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Jia H, Chen Y, Chen Y, Liu R, Zhang Q, Bartlam M. Structure and function of the pyridoxal 5'-phosphate-dependent (PLP) threonine deaminase IlvA1 from Pseudomonas aeruginosa PAO1. Biochem Biophys Res Commun 2024; 704:149710. [PMID: 38417345 DOI: 10.1016/j.bbrc.2024.149710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
IlvA1, a pyridoxal phosphate-dependent (PLP) enzyme, catalyzes the deamination of l-threonine and l-serine to yield 2-ketobutyric acid or pyruvate. To gain insights into the function of IlvA1, we determined its crystal structure from Pseudomonas aeruginosa to 2.3 Å. Density for a 2-ketobutyric acid product was identified in the active site and a putative allosteric site. Activity and substrate binding assays confirmed that IlvA1 utilizes l-threonine, l-serine, and L-allo-threonine as substrates. The enzymatic activity is regulated by the end products l-isoleucine and l-valine. Additionally, the efficiency of d-cycloserine and l-cycloserine inhibitors on IlvA1 enzymatic activity was examined. Notably, site-directed mutagenesis confirmed the active site residues and revealed that Gln165 enhances the enzyme activity, emphasizing its role in substrate access. This work provides crucial insights into the structure and mechanism of IlvA1 and serves as a starting point for further functional and mechanistic studies of the threonine deaminase in P. aeruginosa.
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Affiliation(s)
- Haizhu Jia
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, Tianjin, 300071, China; Chinese Academy of Medical Sciences & Peking Union Medical College (State Key Laboratory of Bioactive Substance and Function of Natural Medicines & NHC Key Laboratory of Biosynthesis of Natural Products), Institute of Materia Medica, Beijing, 100050, China
| | - Yujing Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, Tianjin, 300071, China; College of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, China
| | - Yuan Chen
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science, and College of Life Sciences, Nankai University, Tianjin, 300071, China.
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2
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Klenner F, Bönigk J, Napoleoni M, Hillier J, Khawaja N, Olsson-Francis K, Cable ML, Malaska MJ, Kempf S, Abel B, Postberg F. How to identify cell material in a single ice grain emitted from Enceladus or Europa. SCIENCE ADVANCES 2024; 10:eadl0849. [PMID: 38517965 PMCID: PMC10959401 DOI: 10.1126/sciadv.adl0849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/20/2024] [Indexed: 03/24/2024]
Abstract
Icy moons like Enceladus, and perhaps Europa, emit material sourced from their subsurface oceans into space via plumes of ice grains and gas. Both moons are prime targets for astrobiology investigations. Cassini measurements revealed a large compositional diversity of emitted ice grains with only 1 to 4% of Enceladus's plume ice grains containing organic material in high concentrations. Here, we report experiments simulating mass spectra of ice grains containing one bacterial cell, or fractions thereof, as encountered by advanced instruments on board future space missions to Enceladus or Europa, such as the SUrface Dust Analyzer onboard NASA's upcoming Europa Clipper mission at flyby speeds of 4 to 6 kilometers per second. Mass spectral signals characteristic of the bacteria are shown to be clearly identifiable by future missions, even if an ice grain contains much less than one cell. Our results demonstrate the advantage of analyses of individual ice grains compared to a diluted bulk sample in a heterogeneous plume.
