate-based pathway. Microb Biotechnol 2024; 17:e14429. [PMID: 38483038 PMCID: PMC10938345 DOI: 10.1111/1751-7915.14429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/16/2024] [Accepted: 02/09/2024] [Indexed: 03/17/2024] Open
Abstract
Glutamate serves as the major cellular amino group donor. In Bacillus subtilis, glutamate is synthesized by the combined action of the glutamine synthetase and the glutamate synthase (GOGAT). The glutamate dehydrogenases are devoted to glutamate degradation in vivo. To keep the cellular glutamate concentration high, the genes and the encoded enzymes involved in glutamate biosynthesis and degradation need to be tightly regulated depending on the available carbon and nitrogen sources. Serendipitously, we found that the inactivation of the ansR and citG genes encoding the repressor of the ansAB genes and the fumarase, respectively, enables the GOGAT-deficient B. subtilis mutant to synthesize glutamate via a non-canonical fumarate-based ammonium assimilation pathway. We also show that the de-repression of the ansAB genes is sufficient to restore aspartate prototrophy of an aspB aspartate transaminase mutant. Moreover, in the presence of arginine, B. subtilis mutants lacking fumarase activity show a growth defect that can be relieved by aspB overexpression, by reducing arginine uptake and by decreasing the metabolic flux through the TCA cycle.
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Affiliation(s)
| | - Johanna Rapp
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
- Campus Institute Data ScienceUniversity of GöttingenGöttingenGermany
| | - Katrin Gunka
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
| | - Hannes Link
- Interfaculty Institute for Microbiology and Infection Medicine TübingenUniversity of TübingenTübingenGermany
| | - Jan Marienhagen
- Institute of Bio‐ and Geosciences, IBG‐1: BiotechnologyForschungszentrum JülichJülichGermany
- Institut of BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute of Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
- Campus Institute Data ScienceUniversity of GöttingenGöttingenGermany
| | - Jörg Stülke
- Department of General Microbiology, Institute for Microbiology and Genetics, GZMBGeorg‐August‐University GöttingenGöttingenGermany
| | - Fabian M. Commichau
- FG Molecular Microbiology, Institute for BiologyUniversity of HohenheimStuttgartGermany
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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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Yang S, Wang A, Li J, Shao Y, Sun F, Li S, Cao K, Liu H, Xiong P, Gao Z. Improved biosynthesis of heme in Bacillus subtilis through metabolic engineering assisted fed-batch fermentation. Microb Cell Fact 2023; 22:102. [PMID: 37198628 DOI: 10.1186/s12934-023-02077-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/31/2023] [Indexed: 05/19/2023] Open
Abstract
BACKGROUND Heme is an iron/porphyrin complex compound, widely used in the health care, food, and pharmaceutical industries. It is more advantageous and attractive to develop microbial cell factories to produce heme by fermentation, with lower production costs and environmentally more friendly procedures than those of the traditional extraction based on animal blood. In this study, Bacillus subtilis, a typical industrial model microorganism of food safety grade, was used for the first time as the host to synthesize heme. RESULTS The heme biosynthetic pathway was engineered as four modules, the endogenous C5 pathway, the heterologous C4 pathway, the uroporphyrinogen (urogen) III synthesis pathway, and the downstream synthesis pathway. Knockout of hemX encoding the negative effector of the concentration of HemA, overexpression of hemA encoding glutamyl-tRNA reductase, and knockout of rocG encoding the major glutamate dehydrogenase in the C5 pathway, resulted in an increase of 427% in heme production. Introduction of the heterologous C4 pathway showed a negligible effect on heme biosynthesis. Overexpression of hemCDB, which encoded hydroxymethylbilane synthase, urogen III synthase, and porphobilinogen synthase participating in the urogen III synthesis pathway, increased heme production by 39%. Knockouts of uroporphyrinogen methyltransferase gene nasF and both heme monooxygenase genes hmoA and hmoB in the downstream synthesis pathway increased heme production by 52%. The engineered B. subtilis produced 248.26 ± 6.97 mg/L of total heme with 221.83 ± 4.71 mg/L of extracellular heme during the fed-batch fermentation in 10 L fermenter. CONCLUSIONS Strengthening endogenous C5 pathway, urogen III synthesis pathway and downstream synthesis pathway promoted the biosynthesis of heme in B. subtilis. The engineered B. subtilis strain has great potential as a microbial cell factory for efficient industrial heme production.
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Affiliation(s)
- Shaomei Yang
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Anlong Wang
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Jiachang Li
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Yunhang Shao
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, 30043, USA
| | - Shucheng Li
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Kai Cao
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Hongliang Liu
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, 266 Xincun West Road, Zibo, 255000, China.
| | - Zhengquan Gao
- School of Pharmacy, Binzhou Medical University, 346 Guanhai Road, Yantai, 256603, China.
