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De Luca V, Giovannuzzi S, Supuran CT, Capasso C. A comprehensive investigation of the anion inhibition profile of a β-carbonic anhydrase from Acinetobacter baumannii for crafting innovative antimicrobial treatments. J Enzyme Inhib Med Chem 2024; 39:2372731. [PMID: 39012078 PMCID: PMC467105 DOI: 10.1080/14756366.2024.2372731] [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: 02/22/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024] Open
Abstract
This study refers to the intricate world of Acinetobacter baumannii, a resilient pathogenic bacterium notorious for its propensity at antibiotic resistance in nosocomial infections. Expanding upon previous findings that emphasised the bifunctional enzyme PaaY, revealing unexpected γ-carbonic anhydrase (CA) activity, our research focuses on a different class of CA identified within the A. baumannii genome, the β-CA, designated as 𝛽-AbauCA (also indicated as CanB), which plays a crucial role in the resistance mechanism mediated by AmpC beta-lactamase. Here, we cloned, expressed, and purified the recombinant 𝛽-AbauCA, unveiling its distinctive kinetic properties and inhibition profile with inorganic anions (classical CA inhibitors). The exploration of 𝛽-AbauCA not only enhances our understanding of the CA repertoire of A. baumannii but also establishes a foundation for targeted therapeutic interventions against this resilient pathogen, promising advancements in combating its adaptability and antibiotic resistance.
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Affiliation(s)
- Viviana De Luca
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy
| | - Simone Giovannuzzi
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Claudiu T. Supuran
- Neurofarba Department, Pharmaceutical and Nutraceutical Section, University of Florence, Sesto Fiorentino, Italy
| | - Clemente Capasso
- Department of Biology, Agriculture and Food Sciences, National Research Council (CNR), Institute of Biosciences and Bioresources, Naples, Italy
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2
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Jiao M, He W, Ouyang Z, Qin Q, Guo Y, Zhang J, Bai Y, Guo X, Yu Q, She J, Hwang PM, Zheng F, Wen Y. Mechanistic and structural insights into the bifunctional enzyme PaaY from Acinetobacter baumannii. Structure 2023; 31:935-947.e4. [PMID: 37329879 DOI: 10.1016/j.str.2023.05.015] [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: 12/01/2022] [Revised: 03/28/2023] [Accepted: 05/23/2023] [Indexed: 06/19/2023]
Abstract
PaaY is a thioesterase that enables toxic metabolites to be degraded through the bacterial phenylacetic acid (PA) pathway. The Acinetobacter baumannii gene FQU82_01591 encodes PaaY, which we demonstrate to possess γ-carbonic anhydrase activity in addition to thioesterase activity. The crystal structure of AbPaaY in complex with bicarbonate reveals a homotrimer with a canonical γ-carbonic anhydrase active site. Thioesterase activity assays demonstrate a preference for lauroyl-CoA as a substrate. The AbPaaY trimer structure shows a unique domain-swapped C-termini, which increases the stability of the enzyme in vitro and decreases its susceptibility to proteolysis in vivo. The domain-swapped C-termini impact thioesterase substrate specificity and enzyme efficacy without affecting carbonic anhydrase activity. AbPaaY knockout reduced the growth of Acinetobacter in media containing PA, decreased biofilm formation, and impaired hydrogen peroxide resistance. Collectively, AbPaaY is a bifunctional enzyme that plays a key role in the metabolism, growth, and stress response mechanisms of A. baumannii.