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Affiliation(s)
- Fabian Klenner
- Department of Earth and Space Sciences, University of Washington, Seattle, WA, USA
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Janine Bönigk
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Maryse Napoleoni
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Jon Hillier
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Nozair Khawaja
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
| | - Karen Olsson-Francis
- Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UK
| | - Morgan L. Cable
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Michael J. Malaska
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Sascha Kempf
- Laboratory for Atmospheric and Space Physics, University of Colorado, Boulder, CO, USA
| | - Bernd Abel
- Institute of Chemical Technology, University of Leipzig, Leipzig, Germany
- Leibniz-Institute of Surface Engineering (IOM), Leipzig, Germany
| | - Frank Postberg
- Institute of Geological Sciences, Freie Universität Berlin, Berlin, Germany
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FK506-binding protein, FKBP12, promotes serine utilization and negatively regulates threonine deaminase in fission yeast. iScience 2022; 25:105659. [PMID: 36505930 PMCID: PMC9730122 DOI: 10.1016/j.isci.2022.105659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/24/2022] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
FK506-binding protein with a molecular weight of 12 kDa (FKBP12) is a receptor of the immunosuppressive drugs, FK506 and rapamycin. The physiological functions of FKBP12 remain ambiguous because of its nonessentiality and multifunctionality. Here, we show that FKBP12 promotes the utilization of serine as a nitrogen source and regulates the isoleucine biosynthetic pathway in fission yeast. In screening for small molecules that inhibit serine assimilation, we found that the growth of fission yeast cells in medium supplemented with serine as the sole nitrogen source, but not in glutamate-supplemented medium, was suppressed by FKBP12 inhibitors. Knockout of FKBP12 phenocopied the action of these compounds in serine-supplemented medium. Metabolome analyses and genetic screens identified the threonine deaminase, Tda1, to be regulated downstream of FKBP12. Genetic and biochemical analyses unveiled the negative regulation of Tda1 by FKBP12. Our findings reveal new roles of FKBP12 in amino acid biosynthesis and nitrogen metabolism homeostasis.
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Identification and biochemical characterization of threonine dehydratase from the hyperthermophile Thermotoga maritima. Amino Acids 2021; 53:903-915. [PMID: 33938999 DOI: 10.1007/s00726-021-02993-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/21/2021] [Indexed: 01/14/2023]
Abstract
The peptidoglycan of the hyperthermophile Thermotoga maritima contains an unusual component, D-lysine (D-Lys), in addition to the typical D-alanine (D-Ala) and D-glutamate (D-Glu). In a previous study, we identified a Lys racemase that is presumably associated with D-Lys biosynthesis. However, our understanding of D-amino acid metabolism in T. maritima and other bacteria remains limited, although D-amino acids in the peptidoglycan are crucial for preserving bacterial cell structure and resistance to environmental threats. Herein, we characterized enzymatic and structural properties of TM0356 that shares a high amino acid sequence identity with serine (Ser) racemase. The results revealed that TM0356 forms a tetramer with each subunit containing a pyridoxal 5'-phosphate as a cofactor. The enzyme did not exhibit racemase activity toward various amino acids including Ser, and dehydratase activity was highest toward L-threonine (L-Thr). It also acted on L-Ser and L-allo-Thr, but not on the corresponding D-amino acids. The catalytic mechanism did not follow typical Michaelis-Menten kinetics; it displayed a sigmoidal dependence on substrate concentration, with highest catalytic efficiency (kcat/K0.5) toward L-Thr. Interestingly, dehydratase activity was insensitive to allosteric regulators L-valine and L-isoleucine (L-Ile) at low concentrations, while these L-amino acids are inhibitors at high concentrations. Thus, TM0356 is a biosynthetic Thr dehydratase responsible for the conversion of L-Thr to α-ketobutyrate and ammonia, which is presumably involved in the first step of the biosynthesis of L-Ile.
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Marinho CM, Dos Santos PT, Kallipolitis BH, Johansson J, Ignatov D, Guerreiro DN, Piveteau P, O’Byrne CP. The σ B-dependent regulatory sRNA Rli47 represses isoleucine biosynthesis in Listeria monocytogenes through a direct interaction with the ilvA transcript. RNA Biol 2019; 16:1424-1437. [PMID: 31242083 PMCID: PMC6779388 DOI: 10.1080/15476286.2019.1632776] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 12/25/2022] Open
Abstract
The facultative intracellular pathogen Listeria monocytogenes can persist and grow in a diverse range of environmental conditions, both outside and within its mammalian host. The alternative sigma factor Sigma B (σB) plays an important role in this adaptability and is critical for the transition into the host. While some of the functions of the σB regulon in facilitating this transition are understood the role of σB-dependent small regulatory RNAs (sRNAs) remain poorly characterized. In this study, we focused on elucidating the function of Rli47, a σB-dependent sRNA that is highly induced in the intestine and in macrophages. Using a combination of in silico and in vivo approaches, a binding interaction was predicted with the Shine-Dalgarno region of the ilvA mRNA, which encodes threonine deaminase, an enzyme required for branched-chain amino acid biosynthesis. Both ilvA transcript levels and threonine deaminase activity were increased in a deletion mutant lacking the rli47 gene. The Δrli47 mutant displayed a shorter growth lag in isoleucine-depleted growth media relative to the wild-type, and a similar phenotype was also observed in a mutant lacking σB. The impact of the Δrli47 on the global transcription profile of the cell was investigated using RNA-seq, and a significant role for Rli47 in modulating amino acid metabolism was uncovered. Taken together, the data point to a model where Rli47 is responsible for specifically repressing isoleucine biosynthesis as a way to restrict growth under harsh conditions, potentially contributing to the survival of L. monocytogenes in niches both outside and within the mammalian host.
