1
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Wang X, Sun B. Metabolic proteins with crucial roles in Edwardsiella tarda antioxidative adaptation and intracellular proliferation. mSystems 2023; 8:e0039123. [PMID: 37729581 PMCID: PMC10654080 DOI: 10.1128/msystems.00391-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Edwardsiella tarda is a significant fish pathogen that can live in challenging environments of reactive oxygen species (ROS), such as inside the phagocytes. Metabolic reconfiguration has been increasingly associated with bacterial oxidative tolerance and virulence. However, the metabolic proteins of E. tarda involved in such processes remain elusive. By proteomic analysis and functional characterization of protein null mutants, the present study identified eight crucial proteins for bacterial oxidative resistance and intracellular infection. Seven of them are metabolic proteins dictating the metabolic flux toward the generation of pyruvate, a key metabolite capable of scavenging ROS molecules. Furthermore, L-aspartate uptake, which can fuel the pyruvate generation, was found essential for the full antioxidative capacity of E. tarda. These findings identified seven metabolic proteins involved in bacterial oxidative adaptation and indicate that metabolic reprogramming toward pyruvate was likely a pivotal strategy of bacteria for antioxidative adaptation and intracellular survival.
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Affiliation(s)
- Xinhui Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
| | - Boguang Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
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2
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Yang H, Yu H, Stolarzewicz IA, Tang W. Enantioselective Transformations in the Synthesis of Therapeutic Agents. Chem Rev 2023; 123:9397-9446. [PMID: 37417731 DOI: 10.1021/acs.chemrev.3c00010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The proportion of approved chiral drugs and drug candidates under medical studies has surged dramatically over the past two decades. As a consequence, the efficient synthesis of enantiopure pharmaceuticals or their synthetic intermediates poses a profound challenge to medicinal and process chemists. The significant advancement in asymmetric catalysis has provided an effective and reliable solution to this challenge. The successful application of transition metal catalysis, organocatalysis, and biocatalysis to the medicinal and pharmaceutical industries has promoted drug discovery by efficient and precise preparation of enantio-enriched therapeutic agents, and facilitated the industrial production of active pharmaceutical ingredient in an economic and environmentally friendly fashion. The present review summarizes the most recent applications (2008-2022) of asymmetric catalysis in the pharmaceutical industry ranging from process scales to pilot and industrial levels. It also showcases the latest achievements and trends in the asymmetric synthesis of therapeutic agents with state of the art technologies of asymmetric catalysis.
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Affiliation(s)
- He Yang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Hanxiao Yu
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Izabela A Stolarzewicz
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenjun Tang
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
- School of Chemistry and Material Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
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3
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Tikhomirova A, Zilm PS, Trappetti C, Paton JC, Kidd SP. The central role of arginine in Haemophilus influenzae survival in a polymicrobial environment with Streptococcus pneumoniae and Moraxella catarrhalis. PLoS One 2022; 17:e0271912. [PMID: 35877653 PMCID: PMC9312370 DOI: 10.1371/journal.pone.0271912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis are bacterial species which frequently co-colonise the nasopharynx, but can also transit to the middle ear to cause otitis media. Chronic otitis media is often associated with a polymicrobial infection by these bacteria. However, despite being present in polymicrobial infections, the molecular interactions between these bacterial species remain poorly understood. We have previously reported competitive interactions driven by pH and growth phase between H. influenzae and S. pneumoniae. In this study, we have revealed competitive interactions between the three otopathogens, which resulted in reduction of H. influenzae viability in co-culture with S. pneumoniae and in triple-species culture. Transcriptomic analysis by mRNA sequencing identified a central role of arginine in mediating these interactions. Arginine supplementation was able to increase H. influenzae survival in a dual-species environment with S. pneumoniae, and in a triple-species environment. Arginine was used by H. influenzae for ATP production, and levels of ATP generated in dual- and triple-species co-culture at early stages of growth were significantly higher than the combined ATP levels of single-species cultures. These results indicate a central role for arginine-mediated ATP production by H. influenzae in the polymicrobial community.
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Affiliation(s)
- Alexandra Tikhomirova
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Peter S. Zilm
- Department of Oral Microbiology, School of Dentistry, University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Claudia Trappetti
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - James C. Paton
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
| | - Stephen P. Kidd
- Department of Molecular and Biomedical Science, Research Centre for Infectious Diseases, University of Adelaide, Adelaide, Australia
- Australian Centre for Antimicrobial Resistance Ecology, The University of Adelaide, Adelaide, Australia
- * E-mail:
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4
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Csuka P, Molnár Z, Tóth V, Imarah AO, Balogh‐Weiser D, Vértessy BG, Poppe L. Immobilization of the Aspartate Ammonia-Lyase from Pseudomonas fluorescens R124 on Magnetic Nanoparticles: Characterization and Kinetics. Chembiochem 2022; 23:e202100708. [PMID: 35114050 PMCID: PMC9307013 DOI: 10.1002/cbic.202100708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/02/2022] [Indexed: 11/07/2022]
Abstract
Aspartate ammonia-lyases (AALs) catalyze the non-oxidative elimination of ammonia from l-aspartate to give fumarate and ammonia. In this work the AAL coding gene from Pseudomonas fluorescens R124 was identified, isolated, and cloned into the pET-15b expression vector and expressed in E. coli. The purified enzyme (PfAAL) showed optimal activity at pH 8.8, Michaelis-Menten kinetics in the ammonia elimination from l-aspartate, and no strong dependence on divalent metal ions for its activity. The purified PfAAL was covalently immobilized on epoxy-functionalized magnetic nanoparticles (MNP), and effective kinetics of the immobilized PfAAL-MNP was compared to the native solution form. Glycerol addition significantly enhanced the storability of PfAAL-MNP. Inhibiting effect of the growing viscosity (modulated by addition of glycerol or glucose) on the enzymatic activity was observed for the native and immobilized form of PfAAL, as previously described for other free enzymes. The storage stability and recyclability of PfAAL-MNP is promising for further biocatalytic applications.