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Affiliation(s)
- Min Jiao
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Wenbo He
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Zhenlin Ouyang
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qian Qin
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yucheng Guo
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jiaxin Zhang
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yixin Bai
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaolong Guo
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qinyue Yu
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Junjun She
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China
| | - Peter M Hwang
- Departments of Medicine and Biochemistry, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Fang Zheng
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Yurong Wen
- Center for Microbiome Research of Med-X Institute, Shaanxi Provincial Key Laboratory of Sepsis in Critical Care Medicine, The First Affiliated Hospital, Xi'an Jiaotong University, Xi'an 710061, China; The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
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3
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Jiao M, He W, Ouyang Z, Shi Q, Wen Y. Progress in structural and functional study of the bacterial phenylacetic acid catabolic pathway, its role in pathogenicity and antibiotic resistance. Front Microbiol 2022; 13:964019. [PMID: 36160191 PMCID: PMC9493321 DOI: 10.3389/fmicb.2022.964019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Phenylacetic acid (PAA) is a central intermediate metabolite involved in bacterial degradation of aromatic components. The bacterial PAA pathway mainly contains 12 enzymes and a transcriptional regulator, which are involved in biofilm formation and antimicrobial activity. They are present in approximately 16% of the sequenced bacterial genome. In this review, we have summarized the PAA distribution in microbes, recent structural and functional study progress of the enzyme families of the bacterial PAA pathway, and their role in bacterial pathogenicity and antibiotic resistance. The enzymes of the bacterial PAA pathway have shown potential as an antimicrobial drug target for biotechnological applications in metabolic engineering.
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Affiliation(s)
- Min Jiao
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Wenbo He
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Zhenlin Ouyang
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Qindong Shi
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
| | - Yurong Wen
- Department of Critical Care Medicine, Center for Microbiome Research of Med-X Institute, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- Department of Critical Care Medicine, The First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, China
- The Key Laboratory of Environment and Genes Related to Disease of Ministry of Education Health Science Center, Xi’an Jiaotong University, Xi’an, China
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4
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Duan Y, Toplak M, Hou A, Brock NL, Dickschat JS, Teufel R. A Flavoprotein Dioxygenase Steers Bacterial Tropone Biosynthesis via Coenzyme A-Ester Oxygenolysis and Ring Epoxidation. J Am Chem Soc 2021; 143:10413-10421. [PMID: 34196542 PMCID: PMC8283759 DOI: 10.1021/jacs.1c04996] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Bacterial tropone
natural products such as tropolone, tropodithietic
acid, or the roseobacticides play crucial roles in various terrestrial
and marine symbiotic interactions as virulence factors, antibiotics,
algaecides, or quorum sensing signals. We now show that their poorly
understood biosynthesis depends on a shunt product from aerobic CoA-dependent
phenylacetic acid catabolism that is salvaged by the dedicated acyl-CoA
dehydrogenase-like flavoenzyme TdaE. Further characterization of TdaE
revealed an unanticipated complex catalysis, comprising substrate
dehydrogenation, noncanonical CoA-ester oxygenolysis, and final ring
epoxidation. The enzyme thereby functions as an archetypal flavoprotein
dioxygenase that incorporates both oxygen atoms from O2 into the substrate, most likely involving flavin-N5-peroxide and
flavin-N5-oxide species for consecutive CoA-ester cleavage and epoxidation,
respectively. The subsequent spontaneous decarboxylation of the reactive
enzyme product yields tropolone, which serves as a key virulence factor
in rice panicle blight caused by pathogenic edaphic Burkholderia
plantarii. Alternatively, the TdaE product is most likely
converted to more complex sulfur-containing secondary metabolites
such as tropodithietic acid from predominant marine Rhodobacteraceae (e.g., Phaeobacter inhibens).
