1
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Amala M, Nagarajan H, Ahila M, Nachiappan M, Veerapandiyan M, Vetrivel U, Jeyakanthan J. Unveiling the intricacies of allosteric regulation in aspartate kinase from the Wolbachia endosymbiont of Brugia Malayi: Mechanistic and therapeutic insights. Int J Biol Macromol 2024; 267:131326. [PMID: 38569988 DOI: 10.1016/j.ijbiomac.2024.131326] [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: 09/10/2023] [Revised: 03/04/2024] [Accepted: 03/31/2024] [Indexed: 04/05/2024]
Abstract
Aspartate kinase (AK), an enzyme from the Wolbachia endosymbiont of Brugia malayi (WBm), plays a pivotal role in the bacterial cell wall and amino acid biosynthesis, rendering it an attractive candidate for therapeutic intervention. Allosteric inhibition of aspartate kinase is a prevalent mode of regulation across microorganisms and plants, often modulated by end products such as lysine, threonine, methionine, or meso-diaminopimelate. The intricate and diverse nature of microbial allosteric regulation underscores the need for rigorous investigation. This study employs a combined experimental and computational approach to decipher the allosteric regulation of WBmAK. Molecular Dynamics (MD) simulations elucidate that ATP (cofactor) and ASP (substrate) binding induce a closed conformation, promoting enzymatic activity. In contrast, the binding of lysine (allosteric inhibitor) leads to enzyme inactivation and an open conformation. The enzymatic assay demonstrates the optimal activity of WBmAK at 28 °C and a pH of 8.0. Notably, the allosteric inhibition study highlights lysine as a more potent inhibitor compared to threonine. Importantly, this investigation sheds light on the allosteric mechanism governing WBmAK and imparts novel insights into structure-based drug discovery, paving the way for the development of effective inhibitors against filarial pathogens.
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Affiliation(s)
- Mathimaran Amala
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India
| | - Hemavathy Nagarajan
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India
| | - Mathimaran Ahila
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India
| | - Mutharasappan Nachiappan
- Structural and Computational Biology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110 067, India
| | - Malaisamy Veerapandiyan
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India
| | - Umashankar Vetrivel
- Virology & Biotechnology/Bioinformatics Division, ICMR-National Institute for Research in Tuberculosis, Chennai, Tamil Nadu 600 031, India
| | - Jeyaraman Jeyakanthan
- Structural Biology and Biocomputing Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630004, Tamil Nadu, India.
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2
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Naz S, Liu P, Farooq U, Ma H. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microb Cell Fact 2023; 22:161. [PMID: 37612753 PMCID: PMC10464499 DOI: 10.1186/s12934-023-02178-z] [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: 06/07/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023] Open
Abstract
Regulation of amino acid's biosynthetic pathway is of significant importance to maintain homeostasis and cell functions. Amino acids regulate their biosynthetic pathway by end-product feedback inhibition of enzymes catalyzing committed steps of a pathway. Discovery of new feedback resistant enzyme variants to enhance industrial production of amino acids is a key objective in industrial biotechnology. Deregulation of feedback inhibition has been achieved for various enzymes using in vitro and in silico mutagenesis techniques. As enzyme's function, its substrate binding capacity, catalysis activity, regulation and stability are dependent on its structural characteristics, here, we provide detailed structural analysis of all feedback sensitive enzyme targets in amino acid biosynthetic pathways. Current review summarizes information regarding structural characteristics of various enzyme targets and effect of mutations on their structures and functions especially in terms of deregulation of feedback inhibition. Furthermore, applicability of various experimental as well as computational mutagenesis techniques to accomplish feedback resistance has also been discussed in detail to have an insight into various aspects of research work reported in this particular field of study.
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Affiliation(s)
- Sadia Naz
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Pi Liu
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Islamabad, 22060, Pakistan
| | - Hongwu Ma
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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3
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Chen Z, Fu Y, Liu S, Huang X, Kong X, Mao Z, Hu N, Zhang F, Han C. Characterization of aspartokinase double mutants using a combination of experiments and simulations. Heliyon 2023; 9:e13133. [PMID: 36747545 PMCID: PMC9898291 DOI: 10.1016/j.heliyon.2023.e13133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/29/2023] Open
Abstract
Aspartokinase (AK) is synergistically suppressed by Thr and Lys in the Corynebacterium metabolic pathway. Site-directed mutations can significantly improve AK inhibition. Our previous studies confirmed that sites 379 and 380 were important sites affecting enzyme activity, so we further screen the double mutants with excellent enzymatic properties from sites 379 and 380, and discuss the difference of enzyme activity between the double mutants and single mutants. Here, a double mutant, T379L/A380 M, with improved enzyme activity (2.74-fold) was obtained. Enzymatic property experiments showed that the optimum temperature of T379L/A380 M increased from 26 °C (recombinant Escherichia coli; WT-AK) to 45 °C and that the optimal pH decreased from 8.0 (WT-AK) to 7.5. Further, the half-life decreased from 4.5 to 3.32 h. These enzymatic properties were better than other mutant strains. Inhibition was diminished with low concentrations of Lys, and Lys + Thr presented an activating role. Subsequently, the reasons for the improved AK enzyme activity were illustrated with microscale thermophoresis (MST) experiments and molecular dynamic (MD) simulation by measuring ligand affinity and AK conformational changes. MST showed that the affinity between T379L/A380 M and Lys decreased, but the affinity between T379L/A380 M and Asp increased, promoting T379L/A380 M enzyme activity. MD experiments showed that T379L/A380 M enhanced the Asp-ATP affinity and catalyzed the transfer of residues S192 and D193 to Asp, promoting T379L/A380 M enzyme activity. However, the mutation did not cause fluctuations in the substrate Asp and ATP pockets. This might be why the enzyme activity was inferior to that of the single mutants (T379L and A380 M).
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Affiliation(s)
- Zhijie Chen
- School of Pharmaceutical Sciences, Tsinghua University, 100084, Beijing, China
| | - Yu Fu
- School of Public Health, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Shimeng Liu
- Jiaxing Xinbeilai Biotechnology Co., Ltd, China
| | - Xinyu Huang
- School of Public Health, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Xiaoting Kong
- School of Public Health, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Zhaojie Mao
- School of Public Health, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Ning Hu
- School of Public Health, Weifang Medical University, Weifang, 261053, Shandong, China
| | - Fengxiang Zhang
- School of Public Health, Weifang Medical University, Weifang, 261053, Shandong, China
- Corresponding author.
| | - Caijing Han
- School of Public Health, Weifang Medical University, Weifang, 261053, Shandong, China
- Corresponding author.