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Affiliation(s)
- Pál Csuka
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - Zsófia Molnár
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
- Institute of EnzymologyELKH Research Center of Natural SciencesMagyar tudósok krt. 21117BudapestHungary
| | - Veronika Tóth
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - Ali Obaid Imarah
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - Diána Balogh‐Weiser
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
- Department of Physical Chemistry and Materials ScienceBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - Beáta G. Vértessy
- Institute of EnzymologyELKH Research Center of Natural SciencesMagyar tudósok krt. 21117BudapestHungary
- Department of Applied Biotechnology and Food ScienceBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
| | - László Poppe
- Department of Organic Chemistry and TechnologyBudapest University of Technology and EconomicsMűegyetem rkp. 31111BudapestHungary
- Biocatalysis and Biotransformation Research CenterFaculty of Chemistry and Chemical EngineeringBabeş-Bolyai University of Cluj-NapocaArany János Str. 11400028Cluj-NapocaRomania
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5
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Wang JY, Rao ZM, Xu JZ, Zhang WG. Enhancing β-alanine production from glucose in genetically modified Corynebacterium glutamicum by metabolic pathway engineering. Appl Microbiol Biotechnol 2021; 105:9153-9166. [PMID: 34837493 DOI: 10.1007/s00253-021-11696-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 10/19/2022]
Abstract
To directly produce β-alanine from glucose by microbial fermentation, a recombinant Corynebacterium glutamicum strain with high efficiency of β-alanine production was constructed in this study. To do this, the biosynthetic pathway of β-alanine in an L-lysine-producing strain XQ-5 was modified by enhancing carbon flux in biosynthetic pathway and limiting carbon flux in competitive pathway. This study showed that replacement of L-aspartate kinase (AK) with wild-type AK and disruption of lactate dehydrogenase and alanine/valine aminotransferases increase β-alanine production because of decreasing the by-products accumulation. Moreover, L-aspartate-α-decarboxylase (ADC) from Bacillus subtilis was designed as the best enzyme for increasing β-alanine production, and its variant (BsADCE56S/I88M) showed the highest activity for catalyzing L-aspartate to generate β-alanine. To further increase β-alanine production, expression level of BsADCE56S/I88M was controlled by optimizing promoter and RBS, indicating that Pgro plus ThirRBS is the best combination for BsADCE56S/I88M expression and β-alanine production. The resultant strain XQ-5.5 produced 30.7 ± 2.3 g/L of β-alanine with a low accumulation of lactate (from 5.2 ± 0.14 to 0.2 ± 0.09 g/L) and L-alanine (from 7.6 ± 0.22 to 3.8 ± 0. 32 g/L) in shake-flask fermentation and produced 56.5 ± 3.2 g/L of β-alanine with a productivity of 0.79 g/(L·h) and the glucose conversion efficiency (α) of 39.5% in feed-batch fermentation. This is the first report of genetically modifying the biosynthetic pathway of β-alanine that improves the efficiency of β-alanine production in an L-lysine-producing strain, and these results give us a new insight for constructing the other valuable biochemical. KEY POINTS: • Optimization and overexpression of the key enzyme BsADC increased the accumulation of β-alanine. • The AK was replaced with wild-type AK to increase the conversion of aspartic acid to β-alanine. • A 56.5-g/L β-alanine production in fed-batch fermentation was achieved.
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Affiliation(s)
- Jin-Yu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China
| | - Zhi-Ming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China.,National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, Wuxi, 214122, People's Republic of China.
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6
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Ni ZF, Xu P, Zong MH, Lou WY. Structure-guided protein engineering of ammonia lyase for efficient synthesis of sterically bulky unnatural amino acids. BIORESOUR BIOPROCESS 2021; 8:103. [PMID: 38650190 PMCID: PMC10992142 DOI: 10.1186/s40643-021-00456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/08/2021] [Indexed: 11/10/2022] Open
Abstract
Enzymatic asymmetric amination addition is seen as a promising approach for synthesizing amine derivatives, especially unnatural amino acids, which are valuable precursors to fine chemicals and drugs. Despite the broad substrate spectrum of methylaspartate lyase (MAL), some bulky substrates, such as caffeic acid, cannot be effectively accepted. Herein, we report a group of variants structurally derived from Escherichia coli O157:H7 MAL (EcMAL). A combined mutagenesis strategy was used to simultaneously redesign the key residues of the entrance tunnel and binding pocket to explore the possibility of accepting bulky substrates with potential application to chiral drug synthesis. Libraries of residues capable of lining the active center of EcMAL were then constructed and screened by an effective activity solid-phase color screening method using tyrosinase as a cascade catalyst system. Activity assays and molecular dynamics studies of the resultant variants showed that the substrate specificity of EcMAL was modified by adjusting the polarity of the binding pocket and the degree of flexibility of the entrance tunnel. Compared to M3, the optimal variant M8 was obtained with a 15-fold increase in catalytic activity. This structure-based protein engineering of EcMAL can be used to open new application directions or to develop practical multi-enzymatic processes for the production of various useful compounds.