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Cai DS, Yang XY, Yang YQ, Gao F, Cheng XH, Zhao YJ, Qi R, Zhang YZ, Lu JH, Lin XY, Liu YJ, Xu B, Wang PL, Lei HM. Design and synthesis of novel anti-multidrug-resistant staphylococcus aureus derivatives of glycyrrhetinic acid by blocking arginine biosynthesis, metabolic and H 2S biogenesis. Bioorg Chem 2023; 131:106337. [PMID: 36603244 DOI: 10.1016/j.bioorg.2022.106337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/12/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022]
Abstract
With the soaring number of multidrug-resistant bacteria, it is imperative to develop novel efficient antibacterial agents and discovery new antibacterial pathways. Herein, we designed and synthesized a series of structurally novel glycyrrhetinic acid (GA) derivatives against multidrug-resistant Staphylococcus aureus (MRSA). The in vitro antibacterial activity of these compounds was evaluated using the microbroth dilution method, agar plate coating experiments and real-time growth curves, respectively. Most of the target derivatives showed moderate antibacterial activity against Staphylococcus aureus (S. aureus) and MRSA (MIC = 3.125-25 μM), but inactivity against Escherichia coli (E. Coli) and Pseudomonas aeruginosa (P. aeruginosa) (MIC > 200 μM). Among them, compound 11 had the strongest antibacterial activity against MRSA, with an MIC value of 3.125 μM, which was 32 times and 64 times than the first-line antibiotics penicillin and norfloxacin, respectively. Additionally, transcriptomic (RNA-seq) and quantitative polymerase chain reaction (qPCR) analysis revealed that the antibacterial mechanism of compound 11 was through blocking the arginine biosynthesis and metabolic and the H2S biogenesis. Importantly, compound 11 was confirmed to have good biocompatibility through the in vitro hemolysis tests, cytotoxicity assays and the in vivo quail chicken chorioallantoic membrane (qCAM) experiments. Current study provided new potential antibacterial candidates from glycyrrhetinic acid derivatives for clinical treatment of MRSA infections.
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Affiliation(s)
- De-Sheng Cai
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Xiao-Yun Yang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Yu-Qin Yang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Feng Gao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Xue-Hao Cheng
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Ya-Juan Zhao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Rui Qi
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Yao-Zhi Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Ji-Hui Lu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Xiao-Yu Lin
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Yi-Jing Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China
| | - Bing Xu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China.
| | - Peng-Long Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China.
| | - Hai-Min Lei
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, Beijing 102488, PR China.
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Yeak KYC, Boekhorst J, Wels M, Abee T, Wells-Bennik MHJ. Prediction and validation of novel SigB regulon members in Bacillus subtilis and regulon structure comparison to Bacillales members. BMC Microbiol 2023; 23:17. [PMID: 36653740 PMCID: PMC9847131 DOI: 10.1186/s12866-022-02700-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 11/11/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Sigma factor B (SigB) is the central regulator of the general stress response in Bacillus subtilis and regulates a group of genes in response to various stressors, known as the SigB regulon members. Genes that are directly regulated by SigB contain a promotor binding motif (PBM) with a previously identified consensus sequence. RESULTS In this study, refined SigB PBMs were derived and different spacer compositions and lengths (N12-N17) were taken into account. These were used to identify putative SigB-regulated genes in the B. subtilis genome, revealing 255 genes: 99 had been described in the literature and 156 genes were newly identified, increasing the number of SigB putative regulon members (with and without a SigB PBM) to > 500 in B. subtilis. The 255 genes were assigned to five categories (I-V) based on their similarity to the original SigB consensus sequences. The functionalities of selected representatives per category were assessed using promoter-reporter fusions in wt and ΔsigB mutants upon exposure to heat, ethanol, and salt stress. The activity of the PrsbV (I) positive control was induced upon exposure to all three stressors. PytoQ (II) showed SigB-dependent activity only upon exposure to ethanol, whereas PpucI (II) with a N17 spacer and PylaL (III) with a N16 spacer showed mild induction regardless of heat/ethanol/salt stress. PywzA (III) and PyaaI (IV) displayed ethanol-specific SigB-dependent activities despite a lower-level conserved - 10 binding motif. PgtaB (V) was SigB-induced under ethanol and salt stress while lacking a conserved - 10 binding region. The activities of PygaO and PykaA (III) did not show evident changes under the conditions tested despite having a SigB PBM that highly resembled the consensus. The identified extended SigB regulon candidates in B. subtilis are mainly involved in coping with stress but are also engaged in other cellular processes. Orthologs of SigB regulon candidates with SigB PBMs were identified in other Bacillales genomes, but not all showed a SigB PBM. Additionally, genes involved in the integration of stress signals to activate SigB were predicted in these genomes, indicating that SigB signaling and regulon genes are species-specific. CONCLUSION The entire SigB regulatory network is sophisticated and not yet fully understood even for the well-characterized organism B. subtilis 168. Knowledge and information gained in this study can be used in further SigB studies to uncover a complete picture of the role of SigB in B. subtilis and other species.