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4
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Fan Z, Fang L, Wu L, Wang Z, Wang Y, Han C, Liu X. Improved catalytic activity of a novel aspartate kinase by site-directed saturation mutagenesis. Bioprocess Biosyst Eng 2022; 45:541-551. [DOI: 10.1007/s00449-021-02677-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/30/2021] [Indexed: 11/02/2022]
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5
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Kawaguchi H, Hasunuma T, Ohnishi Y, Sazuka T, Kondo A, Ogino C. Enhanced production of γ-amino acid 3-amino-4-hydroxybenzoic acid by recombinant Corynebacterium glutamicum under oxygen limitation. Microb Cell Fact 2021; 20:228. [PMID: 34949178 PMCID: PMC8697445 DOI: 10.1186/s12934-021-01714-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Bio-based aromatic compounds are of great interest to the industry, as commercial production of aromatic compounds depends exclusively on the unsustainable use of fossil resources or extraction from plant resources. γ-amino acid 3-amino-4-hydroxybenzoic acid (3,4-AHBA) serves as a precursor for thermostable bioplastics. Results Under aerobic conditions, a recombinant Corynebacterium glutamicum strain KT01 expressing griH and griI genes derived from Streptomyces griseus produced 3,4-AHBA with large amounts of amino acids as by-products. The specific productivity of 3,4-AHBA increased with decreasing levels of dissolved oxygen (DO) and was eightfold higher under oxygen limitation (DO = 0 ppm) than under aerobic conditions (DO ≥ 2.6 ppm). Metabolic profiles during 3,4-AHBA production were compared at three different DO levels (0, 2.6, and 5.3 ppm) using the DO-stat method. Results of the metabolome analysis revealed metabolic shifts in both the central metabolic pathway and amino acid metabolism at a DO of < 33% saturated oxygen. Based on this metabolome analysis, metabolic pathways were rationally designed for oxygen limitation. An ldh deletion mutant, with the loss of lactate dehydrogenase, exhibited 3.7-fold higher specific productivity of 3,4-AHBA at DO = 0 ppm as compared to the parent strain KT01 and produced 5.6 g/L 3,4-AHBA in a glucose fed-batch culture. Conclusions Our results revealed changes in the metabolic state in response to DO concentration and provided insights into oxygen supply during fermentation and the rational design of metabolic pathways for improved production of related amino acids and their derivatives. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01714-z.
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Affiliation(s)
- Hideo Kawaguchi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo, Tokyo, 113-8657, Japan
| | - Takashi Sazuka
- Bioscience and Biotechnology Center, Nagoya University, Furo, Chikusa, Nagoya, 464-8601, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Biomass Engineering Research Division, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
| | - Chiaki Ogino
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
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6
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Tsuge Y, Matsuzawa H. Recent progress in production of amino acid-derived chemicals using Corynebacterium glutamicum. World J Microbiol Biotechnol 2021; 37:49. [PMID: 33569648 DOI: 10.1007/s11274-021-03007-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/17/2021] [Indexed: 01/07/2023]
Abstract
Green chemical production by microbial processes is critical for the development of a sustainable society in the twenty-first century. Among the important industrial microorganisms, the gram-positive bacterium Corynebacterium glutamicum has been utilized for amino acid fermentation, which is one of the largest microbial-based industries. To date, several amino acids, including L-glutamic acid, L-lysine, and L-threonine, have been produced by C. glutamicum. The capability to produce substantial amounts of amino acids has gained immense attention because the amino acids can be used as a precursor to produce other high-value-added chemicals. Recent developments in metabolic engineering and synthetic biology technologies have enabled the extension of metabolic pathways from amino acids. The present review provides an overview of the recent progress in the microbial production of amino acid-derived bio-based monomers such as 1,4-diaminobutane, 1,5-diaminopentane, glutaric acid, 5-aminolevulinic acid, L-pipecolic acid, 4-amino-1-butanol, and 5-aminolevulinic acid, as well as building blocks for healthcare products and pharmaceuticals such as ectoine, L-theanine, and gamma-aminobutyric acid by metabolically engineered C. glutamicum.
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Affiliation(s)
- Yota Tsuge
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan. .,Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan.
| | - Hiroki Matsuzawa
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Ishikawa, 920-1192, Japan
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7
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Kim DH, Nguyen QT, Ko, GS, Yang JK. Molecular and Enzymatic Features of Homoserine Dehydrogenase from Bacillus subtilis. J Microbiol Biotechnol 2020; 30:1905-1911. [PMID: 33046675 PMCID: PMC9728202 DOI: 10.4014/jmb.2004.04060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022]
Abstract
Homoserine dehydrogenase (HSD) catalyzes the reversible conversion of L-aspartate-4- semialdehyde to L-homoserine in the aspartate pathway for the biosynthesis of lysine, methionine, threonine, and isoleucine. HSD has attracted great attention for medical and industrial purposes due to its recognized application in the development of pesticides and is being utilized in the large scale production of L-lysine. In this study, HSD from Bacillus subtilis (BsHSD) was overexpressed in Escherichia coli and purified to homogeneity for biochemical characterization. We examined the enzymatic activity of BsHSD for L-homoserine oxidation and found that BsHSD exclusively prefers NADP+ to NAD+ and that its activity was maximal at pH 9.0 and in the presence of 0.4 M NaCl. By kinetic analysis, Km values for L-homoserine and NADP+ were found to be 35.08 ± 2.91 mM and 0.39 ± 0.05 mM, respectively, and the Vmax values were 2.72 ± 0.06 μmol/min-1 mg-1 and 2.79 ± 0.11 μmol/min-1 mg-1, respectively. The apparent molecular mass determined with size-exclusion chromatography indicated that BsHSD forms a tetramer, in contrast to the previously reported dimeric HSDs from other organisms. This novel oligomeric assembly can be attributed to the additional C-terminal ACT domain of BsHSD. Thermal denaturation monitoring by circular dichroism spectroscopy was used to determine its melting temperature, which was 54.8°C. The molecular and biochemical features of BsHSD revealed in this study may lay the foundation for future studies on amino acid metabolism and its application for industrial and medical purposes.
