151
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Nofiani R, Philmus B, Nindita Y, Mahmud T. 3-Ketoacyl-ACP synthase (KAS) III homologues and their roles in natural product biosynthesis. MEDCHEMCOMM 2019; 10:1517-1530. [PMID: 31673313 DOI: 10.1039/c9md00162j] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 11/21/2022]
Abstract
The 3-ketoacyl-ACP synthase (KAS) III proteins are one of the most abundant enzymes in nature, as they are involved in the biosynthesis of fatty acids and natural products. KAS III enzymes catalyse a carbon-carbon bond formation reaction that involves the α-carbon of a thioester and the carbonyl carbon of another thioester. In addition to the typical KAS III enzymes involved in fatty acid and polyketide biosynthesis, there are proteins homologous to KAS III enzymes that catalyse reactions that are different from that of the traditional KAS III enzymes. Those include enzymes that are responsible for a head-to-head condensation reaction, the formation of acetoacetyl-CoA in mevalonate biosynthesis, tailoring processes via C-O bond formation or esterification, as well as amide formation. This review article highlights the diverse reactions catalysed by this class of enzymes and their role in natural product biosynthesis.
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Affiliation(s)
- Risa Nofiani
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA . .,Department of Chemistry , Universitas Tanjungpura , Pontianak , Indonesia
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Yosi Nindita
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
| | - Taifo Mahmud
- Department of Pharmaceutical Sciences , Oregon State University , Corvallis , OR 97333 , USA .
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152
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Schaub AJ, Moreno GO, Zhao S, Truong HV, Luo R, Tsai SC. Computational structural enzymology methodologies for the study and engineering of fatty acid synthases, polyketide synthases and nonribosomal peptide synthetases. Methods Enzymol 2019; 622:375-409. [PMID: 31155062 PMCID: PMC7197764 DOI: 10.1016/bs.mie.2019.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Various computational methodologies can be applied to enzymological studies on enzymes in the fatty acid, polyketide, and non-ribosomal peptide biosynthetic pathways. These multi-domain complexes are called fatty acid synthases, polyketide synthases, and non-ribosomal peptide synthetases. These mega-synthases biosynthesize chemically diverse and complex bioactive molecules, with the intermediates being chauffeured between catalytic partners via a carrier protein. Recent efforts have been made to engineer these systems to expand their product diversity. A major stumbling block is our poor understanding of the transient protein-protein and protein-substrate interactions between the carrier protein and its many catalytic partner domains and product intermediates. The innate reactivity of pathway intermediates in two major classes of polyketide synthases has frustrated our mechanistic understanding of these interactions during the biosynthesis of these natural products, ultimately impeding the engineering of these systems for the generation of engineered natural products. Computational techniques described in this chapter can aid data interpretation or used to generate testable models of these experimentally intractable transient interactions, thereby providing insight into key interactions that are difficult to capture otherwise, with the potential to expand the diversity in these systems.
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Affiliation(s)
- Andrew J Schaub
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Gabriel O Moreno
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Shiji Zhao
- Mathematical, Computational and Systems Biology Program, Center for Complex Biological Systems, University of California, Irvine, CA, United States
| | - Hau V Truong
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, CA, United States.
| | - Shiou-Chuan Tsai
- Department of Molecular Biology and Biochemistry, Chemistry, Pharmaceutical Sciences, University of California, Irvine, CA, United States.
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153
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New Frontiers in Lipidomics Analyses using Structurally Selective Ion Mobility-Mass Spectrometry. Trends Analyt Chem 2019; 116:316-323. [PMID: 31983792 DOI: 10.1016/j.trac.2019.03.031] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The growth of lipidomics and the high isomeric complexity of the lipidome has revealed a need for analytical techniques capable of structurally characterizing lipids with a high degree of specificity. Lipids are morphologically diverse molecules that can exist as any one of a large number of isomeric species, and as such are often indistinguishable by mass spectrometry without a complementary separation method. Recent developments in the field of lipidomics aim to address these challenges by utilizing a combination of multiple analytical techniques which are selective to lipid primary structure. This review summarizes two emerging strategies for lipidomic analysis, namely, ion mobility-mass spectrometry and ion fragmentation via ozonolysis.
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154
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Target Proteins of Phloretin for Its Anti-Inflammatory and Antibacterial Activities Against Propionibacterium acnes-Induced Skin Infection. Molecules 2019; 24:molecules24071319. [PMID: 30987239 PMCID: PMC6479541 DOI: 10.3390/molecules24071319] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/25/2019] [Accepted: 04/02/2019] [Indexed: 12/17/2022] Open
Abstract
Phloretin is a natural chalcone with antibacterial and anti-inflammatory effects. This study investigated the anti-acne activity of phloretin against Propionibacterium acnes-induced skin infection and the potential target proteins of its anti-inflammatory and antibacterial effects. Phloretin potently inhibited the growth of P. acnes and P. acnes-induced Toll-like receptor (TLR) 2-mediated inflammatory signaling in human keratinocytes. Secreted embryonic alkaline phosphatase assay confirmed that the anti-inflammatory activity of phloretin is associated with the P. acnes-stimulated TLR2-mediated NF-κB signaling pathway. Phloretin significantly decreased the level of phosphorylated c-Jun N-terminal kinase (JNK), showing a binding affinity of 1.184 × 10−5 M−1. We also found that phloretin binds with micromolar affinity to P. acnes β-ketoacyl acyl carrier protein (ACP) synthase III (KAS III), an enzyme involved in fatty acid synthesis. Conformation-sensitive native polyacrylamide gel electrophoresis showed that phloretin reduced KAS III-mediated 3-ketoacyl ACP production by over 66%. A docking study revealed that phloretin interacts with the active sites of JNK1 and KAS III, suggesting their involvement in P. acnes-induced inflammation and their potential as targets for the antibacterial activity of phloretin. These results demonstrate that phloretin may be useful in the prevention or treatment of P. acnes infection.
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155
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Malina C, Larsson C, Nielsen J. Yeast mitochondria: an overview of mitochondrial biology and the potential of mitochondrial systems biology. FEMS Yeast Res 2019; 18:4969682. [PMID: 29788060 DOI: 10.1093/femsyr/foy040] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/10/2018] [Indexed: 12/29/2022] Open
Abstract
Mitochondria are dynamic organelles of endosymbiotic origin that are essential components of eukaryal cells. They contain their own genetic machinery, have multicopy genomes and like their bacterial ancestors they consist of two membranes. However, the majority of the ancestral genome has been lost or transferred to the nuclear genome of the host, preserving only a core set of genes involved in oxidative phosphorylation. Mitochondria perform numerous biological tasks ranging from bioenergetics to production of protein co-factors, including heme and iron-sulfur clusters. Due to the importance of mitochondria in many cellular processes, mitochondrial dysfunction is implicated in a wide variety of human disorders. Much of our current knowledge on mitochondrial function and dysfunction comes from studies using Saccharomyces cerevisiae. This yeast has good fermenting capacity, rendering tolerance to mutations that inactivate oxidative phosphorylation and complete loss of mitochondrial DNA. Here, we review yeast mitochondrial metabolism and function with focus on S. cerevisiae and its contribution in understanding mitochondrial biology. We further review how systems biology studies, including mathematical modeling, has allowed gaining new insight into mitochondrial function, and argue that this approach may enable us to gain a holistic view on how mitochondrial function interacts with different cellular processes.
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Affiliation(s)
- Carl Malina
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Christer Larsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Wallenberg Center for Protein Research, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Lyngby, Denmark
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156
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Shi YM, Brachmann AO, Westphalen MA, Neubacher N, Tobias NJ, Bode HB. Dual phenazine gene clusters enable diversification during biosynthesis. Nat Chem Biol 2019; 15:331-339. [PMID: 30886436 DOI: 10.1038/s41589-019-0246-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Accepted: 02/13/2019] [Indexed: 11/10/2022]
Abstract
Biosynthetic gene clusters (BGCs) bridging genotype and phenotype continuously evolve through gene mutations and recombinations to generate chemical diversity. Phenazine BGCs are widespread in bacteria, and the biosynthetic mechanisms of the formation of the phenazine structural core have been illuminated in the last decade. However, little is known about the complex phenazine core-modification machinery. Here, we report the diversity-oriented modifications of the phenazine core through two distinct BGCs in the entomopathogenic bacterium Xenorhabdus szentirmaii, which lives in symbiosis with nematodes. A previously unidentified aldehyde intermediate, which can be modified by multiple enzymatic and non-enzymatic reactions, is a common intermediate bridging the pathways encoded by these BGCs. Evaluation of the antibiotic activity of the resulting phenazine derivatives suggests a highly effective strategy to convert Gram-positive specific phenazines into broad-spectrum antibiotics, which might help the bacteria-nematode complex to maintain its special environmental niche.
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Affiliation(s)
- Yi-Ming Shi
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Alexander O Brachmann
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany.,Institute of Microbiology, Eidgenössische Technische Hochschule Zurich, Zurich, Switzerland
| | - Margaretha A Westphalen
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Nick Neubacher
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Nicholas J Tobias
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B Bode
- Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe Universität Frankfurt, Frankfurt am Main, Germany. .,Buchmann Institute for Molecular Life Sciences, Goethe Universität Frankfurt, Frankfurt am Main, Germany.
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157
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Biswas R, Singh BK, Dutta D, Das PK, Maiti MK, Basak A, Das AK. Decrypting the oscillating nature of the 4'-phosphopantetheine arm in acyl carrier protein AcpM of Mycobacterium tuberculosis. FEBS Lett 2019; 593:622-633. [PMID: 30847903 DOI: 10.1002/1873-3468.13339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/04/2019] [Accepted: 02/11/2019] [Indexed: 12/28/2022]
Abstract
In Mycobacterium tuberculosis, acyl carrier protein (AcpM)-mediated fatty acid synthase type II is integral for the synthesis of mycolic acids. AcpM, designated as an atypical ACP, comprises of a putative 33 amino acid long C-terminal extension which is distinctive in nature. Here, we aimed at devising an 'easy-to-go' method for the generation of crypto-AcpM loaded with a solvatochromic probe 7-Nitrobenz-2-oxa-1,3-diazol-4-yl, which is linked to the 4'-phosphopantetheine (Ppant) prosthetic group of AcpM. The crypto-AcpM, coupled with fluorescence spectroscopy and molecular dynamics simulation studies, was employed to explore the elusive dynamics of Ppant arm in AcpM. This investigation establishes the role of the flexible C-terminal extension of AcpM in regulating the prosthetic group sequestration ability by modulating the 'Asp-Ser-Leu' motif.