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Affiliation(s)
- Zi-Fu Ni
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Pei Xu
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Min-Hua Zong
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China
| | - Wen-Yong Lou
- Laboratory of Applied Biocatalysis, School of Food Science and Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou, 510640, Guangdong, China.
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7
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Development of a versatile and efficient C–N lyase platform for asymmetric hydroamination via computational enzyme redesign. Nat Catal 2021. [DOI: 10.1038/s41929-021-00604-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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8
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Magnetically Agitated Nanoparticle-Based Batch Reactors for Biocatalysis with Immobilized Aspartate Ammonia-Lyase. Catalysts 2021. [DOI: 10.3390/catal11040483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this study, we investigated the influence of different modes of magnetic mixing on effective enzyme activity of aspartate ammonia-lyase from Pseudomonas fluorescens immobilized onto epoxy-functionalized magnetic nanoparticles by covalent binding (AAL-MNP). The effective specific enzyme activity of AAL-MNPs in traditional shake vial method was compared to the specific activity of the MNP-based biocatalyst in two devices designed for magnetic agitation. The first device agitated the AAL-MNPs by moving two permanent magnets at two opposite sides of a vial in x-axis direction (being perpendicular to the y-axis of the vial); the second device unsettled the MNP biocatalyst by rotating the two permanent magnets around the y-axis of the vial. In a traditional shake vial, the substrate and biocatalyst move in the same direction with the same pattern. In magnetic agitation modes, the MNPs responded differently to the external magnetic field of two permanent magnets. In the axial agitation mode, MNPs formed a moving cloud inside the vial, whereas in the rotating agitation mode, they formed a ring. Especially, the rotating agitation of the MNPs generated small fluid flow inside the vial enabling the mixing of the reaction mixture, leading to enhanced effective activity of AAL-MNPs compared to shake vial agitation.
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9
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Transcriptional profiling of biofilms formed on chilled beef by psychrotrophic meat spoilage bacterium, Pseudomonas fragi 1793. Biofilm 2021; 3:100045. [PMID: 33718862 PMCID: PMC7921472 DOI: 10.1016/j.bioflm.2021.100045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 11/21/2022] Open
Abstract
Pseudomonas fragi is the predominant bacterial species associated with spoiled aerobically stored chilled meat worldwide. It readily forms biofilms on meat under refrigerated temperature conditions used in the meat industry. Biofilm growth leads to slime development on meat which in turn becomes a major quality defect. To understand the genetic regulation that aids P. fragi to survive under chilled conditions used in the meat industry, as well to obtain an overview of the transcriptomic behavior of this organism when grown as biofilms, RNA sequencing was carried out for the main stages of the P. fragi 1793 biofilm. RNA was extracted at different stages of the biofilm cycle namely initiation, maturation and dispersal. At the same time, the biofilm growth was assessed by fluorescent staining and imaging using confocal laser scanning microscope. The results of RNA sequencing were verified by qRT-PCR using twelve genes that were most significantly up and down regulated at each stage. Differential expression analysis at biofilm maturation revealed 332 significantly upregulated genes and 37 downregulated genes relative to initiation. Differential expression analysis at biofilm dispersal reveled 658 upregulated and 275 downregulated genes relative to initiation. During biofilm maturation and dispersal, genes coding for flp family type IVb pilin, ribosome modulation factor, creatininase were the most upregulated genes while genes encoding for iron uptake systems including TonB-dependent siderophore receptor and taurine transport were significantly down regulated. The results show that protein synthesis and cellular multiplication cease after the biofilm population maximum has reached.