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Affiliation(s)
- Do Hyeon Kim
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Quyet Thang Nguyen
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea,Department of Information Communication, Materials, and Chemistry Convergence Technology, Soongsil University, Seoul 06978, Republic of Korea
| | - Gyeong Soo Ko,
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea
| | - Jin Kuk Yang
- Department of Chemistry, College of Natural Sciences, Soongsil University, Seoul 06978, Republic of Korea,Corresponding author Phone: +82-2-820-0433 Fax: +82-2-824-4383 E-mail:
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8
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Liu X, Han C, Fang L, Fan Z, Wang Y, Gao X, Shi J, Min W. Mechanism of the feedback-inhibition resistance in aspartate kinase of Corynebacterium pekinense: from experiment to MD simulations. RSC Adv 2020; 11:30-38. [PMID: 35423034 PMCID: PMC8690038 DOI: 10.1039/d0ra09153g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/14/2020] [Indexed: 11/21/2022] Open
Abstract
In microorganisms and plants, aspartate kinase (AK) is the initial committed enzyme of the biosynthesis of the aspartate acid family amino acids and is inhibited by end products. In the paper, we mutated the key allosteric regulatory site A380 around the binding site of the Lys inhibitor in Corynebacterium pekinense AK (CpAK). A single-mutant A380C was obtained with 12.35-fold higher enzyme activity through high-throughput screening. On this basis, T379 as another key allosteric regulatory site was further modified, and the double-mutant T379N/A380C with 22.79-fold higher enzyme activity was obtained. Molecular dynamics (MD) simulations were used to investigate the mechanism of allosteric inhibition by Lys. The results indicated that the binding of Lys with CpAK resulted in conformational changes and a larger distance between the phosphorus atom of ATP and the oxygen atom of Asp, which was detrimental for the catalytic reaction. However, the mutation of allosteric sites opens the "switch" of allosteric regulation and can prevent the conformational transformation. Some key residues such as G168, R203, and D193 play an important role in maintaining the substrate binding with CpAK and further enhance the enzyme activity.
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Affiliation(s)
- Xiaoting Liu
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Caijing Han
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
- School of Public Health, Weifang Medical University Weifang 261042 Shandong China
| | - Li Fang
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Zhanqing Fan
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Yanan Wang
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Xin Gao
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Junhua Shi
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
| | - Weihong Min
- College of Food Science and Engineering, National Engineering Laboratory of Wheat and Corn Deep Processing, Jilin Agricultural University Changchun 130118 Jilin People's Republic of China +86-431-8451-7235 +86-139-4491-9697
- National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 Jilin China
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9
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Han C, Liu S, Liu C, Xie X, Fang L, Min W. The mutant T379L of novel aspartokinase from Corynebacterium pekinense: A combined experimental and molecular dynamics simulation study. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.04.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Gao Y, Han C, Liu C, Wang J, Zhao L, Fang L, Min W. Enzymatic characterization and molecular mechanism of a novel aspartokinase mutant M372I/T379W from Corynebacterium pekinense. RSC Adv 2019; 9:21344-21354. [PMID: 35521304 PMCID: PMC9066179 DOI: 10.1039/c9ra03293b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 07/03/2019] [Indexed: 02/01/2023] Open
Abstract
A novel aspartokinase mutant M372I/T379W from Corynebacterium pekinense was constructed by using site-directed mutagenesis. The enzyme was then purified, characterized, and its molecular mechanism was comprehensively analyzed. Compared with wild-type AK, the catalytic activity of M372I/T379W AK was 16.51 fold higher and the optimum temperature increased from 28 to 35 °C. The thermostability of M372I/T379W AK was significantly improved. Microscale thermophoresis analysis indicated that M372I/T379W AK not only weakened the inhibitory effect of Lys, but also had stronger binding force with Asp. Molecular dynamics simulation showed that mutations M372I and T379W could regulate the activity of CpAK through affecting the flexibility of Asp and ATP binding pocket residues and the hydrogen bond between CpAK and Asp. In addition, mutations could affect the relative position of protein domains. The width of the Asp binding pocket entrance gate Arg169-Ala60 of M372I/T379W AK was greater than that in wild-type AK and the CpAK switched from T-state to R-state, which promoted the binding of the enzyme to Asp and improving the catalytic efficiency of this enzyme. These results explain the molecular mechanism of M372I/T379W AK, which will greatly facilitate the rational design of more aspartokinase mutants, with have potential applications in aspartic acid metabolism.
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Affiliation(s)
- Yunna Gao
- College of Food Science and Engineering, Jilin Agricultural University Changchun 130118 China +86-138-4486-2551.,National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 China +86-139-4491-9697
| | - Caijing Han
- College of Food Science and Engineering, Jilin Agricultural University Changchun 130118 China +86-138-4486-2551.,National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 China +86-139-4491-9697
| | - Chunlei Liu
- College of Food Science and Engineering, Jilin Agricultural University Changchun 130118 China +86-138-4486-2551.,National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 China +86-139-4491-9697
| | - Ji Wang
- College of Food Science and Engineering, Jilin Agricultural University Changchun 130118 China +86-138-4486-2551.,National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 China +86-139-4491-9697
| | - Lan Zhao
- College of Food Science and Engineering, Jilin Agricultural University Changchun 130118 China +86-138-4486-2551.,National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 China +86-139-4491-9697
| | - Li Fang
- College of Food Science and Engineering, Jilin Agricultural University Changchun 130118 China +86-138-4486-2551.,National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 China +86-139-4491-9697
| | - Weihong Min
- College of Food Science and Engineering, Jilin Agricultural University Changchun 130118 China +86-138-4486-2551.,National Engineering Laboratory of Wheat and Corn Deep Processing Changchun 130118 China +86-139-4491-9697
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11
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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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12
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Construction of Novel Aspartokinase Mutant A380I and Its Characterization by Molecular Dynamics Simulation. Molecules 2018; 23:molecules23123379. [PMID: 30572676 PMCID: PMC6321352 DOI: 10.3390/molecules23123379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/15/2018] [Accepted: 12/17/2018] [Indexed: 02/01/2023] Open
Abstract
In this study, a novel monomer aspartokinase (AK) from Corynebacterium pekinense was identified, and its monomer model was constructed. Site 380 was identified by homologous sequencing and monomer model comparison as the key site which was conserved and located around the binding site of the inhibitor Lys. Furthermore, the mutant A380I with enzyme activity 11.32-fold higher than wild type AK (WT-AK), was obtained by site-directed mutagenesis and high throughput screening. In the mutant A380I, the optimal temperature was raised from 26 °C (WT-AK) to 28 °C, the optimal pH remained unchanged at 8.0, and the half-life was prolonged from 4.5 h (WT-AK) to 6.0 h, indicating enhanced thermal stability. The inhibition of A380I was weakened at various inhibitor concentrations and even activated at certain inhibitor concentrations (10 mM of Lys, 5 mM or 10 mM of Lys + Thr, 10 mM of Lys + Met, 5 mM of Lys + Thr + Met). Molecular dynamics simulation results indicated that the occupancy rate of hydrogen bond between A380I and ATP was enhanced, the effect of Lys (inhibitor) on the protein was weakened, and the angle between Ser281-Tyre358 and Asp359-Gly427 was increased after mutation, leading to an open conformation (R-state) that favored the binding of substrate.