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Affiliation(s)
- Rupam Biswas
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Bina Kumari Singh
- School of Biosciences, Indian Institute of Technology, Kharagpur, India
| | - Debajyoti Dutta
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Prabir Kumar Das
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Mrinal Kumar Maiti
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India
| | - Amit Basak
- School of Biosciences, Indian Institute of Technology, Kharagpur, India.,Department of Chemistry, Indian Institute of Technology, Kharagpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology, Kharagpur, India.,School of Biosciences, Indian Institute of Technology, Kharagpur, India
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158
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Zhang D, Zhang F, Liu W. A KAS-III Heterodimer in Lipstatin Biosynthesis Nondecarboxylatively Condenses C 8 and C 14 Fatty Acyl-CoA Substrates by a Variable Mechanism during the Establishment of a C 22 Aliphatic Skeleton. J Am Chem Soc 2019; 141:3993-4001. [PMID: 30763089 DOI: 10.1021/jacs.8b12843] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
β-Ketoacyl-acyl carrier protein synthase-III (KAS-III) and its homologues are thiolase-fold proteins that typically behave as homodimers functioning in diverse thioester-based reactions for C-C, C-O, or C-N bond formation. Here, we report an exception observed in the biosynthesis of lipstatin. During the establishment of the C22 aliphatic skeleton of this β-lactone lipase inhibitor, LstA and LstB, which both are KAS-III homologues but phylogenetically distinct from each other, function together by forming an unusual heterodimer to catalyze a nondecarboxylating Claisen condensation of C8 and C14 fatty acyl-CoA substrates. The resulting C22 α-alkyl β-ketoacid, which is unstable and tends to be spontaneously decarboxylated to a shunt C21 hydrocarbon product, is transformed by the stereoselective β-ketoreductase LstD into a relatively stable C22 α-alkyl β-hydroxyacid for further transformation. LstAB activity tolerates changes in the stereochemistry, saturation degree, and thioester form of both long-chain fatty acyl-CoA substrates. This flexibility, along with the characterization of catalytic residues, benefits our investigations into the individual roles of the two KAS-III homologues in the heterodimer-catalyzed reactions. The large subunit LstA contains a characteristic Cys-His-Asn triad and likely reacts with C8 acyl-CoA to form an acyl-Cys enzyme intermediate. In contrast, the small subunit LstB lacks this triad but possesses a catalytic Glu residue, which can act on the C8 acyl-Cys enzyme intermediate in a substrate-dependent manner, either as a base for Cα deprotonation or as a nucleophile for a Michael-type addition-initiated cascade reaction, to produce an enolate anion for head-to-head assembly with C14 acyl-CoA through a unidirectional nucleophilic substitution. Uncovering LstAB catalysis draws attention to thiolase-fold proteins that are noncanonical in both active form and catalytic reaction/mechanism. LstAB homologues are widespread in bacteria and remain to be functionally assigned, generating great interest in their corresponding products and associated biological functions.
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Affiliation(s)
- Daozhong Zhang
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , University of Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China
| | - Fang Zhang
- Innovation Research Institute of Traditional Chinese Medicine , Shanghai University of Traditional Chinese Medicine , 1200 Cailun Road , Shanghai 201203 , China
| | - Wen Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry , University of Chinese Academy of Sciences , 345 Lingling Road , Shanghai 200032 , China.,Huzhou Center of Bio-Synthetic Innovation , 1366 Hongfeng Road , Huzhou 313000 , China
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159
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Xin X, Huang G, An C, Raina-Fulton R, Weger H. Insights into Long-Term Toxicity of Triclosan to Freshwater Green Algae in Lake Erie. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:2189-2198. [PMID: 30673261 DOI: 10.1021/acs.est.9b00259] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This study explored the long-term impacts of a pulse disturbance of triclosan on five nontarget green algae in Lake Erie. Comprehensive analyses were performed using multiple physiological end points at community and subcellular scales. The toxic mechanism of triclosan in a wide range of concentrations was analyzed. The diverse sensitivity of algae species and complex interrelationships among multiple end points were revealed. The results showed the taxonomic groups of algae were the key issue for sensitivity difference. High doses of triclosan caused irreversible damage on algae, and environmentally relevant doses initiated either inhibition or stimulation. Smaller cells had higher sensitivity to triclosan, while larger cells had a wider size variation after exposure. Colonial cells were less sensitive than unicells. For chlorophyll, there were better dose-response relationships in Chlorococcum sp., Chlamydomonas reinhardtii CPCC 12 and 243 than Asterococcus superbus and Eremosphaera viridis. For chlorophyll fluorescence, Fv/ Fm was the most sensitive parameter, and qN was more sensitive than qP. Triclosan showed long-term effects on biochemical components, such as lipids, proteins, and nucleic acids. The findings will be helpful for a systematic and complete assessment of triclosan toxicity in natural waters and the development of appropriate strategies for its risk management.
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Affiliation(s)
- Xiaying Xin
- Institute for Energy, Environment and Sustainable Communities , University of Regina , Regina , Canada S4S 0A2
| | - Gordon Huang
- Institute for Energy, Environment and Sustainable Communities , University of Regina , Regina , Canada S4S 0A2
| | - Chunjiang An
- Department of Building, Civil and Environmental Engineering , Concordia University , Montreal , Canada H3G 1M8
| | - Renata Raina-Fulton
- Department of Chemistry and Biochemistry , University of Regina , Regina , Canada S4S 0A2
| | - Harold Weger
- Department of Biology , University of Regina , Regina , Canada S4S 0A2
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160
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Kalia M, Yadav VK, Singh PK, Dohare S, Sharma D, Narvi SS, Agarwal V. Designing quorum sensing inhibitors of Pseudomonas aeruginosa utilizing FabI: an enzymic drug target from fatty acid synthesis pathway. 3 Biotech 2019; 9:40. [PMID: 30675450 DOI: 10.1007/s13205-019-1567-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 01/03/2019] [Indexed: 01/24/2023] Open
Abstract
Pseudomonas aeruginosa infections are a leading cause of death in patients suffering from respiratory diseases. The multidrug-resistant nature of Pseudomonas is potentiated by a process known as quorum sensing. The aim of this study was to reveal new inhibitors of a well-validated but quite unexplored target, enoyl-ACP reductase, which contributes acyl chain lengths of N-acyl homoserine lactones that are major signaling molecules in gram-negative bacteria. In the present study, the crystal structure of FabI (PDB, ID 4NR0) was used for the structure-based identification of quorum sensing inhibitors of Pseudomonas aeruginosa. Active site residues of FabI were identified from the complex of FabI with triclosan and these active site residues were further used to screen for potential inhibitors from natural database. Three-dimensional structures of the 75 natural compounds were retrieved from the ZINC database and screened using PyRX software against FabI. Thirty-eight molecules from the initial screening were sorted on the basis of binding energy, using the known inhibitor triclosan as a standard. These molecules were subjected to various secondary filters, such as Lipinski's Rule of Five, ADME, and toxicity. Finally, eight lead-like molecules were obtained after their evaluation for drug-like characteristics. The present study will open a new window for designing QS inhibitors against P. aeruginosa.
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Affiliation(s)
- Manmohit Kalia
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, India
| | - Vivek Kumar Yadav
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, India
| | - Pradeep Kumar Singh
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, India
| | - Suhaga Dohare
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, India
| | - Deepmala Sharma
- 2Department of Mathematics, National Institute of Technology Raipur, Raipur, India
| | - Shahid Suhail Narvi
- 3Department of Chemistry, Motilal Nehru National Institute of Technology Allahabad, Allahabad, India
| | - Vishnu Agarwal
- 1Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Allahabad, India
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161
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Koeda S, Sato K, Saito H, Nagano AJ, Yasugi M, Kudoh H, Tanaka Y. Mutation in the putative ketoacyl-ACP reductase CaKR1 induces loss of pungency in Capsicum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:65-80. [PMID: 30267113 DOI: 10.1007/s00122-018-3195-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 09/20/2018] [Indexed: 05/13/2023]
Abstract
A putative ketoacyl-ACP reductase (CaKR1) that was not previously known to be associated with pungency of Capsicum was identified from map-based cloning and functional characterization. The pungency of chili pepper fruits is due to the presence of capsaicinoids, which are synthesized through the convergence of the phenylpropanoid and branched-chain fatty acid pathways. The extensive, global use of pungent and non-pungent peppers underlines the importance of understanding the genetic mechanism underlying capsaicinoid biosynthesis for breeding pepper cultivars. Although Capsicum is one of the earliest domesticated plant genera, the only reported genetic causes of its loss of pungency are mutations in acyltransferase (Pun1) and putative aminotransferase (pAMT). In this study, a single recessive gene responsible for the non-pungency of pepper No.3341 (C. chinense) was identified on chromosome 10 using an F2 population derived from a cross between Habanero and No.3341. Five candidate genes were identified in the target region, within a distance of 220 kb. A candidate gene, a putative ketoacyl-ACP reductase (CaKR1), of No.3341 had an insertion of a 4.5-kb transposable element (TE) sequence in the first intron, resulting in the production of a truncated transcript missing the region coding the catalytic domain. Virus-induced gene silencing of CaKR1 in pungent peppers resulted in the decreased accumulation of capsaicinoids, a phenotype consistent with No.3341. Moreover, GC-MS analysis of 8-methyl-6-nonenoic acid, which is predicted to be synthesized during the elongation cycle of branched-chain fatty acid biosynthesis, revealed that its deficiency in No.3341. Genetic, genomic, transcriptional, silencing, and biochemical precursor analyses performed in combination provide a solid ground for the conclusion that CaKR1 is involved in capsaicinoid biosynthesis and that its disruption results in a loss of pungency.
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Affiliation(s)
- Sota Koeda
- Faculty of Agriculture, Kindai University, Nara, Nara, 631-8505, Japan.
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, 619-0218, Japan.
| | - Kosuke Sato
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, 619-0218, Japan
| | - Hiroki Saito
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, 619-0218, Japan
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, Okinawa, 907-0002, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2914, Japan
| | - Masaki Yasugi
- Faculty of Engineering, Utsunomiya University, Utsunomiya, Tochigi, 321-8585, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Yoshiyuki Tanaka
- Graduate School of Environmental and Life Science, Okayama University, Okayama, 700-8530, Japan
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162
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Konno S, La Clair JJ, Burkart MD. Trapping the Complex Molecular Machinery of Polyketide and Fatty Acid Synthases with Tunable Silylcyanohydrin Crosslinkers. Angew Chem Int Ed Engl 2018; 57:17009-17013. [PMID: 30379389 PMCID: PMC6407627 DOI: 10.1002/anie.201806865] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 09/19/2018] [Indexed: 12/14/2022]
Abstract
Many families of natural products are synthesized by large multidomain biological machines commonly referred to as megasynthases. While the advance of mechanism-based tools has opened new windows into the structural features within the protein-protein interfaces guiding carrier protein dependent enzymes, there is an immediate need for tools that can be engaged to link co-translated domains in a site-selective manner. Now, the use of silylcyanohydrins is demonstrated in a two-step, two-site selective crosslinking for the trapping of carrier-protein interactions within megasynthases. This advance provides a new tool to trap intermediate states within multimodular systems, a key step toward understanding the specificities within fatty acid (FAS) and polyketide (PKS) synthases.