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10
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Surface charge-based rational design of aspartase modifies the optimal pH for efficient β-aminobutyric acid production. Int J Biol Macromol 2020; 164:4165-4172. [DOI: 10.1016/j.ijbiomac.2020.08.229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/29/2020] [Accepted: 08/29/2020] [Indexed: 12/19/2022]
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11
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Blocks in Tricarboxylic Acid Cycle of Salmonella enterica Cause Global Perturbation of Carbon Storage, Motility, and Host-Pathogen Interaction. mSphere 2019; 4:4/6/e00796-19. [PMID: 31826974 PMCID: PMC6908425 DOI: 10.1128/msphere.00796-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed perturbation analyses of the tricarboxylic acid cycle of the gastrointestinal pathogen Salmonella enterica serovar Typhimurium. The defect of fumarase activity led to accumulation of fumarate but also resulted in a global alteration of carbon fluxes, leading to increased storage of glycogen. Gross alterations were observed in proteome and metabolome compositions of fumarase-deficient Salmonella. In turn, these changes were linked to aberrant motility patterns of the mutant strain and resulted in highly increased phagocytic uptake by macrophages. Our findings indicate that basic cellular functions and specific virulence functions in Salmonella critically depend on the proper function of the primary metabolism. The tricarboxylic acid (TCA) cycle is a central metabolic hub in most cells. Virulence functions of bacterial pathogens such as facultative intracellular Salmonella enterica serovar Typhimurium (S. Typhimurium) are closely connected to cellular metabolism. During systematic analyses of mutant strains with defects in the TCA cycle, a strain deficient in all fumarase isoforms (ΔfumABC) elicited a unique metabolic profile. Alongside fumarate, S. Typhimurium ΔfumABC accumulates intermediates of the glycolysis and pentose phosphate pathway. Analyses by metabolomics and proteomics revealed that fumarate accumulation redirects carbon fluxes toward glycogen synthesis due to high (p)ppGpp levels. In addition, we observed reduced abundance of CheY, leading to altered motility and increased phagocytosis of S. Typhimurium by macrophages. Deletion of glycogen synthase restored normal carbon fluxes and phagocytosis and partially restored levels of CheY. We propose that utilization of accumulated fumarate as carbon source induces a status similar to exponential- to stationary-growth-phase transition by switching from preferred carbon sources to fumarate, which increases (p)ppGpp levels and thereby glycogen synthesis. Thus, we observed a new form of interplay between metabolism of S. Typhimurium and cellular functions and virulence. IMPORTANCE We performed perturbation analyses of the tricarboxylic acid cycle of the gastrointestinal pathogen Salmonella enterica serovar Typhimurium. The defect of fumarase activity led to accumulation of fumarate but also resulted in a global alteration of carbon fluxes, leading to increased storage of glycogen. Gross alterations were observed in proteome and metabolome compositions of fumarase-deficient Salmonella. In turn, these changes were linked to aberrant motility patterns of the mutant strain and resulted in highly increased phagocytic uptake by macrophages. Our findings indicate that basic cellular functions and specific virulence functions in Salmonella critically depend on the proper function of the primary metabolism.
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12
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Stuttgen GM, Grosskopf JD, Berger CR, May JF, Bhattacharyya B, Weaver TM. Closed fumarase C active‐site structures reveal SS Loop residue contribution in catalysis. FEBS Lett 2019; 594:337-357. [DOI: 10.1002/1873-3468.13603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/26/2019] [Accepted: 09/05/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Gage M. Stuttgen
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
| | - Julian D. Grosskopf
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
| | - Colton R. Berger
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
| | - John F. May
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
| | | | - Todd M. Weaver
- Department of Chemistry and Biochemistry University Wisconsin – La Crosse WI USA
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13
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Paul A, Mishra A, Surolia A, Vijayan M. Structural studies on
M. tuberculosis
argininosuccinate lyase and its liganded complex: Insights into catalytic mechanism. IUBMB Life 2019; 71:643-652. [DOI: 10.1002/iub.2000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Anju Paul
- Molecular Biophysics UnitIndian Institute of Science Bangalore India
| | - Archita Mishra
- Molecular Biophysics UnitIndian Institute of Science Bangalore India
| | - Avadhesha Surolia
- Molecular Biophysics UnitIndian Institute of Science Bangalore India
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14
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Li R, Wijma HJ, Song L, Cui Y, Otzen M, Tian Y, Du J, Li T, Niu D, Chen Y, Feng J, Han J, Chen H, Tao Y, Janssen DB, Wu B. Computational redesign of enzymes for regio- and enantioselective hydroamination. Nat Chem Biol 2018; 14:664-670. [PMID: 29785057 DOI: 10.1038/s41589-018-0053-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/09/2018] [Indexed: 12/29/2022]
Abstract
Introduction of innovative biocatalytic processes offers great promise for applications in green chemistry. However, owing to limited catalytic performance, the enzymes harvested from nature's biodiversity often need to be improved for their desired functions by time-consuming iterative rounds of laboratory evolution. Here we describe the use of structure-based computational enzyme design to convert Bacillus sp. YM55-1 aspartase, an enzyme with a very narrow substrate scope, to a set of complementary hydroamination biocatalysts. The redesigned enzymes catalyze asymmetric addition of ammonia to substituted acrylates, affording enantiopure aliphatic, polar and aromatic β-amino acids that are valuable building blocks for the synthesis of pharmaceuticals and bioactive compounds. Without a requirement for further optimization by laboratory evolution, the redesigned enzymes exhibit substrate tolerance up to a concentration of 300 g/L, conversion up to 99%, β-regioselectivity >99% and product enantiomeric excess >99%. The results highlight the use of computational design to rapidly adapt an enzyme to industrially viable reactions.
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Affiliation(s)
- Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Transducer Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hein J Wijma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Lu Song
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Transducer Technology, Chinese Academy of Sciences, Beijing, China
| | - Marleen Otzen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Yu'e Tian
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiawei Du
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dingding Niu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanchun Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Feng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jian Han
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hao Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dick B Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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15
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Poddar H, de Villiers J, Zhang J, Puthan Veetil V, Raj H, Thunnissen AMWH, Poelarends GJ. Structural Basis for the Catalytic Mechanism of Ethylenediamine- N, N'-disuccinic Acid Lyase, a Carbon-Nitrogen Bond-Forming Enzyme with a Broad Substrate Scope. Biochemistry 2018; 57:3752-3763. [PMID: 29741885 PMCID: PMC6034166 DOI: 10.1021/acs.biochem.8b00406] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The
natural aminocarboxylic acid product ethylenediamine-N,N′-disuccinic acid [(S,S)-EDDS] is able to form a stable complex with
metal ions, making it an attractive biodegradable alternative for
the synthetic metal chelator ethylenediaminetetraacetic acid (EDTA),
which is currently used on a large scale in numerous applications.