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Affiliation(s)
- Kah Yen Claire Yeak
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Jos Boekhorst
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.4818.50000 0001 0791 5666Host Microbe Interactomics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Michiel Wels
- grid.419921.60000 0004 0588 7915NIZO, Ede, The Netherlands ,grid.426040.4Rijk Zwaan Breeding B.V, Fijnaart, The Netherlands
| | - Tjakko Abee
- grid.4818.50000 0001 0791 5666Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
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He H, Li Y, Zhang L, Ding Z, Shi G. Understanding and application of Bacillus nitrogen regulation: A synthetic biology perspective. J Adv Res 2022:S2090-1232(22)00205-3. [PMID: 36103961 DOI: 10.1016/j.jare.2022.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/22/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022] Open
Abstract
BACKGROUND Nitrogen sources play an essential role in maintaining the physiological and biochemical activity of bacteria. Nitrogen metabolism, which is the core of microorganism metabolism, makes bacteria able to autonomously respond to different external nitrogen environments by exercising complex internal regulatory networks to help them stay in an ideal state. Although various studies have been put forth to better understand this regulation in Bacillus, and many valuable viewpoints have been obtained, these views need to be presented systematically and their possible applications need to be specified. AIM OF REVIEW The intention is to provide a deep and comprehensive understanding of nitrogen metabolism in Bacillus, an important industrial microorganism, and thereby apply this regulatory logic to synthetic biology to improve biosynthesis competitiveness. In addition, the potential researches in the future are also discussed. KEY SCIENTIFIC CONCEPT OF REVIEW Understanding the meticulous regulation process of nitrogen metabolism in Bacillus not only could facilitate research on metabolic engineering but also could provide constructive insights and inspiration for studies of other microorganisms.
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Affiliation(s)
- Hehe He
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China.
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu Province 214122, PR China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu Province 214122, PR China.
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7
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Frank C, Hoffmann T, Zelder O, Felle MF, Bremer E. Enhanced Glutamate Synthesis and Export by the Thermotolerant Emerging Industrial Workhorse Bacillus methanolicus in Response to High Osmolarity. Front Microbiol 2021; 12:640980. [PMID: 33897645 PMCID: PMC8060640 DOI: 10.3389/fmicb.2021.640980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/01/2021] [Indexed: 11/13/2022] Open
Abstract
The thermotolerant methylotroph Bacillus methanolicus MGA3 was originally isolated from freshwater marsh soil. Due to its ability to use methanol as sole carbon and energy source, B. methanolicus is increasingly explored as a cell factory for the production of amino acids, fine chemicals, and proteins of biotechnological interest. During high cell density fermentation in industrial settings with the membrane-permeable methanol as the feed, the excretion of low molecular weight products synthesized from it will increase the osmotic pressure of the medium. This in turn will impair cell growth and productivity of the overall biotechnological production process. With this in mind, we have analyzed the core of the physiological adjustment process of B. methanolicus MGA3 to sustained high osmolarity surroundings. Through growth assays, we found that B. methanolicus MGA3 possesses only a restricted ability to cope with sustained osmotic stress. This finding is consistent with the ecophysiological conditions in the habitat from which it was originally isolated. None of the externally provided compatible solutes and proline-containing peptides affording osmostress protection for Bacillus subtilis were able to stimulate growth of B. methanolicus MGA3 at high salinity. B. methanolicus MGA3 synthesized the moderately effective compatible solute L-glutamate in a pattern such that the cellular pool increased concomitantly with increases in the external osmolarity. Counterintuitively, a large portion of the newly synthesized L-glutamate was excreted. The expression of the genes (gltAB and gltA2) for two L-glutamate synthases were upregulated in response to high salinity along with that of the gltC regulatory gene. Such a regulatory pattern of the system(s) for L-glutamate synthesis in Bacilli is new. Our findings might thus be generally relevant to understand the production of the osmostress protectant L-glutamate by those Bacilli that exclusively rely on this compatible solute for their physiological adjustment to high osmolarity surroundings.
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Affiliation(s)
- Christine Frank
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Tamara Hoffmann
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
| | - Oskar Zelder
- BASF SE, RWB/EC - A030 - L3/10, Ludwigshafen, Germany
| | - Max F Felle
- BASF SE, RWB/EC - A030 - L3/10, Ludwigshafen, Germany
| | - Erhard Bremer
- Laboratory for Microbiology, Department of Biology, Philipps-University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-University Marburg, Marburg, Germany
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8
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Sidiq KR, Chow MW, Zhao Z, Daniel RA. Alanine metabolism in Bacillus subtilis. Mol Microbiol 2020; 115:739-757. [PMID: 33155333 DOI: 10.1111/mmi.14640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022]
Abstract
Both isomeric forms of alanine play a crucial role in bacterial growth and viability; the L-isomer of this amino acid is one of the building blocks for protein synthesis, and the D-isomer is incorporated into the bacterial cell wall. Despite a long history of genetic manipulation of Bacillus subtilis using auxotrophic markers, the genes involved in alanine metabolism have not been characterized fully. In this work, we genetically characterized the major enzymes involved in B. subtilis alanine biosynthesis and identified an alanine permease, AlaP (YtnA), which we show has a major role in the assimilation of D-alanine from the environment. Our results provide explanations for the puzzling fact that growth of B. subtilis does not result in the significant accumulation of extracellular D-alanine. Interestingly, we find that in B. subtilis, unlike E. coli where multiple enzymes have a biochemical activity that can generate alanine, the primary synthetic enzyme for alanine is encoded by alaT, although a second gene, dat, can support slow growth of an L-alanine auxotroph. However, our results also show that Dat mediates the synthesis of D-alanine and its activity is influenced by the abundance of L-alanine. This work provides valuable insights into alanine metabolism that suggests that the relative abundance of D- and L-alanine might be linked with cytosolic pool of D and L-glutamate, thereby coupling protein and cell envelope synthesis with the metabolic status of the cell. The results also suggest that, although some of the purified enzymes involved in alanine biosynthesis have been shown to catalyze reversible reactions in vitro, most of them function unidirectionally in vivo.