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Affiliation(s)
- Catarina M. Marinho
- Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
- Bacterial Stress Response Group, National University of Ireland, Galway, Ireland
| | - Patrícia T. Dos Santos
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Birgitte H. Kallipolitis
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jörgen Johansson
- Department of Molecular Biology; Molecular Infection Medicine, Sweden (MIMS), Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Dmitriy Ignatov
- Department of Molecular Biology; Molecular Infection Medicine, Sweden (MIMS), Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | - Duarte N. Guerreiro
- Bacterial Stress Response Group, National University of Ireland, Galway, Ireland
| | - Pascal Piveteau
- Agroécologie, AgroSup Dijon, INRA, Université de Bourgogne Franche-Comté, Dijon, France
| | - Conor P. O’Byrne
- Bacterial Stress Response Group, National University of Ireland, Galway, Ireland
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Formation of alanine, α-aminobutyrate, acetate, and 2-butanol during cheese ripening by Pediococcus acidilactici FAM18098. Int Dairy J 2019. [DOI: 10.1016/j.idairyj.2019.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Strategy for improving L-isoleucine production efficiency in Corynebacterium glutamicum. Appl Microbiol Biotechnol 2019; 103:2101-2111. [DOI: 10.1007/s00253-019-09632-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/06/2019] [Accepted: 01/07/2019] [Indexed: 01/25/2023]
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Favrot L, Amorim Franco TM, Blanchard JS. Biochemical Characterization of the Mycobacterium smegmatis Threonine Deaminase. Biochemistry 2018; 57:6003-6012. [PMID: 30226377 DOI: 10.1021/acs.biochem.8b00871] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The biosynthesis of branched-chain amino acids or BCAAs (l-isoleucine, l-leucine, and l-valine) is essential in eubacteria, but mammals are branched-chain amino acid auxotrophs, making the enzymes in the pathway excellent targets for antibacterial drug development. The biosynthesis of l-isoleucine, l-leucine, and l-valine is very efficient, requiring only eight enzymes. Threonine dehydratase (TD), a pyridoxal 5'-phosphate (PLP)-dependent enzyme encoded by the ilvA gene, is the enzyme responsible for the conversion of l-threonine (l-Thr) to α-ketobutyrate, ammonia, and water, which is the first step in the biosynthesis of l-isoleucine. We have cloned, expressed, and biochemically characterized the reaction catalyzed by Mycobacterium smegmatis TD (abbreviated as MsIlvA) using steady-state kinetics and kinetic isotope effects. We show here that in addition to l-threonine, l-allo-threonine and l-serine are also used as substrates by TD, and all exhibit sigmoidal, non-Michaelis-Menten kinetics. Curiously, β-chloro-l-alanine was also a substrate rather than an inhibitor as expected. The enzymatic activity of TD is sensitive to the presence of allosteric regulators, including the activator l-valine or the end product feedback inhibitor of the BCAA pathway in which TD is involved, l-isoleucine. Primary deuterium kinetic isotopes are small, suggesting Cα proton abstraction is only partially rate-limiting. Solvent kinetic isotopes were significantly larger, indicating that a proton transfer occurring during the reaction is also partially rate-limiting. Finally, we demonstrate that l-cycloserine, a general inhibitor of PLP-dependent enzymes, is an excellent inhibitor of threonine deaminase.