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13
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Tomita T. Structure, function, and regulation of enzymes involved in amino acid metabolism of bacteria and archaea. Biosci Biotechnol Biochem 2017; 81:2050-2061. [PMID: 28840778 DOI: 10.1080/09168451.2017.1365593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Amino acids are essential components in all organisms because they are building blocks of proteins. They are also produced industrially and used for various purposes. For example, L-glutamate is used as the component of "umami" taste and lysine has been used as livestock feed. Recently, many kinds of amino acids have attracted attention as biological regulators and are used for a healthy life. Thus, to clarify the mechanism of how amino acids are biosynthesized and how they work as biological regulators will lead to further effective utilization of them. Here, I review the leucine-induced-allosteric activation of glutamate dehydrogenase (GDH) from Thermus thermophilus and the relationship with the allosteric regulation of GDH from mammals. Next, I describe structural insights into the efficient production of L-glutamate by GDH from an excellent L-glutamate producer, Corynebacterium glutamicum. Finally, I review the structural biology of lysine biosynthesis of thermophilic bacterium and archaea.
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Affiliation(s)
- Takeo Tomita
- a Department of Biotechnology, Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
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14
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da Luz JA, Hans E, Frank D, Zeng AP. Analysis of intracellular metabolites of Corynebacterium glutamicum at high cell density with automated sampling and filtration and assessment of engineered enzymes for effective l-lysine production. Eng Life Sci 2016; 17:512-522. [PMID: 32624795 DOI: 10.1002/elsc.201600163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/13/2016] [Accepted: 10/27/2016] [Indexed: 01/18/2023] Open
Abstract
Engineering of enzymes and pathways is generally required for the development of efficient strains for bioproduction processes. To this end, quantitative and reliable data of intracellular metabolites are highly desired, but often not available, especially for conditions more close to industrial applications, i.e. at high cell density and product concentration. Here, we investigated the intracellular metabolite profiles of an engineered l-lysine-producing Corynebacterium glutamicum strain and the corresponding wild-type strain to assess the impacts of deregulation of product inhibition of the key enzymes aspartate kinase and phosphoenolpyruvate carboxylase and to identify potentials for their further improvement. A bioreactor system with automated fast-sampling, filtration and on-filter quenching of the metabolism was used for a more reliable determination of intracellular metabolites in batch cultures with optical cell density (OD660) up to 40. The l-lysine-producing strain showed substantially different metabolite profiles in the amino acid metabolism, including increased intracellular pool sizes in the l-lysine-, l-homoserine- and l-threonine pathways and decreased intracellular pool sizes for all other determined amino acids. By comparing data of in vitro inhibition of the engineered enzymes and determined intracellular concentrations of the inhibitors it was found that the inferred in vivo activities of these enzymes are still significantly below their in vitro maximums. This work demonstrates the usefulness of metabolic analysis for assessing the impact of engineered enzymes and identifying targets for further strain development.
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Affiliation(s)
- Julian A da Luz
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Enrico Hans
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - Doinita Frank
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess- and Biosystems Engineering Hamburg University of Technology Hamburg Germany
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Tsujimoto M, Yoshida A, Shimizu T, Tomita T, Ohnishi Y, Kuzuyama T, Nishiyama M. Aspartate kinase involved in 4-hydroxy-3-nitrosobenzamide biosynthesis in Streptomyces murayamaensis. Biosci Biotechnol Biochem 2016; 80:2255-2263. [PMID: 27485103 DOI: 10.1080/09168451.2016.1214534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Streptomyces murayamensis carries two aspartate kinase (AK) genes: one for the biosynthesis of lysine, threonine, and methionine, and the other (nspJ) contained in the biosynthetic gene cluster for the secondary metabolite, 4-hydroxy-3-nitrosobenzamide, for catalyzing the first reaction. AKs involved in the biosynthesis of amino acids are often regulated allosterically by the end products. In the present study, we characterized NspJ to investigate whether AKs involved in secondary metabolism were also allosterically regulated. NspJ was in α2β2 and (α2β2)2 heterooligomeric forms, and was insensitive to all the compounds tested including lysine, threonine, and methionine. The reduction in the activity following the removal of ammonium sulfate, which induced subunit dissociation, suggests that the β subunit may be involved in stabilizing the structure of the α subunit in order to exhibit its activity. This study has provided the first example of a feedback-insensitive α2β2-type AK, which is involved in the secondary metabolism.