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Affiliation(s)
- Karzan R Sidiq
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Man W Chow
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Zhao Zhao
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
| | - Richard A Daniel
- Centre for Bacterial Cell Biology, Biosciences Institute, Medical Faculty, Newcastle University, Newcastle Upon Tyne, UK
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9
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Jingjing E, Lili M, Zichao C, Rongze M, Qiaoling Z, Ruiyin S, Zongbai H, Junguo W. Effects of buffer salts on the freeze-drying survival rate of Lactobacillus plantarum LIP-1 based on transcriptome and proteome analyses. Food Chem 2020; 326:126849. [DOI: 10.1016/j.foodchem.2020.126849] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/16/2020] [Accepted: 04/17/2020] [Indexed: 10/24/2022]
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10
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Role of Glutamate Synthase in Biofilm Formation by Bacillus subtilis. J Bacteriol 2020; 202:JB.00120-20. [PMID: 32393519 DOI: 10.1128/jb.00120-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/04/2020] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis forms robust biofilms in the presence of large amounts of carbon sources, such as glycerol. However, little is known about the importance of the metabolic systems, or the relationship between metabolic systems and regulatory systems, involved in biofilm formation. Glutamate synthase, encoded by gltAB, is an enzyme that converts 2-ketoglutarate (a tricarboxylic acid [TCA] cycle intermediate) and glutamine into glutamate, which is a general amino group donor in metabolism. Here, we show that a ΔgltA mutant exhibited early arrest of biofilm formation in complex medium containing glycerol. This phenotype was not due to glutamate auxotrophy. Consistent with its biofilm formation phenotype, the ΔgltA mutant exhibited an early decrease in expression of the epsA and tapA operons, which are responsible for production of biofilm matrix polymers. This resulted from decreased activity of their regulator, Spo0A, as evidenced by reduced expression of other Spo0A-regulated genes in the ΔgltA mutant. The ΔgltA mutation prevented biofilm formation only in the presence of large amounts of glycerol. Moreover, limited expression of citrate synthase (but not other TCA enzymes) restored biofilm-forming ability to the ΔgltA mutant. These results indicate that the ΔgltA mutant accumulates an inhibitory intermediate (citrate) in the TCA cycle in the presence of large amounts of glycerol. The ΔgltA mutant formed biofilms when excess iron was added to the medium. Taken together, the data suggest that accumulation of citrate ions by the ΔgltA mutant causes iron shortage due to chelation, which prevents activation of Spo0A and causes defective biofilm formation.IMPORTANCE Bacillus subtilis, a model organism for bacterial biofilm formation, forms robust biofilms in a medium-dependent manner. Although the regulatory network that controls biofilm formation has been well studied, the importance of the underlying metabolic systems remains to be elucidated. The present study demonstrates that a metabolic disorder in a well-conserved metabolic system causes accumulation of an inhibitory metabolic intermediate that prevents activation of the system that regulates biofilm formation. These findings increase our understanding of the coordination between cellular metabolic status and the regulatory networks governing biofilm formation.
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11
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Gibhardt J, Heidemann JL, Bremenkamp R, Rosenberg J, Seifert R, Kaever V, Ficner R, Commichau FM. An extracytoplasmic protein and a moonlighting enzyme modulate synthesis of c-di-AMP in Listeria monocytogenes. Environ Microbiol 2020; 22:2771-2791. [PMID: 32250026 DOI: 10.1111/1462-2920.15008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/17/2020] [Accepted: 03/31/2020] [Indexed: 01/06/2023]
Abstract
The second messenger cyclic di-AMP (c-di-AMP) is essential for growth of many bacteria because it controls osmolyte homeostasis. c-di-AMP can regulate the synthesis of potassium uptake systems in some bacteria and it also directly inhibits and activates potassium import and export systems, respectively. Therefore, c-di-AMP production and degradation have to be tightly regulated depending on the environmental osmolarity. The Gram-positive pathogen Listeria monocytogenes relies on the membrane-bound diadenylate cyclase CdaA for c-di-AMP production and degrades the nucleotide with two phosphodiesterases. While the enzymes producing and degrading the dinucleotide have been reasonably well examined, the regulation of c-di-AMP production is not well understood yet. Here we demonstrate that the extracytoplasmic regulator CdaR interacts with CdaA via its transmembrane helix to modulate c-di-AMP production. Moreover, we show that the phosphoglucosamine mutase GlmM forms a complex with CdaA and inhibits the diadenylate cyclase activity in vitro. We also found that GlmM inhibits c-di-AMP production in L. monocytogenes when the bacteria encounter osmotic stress. Thus, GlmM is the major factor controlling the activity of CdaA in vivo. GlmM can be assigned to the class of moonlighting proteins because it is active in metabolism and adjusts the cellular turgor depending on environmental osmolarity.
