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Katsube S, Sakai K, Ando T, Tobe R, Yoneyama H. l-Alanine Exporter AlaE Functions as One of the d-Alanine Exporters in Escherichia coli. Int J Mol Sci 2023; 24:10242. [PMID: 37373388 DOI: 10.3390/ijms241210242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
d-amino acids have recently been found to be present in the extracellular milieu at millimolar levels and are therefore assumed to play a physiological function. However, the pathway (or potential pathways) by which these d-amino acids are secreted remains unknown. Recently, Escherichia coli has been found to possess one or more energy-dependent d-alanine export systems. To gain insight into these systems, we developed a novel screening system in which cells expressing a putative d-alanine exporter could support the growth of d-alanine auxotrophs in the presence of l-alanyl-l-alanine. In the initial screening, five d-alanine exporter candidates, AlaE, YmcD, YciC, YraM, and YidH, were identified. Transport assays of radiolabeled d-alanine in cells expressing these candidates indicated that YciC and AlaE resulted in lower intracellular levels of d-alanine. Further detailed transport assays of AlaE in intact cells showed that it exports d-alanine in an expression-dependent manner. In addition, the growth constraints on cells in the presence of 90 mM d-alanine were mitigated by the overexpression of AlaE, implying that AlaE could export free d-alanine in addition to l-alanine under conditions in which intracellular d/l-alanine levels are raised. This study also shows, for the first time, that YciC could function as a d-alanine exporter in intact cells.
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Affiliation(s)
- Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Keiichiro Sakai
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Tasuke Ando
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Ryuta Tobe
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Hiroshi Yoneyama
- Laboratory of Animal Microbiology, Department of Animal Science, Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai 980-0845, Japan
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2
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Pavao A, Girinathan B, Peltier J, Altamirano Silva P, Dupuy B, Muti IH, Malloy C, Cheng LL, Bry L. Elucidating dynamic anaerobe metabolism with HRMAS 13C NMR and genome-scale modeling. Nat Chem Biol 2023; 19:556-564. [PMID: 36894723 PMCID: PMC10154198 DOI: 10.1038/s41589-023-01275-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
Anaerobic microbial metabolism drives critical functions within global ecosystems, host-microbiota interactions, and industrial applications, yet remains ill-defined. Here we advance a versatile approach to elaborate cellular metabolism in obligate anaerobes using the pathogen Clostridioides difficile, an amino acid and carbohydrate-fermenting Clostridia. High-resolution magic angle spinning nuclear magnetic resonance (NMR) spectroscopy of C. difficile, grown with fermentable 13C substrates, informed dynamic flux balance analysis (dFBA) of the pathogen's genome-scale metabolism. Analyses identified dynamic recruitment of oxidative and supporting reductive pathways, with integration of high-flux amino acid and glycolytic metabolism at alanine's biosynthesis to support efficient energy generation, nitrogen handling and biomass generation. Model predictions informed an approach leveraging the sensitivity of 13C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow from [U-13C]glucose and [15N]leucine, confirming the formation of [13C,15N]alanine. Findings identify metabolic strategies used by C. difficile to support its rapid colonization and expansion in gut ecosystems.
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Affiliation(s)
- Aidan Pavao
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brintha Girinathan
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Ginkgo Bioworks, The Innovation and Design Building, Boston, MA, USA
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
- Institute for Integrative Biology of the Cell (I2BC), 91198, University of Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Pamela Altamirano Silva
- Centre for Investigations in Tropical Diseases, Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Isabella H Muti
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Craig Malloy
- Department of Radiology, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Leo L Cheng
- Departments of Radiology and Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Chaves GL, Batista RS, Cunha JDS, Oliveira DB, da Silva MR, Pisani GFD, Selistre-de-Araújo HS, Zangirolami TC, da Silva AJ. Improving 3-hydroxypropionic acid production in E. coli by in silico prediction of new metabolic targets. N Biotechnol 2022; 72:80-88. [PMID: 36272546 DOI: 10.1016/j.nbt.2022.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
3-Hydroxypropionic acid (3-HP) production from renewable feedstocks is of great interest in efforts to develop greener processes for obtaining this chemical platform. Here we report an engineered E. coli strain for 3-HP production through the β-alanine pathway. To obtain a new strain capable of producing 3-HP, the pathway was established by overexpressing the enzymes pyruvate aminotransferase, 3-hydroxyacid dehydrogenase, and L-aspartate-1-decarboxylase. Further increase of the 3-HP titer was achieved using evolutionary optimizations of a genome-scale metabolic model of E. coli containing the adopted pathway. From these optimizations, three non-intuitive targets for in vivo assessment were identified: L-alanine aminotransferase and alanine racemase overexpression, and L-valine transaminase knock-out. The implementation of these targets in the production strain resulted in a 40% increase in 3-HP titer. The strain was further engineered to overexpress phosphoenolpyruvate carboxylase, reaching 0.79 ± 0.02 g/L of 3-HP when grown using glucose. Surprisingly, this strain produced 63% more of the desired product when grown using a mixture of glucose and xylose (1:1, C-mol), and gene expression analysis showed that the cellular adjustment to consume xylose had a positive impact on 3-HP accumulation. Fed-batch culture with xylose feeding led to a final titer of 29.1 g/L. These results reinforce the value of computational methods in strain engineering, enabling the design of more efficient strategies to be assessed. Moreover, higher production of 3-HP under a sugar mixture condition points towards the development of bioprocesses based on renewable resources, such as hemicellulose hydrolysates.