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Affiliation(s)
- Lorenza Favrot
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - Tathyana M Amorim Franco
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
| | - John S Blanchard
- Department of Biochemistry , Albert Einstein College of Medicine , 1300 Morris Park Avenue , Bronx , New York 10461 , United States
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9
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Wang X, Zhang H, Quinn PJ. Production of l-valine from metabolically engineered Corynebacterium glutamicum. Appl Microbiol Biotechnol 2018; 102:4319-4330. [DOI: 10.1007/s00253-018-8952-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/15/2018] [Accepted: 03/16/2018] [Indexed: 01/25/2023]
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10
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Liu Y, Li Y, Wang X. Molecular evolution of acetohydroxyacid synthase in bacteria. Microbiologyopen 2017; 6. [PMID: 28782269 PMCID: PMC5727371 DOI: 10.1002/mbo3.524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/21/2017] [Accepted: 06/29/2017] [Indexed: 11/16/2022] Open
Abstract
Acetohydroxyacid synthase (AHAS) is the key enzyme in the biosynthetic pathways of branched chain amino acids in bacteria. Since it does not exist in animal and plant cells, AHAS is an attractive target for developing antimicrobials and herbicides. In some bacteria, there is a single copy of AHAS, while in others there are multiple copies. Therefore, it is necessary to investigate the origin and evolutionary pathway of various AHASs in bacteria. In this study, all the available protein sequences of AHAS in bacteria were investigated, and an evolutionary model of AHAS in bacteria is proposed, according to gene structure, organization and phylogeny. Multiple copies of AHAS in some bacteria might be evolved from the single copy of AHAS, the ancestor. Gene duplication, domain deletion and horizontal gene transfer might occur during the evolution of this enzyme. The results show the biological significance of AHAS, help to understand the functions of various AHASs in bacteria, and would be useful for developing industrial production strains of branched chain amino acids or novel antimicrobials.
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Affiliation(s)
- Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yanyan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China.,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, China
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Sharma R, Keshari D, Singh KS, Singh SK. Biochemical and functional characterization of MRA_1571 of Mycobacterium tuberculosis H37Ra and effect of its down-regulation on survival in macrophages. Biochem Biophys Res Commun 2017; 487:892-897. [PMID: 28465237 DOI: 10.1016/j.bbrc.2017.04.149] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 04/29/2017] [Indexed: 12/31/2022]
Abstract
Amino acid biosynthesis has emerged as a source of new drug targets as many bacterial strains auxotrophic for amino acids fail to proliferate under in vivo conditions. Branch chain amino acids (BCAAs) are important for Mycobacterium tuberculosis (Mtb) survival and strains deficient in their biosynthesis were attenuated for growth in mice. Threonine dehydratase (IlvA) is a pyridoxal-5-phosphate (PLP) dependent enzyme that catalyzes the first step in isoleucine biosynthesis. The MRA_1571 of Mycobacterium tuberculosis H37Ra (Mtb-Ra), annotated to be coding for IlvA, was cloned, expressed and purified. Purified protein was subsequently used for developing enzyme assay and to study its biochemical properties. Also, E. coli BL21 (DE3) IlvA knockout (E. coli-ΔilvA) was developed and genetically complemented with Mtb-Ra ilvA expression construct (pET32a-ilvA) to make complemented E. coli strain (E. coli-ΔilvA + pET32a-ilvA). The E. coli-ΔilvA showed growth failure in minimal medium but growth restoration was observed in E. coli-ΔilvA + pET32a-ilvA. E. coli-ΔilvA growth was also restored in the presence of isoleucine. The IlvA localization studies detected its distribution in cell wall and membrane fractions with relatively minor presence in cytosolic fraction. Maximum IlvA expression was observed at 72 h in wild-type (WT) Mtb-Ra infecting macrophages. Also, Mtb-Ra IlvA knockdown (KD) showed reduced survival in macrophages compared to WT and complemented strain (KDC).
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Affiliation(s)
- Rishabh Sharma
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow - 226031, India
| | - Deepa Keshari
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow - 226031, India
| | - Kumar Sachin Singh
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow - 226031, India
| | - Sudheer Kumar Singh
- Microbiology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow - 226031, India; Academy of Scientific and Industrial Research (AcSIR), New Delhi, India.
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