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Affiliation(s)
- Johannes Gibhardt
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany.,FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Jana L Heidemann
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, University of Goettingen, 37077, Göttingen, Germany
| | - Rica Bremenkamp
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Jonathan Rosenberg
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Roland Seifert
- Institute of Pharmacology & Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Volkhard Kaever
- Institute of Pharmacology & Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute for Microbiology and Genetics, GZMB, University of Goettingen, 37077, Göttingen, Germany
| | - Fabian M Commichau
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
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12
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Garde R, Ibrahim B, Kovács ÁT, Schuster S. Differential equation-based minimal model describing metabolic oscillations in Bacillus subtilis biofilms. ROYAL SOCIETY OPEN SCIENCE 2020; 7:190810. [PMID: 32257302 PMCID: PMC7062081 DOI: 10.1098/rsos.190810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 01/15/2020] [Indexed: 06/11/2023]
Abstract
Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in Bacillus subtilis biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
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Affiliation(s)
- Ravindra Garde
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
- Max Planck Institute for Chemical Ecology, Hans-Knöll-Strasse 8, 07745 Jena, Germany
| | - Bashar Ibrahim
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
- Centre for Applied Mathematics and Bioinformatics, Gulf University for Science and Technology, Hawally 32093, Kuwait
- Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally 32093, Kuwait
| | - Ákos T. Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Søltofts Plads Building 221, 2800 Kgs. Lyngby, Denmark
| | - Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
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13
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Alvarado A, Behrens W, Josenhans C. Protein Activity Sensing in Bacteria in Regulating Metabolism and Motility. Front Microbiol 2020; 10:3055. [PMID: 32010106 PMCID: PMC6978683 DOI: 10.3389/fmicb.2019.03055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved complex sensing and signaling systems to react to their changing environments, most of which are present in all domains of life. Canonical bacterial sensing and signaling modules, such as membrane-bound ligand-binding receptors and kinases, are very well described. However, there are distinct sensing mechanisms in bacteria that are less studied. For instance, the sensing of internal or external cues can also be mediated by changes in protein conformation, which can either be implicated in enzymatic reactions, transport channel formation or other important cellular functions. These activities can then feed into pathways of characterized kinases, which translocate the information to the DNA or other response units. This type of bacterial sensory activity has previously been termed protein activity sensing. In this review, we highlight the recent findings about this non-canonical sensory mechanism, as well as its involvement in metabolic functions and bacterial motility. Additionally, we explore some of the specific proteins and protein-protein interactions that mediate protein activity sensing and their downstream effects. The complex sensory activities covered in this review are important for bacterial navigation and gene regulation in their dynamic environment, be it host-associated, in microbial communities or free-living.
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Affiliation(s)
- Alejandra Alvarado
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany
| | - Wiebke Behrens
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| | - Christine Josenhans
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
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14
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Dormeyer M, Lentes S, Richts B, Heermann R, Ischebeck T, Commichau FM. Variants of the Bacillus subtilis LysR-Type Regulator GltC With Altered Activator and Repressor Function. Front Microbiol 2019; 10:2321. [PMID: 31649652 PMCID: PMC6794564 DOI: 10.3389/fmicb.2019.02321] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/23/2019] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive soil bacterium Bacillus subtilis relies on the glutamine synthetase and the glutamate synthase for glutamate biosynthesis from ammonium and 2-oxoglutarate. During growth with the carbon source glucose, the LysR-type transcriptional regulator GltC activates the expression of the gltAB glutamate synthase genes. With excess of intracellular glutamate, the gltAB genes are not transcribed because the glutamate-degrading glutamate dehydrogenases (GDHs) inhibit GltC. Previous in vitro studies revealed that 2-oxoglutarate and glutamate stimulate the activator and repressor function, respectively, of GltC. Here, we have isolated GltC variants with enhanced activator or repressor function. The majority of the GltC variants with enhanced activator function differentially responded to the GDHs and to glutamate. The GltC variants with enhanced repressor function were still capable of activating the PgltA promoter in the absence of a GDH. Using PgltA promoter variants (PgltA∗) that are active independent of GltC, we show that the wild type GltC and the GltC variants with enhanced repressor function inactivate PgltA∗ promoters in the presence of the native GDHs. These findings suggest that GltC may also act as a repressor of the gltAB genes in vivo. We discuss a model combining previous models that were derived from in vivo and in vitro experiments.
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Affiliation(s)
- Miriam Dormeyer
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Sabine Lentes
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Björn Richts
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Ralf Heermann
- Institut für Molekulare Physiologie, Mikrobiologie und Weinforschung, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Till Ischebeck
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, Göttingen, Germany
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15
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Improvement of l-Leucine Production in Corynebacterium glutamicum by Altering the Redox Flux. Int J Mol Sci 2019; 20:ijms20082020. [PMID: 31022947 PMCID: PMC6515235 DOI: 10.3390/ijms20082020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/13/2019] [Accepted: 04/20/2019] [Indexed: 12/14/2022] Open
Abstract
The production of l-leucine was improved by the disruption of ltbR encoding transcriptional regulator and overexpression of the key genes (leuAilvBNCE) of the l-leucine biosynthesis pathway in Corynebacterium glutamicum XQ-9. In order to improve l-leucine production, we rationally engineered C. glutamicum to enhance l-leucine production, by improving the redox flux. On the basis of this, we manipulated the redox state of the cells by mutating the coenzyme-binding domains of acetohydroxyacid isomeroreductase encoded by ilvC, inserting NAD-specific leucine dehydrogenase, encoded by leuDH from Lysinibacillus sphaericus, and glutamate dehydrogenase encoded by rocG from Bacillus subtilis, instead of endogenous branched-chain amino acid transaminase and glutamate dehydrogenase, respectively. The yield of l-leucine reached 22.62 ± 0.17 g·L-1 by strain ΔLtbR-acetohydroxyacid isomeroreductase (AHAIR)M/ABNCME, and the concentrations of the by-products (l-valine and l-alanine) increased, compared to the strain ΔLtbR/ABNCE. Strain ΔLtbR-AHAIRMLeuDH/ABNCMLDH accumulated 22.87±0.31 g·L-1 l-leucine, but showed a drastically low l-valine accumulation (from 8.06 ± 0.35 g·L-1 to 2.72 ± 0.11 g·L-1), in comparison to strain ΔLtbR-AHAIRM/ABNCME, which indicated that LeuDH has much specificity for l-leucine synthesis but not for l-valine synthesis. Subsequently, the resultant strain ΔLtbR-AHAIRMLeuDHRocG/ABNCMLDH accumulated 23.31 ± 0.24 g·L-1 l-leucine with a glucose conversion efficiency of 0.191 g·g-1.