Previous studies have demonstrated that biodegradation of (S,S)-EDDS may be initiated by an EDDS lyase,
converting (S,S)-EDDS via the intermediate N-(2-aminoethyl)aspartic acid (AEAA) into ethylenediamine
and two molecules of fumarate. However, current knowledge of this
enzyme is limited because of the absence of structural data. Here,
we describe the identification and characterization of an EDDS lyase
from Chelativorans sp. BNC1, which has a broad substrate
scope, accepting various mono- and diamines for addition to fumarate.
We report crystal structures of the enzyme in an unliganded state
and in complex with formate, succinate, fumarate, AEAA, and (S,S)-EDDS. The structures reveal a tertiary
and quaternary fold that is characteristic of the aspartase/fumarase
superfamily and support a mechanism that involves general base-catalyzed,
sequential two-step deamination of (S,S)-EDDS. This work broadens our understanding of mechanistic diversity
within the aspartase/fumarase superfamily and will aid in the optimization
of EDDS lyase for asymmetric synthesis of valuable (metal-chelating)
aminocarboxylic acids.
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Affiliation(s)
- Harshwardhan Poddar
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Jandré de Villiers
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Jielin Zhang
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Vinod Puthan Veetil
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Hans Raj
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
| | - Andy-Mark W H Thunnissen
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute , University of Groningen , Nijenborgh 4 , 9747 AG Groningen , The Netherlands
| | - Gerrit J Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy , University of Groningen , Antonius Deusinglaan 1 , 9713 AV Groningen , The Netherlands
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16
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Katsuyama Y, Sato Y, Sugai Y, Higashiyama Y, Senda M, Senda T, Ohnishi Y. Crystal structure of the nitrosuccinate lyase CreD in complex with fumarate provides insights into the catalytic mechanism for nitrous acid elimination. FEBS J 2018; 285:1540-1555. [PMID: 29505698 DOI: 10.1111/febs.14429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 02/23/2018] [Accepted: 03/01/2018] [Indexed: 01/30/2023]
Abstract
Enzymes belonging to the aspartase/fumarase superfamily catalyze elimination of various functional groups from succinate derivatives and play an important role in primary metabolism and aromatic compound degradation. Recently, an aspartase/fumarase superfamily enzyme, CreD, was discovered in cremeomycin biosynthesis. This enzyme catalyzes the elimination of nitrous acid from nitrosuccinate synthesized from aspartate by CreE, a flavin-dependent monooxygenase. Nitrous acid generated by this pathway is an important precursor of the diazo group of cremeomycin. CreD is the first aspartase/fumarase superfamily enzyme that was reported to catalyze the elimination of nitrous acid, and therefore we aimed to analyze its reaction mechanism. The crystal structure of CreD was determined by the molecular replacement native-single anomalous diffraction method at 2.18 Å resolution. Subsequently, the CreD-fumarate complex structure was determined at 2.30 Å resolution by the soaking method. Similar to other aspartase/fumarase superfamily enzymes, the crystal structure of CreD was composed of three domains and formed a tetramer. Two molecules of fumarate were observed in one subunit of the CreD-fumarate complex. One of them was located in the active site pocket formed by three different subunits. Intriguingly, no histidine residue, which usually functions as a catalytic acid in aspartase/fumarase superfamily enzymes, was found around the fumarate molecule in the active site. Based on the mutational analysis, we propose a catalytic mechanism of CreD, in which Arg325 acts as a catalytic acid. DATABASES The crystal structures of CreD and the CreD-fumarate complex were deposited to PDB under the accession numbers 5XNY and 5XNZ, respectively. ENZYMES Nitrosuccinate lyase CreD, EC4.3.
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Affiliation(s)
- Yohei Katsuyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Yukari Sato
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Yoshinori Sugai
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Yousuke Higashiyama
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Japan.,Department of Materials Structure Science, School of High Energy Accelerator Science, The Graduate University for Advanced Studies (Soken-dai), Tsukuba, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Japan
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17
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Partovi SE, Mus F, Gutknecht AE, Martinez HA, Tripet BP, Lange BM, DuBois JL, Peters JW. Coenzyme M biosynthesis in bacteria involves phosphate elimination by a functionally distinct member of the aspartase/fumarase superfamily. J Biol Chem 2018; 293:5236-5246. [PMID: 29414784 DOI: 10.1074/jbc.ra117.001234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/23/2018] [Indexed: 11/06/2022] Open
Abstract
For nearly 30 years, coenzyme M (CoM) was assumed to be present solely in methanogenic archaea. In the late 1990s, CoM was reported to play a role in bacterial propene metabolism, but no biosynthetic pathway for CoM has yet been identified in bacteria. Here, using bioinformatics and proteomic approaches in the metabolically versatile bacterium Xanthobacter autotrophicus Py2, we identified four putative CoM biosynthetic enzymes encoded by the xcbB1, C1, D1, and E1 genes. Only XcbB1 was homologous to a known CoM biosynthetic enzyme (ComA), indicating that CoM biosynthesis in bacteria involves enzymes different from those in archaea. We verified that the ComA homolog produces phosphosulfolactate from phosphoenolpyruvate (PEP), demonstrating that bacterial CoM biosynthesis is initiated similarly as the phosphoenolpyruvate-dependent methanogenic archaeal pathway. The bioinformatics analysis revealed that XcbC1 and D1 are members of the aspartase/fumarase superfamily (AFS) and that XcbE1 is a pyridoxal 5'-phosphate-containing enzyme with homology to d-cysteine desulfhydrases. Known AFS members catalyze β-elimination reactions of succinyl-containing substrates, yielding fumarate as the common unsaturated elimination product. Unexpectedly, we found that XcbC1 catalyzes β-elimination on phosphosulfolactate, yielding inorganic phosphate and a novel metabolite, sulfoacrylic acid. Phosphate-releasing β-elimination reactions are unprecedented among the AFS, indicating that XcbC1 is an unusual phosphatase. Direct demonstration of phosphosulfolactate synthase activity for XcbB1 and phosphate β-elimination activity for XcbC1 strengthened their hypothetical assignment to a CoM biosynthetic pathway and suggested functions also for XcbD1 and E1. Our results represent a critical first step toward elucidating the CoM pathway in bacteria.