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Affiliation(s)
- Sho Konno
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - James J La Clair
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Michael D Burkart
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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163
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Identification of active site residues implies a two-step catalytic mechanism for acyl-ACP thioesterase. Biochem J 2018; 475:3861-3873. [DOI: 10.1042/bcj20180470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 02/02/2023]
Abstract
In plants and bacteria that use a Type II fatty acid synthase, isozymes of acyl-acyl carrier protein (ACP) thioesterase (TE) hydrolyze the thioester bond of acyl-ACPs, terminating the process of fatty acid biosynthesis. These TEs are therefore critical in determining the fatty acid profiles produced by these organisms. Past characterizations of a limited number of plant-sourced acyl-ACP TEs have suggested a thiol-based, papain-like catalytic mechanism, involving a triad of Cys, His, and Asn residues. In the present study, the sequence alignment of 1019 plant and bacterial acyl-ACP TEs revealed that the previously proposed Cys catalytic residue is not universally conserved and therefore may not be a catalytic residue. Systematic mutagenesis of this residue to either Ser or Ala in three plant acyl-ACP TEs, CvFatB1 and CvFatB2 from Cuphea viscosissima and CnFatB2 from Cocos nucifera, resulted in enzymatically active variants, demonstrating that this Cys residue (Cys348 in CvFatB2) is not catalytic. In contrast, the multiple sequence alignment, together with the structure modeling of CvFatB2, suggests that the highly conserved Asp309 and Glu347, in addition to previously proposed Asn311 and His313, may be involved in catalysis. The substantial loss of catalytic competence associated with site-directed mutants at these positions confirmed the involvement of these residues in catalysis. By comparing the structures of acyl-ACP TE and the Pseudomonas 4-hydroxybenzoyl-CoA TE, both of which fold in the same hotdog tertiary structure and catalyze the hydrolysis reaction of thioester bond, we have proposed a two-step catalytic mechanism for acyl-ACP TE that involves an enzyme-bound anhydride intermediate.
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164
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Abstract
Biocatalytic systems (e.g., multienzyme pathways or complexes) enable the conversion of simple sugars into complex products under ambient conditions and, thus, represent promising platforms for the synthesis of renewable fuels and chemicals. Unfortunately, to date, many of these systems have proven difficult to engineer without a detailed understanding of the kinetic relationships that regulate the concerted action of their constituent enzymes. This study develops a mechanistic kinetic model of the fatty acid synthase (FAS) of Escherichia coli and uses that model to determine how different FAS components work together to control the production of free fatty acids-precursors to a wide range of oleochemicals. Perturbational analyses indicate that the modification or overexpression of a single FAS component can depress fatty acid production (a commonly observed phenomenon) by sequestering the proteins with which it interacts and/or by depleting common substrate pools. Compositional studies, in turn, suggest that simple changes in the ratios of FAS components can alter the average length of fatty acids but show that specialized enzymes (i.e., highly specific ketoacyl synthases or thioesterases) are required for narrow product profiles. Intriguingly, a sensitivity analysis indicates that two components primarily influence-and, thus, enable fine control over-total production, but suggests that the enzymes that regulate product profile are more broadly influential. Findings thus reveal the general importance of kinetic considerations in efforts to engineer fatty acid biosynthesis and provide strategies-and a kinetic model-for incorporating those considerations into FAS designs.
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Affiliation(s)
- Sophia Ruppe
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
| | - Jerome M. Fox
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, 3415 Colorado Avenue, Boulder, Colorado 80303, United States
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165
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Rivas MA, Courouble VC, Baker MC, Cookmeyer DL, Fiore KE, Frost AJ, Godbe KN, Jordan MR, Krasnow EN, Mollo A, Ridings ST, Sawada K, Shroff KD, Studnitzer B, Thiele GAR, Sisto AC, Nawal S, Huff AR, Fairman R, Johnson KA, Beld J, Kokona B, Charkoudian LK. The Effect of Divalent Cations on the Thermostability of Type II Polyketide Synthase Acyl Carrier Proteins. AIChE J 2018; 64:4308-4318. [PMID: 31527922 DOI: 10.1002/aic.16402] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The successful engineering of biosynthetic pathways hinges on understanding the factors that influence acyl carrier protein (ACP) stability and function. The stability and structure of ACPs can be influenced by the presence of divalent cations, but how this relates to primary sequence remains poorly understood. As part of a course-based undergraduate research experience, we investigated the thermostability of type II polyketide synthase (PKS) ACPs. We observed an approximate 40 °C range in the thermostability amongst the 14 ACPs studied, as well as an increase in stability (5 - 26 °C) of the ACPs in the presence of divalent cations. Distribution of charges in the helix II-loop-helix III region was found to impact the enthalpy of denaturation. Taken together, our results reveal clues as to how the sequence of type II PKS ACPs relates to their structural stability, information that can be used to study how ACP sequence relates to function.
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Affiliation(s)
| | - Valentine C. Courouble
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Miranda C. Baker
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Kristen E. Fiore
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Alexander J. Frost
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Michael R. Jordan
- Dept. of Physics Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Emily N. Krasnow
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Aurelio Mollo
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Stephen T. Ridings
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Keisuke Sawada
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Kavita D. Shroff
- Dept. of Biology Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Bradley Studnitzer
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | - Grace A. R. Thiele
- Dept. of Chemistry Haverford College Haverford PA 19041
- Biochemistry 390 (“Biochemistry Superlab”) Haverford College Haverford PA
| | | | - Saadia Nawal
- Dept. of Chemistry Haverford College Haverford PA 19041
| | - Adam R. Huff
- Dept. of Chemistry Haverford College Haverford PA 19041
| | | | | | - Joris Beld
- Dept. of Microbiology and Immunology Drexel University College of Medicine Philadelphia PA 19102
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166
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Konno S, La Clair JJ, Burkart MD. Trapping the Complex Molecular Machinery of Polyketide and Fatty Acid Synthases with Tunable Silylcyanohydrin Crosslinkers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sho Konno
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - James J. La Clair
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Michael D. Burkart
- Department of Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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167
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Wood BM, Santa Maria JP, Matano LM, Vickery CR, Walker S. A partial reconstitution implicates DltD in catalyzing lipoteichoic acid d-alanylation. J Biol Chem 2018; 293:17985-17996. [PMID: 30237166 PMCID: PMC6240853 DOI: 10.1074/jbc.ra118.004561] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/27/2018] [Indexed: 12/19/2022] Open
Abstract
Modifications to the Gram-positive bacterial cell wall play important roles in antibiotic resistance and pathogenesis, but the pathway for the d-alanylation of teichoic acids (DLT pathway), a ubiquitous modification, is poorly understood. The d-alanylation machinery includes two membrane proteins of unclear function, DltB and DltD, which are somehow involved in transfer of d-alanine from a carrier protein inside the cell to teichoic acids on the cell surface. Here, we probed the role of DltD in the human pathogen Staphylococcus aureus using both cell-based and biochemical assays. We first exploited a known synthetic lethal interaction to establish the essentiality of each gene in the DLT pathway for d-alanylation of lipoteichoic acid (LTA) and confirmed this by directly detecting radiolabeled d-Ala-LTA both in cells and in vesicles prepared from mutant strains of S. aureus We developed a partial reconstitution of the pathway by using cell-derived vesicles containing DltB, but no other components of the d-alanylation pathway, and showed that d-alanylation of previously formed lipoteichoic acid in the DltB vesicles requires the presence of purified and reconstituted DltA, DltC, and DltD, but not of the LTA synthase LtaS. Finally, based on the activity of DltD mutants in cells and in our reconstituted system, we determined that Ser-70 and His-361 are essential for d-alanylation activity, and we propose that DltD uses a catalytic dyad to transfer d-alanine to LTA. In summary, we have developed a suite of assays for investigating the bacterial DLT pathway and uncovered a role for DltD in LTA d-alanylation.
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Affiliation(s)
- B McKay Wood
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - John P Santa Maria
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Leigh M Matano
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Christopher R Vickery
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115
| | - Suzanne Walker
- From the Department of Microbiology, Harvard Medical School, Boston, Massachusetts 02115.
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168
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Chen A, Re RN, Burkart MD. Type II fatty acid and polyketide synthases: deciphering protein-protein and protein-substrate interactions. Nat Prod Rep 2018; 35:1029-1045. [PMID: 30046786 PMCID: PMC6233901 DOI: 10.1039/c8np00040a] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Covering: up to April 5, 2018 Metabolites from type II fatty acid synthase (FAS) and polyketide synthase (PKS) pathways differ broadly in their identities and functional roles. The former are considered primary metabolites that are linear hydrocarbon acids, while the latter are complex aromatic or polyunsaturated secondary metabolites. Though the study of bacterial FAS has benefitted from decades of biochemical and structural investigations, type II PKSs have remained less understood. Here we review the recent approaches to understanding the protein-protein and protein-substrate interactions in these pathways, with an emphasis on recent chemical biology and structural applications. New approaches to the study of FAS have highlighted the critical role of the acyl carrier protein (ACP) with regard to how it stabilizes intermediates through sequestration and selectively delivers cargo to successive enzymes within these iterative pathways, utilizing protein-protein interactions to guide and organize enzymatic timing and specificity. Recent tools that have shown promise in FAS elucidation should find new approaches to studying type II PKS systems in the coming years.
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Affiliation(s)
- Aochiu Chen
- Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA.