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16
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Wicke D, Schulz LM, Lentes S, Scholz P, Poehlein A, Gibhardt J, Daniel R, Ischebeck T, Commichau FM. Identification of the first glyphosate transporter by genomic adaptation. Environ Microbiol 2019; 21:1287-1305. [PMID: 30666812 DOI: 10.1111/1462-2920.14534] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/17/2019] [Accepted: 01/18/2019] [Indexed: 01/12/2023]
Abstract
The soil bacterium Bacillus subtilis can get into contact with growth-inhibiting substances, which may be of anthropogenic origin. Glyphosate is such a substance serving as a nonselective herbicide. Glyphosate specifically inhibits the 5-enolpyruvyl-shikimate-3-phosphate (EPSP) synthase, which generates an essential precursor for de novo synthesis of aromatic amino acids in plants, fungi, bacteria and archaea. Inhibition of the EPSP synthase by glyphosate results in depletion of the cellular levels of aromatic amino acids unless the environment provides them. Here, we have assessed the potential of B. subtilis to adapt to glyphosate at the genome level. In contrast to Escherichia coli, which evolves glyphosate resistance by elevating the production and decreasing the glyphosate sensitivity of the EPSP synthase, B. subtilis primarily inactivates the gltT gene encoding the high-affinity glutamate/aspartate symporter GltT. Further adaptation of the gltT mutants to glyphosate led to the inactivation of the gltP gene encoding the glutamate transporter GltP. Metabolome analyses confirmed that GltT is the major entryway of glyphosate into B. subtilis. GltP, the GltT homologue of E. coli also transports glyphosate into B. subtilis. Finally, we found that GltT is involved in uptake of the herbicide glufosinate, which inhibits the glutamine synthetase.
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Affiliation(s)
- Dennis Wicke
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Lisa M Schulz
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Sabine Lentes
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Patricia Scholz
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center of Molecular Biosciences (GZMB), University of Goettingen, 37077, Göttingen, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Johannes Gibhardt
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
| | - Till Ischebeck
- Department for Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Göttingen Center of Molecular Biosciences (GZMB), University of Goettingen, 37077, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute for Microbiology and Genetics, University of Goettingen, 37077, Göttingen, Germany
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17
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Noda-García L, Davidi D, Korenblum E, Elazar A, Putintseva E, Aharoni A, Tawfik DS. Chance and pleiotropy dominate genetic diversity in complex bacterial environments. Nat Microbiol 2019; 4:1221-1230. [PMID: 30936490 DOI: 10.1038/s41564-019-0412-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Abstract
How does environmental complexity affect the evolution of single genes? Here, we measured the effects of a set of Bacillus subtilis glutamate dehydrogenase mutants across 19 different environments-from phenotypically homogeneous single-cell populations in liquid media to heterogeneous biofilms, plant roots and soil populations. The effects of individual gene mutations on organismal fitness were highly reproducible in liquid cultures. However, 84% of the tested alleles showed opposing fitness effects under different growth conditions (sign environmental pleiotropy). In colony biofilms and soil samples, different alleles dominated in parallel replica experiments. Accordingly, we found that in these heterogeneous cell populations the fate of mutations was dictated by a combination of selection and drift. The latter relates to programmed prophage excisions that occurred during biofilm development. Overall, for each condition, a wide range of glutamate dehydrogenase mutations persisted and sometimes fixated as a result of the combined action of selection, pleiotropy and chance. However, over longer periods and in multiple environments, nearly all of this diversity would be lost-across all the environments and conditions that we tested, the wild type was the fittest allele.