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Affiliation(s)
- Sarah E Partovi
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | | | - Andrew E Gutknecht
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Hunter A Martinez
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Brian P Tripet
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
| | - Bernd Markus Lange
- the Institute of Biological Chemistry and.,M. J. Murdock Metabolomics Laboratory, Washington State University, Pullman, Washington 99164
| | - Jennifer L DuBois
- From the Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717 and
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18
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Xue YP, Cao CH, Zheng YG. Enzymatic asymmetric synthesis of chiral amino acids. Chem Soc Rev 2018; 47:1516-1561. [DOI: 10.1039/c7cs00253j] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
This review summarizes the progress achieved in the enzymatic asymmetric synthesis of chiral amino acids from prochiral substrates.
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Affiliation(s)
- Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Cheng-Hao Cao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province
- College of Biotechnology and Bioengineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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19
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Parmeggiani F, Weise NJ, Ahmed ST, Turner NJ. Synthetic and Therapeutic Applications of Ammonia-lyases and Aminomutases. Chem Rev 2017; 118:73-118. [DOI: 10.1021/acs.chemrev.6b00824] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fabio Parmeggiani
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Weise
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Syed T. Ahmed
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
| | - Nicholas J. Turner
- School of Chemistry, Manchester
Institute of Biotechnology, University of Manchester, 131 Princess
Street, M1 7DN, Manchester, United Kingdom
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20
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Bioproduction of l-Aspartic Acid and Cinnamic Acid by l-Aspartate Ammonia Lyase from Pseudomonas aeruginosa PAO1. Appl Biochem Biotechnol 2016; 182:792-803. [DOI: 10.1007/s12010-016-2362-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 12/05/2016] [Indexed: 10/20/2022]
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21
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Joosten RP, Lütteke T. Carbohydrate 3D structure validation. Curr Opin Struct Biol 2016; 44:9-17. [PMID: 27816840 DOI: 10.1016/j.sbi.2016.10.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 12/11/2022]
Abstract
Glycoproteins and protein-carbohydrate complexes in the worldwide Protein Data Bank (wwPDB) can be an excellent source of information for glycoscientists. Unfortunately, a rather large number of errors and inconsistencies is found in the glycan moieties of these 3D structures. This review illustrates frequent problems of carbohydrate moieties in wwPDB entries, such as nomenclature issues, incorrect N-glycan core structures, missing or erroneous linkages, or poor glycan geometry, and describes the carbohydrate-specific validation tools that are designed to identify such problems. Recommendations how to avoid these issues or how to rectify incorrect structures are also given.
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Affiliation(s)
- Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Str. 100, 35392 Giessen, Germany.
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22
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Otzen M, Crismaru CG, Postema CP, Wijma HJ, Heberling MM, Szymanski W, de Wildeman S, Janssen DB. Metabolism of β-valine via a CoA-dependent ammonia lyase pathway. Appl Microbiol Biotechnol 2015; 99:8987-98. [PMID: 26004802 PMCID: PMC4619459 DOI: 10.1007/s00253-015-6551-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/24/2015] [Accepted: 03/17/2015] [Indexed: 11/30/2022]
Abstract
Pseudomonas species strain SBV1 can rapidly grow on medium containing β-valine as a sole nitrogen source. The tertiary amine feature of β-valine prevents direct deamination reactions catalyzed by aminotransferases, amino acid dehydrogenases, and amino acid oxidases. However, lyase- or aminomutase-mediated conversions would be possible. To identify enzymes involved in the degradation of β-valine, a PsSBV1 gene library was prepared and used to complement the β-valine growth deficiency of a closely related Pseudomonas strain. This resulted in the identification of a gene encoding β-valinyl-coenzyme A ligase (BvaA) and two genes encoding β-valinyl-CoA ammonia lyases (BvaB1 and BvaB2). The BvaA protein demonstrated high sequence identity to several known phenylacetate CoA ligases. Purified BvaA enzyme did not convert phenyl acetic acid but was able to activate β-valine in an adenosine triphosphate (ATP)- and CoA-dependent manner. The substrate range of the enzyme appears to be narrow, converting only β-valine and to a lesser extent, 3-aminobutyrate and β-alanine. Characterization of BvaB1 and BvaB2 revealed that both enzymes were able to deaminate β-valinyl-CoA to produce 3-methylcrotonyl-CoA, a common intermediate in the leucine degradation pathway. Interestingly, BvaB1 and BvaB2 demonstrated no significant sequence identity to known CoA-dependent ammonia lyases, suggesting they belong to a new family of enzymes. BLAST searches revealed that BvaB1 and BvaB2 show high sequence identity to each other and to several enoyl-CoA hydratases, a class of enzymes that catalyze a similar reaction with water instead of amine as the leaving group.