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Affiliation(s)
- Ying Duan
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Marina Toplak
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Anwei Hou
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Nelson L Brock
- Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.,Institute of Organic Chemistry, TU Braunschweig, Hagenring 30, 38106 Braunschweig, Germany
| | - Robin Teufel
- Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
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5
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Duan Y, Petzold M, Saleem‐Batcha R, Teufel R. Bacterial Tropone Natural Products and Derivatives: Overview of their Biosynthesis, Bioactivities, Ecological Role and Biotechnological Potential. Chembiochem 2020; 21:2384-2407. [PMID: 32239689 PMCID: PMC7497051 DOI: 10.1002/cbic.201900786] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 04/02/2020] [Indexed: 12/05/2022]
Abstract
Tropone natural products are non-benzene aromatic compounds of significant ecological and pharmaceutical interest. Herein, we highlight current knowledge on bacterial tropones and their derivatives such as tropolones, tropodithietic acid, and roseobacticides. Their unusual biosynthesis depends on a universal CoA-bound precursor featuring a seven-membered carbon ring as backbone, which is generated by a side reaction of the phenylacetic acid catabolic pathway. Enzymes encoded by separate gene clusters then further modify this key intermediate by oxidation, CoA-release, or incorporation of sulfur among other reactions. Tropones play important roles in the terrestrial and marine environment where they act as antibiotics, algaecides, or quorum sensing signals, while their bacterial producers are often involved in symbiotic interactions with plants and marine invertebrates (e. g., algae, corals, sponges, or mollusks). Because of their potent bioactivities and of slowly developing bacterial resistance, tropones and their derivatives hold great promise for biomedical or biotechnological applications, for instance as antibiotics in (shell)fish aquaculture.
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Affiliation(s)
- Ying Duan
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | - Melanie Petzold
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
| | | | - Robin Teufel
- Faculty of BiologyUniversity of Freiburg79104FreiburgGermany
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6
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Spieker M, Saleem-Batcha R, Teufel R. Structural and Mechanistic Basis of an Oxepin-CoA Forming Isomerase in Bacterial Primary and Secondary Metabolism. ACS Chem Biol 2019; 14:2876-2886. [PMID: 31689071 DOI: 10.1021/acschembio.9b00742] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Numerous aromatic compounds are aerobically degraded in bacteria via the central intermediate phenylacetic acid (paa). In one of the key steps of this widespread catabolic pathway, 1,2-epoxyphenylacetyl-CoA is converted by PaaG into the heterocyclic oxepin-CoA. PaaG thereby elegantly generates an α,β-unsaturated CoA ester that is predisposed to undergo β-oxidation subsequent to hydrolytic ring-cleavage. Moreover, oxepin-CoA serves as a precursor for secondary metabolites (e.g., tropodithietic acid) that act as antibiotics and quorum-sensing signals. Here we verify that PaaG adopts a second role in aromatic catabolism by converting cis-3,4-didehydroadipoyl-CoA into trans-2,3-didehydroadipoyl-CoA and corroborate a Δ3,Δ2-enoyl-CoA isomerase-like proton shuttling mechanism for both distinct substrates. Biochemical and structural investigations of PaaG reveal active site adaptations to the structurally different substrates and provide detailed insight into catalysis and control of stereospecificity. This work elucidates the mechanism of action of unusual isomerase PaaG and sheds new light on the ubiquitous enoyl-CoA isomerases of the crotonase superfamily.
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Affiliation(s)
- Melanie Spieker
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Raspudin Saleem-Batcha
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Robin Teufel
- ZBSA, Center for Biological Systems Analysis, University of Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
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7
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Sathyanarayanan N, Cannone G, Gakhar L, Katagihallimath N, Sowdhamini R, Ramaswamy S, Vinothkumar KR. Molecular basis for metabolite channeling in a ring opening enzyme of the phenylacetate degradation pathway. Nat Commun 2019; 10:4127. [PMID: 31511507 PMCID: PMC6739347 DOI: 10.1038/s41467-019-11931-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/13/2019] [Indexed: 02/06/2023] Open
Abstract
Substrate channeling is a mechanism for the internal transfer of hydrophobic, unstable or toxic intermediates from the active site of one enzyme to another. Such transfer has previously been described to be mediated by a hydrophobic tunnel, the use of electrostatic highways or pivoting and by conformational changes. The enzyme PaaZ is used by many bacteria to degrade environmental pollutants. PaaZ is a bifunctional enzyme that catalyzes the ring opening of oxepin-CoA and converts it to 3-oxo-5,6-dehydrosuberyl-CoA. Here we report the structures of PaaZ determined by electron cryomicroscopy with and without bound ligands. The structures reveal that three domain-swapped dimers of the enzyme form a trilobed structure. A combination of small-angle X-ray scattering (SAXS), computational studies, mutagenesis and microbial growth experiments suggests that the key intermediate is transferred from one active site to the other by a mechanism of electrostatic pivoting of the CoA moiety, mediated by a set of conserved positively charged residues.