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Affiliation(s)
- Lianet Noda-García
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Elisa Korenblum
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Assaf Elazar
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
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18
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Visualization of tandem repeat mutagenesis in Bacillus subtilis. DNA Repair (Amst) 2018; 63:10-15. [DOI: 10.1016/j.dnarep.2018.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/10/2018] [Accepted: 01/17/2018] [Indexed: 11/21/2022]
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19
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Reuß DR, Rath H, Thürmer A, Benda M, Daniel R, Völker U, Mäder U, Commichau FM, Stülke J. Changes of DNA topology affect the global transcription landscape and allow rapid growth of a Bacillus subtilis mutant lacking carbon catabolite repression. Metab Eng 2017; 45:171-179. [PMID: 29242163 DOI: 10.1016/j.ymben.2017.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 12/27/2022]
Abstract
Bacteria are able to prioritize preferred carbon sources from complex mixtures. This is achieved by the regulatory phenomenon of carbon catabolite repression. To allow the simultaneous utilization of multiple carbon sources and to prevent the time-consuming adaptation to each individual nutrient in biotechnological applications, mutants lacking carbon catabolite repression can be used. However, such mutants often exhibit pleiotropic growth defects. We have isolated and characterized mutations that overcome the growth defect of Bacillus subtilis ccpA mutants lacking the major regulator of catabolite repression, in particular their glutamate auxotrophy. Here we show, that distinct mutations affecting the essential DNA topoisomerase I (TopA) cause glutamate prototrophy of the ccpA mutant. These suppressing variants of the TopA enzyme exhibit increased activity resulting in enhanced relaxation of the DNA. Reduced DNA supercoiling results in enhanced expression of the gltAB operon encoding the biosynthetic glutamate synthase. This is achieved by a significant re-organization of the global transcription network accompanied by re-routing of metabolism, which results in inactivation of the glutamate dehydrogenase. Our results provide a link between DNA topology, the global transcriptional network, and glutamate metabolism and suggest that specific topA mutants may be well suited for biotechnological purposes.
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Affiliation(s)
- Daniel R Reuß
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Hermann Rath
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Martin Benda
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Ulrike Mäder
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg-August-University Göttingen, Göttingen, Germany; Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany.
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20
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Zhang W, Guo H, Cao C, Li L, Kwok LY, Zhang H, Sun Z. Adaptation of Lactobacillus casei Zhang to Gentamycin Involves an Alkaline Shock Protein. Front Microbiol 2017; 8:2316. [PMID: 29218040 PMCID: PMC5703869 DOI: 10.3389/fmicb.2017.02316] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/09/2017] [Indexed: 12/26/2022] Open
Abstract
Lactobacillus (L. casei) Zhang is a koumiss-originated probiotic strain, which was used as a model in a long-term antibiotics-driven evolution experiment to reveal bacterial evolutionary dynamics; and we isolated gentamycin-resistant L. casei Zhang descendents. To decipher the gentamycin resistance mechanism, here we cultivated the parental L. casei Zhang and its descendent cells in an antibiotics-containing environment to compare their global protein expression profiles using the iTRAQ-based proteomic approach. A total of 72 proteins were significantly up-regulated (>2.0-fold, P < 0.05), whilst 32 proteins were significantly down-regulated <−2.0-fold, P < 0.05) in the descendent line. The gentamycin-resistant descendent line showed elevated expression in some carbohydrates, amino acids, and purine metabolic pathways. Several stress-related proteins were also differentially expressed. Among them, one alkaline shock protein, asp23, was up-regulated most in the gentamycin-resistant strain (21.9-fold increase compared with the parental strain). The asp23 gene disruption mutant was significantly more sensitive to gentamycin compared with the wild type, suggesting an important role of this gene in developing the gentamycin-resistant phenotype in L. casei. Our report has described the adaptation of a probiotic strain that has acquired antibiotics resistance through long-term antibiotics exposure at the proteome level, and we revealed a novel mechanism of gentamycin resistance.
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Affiliation(s)
- Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Huiling Guo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Chenxia Cao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Lina Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot, China
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21
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Rosenberg J, Yeak KC, Commichau FM. A two-step evolutionary process establishes a non-native vitamin B6 pathway in Bacillus subtilis. Environ Microbiol 2017; 20:156-168. [PMID: 29027347 DOI: 10.1111/1462-2920.13950] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 12/11/2022]
Abstract
Pyridoxal 5'-phosphate (PLP), the most important form of vitamin B6 serves as a cofactor for many proteins. Two alternative pathways for de novo PLP biosynthesis are known: the short deoxy-xylulose-5-phosphate (DXP)-independent pathway, which is present in the Gram-positive model bacterium Bacillus subtilis and the longer DXP-dependent pathway, which has been intensively studied in the Gram-negative model bacterium Escherichia coli. Previous studies revealed that bacteria contain many promiscuous enzymes causing a so-called 'underground metabolism', which can be important for the evolution of novel pathways. Here, we evaluated the potential of B. subtilis to use a truncated non-native DXP-dependent PLP pathway from E. coli for PLP synthesis. Adaptive laboratory evolution experiments revealed that two non-native enzymes catalysing the last steps of the DXP-dependent PLP pathway and two genomic alterations are sufficient to allow growth of vitamin B6 auxotrophic bacteria as rapid as the wild type. Thus, the existence of an underground metabolism in B. subtilis facilitates the generation of a pathway for synthesis of PLP using parts of a non-native vitamin B6 pathway. The introduction of non-native enzymes into a metabolic network and rewiring of native metabolism could be helpful to generate pathways that might be optimized for producing valuable substances.