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Affiliation(s)
- Mai Tsujimoto
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Ayako Yoshida
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Tetsu Shimizu
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Takeo Tomita
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Yasuo Ohnishi
- b Department of Biotechnology , Graduate School of Agricultural and Life Sciences, The University of Tokyo , Tokyo , Japan
| | - Tomohisa Kuzuyama
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
| | - Makoto Nishiyama
- a Biotechnology Research Center , The University of Tokyo , Tokyo , Japan
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Characterization of aspartate kinase and homoserine dehydrogenase from Corynebacterium glutamicum IWJ001 and systematic investigation of l-isoleucine biosynthesis. ACTA ACUST UNITED AC 2016; 43:873-85. [DOI: 10.1007/s10295-016-1763-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 03/16/2016] [Indexed: 11/24/2022]
Abstract
Abstract
Previously we have characterized a threonine dehydratase mutant TDF383V (encoded by ilvA1) and an acetohydroxy acid synthase mutant AHASP176S, D426E, L575W (encoded by ilvBN1) in Corynebacterium glutamicum IWJ001, one of the best l-isoleucine producing strains. Here, we further characterized an aspartate kinase mutant AKA279T (encoded by lysC1) and a homoserine dehydrogenase mutant HDG378S (encoded by hom1) in IWJ001, and analyzed the consequences of all these mutant enzymes on amino acids production in the wild type background. In vitro enzyme tests confirmed that AKA279T is completely resistant to feed-back inhibition by l-threonine and l-lysine, and that HDG378S is partially resistant to l-threonine with the half maximal inhibitory concentration between 12 and 14 mM. In C. glutamicum ATCC13869, expressing lysC1 alone led to exclusive l-lysine accumulation, co-expressing hom1 and thrB1 with lysC1 shifted partial carbon flux from l-lysine (decreased by 50.1 %) to l-threonine (4.85 g/L) with minor l-isoleucine and no l-homoserine accumulation, further co-expressing ilvA1 completely depleted l-threonine and strongly shifted carbon flux from l-lysine (decreased by 83.0 %) to l-isoleucine (3.53 g/L). The results demonstrated the strongly feed-back resistant TDF383V might be the main driving force for l-isoleucine over-synthesis in this case, and the partially feed-back resistant HDG378S might prevent the accumulation of toxic intermediates. Information exploited from such mutation-bred production strain would be useful for metabolic engineering.
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Characterization of Aspartate Kinase from Corynebacterium pekinense and the Critical Site of Arg169. Int J Mol Sci 2015; 16:28270-84. [PMID: 26633359 PMCID: PMC4691045 DOI: 10.3390/ijms161226098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 11/21/2022] Open
Abstract
Aspartate kinase (AK) is the key enzyme in the biosynthesis of aspartate-derived amino acids. Recombinant AK was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. Homogeneous AK was predicted as a decamer with a molecular weight of ~48 kDa and a half-life of 4.5 h. The enzymatic activity was enhanced by ethanol and Ni2+. Moreover, steady-state kinetic study confirmed that AK is an allosteric enzyme, and its activity was inhibited by allosteric inhibitors, such as Lys, Met, and Thr. Theoretical results indicated the binding mode of AK and showed that Arg169 is an important residue in substrate binding, catalytic domain, and inhibitor binding. The values of the kinetic parameter Vmax of R169 mutants, namely, R169Y, R169P, R169D, and R169H AK, with l-aspartate as the substrate, were 4.71-, 2.25-, 2.57-, and 2.13-fold higher, respectively, than that of the wild-type AK. Furthermore, experimental and theoretical data showed that Arg169 formed a hydrogen bond with Glu92, which functions as the entrance gate. This study provides a basis to develop new enzymes and elucidate the corresponding amino acid production.
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Evolution of a chimeric aspartate kinase for L-lysine production using a synthetic RNA device. Appl Microbiol Biotechnol 2015; 99:8527-36. [DOI: 10.1007/s00253-015-6615-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/20/2015] [Accepted: 04/15/2015] [Indexed: 10/23/2022]
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Ma CW, Xiu ZL, Zeng AP. Exploring signal transduction in heteromultimeric protein based on energy dissipation model. J Biomol Struct Dyn 2013; 33:134-46. [PMID: 24279729 DOI: 10.1080/07391102.2013.855145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Dynamic intersubunit interactions are key elements in the regulation of many biological systems. A better understanding of how subunits interact with each other and how their interactions are related to dynamic protein structure is a fundamental task in biology. In this paper, a heteromultimeric allosteric protein, Corynebacterium glutamicum aspartokinase, is used as a model system to explore the signal transduction involved in intersubunit interactions and allosteric communication with an emphasis on the intersubunit signaling process. For this purpose, energy dissipation simulation and network construction are conducted for each subunit and the whole protein. Comparison with experimental results shows that the new approach is able to predict all the mutation sites that have been experimentally proved to desensitize allosteric regulation of the enzyme. Additionally, analysis revealed that the function of the effector threonine is to facilitate the binding of the two subunits without contributing to the allosteric communication. During the allosteric regulation upon the binding of the effector lysine, signals can be transferred from the β-subunit to the catalytic site of the α-subunit through both a direct way of intersubunit signal transduction, and an indirect way: first, to the regulatory region of the α-subunit by intersubunit signal transduction and then to the catalytic region by intramolecular signal transduction. Therefore, the new approach is able to illustrate the diversity of the underlying mechanisms when the strength of feedback inhibition by the effector(s) is modulated, providing useful information that has potential applications in engineering heteromultimeric allosteric regulation.
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Affiliation(s)
- Cheng-Wei Ma
- a Institute of Bioprocess and Biosystems Engineering , Hamburg University of Technology , Hamburg D-21073 , Germany
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Co-expression of feedback-resistant threonine dehydratase and acetohydroxy acid synthase increase L-isoleucine production in Corynebacterium glutamicum. Metab Eng 2012; 14:542-50. [PMID: 22771937 DOI: 10.1016/j.ymben.2012.06.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 05/19/2012] [Accepted: 06/26/2012] [Indexed: 11/24/2022]
Abstract
Threonine dehydratase and acetohydroxy acid synthase are critical enzymes in the L-isoleucine biosynthesis pathway of Corynebacterium glutamicum, but their activities are usually feedback-inhibited. In this study, we characterized a feedback-resistant threonine dehydratase and an acetohydroxy acid synthase from an L-isoleucine producing strain C. glutamicum JHI3-156. Sequence analysis showed that there was only a single amino acid substitution (Phe383Val) in the feedback-resistant threonine dehydratase, and there were three mutated amino acids (Pro176Ser, Asp426Glu, and Leu575Trp) in the big subunit of feedback-resistant acetohydroxy acid synthase. The mutated threonine dehydratase over-expressed in E. coli not only showed completely resistance to L-isoleucine inhibition, but also showed enhanced activity. The mutated acetohydroxy acid synthase over-expressed in E. coli showed more resistance to L-isoleucine inhibition than the wild type. Over-expression of the feedback-resistant threonine dehydratase or acetohydroxy acid synthase in C. glutamicum JHI3-156 led to increase of L-isoleucine production; co-expression of them in C. glutamicum JHI3-156 led to 131.7% increase in flask cultivation, and could produce 30.7g/L L-isoleucine in 72-h fed-batch fermentation. These results would be useful to enhance L-isoleucine production in C. glutamicum.