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169
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de Carvalho CCCR, Caramujo MJ. The Various Roles of Fatty Acids. Molecules 2018; 23:molecules23102583. [PMID: 30304860 PMCID: PMC6222795 DOI: 10.3390/molecules23102583] [Citation(s) in RCA: 305] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/01/2018] [Accepted: 10/06/2018] [Indexed: 12/31/2022] Open
Abstract
Lipids comprise a large group of chemically heterogeneous compounds. The majority have fatty acids (FA) as part of their structure, making these compounds suitable tools to examine processes raging from cellular to macroscopic levels of organization. Among the multiple roles of FA, they have structural functions as constituents of phospholipids which are the "building blocks" of cell membranes; as part of neutral lipids FA serve as storage materials in cells; and FA derivatives are involved in cell signalling. Studies on FA and their metabolism are important in numerous research fields, including biology, bacteriology, ecology, human nutrition and health. Specific FA and their ratios in cellular membranes may be used as biomarkers to enable the identification of organisms, to study adaptation of bacterial cells to toxic compounds and environmental conditions and to disclose food web connections. In this review, we discuss the various roles of FA in prokaryotes and eukaryotes and highlight the application of FA analysis to elucidate ecological mechanisms. We briefly describe FA synthesis; analyse the role of FA as modulators of cell membrane properties and FA ability to store and supply energy to cells; and inspect the role of polyunsaturated FA (PUFA) and the suitability of using FA as biomarkers of organisms.
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Affiliation(s)
- Carla C C R de Carvalho
- Institute for Bioengineering and Biosciences, Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Maria José Caramujo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Edifício C2-5º Piso, 1749-016 Lisboa, Portugal.
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170
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Meng Q, Liang H, Gao H. Roles of multiple KASIII homologues of Shewanella oneidensis in initiation of fatty acid synthesis and in cerulenin resistance. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:1153-1163. [DOI: 10.1016/j.bbalip.2018.06.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/02/2018] [Accepted: 06/28/2018] [Indexed: 01/04/2023]
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171
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Rickettsia Lipid A Biosynthesis Utilizes the Late Acyltransferase LpxJ for Secondary Fatty Acid Addition. J Bacteriol 2018; 200:JB.00334-18. [PMID: 30012728 PMCID: PMC6148475 DOI: 10.1128/jb.00334-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 07/06/2018] [Indexed: 12/18/2022] Open
Abstract
Members of the Rickettsia genus are obligate intracellular, Gram-negative coccobacilli that infect mammalian and arthropod hosts. Several rickettsial species are human pathogens and are transmitted by blood-feeding arthropods. In Gram-negative parasites, the outer membrane (OM) sits at the nexus of the host-pathogen interaction and is rich in lipopolysaccharide (LPS). The lipid A component of LPS anchors the molecule to the bacterial surface and is an endotoxic agonist of Toll-like receptor 4 (TLR4). Despite the apparent importance of lipid A in maintaining OM integrity, as well as its inflammatory potential during infection, this molecule is poorly characterized in Rickettsia pathogens. In this work, we have identified and characterized new members of the recently discovered LpxJ family of lipid A acyltransferases in both Rickettsia typhi and Rickettsia rickettsii, the etiological agents of murine typhus and Rocky Mountain spotted fever, respectively. Our results demonstrate that these enzymes catalyze the addition of a secondary acyl chain (C14/C16) to the 3'-linked primary acyl chain of the lipid A moiety in the final steps of the Raetz pathway of lipid A biosynthesis. Since lipid A architecture is fundamental to bacterial OM integrity, we believe that rickettsial LpxJ may be important in maintaining membrane dynamics to facilitate molecular interactions at the host-pathogen interface that are required for adhesion and invasion of mammalian cells. This work contributes to our understanding of rickettsial outer membrane physiology and sets a foundation for further exploration of the envelope and its role in pathogenesis.IMPORTANCE Lipopolysaccharide (LPS) triggers an inflammatory response through the TLR4-MD2 receptor complex and inflammatory caspases, a process mediated by the lipid A moiety of LPS. Species of Rickettsia directly engage both extracellular and intracellular immunosurveillance, yet little is known about rickettsial lipid A. Here, we demonstrate that the alternative lipid A acyltransferase, LpxJ, from Rickettsia typhi and R. rickettsii catalyzes the addition of C16 fatty acid chains into the lipid A 3'-linked primary acyl chain, accounting for major structural differences relative to the highly inflammatory lipid A of Escherichia coli.
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172
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Haga T, Hirakawa H, Nagamune T. Artificial Self‐Sufficient Cytochrome P450 Containing Multiple Auxiliary Proteins Demonstrates Improved Monooxygenase Activity. Biotechnol J 2018; 13:e1800088. [DOI: 10.1002/biot.201800088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/18/2018] [Indexed: 02/04/2023]
Affiliation(s)
- Tomoaki Haga
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Hidehiko Hirakawa
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
| | - Teruyuki Nagamune
- Department of Chemistry and BiotechnologySchool of EngineeringThe University of TokyoTokyo 113‐8656Japan
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173
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Biochemical and Structural Basis of Triclosan Resistance in a Novel Enoyl-Acyl Carrier Protein Reductase. Antimicrob Agents Chemother 2018; 62:AAC.00648-18. [PMID: 29891603 DOI: 10.1128/aac.00648-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/05/2018] [Indexed: 12/24/2022] Open
Abstract
Enoyl-acyl carrier protein reductases (ENR), such as FabI, FabL, FabK, and FabV, catalyze the last reduction step in bacterial type II fatty acid biosynthesis. Previously, we reported metagenome-derived ENR homologs resistant to triclosan (TCL) and highly similar to 7-α hydroxysteroid dehydrogenase (7-AHSDH). These homologs are commonly found in Epsilonproteobacteria, a class that contains several human-pathogenic bacteria, including the genera Helicobacter and Campylobacter Here we report the biochemical and predicted structural basis of TCL resistance in a novel 7-AHSDH-like ENR. The purified protein exhibited NADPH-dependent ENR activity but no 7-AHSDH activity, despite its high homology with 7-AHSDH (69% to 96%). Because this ENR was similar to FabL (41%), we propose that this metagenome-derived ENR be referred to as FabL2. Homology modeling, molecular docking, and molecular dynamic simulation analyses revealed the presence of an extrapolated six-amino-acid loop specific to FabL2 ENR, which prevented the entry of TCL into the active site of FabL2 and was likely responsible for TCL resistance. Elimination of this extrapolated loop via site-directed mutagenesis resulted in the complete loss of TCL resistance but not enzyme activity. Phylogenetic analysis suggested that FabL, FabL2, and 7-AHSDH diverged from a common short-chain dehydrogenase reductase family. This study is the first to report the role of the extrapolated loop of FabL2-type ENRs in conferring TCL resistance. Thus, the FabL2 ENR represents a new drug target specific for pathogenic Epsilonproteobacteria.
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174
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Tsai SC(S. The Structural Enzymology of Iterative Aromatic Polyketide Synthases: A Critical Comparison with Fatty Acid Synthases. Annu Rev Biochem 2018; 87:503-531. [DOI: 10.1146/annurev-biochem-063011-164509] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Polyketides are a large family of structurally complex natural products including compounds with important bioactivities. Polyketides are biosynthesized by polyketide synthases (PKSs), multienzyme complexes derived evolutionarily from fatty acid synthases (FASs). The focus of this review is to critically compare the properties of FASs with iterative aromatic PKSs, including type II PKSs and fungal type I nonreducing PKSs whose chemical logic is distinct from that of modular PKSs. This review focuses on structural and enzymological studies that reveal both similarities and striking differences between FASs and aromatic PKSs. The potential application of FAS and aromatic PKS structures for bioengineering future drugs and biofuels is highlighted.
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Affiliation(s)
- Shiou-Chuan (Sheryl) Tsai
- Departments of Molecular Biology and Biochemistry, Chemistry, and Pharmaceutical Sciences, University of California, Irvine, California 92697, USA
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175
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Marcella AM, Barb AW. Acyl-coenzyme A:(holo-acyl carrier protein) transacylase enzymes as templates for engineering. Appl Microbiol Biotechnol 2018; 102:6333-6341. [PMID: 29858956 DOI: 10.1007/s00253-018-9114-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 01/18/2023]
Abstract
This review will cover the structure, enzymology, and related aspects that are important for structure-based engineering of the transacylase enzymes from fatty acid biosynthesis and polyketide synthesis. Furthermore, this review will focus on in vitro characteristics and not cover engineering of the upstream or downstream reactions or strategies to manipulate metabolic flux in vivo. The malonyl-coenzyme A(CoA)-holo-acyl-carrier protein (holo-ACP) transacylase (FabD) from Escherichia coli serves as a model for this enzyme with thorough descriptions of structure, enzyme mechanism, and effects of mutation on substrate binding presented in the literature. Here, we discuss multiple practical and theoretical considerations regarding engineering transacylase enzymes to accept non-cognate substrates and form novel acyl-ACPs for downstream reactions.
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Affiliation(s)
- Aaron M Marcella
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Ames, IA, 50011, USA
| | - Adam W Barb
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, 2437 Pammel Drive, Molecular Biology Building, rm 4210, Ames, IA, 50011, USA.
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176
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Geethalakshmi R, Sundaramurthi JC, Sarada DVL. Antibacterial activity of flavonoid isolated from Trianthema decandra against Pseudomonas aeruginosa and molecular docking study of FabZ. Microb Pathog 2018; 121:87-92. [PMID: 29763727 DOI: 10.1016/j.micpath.2018.05.016] [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: 04/16/2018] [Revised: 05/10/2018] [Accepted: 05/11/2018] [Indexed: 11/25/2022]
Abstract
The natural product flavonoid demonstrates an extensive sort of pharmacological properties including antimicrobial activity. Although its Pseudomonas aeruginosa inhibition has been discovered, no target for action against flavonoid has been revealed to date. The anti - P. aeruginosa activity of the 2 - (3', 4' dihydroxy-phenyl) - 3, 5, 7-trihydroxy-chromen-4-one isolated from T. decandra was evaluated by disc diffusion and minimum inhibitory concentration methods. The molecular docking of the flavonoid isolated from T. decandra was carried out using CDOCKER (Discovery Studio 2.0). The flavonoid isolated from T. decandra was found to inhibit the growth of P. aeruginosa and the zone of inhibition was found to be 22 ± 0.04 mm at 20 μg/ml while chloramphenicol showed 23 ± 0.05 mm at 30 μg/ml. P. aeruginosa was found to be the most sensitive to both isolated flavonoid and standard control chloramphenicol with MIC values 39.05 μg/ml and 25 μg/ml respectively. Further, the FAS II β-hydroxyacyl-ACP (FabZ) of P. aeruginosa was found to be a potential target of the flavonoid as it docked in silico effectively. Our work has demonstrated the anti - P. aeruginosa activity of flavonoid isolated from T. decandra and also resulted in the elucidation of a plausible mechanism of action of the isolated flavonoid by inhibiting the FabZ using in silico analysis.
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Affiliation(s)
- Rajarathinam Geethalakshmi
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur 603203, Tamil Nadu, India.
| | - Jagadish Chandrabose Sundaramurthi
- ICMR - Biomedical Informatics Centre, National Institute for Research in Tuberculosis (ICMR), (Formerly Tuberculosis Research Centre), Chennai 600031, Tamil Nadu, India.
| | - Dronamraju V L Sarada
- Department of Biotechnology, School of Bioengineering, SRM University, Kattankulathur 603203, Tamil Nadu, India.