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Affiliation(s)
- Marleen Otzen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ciprian G Crismaru
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Christiaan P Postema
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Hein J Wijma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Matthew M Heberling
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Wiktor Szymanski
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Stefaan de Wildeman
- DSM Pharmaceutical Products, Geleen, The Netherlands.,BioBased Materials, Faculty of Humanities and Sciences, Maastricht University, Chemelot, The Netherlands
| | - Dick B Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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23
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Chang C, Huang R, Yan Y, Ma H, Dai Z, Zhang B, Deng Z, Liu W, Qu X. Uncovering the formation and selection of benzylmalonyl-CoA from the biosynthesis of splenocin and enterocin reveals a versatile way to introduce amino acids into polyketide carbon scaffolds. J Am Chem Soc 2015; 137:4183-90. [PMID: 25763681 DOI: 10.1021/jacs.5b00728] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Selective modification of carbon scaffolds via biosynthetic engineering is important for polyketide structural diversification. Yet, this scope is currently restricted to simple aliphatic groups due to (1) limited variety of CoA-linked extender units, which lack aromatic structures and chemical reactivity, and (2) narrow acyltransferase (AT) specificity, which is limited to aliphatic CoA-linked extender units. In this report, we uncovered and characterized the first aromatic CoA-linked extender unit benzylmalonyl-CoA from the biosynthetic pathways of splenocin and enterocin in Streptomyces sp. CNQ431. Its synthesis employs a deamination/reductive carboxylation strategy to convert phenylalanine into benzylmalonyl-CoA, providing a link between amino acid and CoA-linked extender unit synthesis. By characterization of its selection, we further validated that AT domains of splenocin, and antimycin polyketide synthases are able to select this extender unit to introduce the phenyl group into their dilactone scaffolds. The biosynthetic machinery involved in the formation of this extender unit is highly versatile and can be potentially tailored for tyrosine, histidine and aspartic acid. The disclosed aromatic extender unit, amino acid-oriented synthetic pathway, and aromatic-selective AT domains provides a systematic breakthrough toward current knowledge of polyketide extender unit formation and selection, and also opens a route for further engineering of polyketide carbon scaffolds using amino acids.
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Affiliation(s)
- Chenchen Chang
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Rong Huang
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Yan Yan
- ‡State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Hongmin Ma
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Zheng Dai
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Benying Zhang
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Zixin Deng
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
| | - Wen Liu
- ‡State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Xudong Qu
- †Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road, Wuhan 430071, China
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24
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A QM/MM study of the catalytic mechanism of aspartate ammonia lyase. J Mol Graph Model 2014; 51:113-9. [DOI: 10.1016/j.jmgm.2014.05.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/20/2014] [Accepted: 05/05/2014] [Indexed: 11/21/2022]
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25
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Vogel A, Schmiedel R, Hofmann U, Gruber K, Zangger K. Converting Aspartase into a β-Amino Acid Lyase by Cluster Screening. ChemCatChem 2014. [DOI: 10.1002/cctc.201300986] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Banerjee S, Agrawal MJ, Mishra D, Sharan S, Balaram H, Savithri HS, Murthy MRN. Structural and kinetic studies on adenylosuccinate lyase from Mycobacterium smegmatis and Mycobacterium tuberculosis provide new insights on the catalytic residues of the enzyme. FEBS J 2014; 281:1642-58. [PMID: 24479855 DOI: 10.1111/febs.12730] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 01/15/2014] [Accepted: 01/23/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Adenylosuccinate lyase (ASL), an enzyme involved in purine biosynthesis, has been recognized as a drug target against microbial infections. In the present study, ASL from Mycobacterium smegmatis (MsASL) and Mycobacterium tuberculosis (MtbASL) were cloned, purified and crystallized. The X-ray crystal structure of MsASL was determined at a resolution of 2.16 Å. It is the first report of an apo-ASL structure with a partially ordered active site C3 loop. Diffracting crystals of MtbASL could not be obtained and a model for its structure was derived using MsASL as a template. These structures suggest that His149 and either Lys285 or Ser279 of MsASL are the residues most likely to function as the catalytic acid and base, respectively. Most of the active site residues were found to be conserved, with the exception of Ser148 and Gly319 of MsASL. Ser148 is structurally equivalent to a threonine in most other ASLs. Gly319 is replaced by an arginine residue in most ASLs. The two enzymes were catalytically much less active compared to ASLs from other organisms. Arg319Gly substitution and reduced flexibility of the C3 loop might account for the low catalytic activity of mycobacterial ASLs. The low activity is consistent with the slow growth rate of Mycobacteria and their high GC containing genomes, as well as their dependence on other salvage pathways for the supply of purine nucleotides. STRUCTURED DIGITAL ABSTRACT purB and purB bind by x-ray crystallography (View interaction).
