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Panda S, Jayasinghe YP, Shinde DD, Bueno E, Stastny A, Bertrand BP, Chaudhari SS, Kielian T, Cava F, Ronning DR, Thomas VC. Staphylococcus aureus counters organic acid anion-mediated inhibition of peptidoglycan cross-linking through robust alanine racemase activity. bioRxiv 2024:2024.01.15.575639. [PMID: 38293037 PMCID: PMC10827132 DOI: 10.1101/2024.01.15.575639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Weak organic acids are commonly found in host niches colonized by bacteria, and they can inhibit bacterial growth as the environment becomes acidic. This inhibition is often attributed to the toxicity resulting from the accumulation of high concentrations of organic anions in the cytosol, which disrupts cellular homeostasis. However, the precise cellular targets that organic anions poison and the mechanisms used to counter organic anion intoxication in bacteria have not been elucidated. Here, we utilize acetic acid, a weak organic acid abundantly found in the gut to investigate its impact on the growth of Staphylococcus aureus. We demonstrate that acetate anions bind to and inhibit d-alanyl-d-alanine ligase (Ddl) activity in S. aureus. Ddl inhibition reduces intracellular d-alanyl-d-alanine (d-Ala-d-Ala) levels, compromising staphylococcal peptidoglycan cross-linking and cell wall integrity. To overcome the effects of acetate-mediated Ddl inhibition, S. aureus maintains a high intracellular d-Ala pool through alanine racemase (Alr1) activity and additionally limits the flux of d-Ala to d-glutamate by controlling d-alanine aminotransferase (Dat) activity. Surprisingly, the modus operandi of acetate intoxication in S. aureus is common to multiple biologically relevant weak organic acids indicating that Ddl is a conserved target of small organic anions. These findings suggest that S. aureus may have evolved to maintain high intracellular d-Ala concentrations, partly to counter organic anion intoxication.
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Affiliation(s)
- Sasmita Panda
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Yahani P Jayasinghe
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Dhananjay D Shinde
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Emilio Bueno
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umea SE-90187, Sweden
| | - Amanda Stastny
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Blake P Bertrand
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Sujata S Chaudhari
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Tammy Kielian
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umea SE-90187, Sweden
| | - Donald R Ronning
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Vinai C Thomas
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5900, USA
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Ibrahim KA, El-Ashrey MK, Kashef MT, Helmy OM. Alanine racemase a promising Helicobacter pylori drug target inhibited by propanoic acid. Microbes Infect 2023; 25:105167. [PMID: 37271368 DOI: 10.1016/j.micinf.2023.105167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/06/2023]
Abstract
Eradication of Helicobacter pylori, the class 1 carcinogen, faces several obstacles, which demand alternative options to conventional drug development methods. Alanine racemase (Alr) was proposed as H. pylori drug target, inhibited by propanoic acid (PA), in a previous in silico study. We investigated the possible treatment of H. pylori infection through Alr inhibition. A new model of H. pylori Alr was built, validated, and the binding of PA to the active site was modelled via molecular docking with a good docking score. PA minimum inhibitory concentration (MIC) against H. pylori ATCC 43504 and six H. pylori clinical isolates ranged from 312.5 to 416.7 ± 180 μg/ml and remained unchanged after 14 serial passages in increasing PA concentrations. The minimum bactericidal concentration of PA was 625 μg/ml. Selective Alr inhibition was confirmed by a significant PA MIC increase with increasing d-alanine concentrations. Similar PA MIC in other tested pathogens was recorded (312.5-625 μg/ml). PA lacked cytotoxicity in tested cell lines and efficiently eradicated H. pylori in a rat infection model. In conclusion, Alr is a promising broad-spectrum drug target, inhibited by PA without resistance development by repeated exposure for 14 serial passages.