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Affiliation(s)
- Gabriel Luz Chaves
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Raquel Salgado Batista
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Josivan de Sousa Cunha
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Davi Benedito Oliveira
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Mateus Ribeiro da Silva
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), 13083-970 Campinas, SP, Brazil
| | - Graziéle Fernanda Deriggi Pisani
- Department of Physiological Sciences, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | | | - Teresa Cristina Zangirolami
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil
| | - Adilson José da Silva
- Graduate Program of Chemical Engineering, Federal University of São Carlos, Rod. Washington Luís, km 235, São Carlos, SP 13565-905, Brazil.
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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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L-Alanine Exporter, AlaE, of Escherichia coli Functions as a Safety Valve to Enhance Survival under Feast Conditions. Int J Mol Sci 2019; 20:ijms20194942. [PMID: 31591285 PMCID: PMC6801825 DOI: 10.3390/ijms20194942] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022] Open
Abstract
The intracellular level of amino acids is determined by the balance between their anabolic and catabolic pathways. L-alanine is anabolized by three L-alanine synthesizing enzymes and catabolized by two racemases and D-amino acid dehydrogenase (DadA). In addition, its level is regulated by L-alanine movement across the inner membrane. We identified the novel gene alaE, encoding an L-alanine exporter. To elucidate the physiological function of L-Alanine exporter, AlaE, we determined the susceptibility of alaE-, dadA-, and alaE/dadA-deficient mutants, derived from the wild-type strain MG1655, to L-alanyl-L-alanine (Ala-Ala), which shows toxicity to the L-alanine-nonmetabolizing variant lacking alaE. The dadA-deficient mutant has a similar minimum inhibitory concentration (MIC) (>1.25 mg/mL) to that observed in MG1655. However, alaE- and alaE/dadA-deficient mutants had MICs of 0.04 and 0.0025 mg/mL, respectively. The results suggested that the efficacy of AlaE to relieve stress caused by toxic intracellular accumulation of L-alanine was higher than that of DadA. Consistent with this, the intracellular level of alanine in the alaE-mutant was much higher than that in MG1655 and the dadA-mutant. We, therefore, conclude that AlaE functions as a ‘safety-valve’ to prevent the toxic level accumulation of intracellular L-alanine under a peptide-rich environment, such as within the animal intestine.
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Yang B, Jiang L, Wang S, Wang L. Global transcriptional regulation by BirA in enterohemorrhagic Escherichia coli O157:H7. Future Microbiol 2018; 13:757-769. [PMID: 29848069 DOI: 10.2217/fmb-2017-0256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
AIM Determination of the effects of BirA on transcription and virulence in enterohemorrhagic Escherichia coli (EHEC) O157:H7. MATERIALS & METHODS The effect of BirA on EHEC O157:H7 gene expression and phenotypes was assessed by RNA-seq combined with adherence, quantitative biofilm and survival assays. RESULTS Many genes associated with virulence, amino acid synthesis and transport, and zinc transport were upregulated, whereas genes encoding stress proteins were downregulated in ΔbirA::km+Ac_birA. Accordingly, ΔbirA::km+Ac_birA adhesion to Caco-2 cells, biofilm formation and survival during oxidative stress were higher, whereas its survival during heat shock was lower than that of the wild-type. CONCLUSION This study demonstrates the wide-ranging regulatory functions of BirA, especially its role in controlling virulence and stress responses in EHEC O157:H7. [Formula: see text].