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Affiliation(s)
- Nitish Sathyanarayanan
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India
- Institute of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Giuseppe Cannone
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Lokesh Gakhar
- Protein Crystallography Facility and Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Nainesh Katagihallimath
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India
- Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India
| | - Subramanian Ramaswamy
- Institute for Stem Cell Science and Regenerative Medicine, GKVK Campus, Bellary Road, Bangalore, India.
| | - Kutti R Vinothkumar
- National Centre for Biological Sciences TIFR, GKVK Campus, Bellary Road, Bangalore, India.
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8
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Liu L, Li T, Cheng XJ, Peng CT, Li CC, He LH, Ju SM, Wang NY, Ye TH, Lian M, Xiao QJ, Song YJ, Zhu YB, Yu LT, Wang ZL, Bao R. Structural and functional studies on Pseudomonas aeruginosa DspI: implications for its role in DSF biosynthesis. Sci Rep 2018; 8:3928. [PMID: 29500457 PMCID: PMC5834635 DOI: 10.1038/s41598-018-22300-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 02/15/2018] [Indexed: 02/05/2023] Open
Abstract
DspI, a putative enoyl-coenzyme A (CoA) hydratase/isomerase, was proposed to be involved in the synthesis of cis-2-decenoic acid (CDA), a quorum sensing (QS) signal molecule in the pathogen Pseudomonas aeruginosa (P. aeruginosa). The present study provided a structural basis for the dehydration reaction mechanism of DspI during CDA synthesis. Structural analysis reveals that Glu126, Glu146, Cys127, Cys131 and Cys154 are important for its enzymatic function. Moreover, we show that the deletion of dspI results in a remarkable decreased in the pyoverdine production, flagella-dependent swarming motility, and biofilm dispersion as well as attenuated virulence in P. aeruginosa PA14. This study thus unravels the mechanism of DspI in diffusible signal factor (DSF) CDA biosynthesis, providing vital information for developing inhibitors that interfere with DSF associated pathogenicity in P. aeruginosa.
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Affiliation(s)
- Li Liu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Department of Dermatology, Southwest Medical University, affiliated hospital, Luzhou, China
| | - Tao Li
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Xing-Jun Cheng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Cui-Ting Peng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Chang-Cheng Li
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Li-Hui He
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Si-Min Ju
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ning-Yu Wang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Ting-Hong Ye
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Mao Lian
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Qing-Jie Xiao
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ying-Jie Song
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Yi-Bo Zhu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Luo-Ting Yu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.
| | - Zhen-Ling Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.
| | - Rui Bao
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.