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Affiliation(s)
- Jonathan Rosenberg
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - KahYen C Yeak
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany
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22
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Dormeyer M, Lübke AL, Müller P, Lentes S, Reuß DR, Thürmer A, Stülke J, Daniel R, Brantl S, Commichau FM. Hierarchical mutational events compensate for glutamate auxotrophy of a Bacillus subtilis gltC mutant. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:279-289. [PMID: 28294562 DOI: 10.1111/1758-2229.12531] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 03/01/2017] [Accepted: 03/05/2017] [Indexed: 06/06/2023]
Abstract
Glutamate is the major donor of nitrogen for anabolic reactions. The Gram-positive soil bacterium Bacillus subtilis either utilizes exogenously provided glutamate or synthesizes it using the gltAB-encoded glutamate synthase (GOGAT). In the absence of glutamate, the transcription factor GltC activates expression of the GOGAT genes for glutamate production. Consequently, a gltC mutant strain is auxotrophic for glutamate. Using a genetic selection and screening system, we could isolate and differentiate between gltC suppressor mutants in one step. All mutants had acquired the ability to synthesize glutamate, independent of GltC. We identified (i) gain-of-function mutations in the gltR gene, encoding the transcription factor GltR, (ii) mutations in the promoter of the gltAB operon and (iii) massive amplification of the genomic locus containing the gltAB operon. The mutants belonging to the first two classes constitutively expressed the gltAB genes and produced sufficient glutamate for growth. By contrast, mutants that belong to the third class appeared most frequently and solved glutamate limitation by increasing the copy number of the poorly expressed gltAB genes. Thus, glutamate auxotrophy of a B. subtilis gltC mutant can be relieved in multiple ways. Moreover, recombination-dependent amplification of the gltAB genes is the predominant mutational event indicating a hierarchy of mutations.
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Affiliation(s)
- Miriam Dormeyer
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Anastasia L Lübke
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Peter Müller
- Department of Genetics, Bacterial Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, 07743, Germany
| | - Sabine Lentes
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Daniel R Reuß
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Jörg Stülke
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
| | - Sabine Brantl
- Department of Genetics, Bacterial Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, 07743, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg August University Göttingen, Grisebachstr. 8, Göttingen, 37077, Germany
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23
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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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24
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Glutamate dehydrogenase (RocG) in Bacillus licheniformis WX-02: Enzymatic properties and specific functions in glutamic acid synthesis for poly-γ-glutamic acid production. Enzyme Microb Technol 2017; 99:9-15. [DOI: 10.1016/j.enzmictec.2017.01.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 11/21/2022]
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25
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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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26
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Schaletzki Y, Kromrey ML, Bröderdorf S, Hammer E, Grube M, Hagen P, Sucic S, Freissmuth M, Völker U, Greinacher A, Rauch BH, Kroemer HK, Jedlitschky G. Several adaptor proteins promote intracellular localisation of the transporter MRP4/ABCC4 in platelets and haematopoietic cells. Thromb Haemost 2016; 117:105-115. [PMID: 27761583 DOI: 10.1160/th16-01-0045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 09/20/2016] [Indexed: 12/29/2022]
Abstract
The multidrug resistance protein 4 (MRP4/ABCC4) has been identified as an important transporter for signalling molecules including cyclic nucleotides and several lipid mediators in platelets and may thus represent a novel target to interfere with platelet function. Besides its localisation in the plasma membrane, MRP4 has been also detected in the membrane of dense granules in resting platelets. In polarised cells it is localised at the basolateral or apical plasma membrane. To date, the mechanism of MRP4 trafficking has not been elucidated; protein interactions may regulate both the localisation and function of this transporter. We approached this issue by searching for interacting proteins by in vitro binding assays, followed by immunoblotting and mass spectrometry, and by visualising their co-localisation in platelets and haematopoietic cells. We identified the PDZ domain containing scaffold proteins ezrin-binding protein 50 (EBP50/NHERF1), postsynaptic density protein 95 (PSD95), and sorting nexin 27 (SNX27), but also the adaptor protein complex 3 subunit β3A (AP3B1) and the heat shock protein HSP90 as putative interaction partners of MRP4. The knock-down of SNX27, PSD95, and AP3B1 by siRNA in megakaryoblastic leukaemia cells led to a redistribution of MRP4 from intracellular structures to the plasma membrane. Inhibition of HSP90 led to a diminished expression and retention of MRP4 in the endoplasmic reticulum. These results indicate that MRP4 localisation and function are regulated by multiple protein interactions. Changes in the adaptor proteins can hence lead to altered localisation and function of the transporter.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Gabriele Jedlitschky
- Gabriele Jedlitschky PhD, Department of Pharmacology, Center of Drug Absorption and Transport (C_DAT), University Medicine Greifswald, Felix-Hausdorff-Str. 3, 17487 Greifswald, Germany, Tel.: +49 3834 8622146, Fax: +49 3834 865631, E-mail:
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27
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Abstract
Cells that reside within a community can cooperate and also compete with each other for resources. It remains unclear how these opposing interactions are resolved at the population level. Here we investigate such an internal conflict within a microbial (Bacillus subtilis) biofilm community: cells in the biofilm periphery not only protect interior cells from external attack but also starve them through nutrient consumption. We discover that this conflict between protection and starvation is resolved through emergence of long-range metabolic co-dependence between peripheral and interior cells. As a result, biofilm growth halts periodically, increasing nutrient availability for the sheltered interior cells. We show that this collective oscillation in biofilm growth benefits the community in the event of a chemical attack. These findings indicate that oscillations support population-level conflict resolution by coordinating competing metabolic demands in space and time, suggesting new strategies to control biofilm growth.
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