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177
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Novel Xanthomonas campestris Long-Chain-Specific 3-Oxoacyl-Acyl Carrier Protein Reductase Involved in Diffusible Signal Factor Synthesis. mBio 2018; 9:mBio.00596-18. [PMID: 29739899 PMCID: PMC5941067 DOI: 10.1128/mbio.00596-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The precursors of the diffusible signal factor (DSF) family signals of Xanthomonas campestris pv. campestris are 3-hydroxyacyl-acyl carrier protein (3-hydroxyacyl-ACP) thioesters having acyl chains of 12 to 13 carbon atoms produced by the fatty acid biosynthetic pathway. We report a novel 3-oxoacyl-ACP reductase encoded by the X. campestris pv. campestris XCC0416 gene (fabG2), which is unable to participate in the initial steps of fatty acyl synthesis. This was shown by the failure of FabG2 expression to allow growth at the nonpermissive temperature of an Escherichia colifabG temperature-sensitive strain. However, when transformed into the E. coli strain together with a plasmid bearing the Vibrio harveyi acyl-ACP synthetase gene (aasS), growth proceeded, but only when the medium contained octanoic acid. In vitro assays showed that FabG2 catalyzes the reduction of long-chain (≥C8) 3-oxoacyl-ACPs to 3-hydroxyacyl-ACPs but is only weakly active with shorter-chain (C4, C6) substrates. FabG1, the housekeeping 3-oxoacyl-ACP reductase encoded within the fatty acid synthesis gene cluster, could be deleted in a strain that overexpressed fabG2 but only in octanoic acid-supplemented media. Growth of the X. campestris pv. campestris ΔfabG1 strain overexpressing fabG2 required fabH for growth with octanoic acid, indicating that octanoyl coenzyme A is elongated by X. campestris pv. campestrisfabH. Deletion of fabG2 reduced DSF family signal production, whereas overproduction of either FabG1 or FabG2 in the ΔfabG2 strain restored DSF family signal levels. Quorum sensing mediated by DSF signaling molecules regulates pathogenesis in several different phytopathogenic bacteria, including Xanthomonas campestris pv. campestris. DSF signaling also plays a key role in infection by the human pathogen Burkholderia cepacia. The acyl chains of the DSF molecules are diverted and remodeled from a key intermediate of the fatty acid synthesis pathway. We report a Xanthomonas campestris pv. campestris fatty acid synthesis enzyme, FabG2, of novel specificity that seems tailored to provide DSF signaling molecule precursors.
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178
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Rullán‐Lind C, Pietri RB, Vázquez‐Cintrón M, Baerga‐Ortiz A. Fused dimerization increases expression, solubility, and activity of bacterial dehydratase enzymes. Protein Sci 2018; 27:969-975. [PMID: 29520922 PMCID: PMC5916124 DOI: 10.1002/pro.3404] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/05/2018] [Accepted: 03/07/2018] [Indexed: 01/12/2023]
Abstract
FabA and FabZ are the two dehydratase enzymes in Escherichia coli that catalyze the dehydration of acyl intermediates in the biosynthesis of fatty acids. Both enzymes form obligate dimers in which the active site contains key amino acids from both subunits. While FabA is a soluble protein that has been relatively straightforward to express and to purify from cultured E. coli, FabZ has shown to be mostly insoluble and only partially active. In an effort to increase the solubility and activity of both dehydratases, we made constructs consisting of two identical subunits of FabA or FabZ fused with a naturally occurring peptide linker, so as to force their dimerization. The fused dimer of FabZ (FabZ-FabZ) was expressed as a soluble enzyme with an ninefold higher activity in vitro than the unfused FabZ. This construct exemplifies a strategy for the improvement of enzymes from the fatty acid biosynthesis pathways, many of which function as dimers, catalyzing critical steps for the production of fatty acids.
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Affiliation(s)
- Carlos Rullán‐Lind
- Department of BiochemistryUniversity of Puerto Rico, Medical Sciences CampusSan Juan00936‐5067Puerto Rico
- Molecular Sciences Research Center, University of Puerto RicoSan JuanPuerto Rico
| | - Ruth B. Pietri
- Department of ChemistryUniversity of Puerto Rico, Cayey CampusCayeyPuerto Rico
| | - Melvin Vázquez‐Cintrón
- Department of BiochemistryUniversity of Puerto Rico, Medical Sciences CampusSan Juan00936‐5067Puerto Rico
- Molecular Sciences Research Center, University of Puerto RicoSan JuanPuerto Rico
| | - Abel Baerga‐Ortiz
- Department of BiochemistryUniversity of Puerto Rico, Medical Sciences CampusSan Juan00936‐5067Puerto Rico
- Molecular Sciences Research Center, University of Puerto RicoSan JuanPuerto Rico
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179
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Lee WC, Jeong MC, Lee Y, Kwak C, Lee JY, Kim Y. Structure and substrate specificity of β-ketoacyl-acyl carrier protein synthase III from Acinetobacter baumannii. Mol Microbiol 2018. [PMID: 29528170 DOI: 10.1111/mmi.13950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Originally annotated as the initiator of fatty acid synthesis (FAS), β-ketoacyl-acyl carrier protein synthase III (KAS III) is a unique component of the bacterial FAS system. Novel variants of KAS III have been identified that promote the de novo use of additional extracellular fatty acids by FAS. These KAS III variants prefer longer acyl-groups, notably octanoyl-CoA. Acinetobacter baumannii, a clinically important nosocomial pathogen, contains such a multifunctional KAS III (AbKAS III). To characterize the structural basis of its substrate specificity, we determined the crystal structures of AbKAS III in the presence of different substrates. The acyl-group binding cavity of AbKAS III and co-crystal structure of AbKAS III and octanoyl-CoA confirmed that the cavity can accommodate acyl groups with longer alkyl chains. Interestingly, Cys264 formed a disulfide bond with residual CoA used in the crystallization, which distorted helices at the putative interface with acyl-carrier proteins. The crystal structure of KAS III in the alternate conformation can also be utilized for designing novel antibiotics.
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Affiliation(s)
- Woo Cheol Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Min-Cheol Jeong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Yeongjoon Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Chulhee Kwak
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jee-Young Lee
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu 41061, Republic of Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
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180
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Rittner A, Paithankar KS, Huu KV, Grininger M. Characterization of the Polyspecific Transferase of Murine Type I Fatty Acid Synthase (FAS) and Implications for Polyketide Synthase (PKS) Engineering. ACS Chem Biol 2018; 13:723-732. [PMID: 29328619 DOI: 10.1021/acschembio.7b00718] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fatty acid synthases (FASs) and polyketide synthases (PKSs) condense acyl compounds to fatty acids and polyketides, respectively. Both, FASs and PKSs, harbor acyltransferases (ATs), which select substrates for condensation by β-ketoacyl synthases (KSs). Here, we present the structural and functional characterization of the polyspecific malonyl/acetyltransferase (MAT) of murine FAS. We assign kinetic constants for the transacylation of the native substrates, acetyl- and malonyl-CoA, and demonstrate the promiscuity of FAS to accept structurally and chemically diverse CoA-esters. X-ray structural data of the KS-MAT didomain in a malonyl-loaded state suggests a MAT-specific role of an active site arginine in transacylation. Owing to its enzymatic properties and its accessibility as a separate domain, MAT of murine FAS may serve as versatile tool for engineering PKSs to provide custom-tailored access to new polyketides that can be applied in antibiotic and antineoplastic therapy.
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Affiliation(s)
- Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Karthik S. Paithankar
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Khanh Vu Huu
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, Cluster of Excellence for Macromolecular Complexes, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
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181
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Two distinct domains contribute to the substrate acyl chain length selectivity of plant acyl-ACP thioesterase. Nat Commun 2018; 9:860. [PMID: 29491418 PMCID: PMC5830452 DOI: 10.1038/s41467-018-03310-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 02/01/2018] [Indexed: 01/12/2023] Open
Abstract
The substrate specificity of acyl-ACP thioesterase (TE) plays an essential role in controlling the fatty acid profile produced by type II fatty acid synthases. Here we identify two groups of residues that synergistically determine different substrate specificities of two acyl-ACP TEs from Cuphea viscosissima (CvFatB1 and CvFatB2). One group (V194, V217, N223, R226, R227, and I268 in CvFatB2) is critical in determining the structure and depth of a hydrophobic cavity in the N-terminal hotdog domain that binds the substrate's acyl moiety. The other group (255-RKLSKI-260 and 285-RKLPKL-289 in CvFatB2) defines positively charged surface patches that may facilitate binding of the ACP moiety. Mutagenesis of residues within these two groups results in distinct synthetic acyl-ACP TEs that efficiently hydrolyze substrates with even shorter chains (C4- to C8-ACPs). These insights into structural determinants of acyl-ACP TE substrate specificity are useful in modifying this enzyme for tailored fatty acid production in engineered organisms.
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182
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Ekström AG, Kelly V, Marles-Wright J, Cockroft SL, Campopiano DJ. Structural evidence for the covalent modification of FabH by 4,5-dichloro-1,2-dithiol-3-one (HR45). Org Biomol Chem 2018; 15:6310-6313. [PMID: 28715001 PMCID: PMC5708339 DOI: 10.1039/c7ob01396e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We use mass spectrometry analysis and molecular modelling to show the established antimicrobial inhibitor 4,5-dichloro-1,2-dithiol-3-one (HR45) acts by forming a covalent adduct with the target β-ketoacyl-ACP synthase III (FabH). The 5-chloro substituent directs attack of the essential active site thiol (C112) via a Michael-type addition elimination reaction mechanism.