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Chen L, Chen Z, Zheng P, Sun J, Zeng AP. Study and reengineering of the binding sites and allosteric regulation of biosynthetic threonine deaminase by isoleucine and valine in Escherichia coli. Appl Microbiol Biotechnol 2012; 97:2939-49. [PMID: 22669632 DOI: 10.1007/s00253-012-4176-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Revised: 05/10/2012] [Accepted: 05/13/2012] [Indexed: 11/26/2022]
Abstract
Biosynthetic threonine deaminase (TD) is a key enzyme for the synthesis of isoleucine which is allosterically inhibited and activated by Ile and Val, respectively. The binding sites of Ile and Val and the mechanism of their regulations in TD are not clear, but essential for a rational design of efficient productive strain(s) for Ile and related amino acids. In this study, structure-based computational approach and site-directed mutagenesis were combined to identify the potential binding sites of Ile and Val in Escherichia coli TD. Our results demonstrated that each regulatory domain of the TD monomer possesses two nonequivalent effector-binding sites. The residues R362, E442, G445, A446, Y369, I460, and S461 only interact with Ile while E347, G350, and F352 are involved not only in the Ile binding but also in the Val binding. By further considering enzyme kinetic data, we propose a concentration-dependent mechanism of the allosteric regulation of TD by Ile and Val. For the construction of Ile overproducing strain, a novel TD mutant with double mutation of F352A/R362F was also created, which showed both higher activity and much stronger resistance to Ile inhibition comparing to those of wild-type enzyme. Overexpression of this mutant TD in E. coli JW3591 significantly increased the production of ketobutyrate and Ile in comparison to the reference strains overexpressing wild-type TD or the catabolic threonine deaminase (TdcB). This work builds a solid basis for the reengineering of TD and related microorganisms for Ile production.
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Affiliation(s)
- Lin Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
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22
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Abstract
L-threonine, one of the three major amino acids produced throughout the world, has a wide application in industry, as an additive or as a precursor for the biosynthesis of other chemicals. It is predominantly produced through microbial fermentation the efficiency of which largely depends on the quality of strains. Metabolic engineering based on a cogent understanding of the metabolic pathways of L-threonine biosynthesis and regulation provides an effective alternative to the traditional breeding for strain development. Continuing efforts have been made in revealing the mechanisms and regulation of L-threonine producing strains, as well as in metabolic engineering of suitable organisms whereby genetically-defined, industrially competitive L-threonine producing strains have been successfully constructed. This review focuses on the global metabolic and regulatory networks responsible for L-threonine biosynthesis, the molecular mechanisms of regulation, and the strategies employed in strain engineering.
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Affiliation(s)
- Xunyan Dong
- Key Laboratory of Industrial Biotechnology of Ministry of Education, School of Biotechnology, JiangnanUniversity, Wuxi, 214122, China
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WONG WINGCHEONG, MAURER-STROH SEBASTIAN, EISENHABER FRANK. THE JANUS-FACED E-VALUES OF HMMER2: EXTREME VALUE DISTRIBUTION OR LOGISTIC FUNCTION? J Bioinform Comput Biol 2011. [DOI: 10.1142/s0219720011005264] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
E-value guided extrapolation of protein domain annotation from libraries such as Pfam with the HMMER suite is indispensable for hypothesizing about the function of experimentally uncharacterized protein sequences. Since the recent release of HMMER3 does not supersede all functions of HMMER2, the latter will remain relevant for ongoing research as well as for the evaluation of annotations that reside in databases and in the literature. In HMMER2, the E-value is computed from the score via a logistic function or via a domain model-specific extreme value distribution (EVD); the lower of the two is returned as E-value for the domain hit in the query sequence. We find that, for thousands of domain models, this treatment results in switching from the EVD to the statistical model with the logistic function when scores grow (for Pfam release 23, 99% in the global mode and 75% in the fragment mode). If the score corresponding to the breakpoint results in an E-value above a user-defined threshold (e.g. 0.1), a critical score region with conflicting E-values from the logistic function (below the threshold) and from EVD (above the threshold) does exist. Thus, this switch will affect E-value guided annotation decisions in an automated mode. To emphasize, switching in the fragment mode is of no practical relevance since it occurs only at E-values far below 0.1. Unfortunately, a critical score region does exist for 185 domain models in the hmmpfam and 1,748 domain models in the hmmsearch global-search mode. For 145 out the respective 185 models, the critical score region is indeed populated by actual sequences. In total, 24.4% of their hits have a logistic function-derived E-value < 0.1 when the EVD provides an E-value > 0.1. We provide examples of false annotations and critically discuss the appropriateness of a logistic function as alternative to the EVD.
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Affiliation(s)
- WING-CHEONG WONG
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A *STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
| | - SEBASTIAN MAURER-STROH
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A *STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 63755, Singapore
| | - FRANK EISENHABER
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A *STAR), 30 Biopolis Street, #07-01, Matrix, Singapore 138671, Singapore
- Department of Biological Sciences (DBS), National University of Singapore (NUS), 8 Medical Drive, Singapore 117597, Singapore
- School of Computer Engineering (SCE), Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Singapore
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The many faces of aspartate kinases. Arch Biochem Biophys 2011; 519:186-93. [PMID: 22079167 DOI: 10.1016/j.abb.2011.10.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/26/2011] [Accepted: 10/28/2011] [Indexed: 10/15/2022]
Abstract
Based on recent X-ray structures and biochemical characterizations of aspartate kinases from different species, we show in this review how various organizations of a regulatory domain have contributed to the different mechanisms of control observed in aspartate kinases allowing simple to complex allosteric controls in branched pathways. The aim of this review is to show the relationships between domain organization, effector binding sites, mechanism of inhibition and regulatory function of an allosteric enzyme in a biosynthetic pathway.