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Affiliation(s)
- Kareem A Ibrahim
- Department of Microbiology and Immunology, Faculty of Pharmacy, Egyptian Russian University, Suez Road, Cairo, 11829, Egypt
| | - Mohamed K El-Ashrey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University, Kasr Elini St., Cairo, 11562, Egypt; Medicinal Chemistry Department, Faculty of Pharmacy, King Salman International University, Ras-Sedr, South Sinai, Egypt
| | - Mona T Kashef
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt.
| | - Omneya M Helmy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
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Chung Y, Ryu Y, An BC, Yoon YS, Choi O, Kim TY, Yoon J, Ahn JY, Park HJ, Kwon SK, Kim JF, Chung MJ. A synthetic probiotic engineered for colorectal cancer therapy modulates gut microbiota. Microbiome 2021; 9:122. [PMID: 34039418 PMCID: PMC8157686 DOI: 10.1186/s40168-021-01071-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 04/06/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Successful chemoprevention or chemotherapy is achieved through targeted delivery of prophylactic agents during initial phases of carcinogenesis or therapeutic agents to malignant tumors. Bacteria can be used as anticancer agents, but efforts to utilize attenuated pathogenic bacteria suffer from the risk of toxicity or infection. Lactic acid bacteria are safe to eat and often confer health benefits, making them ideal candidates for live vehicles engineered to deliver anticancer drugs. RESULTS In this study, we developed an effective bacterial drug delivery system for colorectal cancer (CRC) therapy using the lactic acid bacterium Pediococcus pentosaceus. It is equipped with dual gene cassettes driven by a strong inducible promoter that encode the therapeutic protein P8 fused to a secretion signal peptide and a complementation system. In an inducible CRC cell-derived xenograft mouse model, our synthetic probiotic significantly reduced tumor volume and inhibited tumor growth relative to the control. Mice with colitis-associated CRC induced by azoxymethane and dextran sodium sulfate exhibited polyp regression and recovered taxonomic diversity when the engineered bacterium was orally administered. Further, the synthetic probiotic modulated gut microbiota and alleviated the chemically induced dysbiosis. Correlation analysis demonstrated that specific bacterial taxa potentially associated with eubiosis or dysbiosis, such as Akkermansia or Turicibacter, have positive or negative relationships with other microbial members. CONCLUSIONS Taken together, our work illustrates that an effective and stable synthetic probiotic composed of P. pentosaceus and the P8 therapeutic protein can reduce CRC and contribute to rebiosis, and the validity and feasibility of cell-based designer biopharmaceuticals for both treating CRC and ameliorating impaired microbiota. Video abstract.
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Affiliation(s)
- Yusook Chung
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Yongku Ryu
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Byung Chull An
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Yeo-Sang Yoon
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Oksik Choi
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Tai Yeub Kim
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Jaekyung Yoon
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jun Young Ahn
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Ho Jin Park
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea
| | - Soon-Kyeong Kwon
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
- Division of Applied Life Science (BK21), Gyeongsang National University, 501 Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
| | - Myung Jun Chung
- R&D Center, Cell Biotech, Co., Ltd., 50 Aegibong-ro 409beon-gil, Gaegok-ri, Wolgot-myeon, Gimpo-si, Gyeonggi-do, 10003, Republic of Korea.
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Dong H, Han Q, Guo Y, Ju J, Wang S, Yuan C, Long W, He X, Xu S, Li S. Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1. Biochem Biophys Res Commun 2018; 503:2319-2325. [PMID: 29964014 DOI: 10.1016/j.bbrc.2018.06.155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 06/27/2018] [Indexed: 02/02/2023]
Abstract
Alanine racemase is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l-alanine to d-alanine. d-alanine is an essential constituent in many prokaryotic cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.
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Affiliation(s)
- Hui Dong
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Qingqing Han
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yu Guo
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Shanshan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China
| | - Chao Yuan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; University of Chinese Academy of Sciences, Beijing, 100049, China; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Wei Long
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Xin He
- Key Laboratory of Tianjin Radiation and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300192, China
| | - Shujing Xu
- College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China.
| | - Sheng Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China.