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Affiliation(s)
- Sanchari Banerjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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27
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Álvarez-Ordóñez A, Begley M, Clifford T, Deasy T, Collins B, Hill C. Transposon mutagenesis reveals genes involved in osmotic stress and drying in Cronobacter sakazakii. Food Res Int 2014. [DOI: 10.1016/j.foodres.2013.10.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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28
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Heberling MM, Wu B, Bartsch S, Janssen DB. Priming ammonia lyases and aminomutases for industrial and therapeutic applications. Curr Opin Chem Biol 2013; 17:250-60. [PMID: 23557642 DOI: 10.1016/j.cbpa.2013.02.013] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 02/05/2013] [Indexed: 01/17/2023]
Abstract
Ammonia lyases (AL) and aminomutases (AM) are emerging in green synthetic routes to chiral amines and an AL is being explored as an enzyme therapeutic for treating phenylketonuria and cancer. Although the restricted substrate range of the wild-type enzymes limits their widespread application, the non-reliance on external cofactors and direct functionalization of an olefinic bond make ammonia lyases attractive biocatalysts for use in the synthesis of natural and non-natural amino acids, including β-amino acids. The approach of combining structure-guided enzyme engineering with efficient mutant library screening has extended the synthetic scope of these enzymes in recent years and has resolved important mechanistic issues for AMs and ALs, including those containing the MIO (4-methylideneimidazole-5-one) internal cofactor.
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Affiliation(s)
- Matthew M Heberling
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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29
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Puthan Veetil V, Raj H, de Villiers M, Tepper PG, Dekker FJ, Quax WJ, Poelarends GJ. Enantioselective Synthesis of N-Substituted Aspartic Acids Using an Engineered Variant of Methylaspartate Ammonia Lyase. ChemCatChem 2013. [DOI: 10.1002/cctc.201200906] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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30
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Zhu S, Qiu Z, Ni T, Zhao X, Yan S, Xing F, Zhao Y, Bai Y, Li M. Dinuclear complexes of copper and zinc with m-xylene/cyclohexane-linked bis-aspartic acids: Synthesis, characterization, dioxygen activation, and catalytic oxidation of nitrobenzene in pure aqueous solution. Dalton Trans 2013; 42:10898-911. [DOI: 10.1039/c3dt50923k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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31
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de Villiers M, Puthan Veetil V, Raj H, de Villiers J, Poelarends GJ. Catalytic mechanisms and biocatalytic applications of aspartate and methylaspartate ammonia lyases. ACS Chem Biol 2012; 7:1618-28. [PMID: 22834890 DOI: 10.1021/cb3002792] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ammonia lyases catalyze the formation of α,β-unsaturated bonds by the elimination of ammonia from their substrates. This conceptually straightforward reaction has been the emphasis of many studies, with the main focus on the catalytic mechanism of these enzymes and/or the use of these enzymes as catalysts for the synthesis of enantiomerically pure α-amino acids. In this Review aspartate ammonia lyase and 3-methylaspartate ammonia lyase, which represent two different enzyme superfamilies, are discussed in detail. In the past few years, the three-dimensional structures of these lyases in complex with their natural substrates have revealed the details of two elegant catalytic strategies. These strategies exploit similar deamination mechanisms that involve general-base catalyzed formation of an enzyme-stabilized enolate anion (aci-carboxylate) intermediate. Recent progress in the engineering and application of these enzymes to prepare enantiopure l-aspartic acid derivatives, which are highly valuable as tools for biological research and as chiral building blocks for pharmaceuticals and food additives, is also discussed.
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Affiliation(s)
- Marianne de Villiers
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
| | - Vinod Puthan Veetil
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
| | - Hans Raj
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
| | - Jandré de Villiers
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
| | - Gerrit J. Poelarends
- Department
of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713
AV Groningen, The Netherlands
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32
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Puthan Veetil V, Fibriansah G, Raj H, Thunnissen AMWH, Poelarends GJ. Aspartase/Fumarase Superfamily: A Common Catalytic Strategy Involving General Base-Catalyzed Formation of a Highly Stabilized aci-Carboxylate Intermediate. Biochemistry 2012; 51:4237-43. [DOI: 10.1021/bi300430j] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vinod Puthan Veetil
- Department of Pharmaceutical
Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen,
The Netherlands
| | - Guntur Fibriansah
- Department
of Biophysical Chemistry,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Hans Raj
- Department of Pharmaceutical
Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen,
The Netherlands
| | - Andy-Mark W. H. Thunnissen
- Department
of Biophysical Chemistry,
Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen,
The Netherlands
| | - Gerrit J. Poelarends
- Department of Pharmaceutical
Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen,
The Netherlands
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33
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Mechaly AE, Haouz A, Miras I, Barilone N, Weber P, Shepard W, Alzari PM, Bellinzoni M. Conformational changes upon ligand binding in the essential class II fumarase Rv1098c fromMycobacterium tuberculosis. FEBS Lett 2012; 586:1606-11. [DOI: 10.1016/j.febslet.2012.04.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 03/31/2012] [Accepted: 04/19/2012] [Indexed: 12/17/2022]
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34
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Immobilized l-aspartate ammonia-lyase from Bacillus sp. YM55-1 as biocatalyst for highly concentrated l-aspartate synthesis. Bioprocess Biosyst Eng 2012; 35:1437-44. [DOI: 10.1007/s00449-012-0732-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 03/26/2012] [Indexed: 10/28/2022]
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