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Yang Q, Yu K, Yan L, Li Y, Chen C, Li X. Structural view of the regulatory subunit of aspartate kinase from Mycobacterium tuberculosis. Protein Cell 2011; 2:745-54. [PMID: 21976064 DOI: 10.1007/s13238-011-1094-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 09/01/2011] [Indexed: 12/01/2022] Open
Abstract
The aspartate kinase (AK) from Mycobacterium tuberculosis (Mtb) catalyzes the biosynthesis of aspartate family amino acids, including lysine, threonine, isoleucine and methionine. We determined the crystal structures of the regulatory subunit of aspartate kinase from Mtb alone (referred to as MtbAKβ) and in complex with threonine (referred to as MtbAKβ-Thr) at resolutions of 2.6 Å and 2.0 Å, respectively. MtbAKβ is composed of two perpendicular non-equivalent ACT domains [aspartate kinase, chorismate mutase, and TyrA (prephenate dehydrogenase)] per monomer. Each ACT domain contains two α helices and four antiparallel β strands. The structure of MtbAKβ shares high similarity with the regulatory subunit of the aspartate kinase from Corynebacterium glutamicum (referred to as CgAKβ), suggesting similar regulatory mechanisms. Biochemical assays in our study showed that MtbAK is inhibited by threonine. Based on crystal structure analysis, we discuss the regulatory mechanism of MtbAK.
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Affiliation(s)
- Qingzhu Yang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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26
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Chen Z, Rappert S, Sun J, Zeng AP. Integrating molecular dynamics and co-evolutionary analysis for reliable target prediction and deregulation of the allosteric inhibition of aspartokinase for amino acid production. J Biotechnol 2011; 154:248-54. [DOI: 10.1016/j.jbiotec.2011.05.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/02/2011] [Accepted: 05/09/2011] [Indexed: 10/18/2022]
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Coevolutionary analysis enabled rational deregulation of allosteric enzyme inhibition in Corynebacterium glutamicum for lysine production. Appl Environ Microbiol 2011; 77:4352-60. [PMID: 21531824 DOI: 10.1128/aem.02912-10] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Product feedback inhibition of allosteric enzymes is an essential issue for the development of highly efficient microbial strains for bioproduction. Here we used aspartokinase from Corynebacterium glutamicum (CgAK), a key enzyme controlling the biosynthesis of industrially important aspartate family amino acids, as a model to demonstrate a fast and efficient approach to the deregulation of allostery. In the last 50 years many researchers and companies have made considerable efforts to deregulate this enzyme from allosteric inhibition by lysine and threonine. However, only a limited number of positive mutants have been identified so far, almost exclusively by random mutation and selection. In this study, we used statistical coupling analysis of protein sequences, a method based on coevolutionary analysis, to systematically clarify the interaction network within the regulatory domain of CgAK that is essential for allosteric inhibition. A cluster of interconnected residues linking different inhibitors' binding sites as well as other regions of the protein have been identified, including most of the previously reported positions of successful mutations. Beyond these mutation positions, we have created another 14 mutants that can partially or completely desensitize CgAK from allosteric inhibition, as shown by enzyme activity assays. The introduction of only one of the inhibition-insensitive CgAK mutations (here Q298G) into a wild-type C. glutamicum strain by homologous recombination resulted in an accumulation of 58 g/liter L-lysine within 30 h of fed-batch fermentation in a bioreactor.
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28
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Schuldt L, Suchowersky R, Veith K, Mueller-Dieckmann J, Weiss MS. Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the regulatory domain of aspartokinase (Rv3709c) from Mycobacterium tuberculosis. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:380-5. [PMID: 21393848 PMCID: PMC3053168 DOI: 10.1107/s1744309111000030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 01/03/2011] [Indexed: 03/04/2023]
Abstract
The regulatory domain of Mycobacterium tuberculosis aspartokinase (Mtb-AK, Mtb-Ask, Rv3709c) has been cloned, heterologously expressed in Escherichia coli and purified using standard chromatographic techniques. Screening for initial crystallization conditions using the regulatory domain (AK-β) in the presence of the potential feedback inhibitor threonine identified four conditions which yielded crystals suitable for X-ray diffraction analysis. From these four conditions five different crystal forms of Mtb-AK-β resulted, three of which belonged to the orthorhombic system, one to the tetragonal system and one to the monoclinic system. The highest resolution (1.6 Å) was observed for a crystal form belonging to space group P2(1)2(1)2(1), with unit-cell parameters a=53.70, b=63.43, c=108.85 Å and two molecules per asymmetric unit.
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Affiliation(s)
- Linda Schuldt
- EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.
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29
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Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for the production of l-threonine. Biotechnol Adv 2011; 29:11-23. [DOI: 10.1016/j.biotechadv.2010.07.009] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/17/2010] [Accepted: 07/26/2010] [Indexed: 11/23/2022]
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30
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Yoshida A, Tomita T, Kuzuyama T, Nishiyama M. Mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from Corynebacterium glutamicum. J Biol Chem 2010; 285:27477-27486. [PMID: 20573952 PMCID: PMC2930746 DOI: 10.1074/jbc.m110.111153] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 06/08/2010] [Indexed: 11/06/2022] Open
Abstract
Aspartate kinase (AK) is the first and committed enzyme of the biosynthetic pathway producing aspartate family amino acids, lysine, threonine, and methionine. AK from Corynebacterium glutamicum (CgAK), a bacterium used for industrial fermentation of amino acids, including glutamate and lysine, is inhibited by lysine and threonine in a concerted manner. To elucidate the mechanism of this unique regulation in CgAK, we determined the crystal structures in several forms: an inhibitory form complexed with both lysine and threonine, an active form complexed with only threonine, and a feedback inhibition-resistant mutant (S301F) complexed with both lysine and threonine. CgAK has a characteristic alpha(2)beta(2)-type heterotetrameric structure made up of two alpha subunits and two beta subunits. Comparison of the crystal structures between inhibitory and active forms revealed that binding inhibitors causes a conformational change to a closed inhibitory form, and the interaction between the catalytic domain in the alpha subunit and beta subunit (regulatory subunit) is a key event for stabilizing the inhibitory form. This study shows not only the first crystal structures of alpha(2)beta(2)-type AK but also the mechanism of concerted inhibition in CgAK.