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Affiliation(s)
- Alexander G Ekström
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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183
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Khan R, Roy N, Choi K, Lee SW. Distribution of triclosan-resistant genes in major pathogenic microorganisms revealed by metagenome and genome-wide analysis. PLoS One 2018; 13:e0192277. [PMID: 29420585 PMCID: PMC5805296 DOI: 10.1371/journal.pone.0192277] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/18/2018] [Indexed: 12/11/2022] Open
Abstract
The substantial use of triclosan (TCS) has been aimed to kill pathogenic bacteria, but TCS resistance seems to be prevalent in microbial species and limited knowledge exists about TCS resistance determinants in a majority of pathogenic bacteria. We aimed to evaluate the distribution of TCS resistance determinants in major pathogenic bacteria (N = 231) and to assess the enrichment of potentially pathogenic genera in TCS contaminated environments. A TCS-resistant gene (TRG) database was constructed and experimentally validated to predict TCS resistance in major pathogenic bacteria. Genome-wide in silico analysis was performed to define the distribution of TCS-resistant determinants in major pathogens. Microbiome analysis of TCS contaminated soil samples was also performed to investigate the abundance of TCS-resistant pathogens. We experimentally confirmed that TCS resistance could be accurately predicted using genome-wide in silico analysis against TRG database. Predicted TCS resistant phenotypes were observed in all of the tested bacterial strains (N = 17), and heterologous expression of selected TCS resistant genes from those strains conferred expected levels of TCS resistance in an alternative host Escherichia coli. Moreover, genome-wide analysis revealed that potential TCS resistance determinants were abundant among the majority of human-associated pathogens (79%) and soil-borne plant pathogenic bacteria (98%). These included a variety of enoyl-acyl carrier protein reductase (ENRs) homologues, AcrB efflux pumps, and ENR substitutions. FabI ENR, which is the only known effective target for TCS, was either co-localized with other TCS resistance determinants or had TCS resistance-associated substitutions. Furthermore, microbiome analysis revealed that pathogenic genera with intrinsic TCS-resistant determinants exist in TCS contaminated environments. We conclude that TCS may not be as effective against the majority of bacterial pathogens as previously presumed. Further, the excessive use of this biocide in natural environments may selectively enrich for not only TCS-resistant bacterial pathogens, but possibly for additional resistance to multiple antibiotics.
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Affiliation(s)
- Raees Khan
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Nazish Roy
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Kihyuck Choi
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea
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184
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Hevener KE, Santarsiero BD, Lee H, Jones JA, Boci T, Johnson ME, Mehboob S. Structural characterization of Porphyromonas gingivalis enoyl-ACP reductase II (FabK). Acta Crystallogr F Struct Biol Commun 2018; 74:105-112. [PMID: 29400320 PMCID: PMC5947681 DOI: 10.1107/s2053230x18000262] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/04/2018] [Indexed: 01/24/2023] Open
Abstract
Enoyl-acyl carrier protein (ACP) reductase II (FabK) is a critical rate-limiting enzyme in the bacterial type II fatty-acid synthesis (FAS II) pathway. FAS II pathway enzymes are markedly disparate from their mammalian analogs in the FAS I pathway in both structure and mechanism. Enzymes involved in bacterial fatty-acid synthesis represent viable drug targets for Gram-negative pathogens, and historical precedent exists for targeting them in the treatment of diseases of the oral cavity. The Gram-negative organism Porphyromonas gingivalis represents a key causative agent of the costly and highly prevalent disease known as chronic periodontitis, and exclusively expresses FabK as its enoyl reductase enzyme in the FAS-II pathway. Together, these characteristics distinguish P. gingivalis FabK (PgFabK) as an attractive and novel narrow-spectrum antibacterial target candidate. PgFabK is a flavoenzyme that is dependent on FMN and NADPH as cofactors for the enzymatic reaction, which reduces the enoyl substrate via a ping-pong mechanism. Here, the structure of the PgFabK enzyme as determined using X-ray crystallography is reported to 1.9 Å resolution with endogenous FMN fully resolved and the NADPH cofactor partially resolved. PgFabK possesses a TIM-barrel motif, and all flexible loops are visible. The determined structure has allowed insight into the structural basis for the NADPH dependence observed in PgFabK and the role of a monovalent cation that has been observed in previous studies to be stringently required for FabK activity. The PgFabK structure and the insights gleaned from its analysis will facilitate structure-based drug-discovery efforts towards the prevention and treatment of P. gingivalis infection.
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Affiliation(s)
- Kirk E. Hevener
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Avenue, Suite 571, Memphis, TN 38163-2198, USA
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Bernard D. Santarsiero
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Hyun Lee
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Jesse A. Jones
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, 881 Madison Avenue, Suite 571, Memphis, TN 38163-2198, USA
| | - Teuta Boci
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Michael E. Johnson
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
| | - Shahila Mehboob
- Center for Pharmaceutical Biotechnology, University of Illinois at Chicago, 900 South Ashland Avenue, Suite 3100, Chicago, IL 60607-7173, USA
- Novalex Therapeutics, Chicago, IL 60612, USA
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185
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Aguilar-Hernández V, Loyola-Vargas VM. Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1658. [PMID: 30524454 PMCID: PMC6262180 DOI: 10.3389/fpls.2018.01658] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/25/2018] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis (SE) is a cell differentiation process by which a somatic cell changes its genetic program and develops into an embryonic cell. Investigating this process with various explant sources in vitro has allowed us to trace somatic embryo development from germination to plantlets and has led to the generation of new technologies, including genetic transformation, endangered species conservation, and synthetic seed production. A transcriptome data comparison from different stages of the developing somatic embryo has revealed a complex network controlling the somatic cell's fate, suggesting that an interconnected network acts at the protein level. Here, we discuss the current progress on SE using proteomic-based data, focusing on changing patterns of proteins during the establishment of the somatic embryo. Despite the advanced proteomic approaches available so far, deciphering how the somatic embryo is induced is still in its infancy. The new proteomics techniques that lead to the quantification of proteins with different abundances during the induction of SE are opening this area of study for the first time. These quantitative differences can elucidate the different pathways involved in SE induction. We envisage that the application of these proteomic technologies can be pivotal to identifying proteins critical to the process of SE, demonstrating the cellular localization, posttranslational modifications, and turnover protein events required to switch from a somatic cell to a somatic embryo cell and providing new insights into the molecular mechanisms underlying SE. This work will help to develop biotechnological strategies for mass production of quality crop material.
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Affiliation(s)
- Victor Aguilar-Hernández
- Catedrático CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
- *Correspondence: Victor Aguilar-Hernández, orcid.org/0000-0001-8239-4047
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
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186
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de Oliveira Viana J, Scotti MT, Scotti L. Molecular Docking Studies in Multitarget Antitubercular Drug Discovery. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2018. [DOI: 10.1007/7653_2018_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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187
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Santos-Merino M, Garcillán-Barcia MP, de la Cruz F. Engineering the fatty acid synthesis pathway in Synechococcus elongatus PCC 7942 improves omega-3 fatty acid production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:239. [PMID: 30202434 PMCID: PMC6123915 DOI: 10.1186/s13068-018-1243-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/27/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND The microbial production of fatty acids has received great attention in the last few years as feedstock for the production of renewable energy. The main advantage of using cyanobacteria over other organisms is their ability to capture energy from sunlight and to transform CO2 into products of interest by photosynthesis, such as fatty acids. Fatty acid synthesis is a ubiquitous and well-characterized pathway in most bacteria. However, the activity of the enzymes involved in this pathway in cyanobacteria remains poorly explored. RESULTS To characterize the function of some enzymes involved in the saturated fatty acid synthesis in cyanobacteria, we genetically engineered Synechococcus elongatus PCC 7942 by overexpressing or deleting genes encoding enzymes of the fatty acid synthase system and tested the lipid profile of the mutants. These modifications were in turn used to improve alpha-linolenic acid production in this cyanobacterium. The mutant resulting from fabF overexpression and fadD deletion, combined with the overexpression of desA and desB desaturase genes from Synechococcus sp. PCC 7002, produced the highest levels of this omega-3 fatty acid. CONCLUSIONS The fatty acid composition of S. elongatus PCC 7942 can be significantly modified by genetically engineering the expression of genes coding for the enzymes involved in the first reactions of fatty acid synthesis pathway. Variations in fatty acid composition of S. elongatus PCC 7942 mutants did not follow the pattern observed in Escherichia coli derivatives. Some of these modifications can be used to improve omega-3 fatty acid production. This work provides new insights into the saturated fatty acid synthesis pathway and new strategies that might be used to manipulate the fatty acid content of cyanobacteria.
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Affiliation(s)
- María Santos-Merino
- Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria—Consejo Superior de Investigaciones Científicas), Santander, Cantabria Spain
| | - M. Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria—Consejo Superior de Investigaciones Científicas), Santander, Cantabria Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria—Consejo Superior de Investigaciones Científicas), Santander, Cantabria Spain
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188
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Pittera J, Jouhet J, Breton S, Garczarek L, Partensky F, Maréchal É, Nguyen NA, Doré H, Ratin M, Pitt FD, Scanlan DJ, Six C. Thermoacclimation and genome adaptation of the membrane lipidome in marine Synechococcus. Environ Microbiol 2017; 20:612-631. [PMID: 29124854 DOI: 10.1111/1462-2920.13985] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/20/2017] [Accepted: 11/02/2017] [Indexed: 12/01/2022]
Abstract
The marine cyanobacteria of the genus Synechococcus are important primary producers, displaying a wide latitudinal distribution that is underpinned by diversification into temperature ecotypes. The physiological basis underlying these ecotypes is poorly known. In many organisms, regulation of membrane fluidity is crucial for acclimating to variations in temperature. Here, we reveal the detailed composition of the membrane lipidome of the model strain Synechococcus sp. WH7803 and its response to temperature variation. Unlike freshwater strains, membranes are almost devoid of C18, mainly containing C14 and C16 chains with no more than two unsaturations. In response to cold, we observed a rarely observed process of acyl chain shortening that likely induces membrane thinning, along with specific desaturation activities. Both of these mechanisms likely regulate membrane fluidity, facilitating the maintenance of efficient photosynthetic activity. A comprehensive examination of 53 Synechococcus genomes revealed clade-specific gene sets regulating membrane lipids. In particular, the genes encoding desaturase enzymes, which is a key to the temperature stress response, appeared to be temperature ecotype-specific, with some of them originating from lateral transfers. Our study suggests that regulation of membrane fluidity has been among the important adaptation processes for the colonization of different thermal niches by marine Synechococcus.