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Ray S, Das S, Panda PK, Suar M. Identification of a new alanine racemase in Salmonella Enteritidis and its contribution to pathogenesis. Gut Pathog 2018; 10:30. [PMID: 30008809 PMCID: PMC6040060 DOI: 10.1186/s13099-018-0257-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/03/2018] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Non-typhoidal Salmonella (NTS) infections caused primarily by S. Enteritidis and S. Typhimurium particularly in immunocompromised hosts have accounted for a large percentage of fatalities in developed nations. Antibiotics have revolutionized the cure of enteric infections but have also led to the rapid emergence of pathogen resistance. New powerful therapeutics involving metabolic enzymes are expected to be potential targets for combating microbial infections and ensuring effective health management. Therefore, the need for new antimicrobials to fight such health emergencies is paramount. Enteric bacteria successfully evade the gut and colonize their hosts through specialized virulence strategies. An important player, alanine racemase is a key enzyme facilitating bacterial survival. RESULTS This study aims at understanding the contribution of alanine racemase genes alr, dadX and SEN3897 to Salmonella survival in vitro and in vivo. We have shown SEN3897 to function as a unique alanine racemase in S. Enteritidis which displayed essential alanine racemase activity. Interestingly, the sole presence of this gene in alr dadX double mutant showed a strict dependence on d-alanine supplementation both in vitro and in vivo. However, Alr complementation in d-alanine auxotrophic strain restored the alanine racemase deficiency. The Km and Vmax of SEN3897 was 89.15 ± 10.2 mM, 400 ± 25.6 µmol/(min mg) for l-alanine and 35 ± 6 mM, 132.5 ± 11.3 µmol/(min mg) for d-alanine, respectively. In vitro assays for invasion and survival as well as in vivo virulence assays involving SEN3897 mutant showed attenuated phenotypes. Further, this study also showed attenuation of d-alanine auxotrophic strain in vivo for the development of potential targets against Salmonella that can be investigated further. CONCLUSION This study identified a third alanine racemase gene unique in S. Enteritidis which had a potential effect on survival and pathogenesis in vitro and in vivo. Our results also confirmed that SEN3897 by itself wasn't able to rescue d-alanine auxotrophy in S. Enteritidis which further contributed to its virulence properties.
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Affiliation(s)
- Shilpa Ray
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha India
| | - Susmita Das
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha India
| | | | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar, Odisha India
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Yang H, Singh M, Kim SJ, Schaefer J. Characterization of the tertiary structure of the peptidoglycan of Enterococcus faecalis. Biochim Biophys Acta Biomembr 2017; 1859:2171-2180. [PMID: 28784459 PMCID: PMC5610627 DOI: 10.1016/j.bbamem.2017.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/29/2022]
Abstract
Solid-state NMR spectra of whole cells and isolated cell walls of Enterococcus faecalis grown in media containing combinations of 13C and 15N specific labels in d- and l-alanine and l-lysine (in the presence of an alanine racemase inhibitor alaphosphin) have been used to determine the composition and architecture of the cell-wall peptidoglycan. The compositional variables include the concentrations of (i) peptidoglycan stems without bridges, (ii) d-alanylated wall teichoic acid, (iii) cross-links, and (iv) uncross-linked tripeptide and tetra/pentapeptide stems. Connectivities of l-alanyl carbonyl‑carbon bridge labels to d-[3-13C]alanyl and l-[ε-15N]lysyl stem labels prove that the peptidoglycan of E. faecalis has the same hybrid short-bridge architecture (with a mix of parallel and perpendicular stems) as the FemA mutant of Staphylococcus aureus, in which the cross-linked stems are perpendicular to one another and the cross-linking is close to the ideal 50% value. This is the first determination of the cell-wall chemical and geometrical architecture of whole cells of E. faecalis, a major source of nosocomial infections worldwide.
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Affiliation(s)
- Hao Yang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA.
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Wang Y, Yang C, Xue W, Zhang T, Liu X, Ju J, Zhao B, Liu D. Selection and characterization of alanine racemase inhibitors against Aeromonas hydrophila. BMC Microbiol 2017; 17:122. [PMID: 28545531 PMCID: PMC5445283 DOI: 10.1186/s12866-017-1010-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 04/13/2017] [Indexed: 02/02/2023] Open
Abstract
Background Combining experimental and computational screening methods has been of keen interest in drug discovery. In the present study, we developed an efficient screening method that has been used to screen 2100 small-molecule compounds for alanine racemase Alr-2 inhibitors. Results We identified ten novel non-substrate Alr-2 inhibitors, of which patulin, homogentisic acid, and hydroquinone were active against Aeromonas hydrophila. The compounds were found to be capable of inhibiting Alr-2 to different extents with 50% inhibitory concentrations (IC50) ranging from 6.6 to 17.7 μM. These compounds inhibited the growth of A. hydrophila with minimal inhibitory concentrations (MICs) ranging from 20 to 120 μg/ml. These compounds have no activity on horseradish peroxidase and d-amino acid oxidase at a concentration of 50 μM. The MTT assay revealed that homogentisic acid and hydroquinone have minimal cytotoxicity against mammalian cells. The kinetic studies indicated a competitive inhibition of homogentisic acid against Alr-2 with an inhibition constant (Ki) of 51.7 μM, while hydroquinone was a noncompetitive inhibitor with a Ki of 212 μM. Molecular docking studies suggested that homogentisic acid binds to the active site of racemase, while hydroquinone lies near the active center of alanine racemase. Conclusions Our findings suggested that combining experimental and computational methods could be used for an efficient, large-scale screening of alanine racemase inhibitors against A. hydrophila that could be applied in the development of new antibiotics against A. hydrophila. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1010-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yaping Wang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Chao Yang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Wen Xue
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Ting Zhang
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xipei Liu
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Jiansong Ju
- College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Baohua Zhao
- College of Life Science, Hebei Normal University, Shijiazhuang, China.