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Affiliation(s)
- Ayako Yoshida
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takeo Tomita
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tomohisa Kuzuyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Makoto Nishiyama
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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A new mode of dimerization of allosteric enzymes with ACT domains revealed by the crystal structure of the aspartate kinase from Cyanobacteria. J Mol Biol 2010; 399:283-93. [PMID: 20398676 DOI: 10.1016/j.jmb.2010.04.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2010] [Revised: 03/31/2010] [Accepted: 04/07/2010] [Indexed: 11/22/2022]
Abstract
Aspartate kinases (AKs) can be divided in two subhomology divisions, AKalpha and AKbeta, depending on the presence of an extra sequence of about 60 amino acids, which is found only in the N-terminus of all AKalpha's. To date, the structures of AKalpha failed to provide a role for this additional N-terminal sequence. In this study, the structure of the AKbeta from the Cyanobacteria Synechocystis reveals that this supplementary sequence is linked to the dimerization mode of AKs. Its absence in AKbeta leads to the dimerization by the catalytic domain instead of involving the ACT domains [Pfam 01842; small regulatory domains initially found in AK, chorismate mutase and TyrA (prephenate dehydrogenase)] as observed in AKalpha. Thus, the structural analysis of the Synechocystis AKbeta revealed a dimer with a novel architecture. The four ACT domains of each monomer interact together and do not make any contact with those of the second monomer. The enzyme is inhibited synergistically by threonine and lysine with the binding of threonine first. The interaction between ACT1 and ACT4 or between ACT2 and ACT3 generates a threonine binding site and a lysine binding site at each interface, making a total of eight regulatory sites per dimer and allowing a fine-tuning of the AK activity by the end products, threonine and lysine.
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Cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. Microbiol Mol Biol Rev 2010; 73:594-651. [PMID: 19946135 DOI: 10.1128/mmbr.00024-09] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspartokinase (Ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. Lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ASK network or from alternative pathways. Ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. Two subhomology divisions, ASK(alpha) and ASK(beta), have been recognized. The ASK(alpha) subhomology division is the most ancient, being widely distributed throughout the Archaea and Eukarya and in some Bacteria. Within an indel region of about 75 amino acids near the N terminus, ASK(beta) sequences differ from ASK(alpha) sequences by the possession of a proposed ancient deletion. ASK(beta) sequences are present in most Bacteria and usually exhibit an in-frame internal translational start site that can generate a small Ask subunit that is identical to the C-terminal portion of the larger subunit of a heterodimeric unit. Particularly novel are ask genes embedded in gene contexts that imply specialization for ectoine (osmotic agent) or aromatic amino acids. The cohesion group approach is well suited for the easy recognition of relatively recent lateral gene transfer (LGT) events, and many examples of these are described. Given the current density of genome representation for Proteobacteria, it is possible to reconstruct more ancient landmark LGT events. Thus, a plausible scenario in which the three well-studied and iconic Ask homologs of Escherichia coli are not within the vertical genealogy of Gammaproteobacteria, but rather originated via LGT from a Bacteroidetes donor, is supported.
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Molecular basis of the inhibitor selectivity and insights into the feedback inhibition mechanism of citramalate synthase from Leptospira interrogans. Biochem J 2009; 421:133-43. [PMID: 19351325 DOI: 10.1042/bj20090336] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
LiCMS (Leptospira interrogans citramalate synthase) catalyses the first reaction of the isoleucine biosynthesis pathway in L. interrogans, the pathogen of leptospirosis. The catalytic reaction is regulated through feedback inhibition by its end product isoleucine. To understand the molecular basis of the high selectivity of the inhibitor and the mechanism of feedback inhibition, we determined the crystal structure of LiCMSC (C-terminal regulatory domain of LiCMS) in complex with isoleucine, and performed a biochemical study of the inhibition of LiCMS using mutagenesis and kinetic methods. LiCMSC forms a dimer of dimers in both the crystal structure and solution and the dimeric LiCMSC is the basic functional unit. LiCMSC consists of six beta-strands forming two anti-parallel beta-sheets and two alpha-helices and assumes a betaalphabeta three-layer sandwich structure. The inhibitor isoleucine is bound in a pocket at the dimer interface and has both hydrophobic and hydrogen-bonding interactions with several conserved residues of both subunits. The high selectivity of LiCMS for isoleucine over leucine is primarily dictated by the residues, Tyr430, Leu451, Tyr454, Ile458 and Val468, that form a hydrophobic pocket to accommodate the side chain of the inhibitor. The binding of isoleucine has inhibitory effects on the binding of both the substrate, pyruvate, and coenzyme, acetyl-CoA, in a typical pattern of K-type inhibition. The structural and biochemical data from the present study together suggest that the binding of isoleucine affects the binding of the substrate and coenzyme at the active site, possibly via conformational change of the dimer interface of the regulatory domain, leading to inhibition of the catalytic reaction.
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Yoshida A, Tomita T, Kono H, Fushinobu S, Kuzuyama T, Nishiyama M. Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase fromThermus thermophilus. FEBS J 2009; 276:3124-36. [DOI: 10.1111/j.1742-4658.2009.07030.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Curien G, Biou V, Mas-Droux C, Robert-Genthon M, Ferrer JL, Dumas R. Amino acid biosynthesis: new architectures in allosteric enzymes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:325-339. [PMID: 18272376 DOI: 10.1016/j.plaphy.2007.12.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Indexed: 05/25/2023]
Abstract
This review focuses on the allosteric controls in the Aspartate-derived and the branched-chain amino acid biosynthetic pathways examined both from kinetic and structural points of view. The objective is to show the differences that exist among the plant and microbial worlds concerning the allosteric regulation of these pathways and to unveil the structural bases of this diversity. Indeed, crystallographic structures of enzymes from these pathways have been determined in bacteria, fungi and plants, providing a wonderful opportunity to obtain insight into the acquisition and modulation of allosteric controls in the course of evolution. This will be examined using two enzymes, threonine synthase and the ACT domain containing enzyme aspartate kinase. In a last part, as many enzymes in these pathways display regulatory domains containing the conserved ACT module, the organization of ACT domains in this kind of allosteric enzymes will be reviewed, providing explanations for the variety of allosteric effectors and type of controls observed.
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Affiliation(s)
- Gilles Curien
- Laboratoire de Physiologie Cellulaire Végétale, Université Joseph Fourier, Commissariat à l'Energie Atomique, Institut de Recherche et de Technologie des Sciences du Vivant, 38054 Grenoble, France
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Kallio P, Liu Z, Mäntsälä P, Niemi J, Metsä-Ketelä M. A Nested Gene in Streptomyces Bacteria Encodes a Protein Involved in Quaternary Complex Formation. J Mol Biol 2008; 375:1212-21. [DOI: 10.1016/j.jmb.2007.11.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 11/07/2007] [Accepted: 11/12/2007] [Indexed: 12/01/2022]
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