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Affiliation(s)
- Justine Pittera
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Juliette Jouhet
- Institut de Biosciences et Biotechnologies de Grenoble, CEA Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, 38054 Grenoble cedex 9, France
| | - Solène Breton
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Laurence Garczarek
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Frédéric Partensky
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Éric Maréchal
- Institut de Biosciences et Biotechnologies de Grenoble, CEA Grenoble, Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168 Centre National de la Recherche Scientifique, Commissariat à l'Energie Atomique, Institut National de la Recherche Agronomique, Université Grenoble Alpes, 38054 Grenoble cedex 9, France
| | - Ngoc A Nguyen
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Hugo Doré
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Morgane Ratin
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
| | - Frances D Pitt
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Christophe Six
- Marine Phototrophic Prokaryotes group, Station Biologique, Place Georges Teissier, Sorbonne Universités, Université Pierre and Marie Curie (Paris 06) and Centre National de la Recherche Scientifique, UMR 7144, 29688 Roscoff cedex, CS 90074, France
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189
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Li KH, Yu YH, Dong HJ, Zhang WB, Ma JC, Wang HH. Biological Functions of ilvC in Branched-Chain Fatty Acid Synthesis and Diffusible Signal Factor Family Production in Xanthomonas campestris. Front Microbiol 2017; 8:2486. [PMID: 29312195 PMCID: PMC5733099 DOI: 10.3389/fmicb.2017.02486] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022] Open
Abstract
In bacteria, the metabolism of branched-chain amino acids (BCAAs) is tightly associated with branched-chain fatty acids (BCFAs) synthetic pathways. Although previous studies have reported on BCFAs biosynthesis, more detailed associations between BCAAs metabolism and BCFAs biosynthesis remain to be addressed. In this study, we deleted the ilvC gene, which encodes ketol-acid reductoisomerase in the BCAAs synthetic pathway, from the Xanthomonas campestris pv. campestris (Xcc) genome. We characterized gene functions in BCFAs biosynthesis and production of the diffusible signal factor (DSF) family signals. Disruption of ilvC caused Xcc to become auxotrophic for valine and isoleucine, and lose the ability to synthesize BCFAs via carbohydrate metabolism. Furthermore, ilvC mutant reduced the ability to produce DSF-family signals, especially branched-chain DSF-family signals, which might be the main reason for Xcc reduction of pathogenesis toward host plants. In this report, we confirmed that BCFAs do not have major functions in acclimatizing Xcc cells to low temperatures.
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Affiliation(s)
- Kai-Huai Li
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yong-Hong Yu
- Guangdong Food and Drug Vocational College, Guangzhou, China
| | - Hui-Juan Dong
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Wen-Bin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jin-Cheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai-Hong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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190
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Seifar F, Khalili M, Khaledyan H, Amiri Moghadam S, Izadi A, Azimi A, Shakouri SK. α-Lipoic acid, functional fatty acid, as a novel therapeutic alternative for central nervous system diseases: A review. Nutr Neurosci 2017; 22:306-316. [DOI: 10.1080/1028415x.2017.1386755] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Fatemeh Seifar
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Khalili
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Multiple Sclerosis Research Center, Tehran, Iran
| | - Habib Khaledyan
- Physical Medicine and Rehabilitation Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shirin Amiri Moghadam
- Faculty of Medicine, Department of Community Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Azimeh Izadi
- Faculty of Nutrition and Food Science, Department of Biochemistry and Diet Therapy, Nutrition Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Seied Kazem Shakouri
- Physical Medicine and Rehabilitation Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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191
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Zhang J, Burgess JG. Enhanced eicosapentaenoic acid production by a new deep-sea marine bacterium Shewanella electrodiphila MAR441T. PLoS One 2017; 12:e0188081. [PMID: 29176835 PMCID: PMC5703452 DOI: 10.1371/journal.pone.0188081] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 10/31/2017] [Indexed: 02/05/2023] Open
Abstract
Omega-3 fatty acids are products of secondary metabolism, essential for growth and important for human health. Although there are numerous reports of bacterial production of omega-3 fatty acids, less information is available on the biotechnological production of these compounds from bacteria. The production of eicosapentaenoic acid (EPA, 20:5ω3) by a new species of marine bacteria Shewanella electrodiphila MAR441T was investigated under different fermentation conditions. This strain produced a high percentage (up to 26%) of total fatty acids and high yields (mg / g of biomass) of EPA at or below the optimal growth temperature. At higher growth temperatures these values decreased greatly. The amount of EPA produced was affected by the carbon source, which also influenced fatty acid composition. This strain required Na+ for growth and EPA synthesis and cells harvested at late exponential or early stationary phase had a higher EPA content. Both the highest amounts (20 mg g-1) and highest percent EPA content (18%) occurred with growth on L-proline and (NH4)2SO4. The addition of cerulenin further enhanced EPA production to 30 mg g-1. Chemical mutagenesis using NTG allowed the isolation of mutants with improved levels of EPA content (from 9.7 to 15.8 mg g-1) when grown at 15°C. Thus, the yields of EPA could be substantially enhanced without the need for recombinant DNA technology, often a commercial requirement for food supplement manufacture.
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Affiliation(s)
- Jinwei Zhang
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratory, Exeter, United Kingdom
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - J. Grant Burgess
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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192
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Increased Biosynthetic Gene Dosage in a Genome-Reduced Defensive Bacterial Symbiont. mSystems 2017; 2:mSystems00096-17. [PMID: 29181447 PMCID: PMC5698493 DOI: 10.1128/msystems.00096-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/18/2017] [Indexed: 12/31/2022] Open
Abstract
Secondary metabolites, which are small-molecule organic compounds produced by living organisms, provide or inspire drugs for many different diseases. These natural products have evolved over millions of years to provide a survival benefit to the producing organism and often display potent biological activity with important therapeutic applications. For instance, defensive compounds in the environment may be cytotoxic to eukaryotic cells, a property exploitable for cancer treatment. Here, we describe the genome of an uncultured symbiotic bacterium that makes such a cytotoxic metabolite. This symbiont is losing genes that do not endow a selective advantage in a hospitable host environment. Secondary metabolism genes, however, are repeated multiple times in the genome, directly demonstrating their selective advantage. This finding shows the strength of selective forces in symbiotic relationships and suggests that uncultured bacteria in such relationships should be targeted for drug discovery efforts. A symbiotic lifestyle frequently results in genome reduction in bacteria; the isolation of small populations promotes genetic drift and the fixation of deletions and deleterious mutations over time. Transitions in lifestyle, including host restriction or adaptation to an intracellular habitat, are thought to precipitate a wave of sequence degradation events and consequent proliferation of pseudogenes. We describe here a verrucomicrobial symbiont of the tunicate Lissoclinum sp. that appears to be undergoing such a transition, with low coding density and many identifiable pseudogenes. However, despite the overall drive toward genome reduction, this symbiont maintains seven copies of a large polyketide synthase (PKS) pathway for the mandelalides (mnd), cytotoxic compounds that likely constitute a chemical defense for the host. There is evidence of ongoing degradation in a small number of these repeats—including variable borders, internal deletions, and single nucleotide polymorphisms (SNPs). However, the gene dosage of most of the pathway is increased at least 5-fold. Correspondingly, this single pathway accounts for 19% of the genome by length and 25.8% of the coding capacity. This increased gene dosage in the face of generalized sequence degradation and genome reduction suggests that mnd genes are under strong purifying selection and are important to the symbiotic relationship. IMPORTANCE Secondary metabolites, which are small-molecule organic compounds produced by living organisms, provide or inspire drugs for many different diseases. These natural products have evolved over millions of years to provide a survival benefit to the producing organism and often display potent biological activity with important therapeutic applications. For instance, defensive compounds in the environment may be cytotoxic to eukaryotic cells, a property exploitable for cancer treatment. Here, we describe the genome of an uncultured symbiotic bacterium that makes such a cytotoxic metabolite. This symbiont is losing genes that do not endow a selective advantage in a hospitable host environment. Secondary metabolism genes, however, are repeated multiple times in the genome, directly demonstrating their selective advantage. This finding shows the strength of selective forces in symbiotic relationships and suggests that uncultured bacteria in such relationships should be targeted for drug discovery efforts. Author Video: An author video summary of this article is available.
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193
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Clomburg JM, Contreras SC, Chou A, Siegel JB, Gonzalez R. Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional β-oxidation reversal. Metab Eng 2017; 45:11-19. [PMID: 29146470 DOI: 10.1016/j.ymben.2017.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/13/2017] [Accepted: 11/04/2017] [Indexed: 01/05/2023]
Abstract
An engineered reversal of the β-oxidation cycle (r-BOX) and the fatty acid biosynthesis (FAB) pathway are promising biological platforms for advanced fuel and chemical production in part due to their iterative nature supporting the synthesis of various chain length products. While diverging in their carbon-carbon elongation reaction mechanism, iterative operation of each pathway relies on common chemical conversions (reduction, dehydration, and reduction) differing only in the attached moiety (acyl carrier protein (ACP) in FAB vs Coenzyme A in r-BOX). Given this similarity, we sought to determine whether FAB enzymes can be used in the context of r-BOX as a means of expanding available r-BOX components with a ubiquitous set of well characterized enzymes. Using enzymes from the type II FAB pathway (FabG, FabZ, and FabI) in conjunction with a thiolase catalyzing a non-decarboxylative condensation, we demonstrate that FAB enzymes support a functional r-BOX. Pathway operation with FAB enzymes was improved through computationally directed protein design to develop FabZ variants with amino acid substitutions designed to disrupt hydrogen bonding at the FabZ-ACP interface and introduce steric and electrostatic repulsion between the FabZ and ACP. FabZ with R126W and R121E substitutions resulted in improved carboxylic acid and alcohol production from one- and multiple-turn r-BOX compared to the wild-type enzyme. Furthermore, the ability for FAB enzymes to operate on functionalized intermediates was exploited to produce branched chain carboxylic acids through an r-BOX with functionalized priming. These results not only provide an expanded set of enzymes within the modular r-BOX pathway, but can also potentially expand the scope of products targeted through this pathway by operating with CoA intermediates containing various functional groups.
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Affiliation(s)
- James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Stephanie C Contreras
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, CA 95616, USA; Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Alexander Chou
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St, Houston, TX 77005, USA
| | - Justin B Siegel
- Department of Chemistry, University of California Davis, One Shields Avenue, Davis, CA 95616, USA; Biochemistry & Molecular Medicine, University of California Davis, One Shields Avenue, Davis, CA 95616, USA; Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA.
| | - Ramon Gonzalez
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main St, Houston, TX 77005, USA; Department of Bioengineering, Rice University, 6100 Main St, Houston, TX 77005, USA.