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9
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Gulevich AY, Skorokhodova AY, Sukhozhenko AV, Debabov VG. Biosynthesis of enantiopure (S)-3-hydroxybutyrate from glucose through the inverted fatty acid β-oxidation pathway by metabolically engineered Escherichia coli. J Biotechnol 2017; 244:16-24. [PMID: 28131860 DOI: 10.1016/j.jbiotec.2017.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/04/2017] [Accepted: 01/24/2017] [Indexed: 11/16/2022]
Abstract
Enantiomers of 3-hydroxybutyric acid (3-HB) can be used as the chiral precursors for the production of various optically active fine chemicals, including drugs, perfumes, and pheromones. In this study, Escherichia coli was engineered to produce (S)-3-HB from glucose through the inverted reactions of the native aerobic fatty acid β-oxidation pathway. Expression of only specific genes encoding enzymes responsible for the conversion of acetyl-CoA to acetoacetyl-CoA, reduction of acetoacetyl-CoA to 3-hydroxybutyryl-CoA and subsequent hydrolysis of 3-hydroxybutyryl-CoA to 3-HB was directly upregulated in an engineered strain. The operation of multiple turns of the inverted fatty acid β-oxidation was precluded by the deletion of gene encoding enzyme that catalyse the terminal stage of the respective cycle. While the overexpression of the C-acetyltransferase gene enabled 3-HB biosynthesis through the inverted fatty acid β-oxidation, the efficient conversion of glucose to the target product was achieved resulting from the additional overexpression of the gene encoding appropriate termination thioesterase II. The engineered strain synthesised the (S)-stereoisomer of 3-HB with an enantiomeric excess of more than 99%. Under microaerobic conditions, up to 9.58g/L of enantiopure (S)-3-HB was produced from glucose, with a yield of 66% of the theoretical maximum.
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Affiliation(s)
- Andrey Yu Gulevich
- Research Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., 1, 117545 Moscow, Russia.
| | - Alexandra Yu Skorokhodova
- Research Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., 1, 117545 Moscow, Russia
| | - Alexey V Sukhozhenko
- Research Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., 1, 117545 Moscow, Russia
| | - Vladimir G Debabov
- Research Institute for Genetics and Selection of Industrial Microorganisms, 1-st Dorozhniy pr., 1, 117545 Moscow, Russia
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10
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Unsaturated Lipid Assimilation by Mycobacteria Requires Auxiliary cis-trans Enoyl CoA Isomerase. ACTA ACUST UNITED AC 2015; 22:1577-87. [DOI: 10.1016/j.chembiol.2015.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/13/2015] [Accepted: 10/15/2015] [Indexed: 11/30/2022]
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11
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Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway. BIOLOGY 2015; 4:424-42. [PMID: 26075354 PMCID: PMC4498308 DOI: 10.3390/biology4020424] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 05/25/2015] [Accepted: 05/29/2015] [Indexed: 11/17/2022]
Abstract
Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism—coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and β-oxidation of fatty acids.
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12
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Ream DC, Bankapur AR, Friedberg I. An event-driven approach for studying gene block evolution in bacteria. ACTA ACUST UNITED AC 2015; 31:2075-83. [PMID: 25717195 PMCID: PMC4481853 DOI: 10.1093/bioinformatics/btv128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/20/2015] [Indexed: 11/24/2022]
Abstract
Motivation: Gene blocks are genes co-located on the chromosome. In many cases, gene blocks are conserved between bacterial species, sometimes as operons, when genes are co-transcribed. The conservation is rarely absolute: gene loss, gain, duplication, block splitting and block fusion are frequently observed. An open question in bacterial molecular evolution is that of the formation and breakup of gene blocks, for which several models have been proposed. These models, however, are not generally applicable to all types of gene blocks, and consequently cannot be used to broadly compare and study gene block evolution. To address this problem, we introduce an event-based method for tracking gene block evolution in bacteria. Results: We show here that the evolution of gene blocks in proteobacteria can be described by a small set of events. Those include the insertion of genes into, or the splitting of genes out of a gene block, gene loss, and gene duplication. We show how the event-based method of gene block evolution allows us to determine the evolutionary rateand may be used to trace the ancestral states of their formation. We conclude that the event-based method can be used to help us understand the formation of these important bacterial genomic structures. Availability and implementation: The software is available under GPLv3 license on http://github.com/reamdc1/gene_block_evolution.git. Supplementary online material: http://iddo-friedberg.net/operon-evolution Contact:i.friedberg@miamioh.edu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- David C Ream
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
| | - Asma R Bankapur
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
| | - Iddo Friedberg
- Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA Department of Microbiology, Miami University, Oxford, OH, USA and Department of Computer Science and Software Engineering, Miami University, Oxford, OH, USA
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