| | - Dong Liu
- College of Life Science, Hebei Normal University, Shijiazhuang, China.
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Sak-Ubol S, Namvijitr P, Pechsrichuang P, Haltrich D, Nguyen TH, Mathiesen G, Eijsink VGH, Yamabhai M. Secretory production of a beta-mannanase and a chitosanase using a Lactobacillus plantarum expression system. Microb Cell Fact 2016; 15:81. [PMID: 27176608 PMCID: PMC4866359 DOI: 10.1186/s12934-016-0481-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/03/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Heterologous production of hydrolytic enzymes is important for green and white biotechnology since these enzymes serve as efficient biocatalysts for the conversion of a wide variety of raw materials into value-added products. Lactic acid bacteria are interesting cell factories for the expression of hydrolytic enzymes as many of them are generally recognized as safe and require only a simple cultivation process. We are studying a potentially food-grade expression system for secretion of hydrolytic enzymes into the culture medium, since this enables easy harvesting and purification, while allowing direct use of the enzymes in food applications. RESULTS We studied overexpression of a chitosanase (CsnA) and a β-mannanase (ManB), from Bacillus licheniformis and Bacillus subtilis, respectively, in Lactobacillus plantarum, using the pSIP system for inducible expression. The enzymes were over-expressed in three forms: without a signal peptide, with their natural signal peptide and with the well-known OmpA signal peptide from Escherichia coli. The total production levels and secretion efficiencies of CsnA and ManB were highest when using the native signal peptides, and both were reduced considerably when using the OmpA signal. At 20 h after induction with 12.5 ng/mL of inducing peptide in MRS media containing 20 g/L glucose, the yields and secretion efficiencies of the proteins with their native signal peptides were 50 kU/L and 84% for ManB, and 79 kU/L and 56% for CsnA, respectively. In addition, to avoid using antibiotics, the erythromycin resistance gene was replaced on the expression plasmid with the alanine racemase (alr) gene, which led to comparable levels of protein production and secretion efficiency in a suitable, alr-deficient L. plantarum host. CONCLUSIONS ManB and CsnA were efficiently produced and secreted in L. plantarum using pSIP-based expression vectors containing either an erythromycin resistance or the alr gene as selection marker.