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194
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Ma JC, Wu YQ, Cao D, Zhang WB, Wang HH. Only Acyl Carrier Protein 1 (AcpP1) Functions in Pseudomonas aeruginosa Fatty Acid Synthesis. Front Microbiol 2017; 8:2186. [PMID: 29176964 PMCID: PMC5686131 DOI: 10.3389/fmicb.2017.02186] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/25/2017] [Indexed: 11/21/2022] Open
Abstract
The genome of Pseudomonas aeruginosa contains three open reading frames, PA2966, PA1869, and PA3334, which encode putative acyl carrier proteins, AcpP1, AcpP2, and AcpP3, respectively. In this study, we found that, although these apo-ACPs were successfully phosphopantetheinylated by P. aeruginosa phosphopantetheinyl transferase (PcpS) and all holo-forms of these proteins could be acylated by Vibrio harveyi acyl-ACP synthetase (AasS), only AcpP1 could be used as a substrate for the synthesis of fatty acids, catalyzed by P. aeruginosa cell free extracts in vitro, and only acpP1 gene could restore growth in the Escherichia coliacpP mutant strain CY1877. And P. aeruginosaacpP1 could not be deleted, while disruption of acpP2 or acpP3 in the P. aeruginosa genome allowed mutant strains to grow as well as the wild type strain. These findings confirmed that only P. aeruginosa AcpP1 functions in fatty acid biosynthesis, and that acpP2 and acpP3 do not play roles in the fatty acid synthetic pathway. Moreover, disruption of acpP2 and acpP3 did not affect the ability of P. aeruginosa to produce N-acylhomoserine lactones (AHL), but replacement of P. aeruginosaacpP1 with E. coliacpP caused P. aeruginosa to reduce the production of AHL molecules, which indicated that neither P. aeruginosa AcpP2 nor AcpP3 can act as a substrate for synthesis of AHL molecules in vivo. Furthermore, replacement of acpP1 with E. coliacpP reduced the ability of P. aeruginosa to produce some exo-products and abolished swarming motility in P. aeruginosa.
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Affiliation(s)
- Jin-Cheng Ma
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yun-Qi Wu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Dan Cao
- Forensic Science Center of Qingyuan, Qingyuan Public Security Department, Qingyuan, China
| | - Wen-Bin Zhang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai-Hong Wang
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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195
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A conserved mammalian mitochondrial isoform of acetyl-CoA carboxylase ACC1 provides the malonyl-CoA essential for mitochondrial biogenesis in tandem with ACSF3. Biochem J 2017; 474:3783-3797. [PMID: 28986507 DOI: 10.1042/bcj20170416] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 01/06/2023]
Abstract
Mitochondrial fatty acid synthesis (mtFAS) is a highly conserved pathway essential for mitochondrial biogenesis. The mtFAS process is required for mitochondrial respiratory chain assembly and function, synthesis of the lipoic acid cofactor indispensable for the function of several mitochondrial enzyme complexes and essential for embryonic development in mice. Mutations in human mtFAS have been reported to lead to neurodegenerative disease. The source of malonyl-CoA for mtFAS in mammals has remained unclear. We report the identification of a conserved vertebrate mitochondrial isoform of ACC1 expressed from an ACACA transcript splicing variant. A specific knockdown (KD) of the corresponding transcript in mouse cells, or CRISPR/Cas9-mediated inactivation of the putative mitochondrial targeting sequence in human cells, leads to decreased lipoylation and mitochondrial fragmentation. Simultaneous KD of ACSF3, encoding a mitochondrial malonyl-CoA synthetase previously implicated in the mtFAS process, resulted in almost complete ablation of protein lipoylation, indicating that these enzymes have a redundant function in mtFAS. The discovery of a mitochondrial isoform of ACC1 required for lipoic acid synthesis has intriguing consequences for our understanding of mitochondrial disorders, metabolic regulation of mitochondrial biogenesis and cancer.
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196
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Marcella AM, Culbertson SJ, Shogren-Knaak MA, Barb AW. Structure, High Affinity, and Negative Cooperativity of the Escherichia coli Holo-(Acyl Carrier Protein):Holo-(Acyl Carrier Protein) Synthase Complex. J Mol Biol 2017; 429:3763-3775. [DOI: 10.1016/j.jmb.2017.10.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/08/2017] [Accepted: 10/11/2017] [Indexed: 01/01/2023]
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197
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Kumar V, Sharma A, Pratap S, Kumar P. Characterization of isoflavonoids as inhibitors of β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from Moraxella catarrhalis: Kinetics, spectroscopic, thermodynamics and in silico studies. Biochim Biophys Acta Gen Subj 2017; 1862:726-744. [PMID: 29092780 DOI: 10.1016/j.bbagen.2017.10.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/14/2017] [Accepted: 10/26/2017] [Indexed: 01/02/2023]
Abstract
BACKGROUD β-hydroxyacyl-acyl carrier protein dehydratase (FabZ) is an essential component of type II fatty acid biosynthesis (FAS II) pathway in bacteria. It performs dehydration of β-hydroxyacyl-ACP to trans-2-acyl-ACP in the elongation cycle of the FAS II pathway. FabZ is ubiquitously expressed and has uniform distribution, which makes FabZ an excellent target for developing novel drugs against pathogenic bacteria. METHODS We focused on the biochemical and biophysical characterization of FabZ from drug-resistant pathogen Moraxella catarrhalis (McFabZ). More importantly, we have identified and characterized new inhibitors against McFabZ using biochemical, biophysical and in silico based studies. RESULTS We have identified three isoflavones (daidzein, biochanin A and genistein) as novel inhibitors against McFabZ. Mode of inhibition of these compounds is competitive with IC50 values lie in the range of 6.85μΜ to 27.7μΜ. Conformational changes observed in secondary and tertiary structure marked by a decrease in the helical and the sheet content in McFabZ structure upon inhibitors binding. In addition, thermodynamic data suggest that biochanin A has a strong binding affinity for McFabZ as compare to daidzein and genistein. Molecular docking studies have revealed that these inhibitors are interacting with the active site of McFabZ and making contacts with catalytic and substrate binding tunnel residues. CONCLUSION AND GENERAL SIGNIFICANCE Three new inhibitors against McFabZ have been identified and characterized. These biochemical and biophysical findings lead to the identification of chemical scaffolds, which can lead to broad-spectrum antimicrobial drugs targeted against FabZ, and modification to existing FabZ inhibitors to improve affinity and potency.
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Affiliation(s)
- Vijay Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Anchal Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Shivendra Pratap
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, 247667, India.
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198
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Marcella AM, Barb AW. The R117A variant of the Escherichia coli transacylase FabD synthesizes novel acyl-(acyl carrier proteins). Appl Microbiol Biotechnol 2017; 101:8431-8441. [DOI: 10.1007/s00253-017-8586-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/29/2017] [Accepted: 10/09/2017] [Indexed: 11/24/2022]
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199
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Dixit SR, Joshi SD, Kulkarni VH, Jalalpure SS, Kumbar VM, Mudaraddi TY, Nadagouda MN, Aminabhavi TM. Pyrrolyl Pyrazoline Carbaldehydes as Enoyl-ACP Reductase Inhibitors: Design, Synthesis and Antitubercular Activity. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2017; 11:92-108. [PMID: 29151986 PMCID: PMC5676022 DOI: 10.2174/1874104501711010092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/20/2017] [Accepted: 08/23/2017] [Indexed: 12/02/2022]
Abstract
Introduction: In efforts to develop new antitubercular (anti-TB) compounds, herein we describe cytotoxic evaluation of 15 newly synthesized pyrrolyl pyrazoline carbaldehydes. Method & Materials: Surflex-Docking method was used to study binding modes of the compounds at the active site of the enzyme enoyl ACP reductase from Mycobacterium tuberculosis (M. tuberculosis), which plays an important role in FAS-II biosynthetic pathway of M. tuberculosis and also it is an important target for designing novel anti-TB agents. Results: Among the synthesized compounds, compounds 4g and 4i showed H-bonding interactions with MET98, TYR158 and co-factor NAD+, all of which fitted well within the binding pocket of InhA. Also, these compounds have shown the same type of interaction as that of 4TZK ligand. The compounds were further evaluated for preliminary anti-TB activities against M. tuberculosis H37Rv strain. Conclusion: Some compounds were also screened for their mammalian cell toxicity using human lung cancer cell-line (A549) that was found to be nontoxic.
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Affiliation(s)
- Sheshagiri R Dixit
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, Soniya Education Trust's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad-580 002, India
| | - Shrinivas D Joshi
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, Soniya Education Trust's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad-580 002, India
| | - Venkatarao H Kulkarni
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, Soniya Education Trust's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad-580 002, India
| | - Sunil S Jalalpure
- KLE University's College of Pharmacy, Nehru Nagar, Belagavi - 590010, Karnataka, India.,Basic Science Research Centre, KLE University, Belagavi - 590010, Karnataka, India
| | - Vijay M Kumbar
- Basic Science Research Centre, KLE University, Belagavi - 590010, Karnataka, India
| | | | - Mallikarjuna N Nadagouda
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, Soniya Education Trust's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad-580 002, India
| | - Tejraj M Aminabhavi
- Novel Drug Design and Discovery Laboratory, Department of Pharmaceutical Chemistry, Soniya Education Trust's College of Pharmacy, Sangolli Rayanna Nagar, Dharwad-580 002, India
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200
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Freund GS, O’Brien TE, Vinson L, Carlin DA, Yao A, Mak WS, Tagkopoulos I, Facciotti MT, Tantillo DJ, Siegel JB. Elucidating Substrate Promiscuity within the FabI Enzyme Family. ACS Chem Biol 2017; 12:2465-2473. [PMID: 28820936 DOI: 10.1021/acschembio.7b00400] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The rapidly growing appreciation of enzymes' catalytic and substrate promiscuity may lead to their expanded use in the fields of chemical synthesis and industrial biotechnology. Here, we explore the substrate promiscuity of enoyl-acyl carrier protein reductases (commonly known as FabI) and how that promiscuity is a function of inherent reactivity and the geometric demands of the enzyme's active site. We demonstrate that these enzymes catalyze the reduction of a wide range of substrates, particularly α,β-unsaturated aldehydes. In addition, we demonstrate that a combination of quantum mechanical hydride affinity calculations and molecular docking can be used to rapidly categorize compounds that FabI can use as substrates. The results here provide new insight into the determinants of catalysis for FabI and set the stage for the development of a new assay for drug discovery, organic synthesis, and novel biocatalysts.
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Affiliation(s)
- Gabriel S. Freund
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Mathematics, University of California Davis, Davis, California United States
| | - Terrence E. O’Brien
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Chemistry, University of California Davis, Davis, California United States
| | - Logan Vinson
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Dylan Alexander Carlin
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Biophysics
Graduate Group, University of California Davis, Davis, California United States
| | - Andrew Yao
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
| | - Wai Shun Mak
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Chemistry, University of California Davis, Davis, California United States
| | - Ilias Tagkopoulos
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Computer Science, University of California Davis, Davis, California United States
| | - Marc T. Facciotti
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Biomedical Engineering, University of California, Davis, California United States
| | - Dean J. Tantillo
- Department
of Chemistry, University of California Davis, Davis, California United States
| | - Justin B. Siegel
- Genome
Center, University of California Davis, One Shields Avenue, Davis, California 95616, United States
- Department
of Chemistry, University of California Davis, Davis, California United States
- Department of Biochemistry & Molecular Medicine, University of CaliforniaDavis, Davis, California United States
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