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Affiliation(s)
- Bin Yang
- TEDA Institute of Biological Sciences & Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Tianjin 300071, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China
| | - Lingyan Jiang
- TEDA Institute of Biological Sciences & Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Tianjin 300071, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China
| | - Shaomeng Wang
- TEDA Institute of Biological Sciences & Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Tianjin 300071, PR China
| | - Lei Wang
- TEDA Institute of Biological Sciences & Biotechnology, Nankai University, TEDA, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology & Technology, Ministry of Education, Tianjin 300071, PR China.,Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin 300457, PR China.,State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, PR China
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7
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Zheng J, Lan X, Huang L, Zhang Y, Wang Z. Kinetic resolution of N-acetyl-DL-alanine methyl ester using immobilized Escherichia coli cells bearing recombinant esterase from Bacillus cereus. Chirality 2018; 30:907-912. [PMID: 29676476 DOI: 10.1002/chir.22863] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/04/2018] [Accepted: 03/14/2018] [Indexed: 12/18/2022]
Abstract
D-alanine is widely used in medicine, food, additives, cosmetics, and other consumer items. Esterase derived from Bacillus cereus WZZ001 exhibits high hydrolytic activity and stereoselectivity. In this study, we expressed the esterase gene in Escherichia coli BL21 (DE3). We analyzed the biocatalytic resolution of N-acetyl-DL-alanine methyl ester by immobilized whole E. coli BL21 (DE3) cells, which were prepared through embedding and cross-linking. We analyzed biocatalytic resolution under the optimal conditions of pH of 7.0, temperature of 40°C and substrate concentration of at 700 mM with an enantiomeric excess of 99.99% and e.e.p of 99.50%. The immobilized recombinant B. cereus esterase E. coli BL21 (DE3) cells exhibited excellent reusability and retained 86.04% of their initial activity after 15 cycles of repeated reactions. The immobilized cells are efficient and stable biocatalysts for the preparation of N-acetyl-D-alanine methyl esters.
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Affiliation(s)
- Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Xing Lan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Lijuan Huang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Yinjun Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
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Hemasa AL, Naumovski N, Maher WA, Ghanem A. Application of Carbon Nanotubes in Chiral and Achiral Separations of Pharmaceuticals, Biologics and Chemicals. NANOMATERIALS 2017; 7:nano7070186. [PMID: 28718832 PMCID: PMC5535252 DOI: 10.3390/nano7070186] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 12/23/2022]
Abstract
Carbon nanotubes (CNTs) possess unique mechanical, physical, electrical and absorbability properties coupled with their nanometer dimensional scale that renders them extremely valuable for applications in many fields including nanotechnology and chromatographic separation. The aim of this review is to provide an updated overview about the applications of CNTs in chiral and achiral separations of pharmaceuticals, biologics and chemicals. Chiral single-walled carbon nanotubes (SWCNTs) and multi-walled carbon nanotubes (MWCNTs) have been directly applied for the enantioseparation of pharmaceuticals and biologicals by using them as stationary or pseudostationary phases in chromatographic separation techniques such as high-performance liquid chromatography (HPLC), capillary electrophoresis (CE) and gas chromatography (GC). Achiral MWCNTs have been used for achiral separations as efficient sorbent objects in solid-phase extraction techniques of biochemicals and drugs. Achiral SWCNTs have been applied in achiral separation of biological samples. Achiral SWCNTs and MWCNTs have been also successfully used to separate achiral mixtures of pharmaceuticals and chemicals. Collectively, functionalized CNTs have been indirectly applied in separation science by enhancing the enantioseparation of different chiral selectors whereas non-functionalized CNTs have shown efficient capabilities for chiral separations by using techniques such as encapsulation or immobilization in polymer monolithic columns.
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Affiliation(s)
- Ayman L Hemasa
- Chirality Program, Biomedical Science, University of Canberra, Bruce, Australian Capital Territory (ACT) 2617, Australia.
| | - Nenad Naumovski
- Collaborative Research in Bioactives and Biomarkers Group (CRIBB), University of Canberra, Bruce, Australian Capital Territory (ACT) 2617, Australia.
| | - William A Maher
- Ecochemistry Laboratory, Institute for Applied Ecology, University of Canberra, Bruce, Australian Capital Territory (ACT) 2617, Australia.
| | - Ashraf Ghanem
- Chirality Program, Biomedical Science, University of Canberra, Bruce, Australian Capital Territory (ACT) 2617, Australia.
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