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Affiliation(s)
- Suttipong Sak-Ubol
- />Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
- />Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peenida Namvijitr
- />Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Phornsiri Pechsrichuang
- />Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Dietmar Haltrich
- />Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Thu-Ha Nguyen
- />Food Biotechnology Laboratory, Department of Food Science and Technology, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
| | - Geir Mathiesen
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Vincent G. H. Eijsink
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Montarop Yamabhai
- />Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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Kobayashi J, Yukimoto J, Shimizu Y, Ohmori T, Suzuki H, Doi K, Ohshima T. Characterization of Lactobacillus salivarius alanine racemase: short-chain carboxylate-activation and the role of A131. Springerplus 2015; 4:639. [PMID: 26543773 PMCID: PMC4628008 DOI: 10.1186/s40064-015-1335-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 12/24/2014] [Indexed: 11/10/2022]
Abstract
Many strains of lactic acid bacteria produce high concentrations of d-amino acids. Among them, Lactobacillus salivarius UCC 118 produces d-alanine at a relative concentration much greater than 50 % of the total d, l-alanine (100d/d, l-alanine). We characterized the L. salivarius alanine racemase (ALR) likely responsible for this d-alanine production and found that the enzyme was activated by carboxylates, which is an unique characteristic among ALRs. In addition, alignment of the amino acid sequences of several ALRs revealed that A131 of L. salivarius ALR is likely involved in the activation. To confirm that finding, an L. salivarius ALR variant with an A131K (ALR(A131K)) substitution was prepared, and its properties were compared with those of ALR. The activity of ALR(A131K) was about three times greater than that of ALR. In addition, whereas L. salivarius ALR was strongly activated by low concentrations (e.g., 1 mM) of short chain carboxylates, and was inhibited at higher concentrations (e.g., 10 mM), ALR(A131K) was clearly inhibited at all carboxylate concentrations tested (1-40 mM). Acetate also increased the stability of ALR such that maximum activity was observed at 35 °C and pH 8.0 without acetate, but at 50 °C in the presence of 1 mM acetate. On the other hand, maximum ALR(A131K) activity was observed at 45 °C and around pH 9.0 with or without acetate. It thus appears that A131 mediates the activation and stabilization of L. salivarius ALR by short chain carboxylates.
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Affiliation(s)
- Jyumpei Kobayashi
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Jotaro Yukimoto
- Applied Molecular Microbiology and Biomass Chemistry Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Yasuhiro Shimizu
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan
| | - Taketo Ohmori
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Omiya, Asahi-ku, Osaka, 535-8585 Japan
| | - Hirokazu Suzuki
- Functional Genomics of Extremophiles, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, 812-8581 Japan
| | - Katsumi Doi
- Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka, 535-8585 Japan
| | - Toshihisa Ohshima
- Microbial Genetics Division, Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan ; Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka, 535-8585 Japan
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Singh M, Kim SJ, Sharif S, Preobrazhenskaya M, Schaefer J. REDOR constraints on the peptidoglycan lattice architecture of Staphylococcus aureus and its FemA mutant. Biochim Biophys Acta 2015; 1848:363-8. [PMID: 24990251 PMCID: PMC4254387 DOI: 10.1016/j.bbamem.2014.05.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/22/2014] [Indexed: 11/23/2022]
Abstract
The peptidoglycan of Gram-positive bacteria consists of glycan chains with attached short peptide stems cross-linked to one another by glycyl bridges. The bridge of Staphylococcus aureus has five glycyl units and that of its FemA mutant has one. These long- and short-bridge cross-links create totally different cell-wall architectures. S. aureus and its FemA mutant grown in the presence of an alanine-racemase inhibitor were labeled with d-[1-¹³C]alanine, l-[3-¹³C]alanine, [2-¹³C]glycine, and l-[5-¹⁹F]lysine to characterize some details of the peptidoglycan tertiary structure. Rotational-echo double-resonance (REDOR) NMR of isolated cell walls was used to measure internuclear distances between ¹³C-labeled alanines and ¹⁹F-labeled lysine incorporated in the peptidoglycan. The alanyl ¹³C labels in the parent strain were preselected for C{F} and C{P} REDOR measurement by their proximity to the glycine label using ¹³C¹³C spin diffusion. The observed ¹³C¹³C and ¹³C³¹P distances are consistent with a tightly packed architecture containing only parallel stems in a repeating structural motif within the peptidoglycan. Dante selection of d-alanine and l-alanine frequencies followed by ¹³C¹³C spin diffusion rules out scrambling of carbon labels. Cell walls of FemA were also labeled by a combination of d-[1-¹³C]alanine and l-[¹⁵N]alanine. Proximity of chains was measured by C{N} and N{C} REDOR distances and asymptotic plateaus, and both were consistent with a mixed-geometry model. Binding of an ¹⁹F-labeled eremomycin analog in the FemA cell wall matches that of binding to the parent-strain cell wall and reveals the proximity of parallel stems in the alternating parallel-perpendicular mixed-geometry model for the FemA peptidoglycan lattice.
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Affiliation(s)
- Manmilan Singh
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Sung Joon Kim
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76706, USA
| | - Shasad Sharif
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
| | - Maria Preobrazhenskaya
- Gause Institute of New Antibiotics, Russian Academy of Medical Sciences, Moscow 119021, Russia
| | - Jacob Schaefer
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA.
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