1
|
Mallik S, Tawfik DS, Levy ED. How gene duplication diversifies the landscape of protein oligomeric state and function. Curr Opin Genet Dev 2022; 76:101966. [PMID: 36007298 PMCID: PMC9548406 DOI: 10.1016/j.gde.2022.101966] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/01/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022]
Abstract
Oligomeric proteins are central to cellular life and the duplication and divergence of their genes is a key driver of evolutionary innovations. The duplication of a gene coding for an oligomeric protein has numerous possible outcomes, which motivates questions on the relationship between structural and functional divergence. How do protein oligomeric states diversify after gene duplication? In the simple case of duplication of a homo-oligomeric protein gene, what properties can influence the fate of descendant paralogs toward forming independent homomers or maintaining their interaction as a complex? Furthermore, how are functional innovations associated with the diversification of oligomeric states? Here, we review recent literature and present specific examples in an attempt to illustrate and answer these questions.
Collapse
Affiliation(s)
- Saurav Mallik
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Dan S Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, The Weizmann Institute of Science, Rehovot 7610001, Israel.
| |
Collapse
|
2
|
Li Y, Wang J, Wang F, Wang L, Wang L, Xu Z, Yuan H, Yang X, Li P, Su J, Wang R. Production of 10-Hydroxy-2-decenoic Acid from Decanoic Acid via Whole-Cell Catalysis in Engineered Escherichia coli. CHEMSUSCHEM 2022; 15:e202102152. [PMID: 34796684 DOI: 10.1002/cssc.202102152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Indexed: 06/13/2023]
Abstract
10-Hydroxy-2-decenoic acid (10-HDA) is a terminal hydroxylated medium-chain α,β-unsaturated carboxylic acid that performs various unique physiological activities and has a wide market value. Therefore, development of an environmentally friendly, safe, and high-efficiency route to synthesize 10-HDA is required. Here, the β-oxidation pathway of Escherichia coli was modified and a P450 terminal hydroxylase (CYP153A33-CPRBM3 ) was rationally designed to synthesize 10-HDA using decanoic acid as a substrate via two-step whole-cell catalysis. Different homologues of FadDs, FadEs, and YdiIs were analyzed in the first step of the conversion of decanoic acid to trans- -2- decenoic acid. In the second step, CYP153A33 (M228L)-CPRBM3 efficiently catalyzed the conversion of trans- -2- decenoic acid to 10-HDA. Finally, 217 mg L-1 10-HDA was obtained with 500 mg L-1 decanoic acid. This study provides a strategy for biosynthesis of 10-HDA and other α, β-unsaturated carboxylic acid derivatives from specific fatty acids.
Collapse
Affiliation(s)
- Yan Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Junqing Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Fen Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Li Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Leilei Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Ziqi Xu
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Haibo Yuan
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Xiaohui Yang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Piwu Li
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Jing Su
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| | - Ruiming Wang
- State Key Laboratory of Biobased Material and Green Papermaking (LBMP), Jinan, Shandong, 250353, P. R. China
- Key Laboratory of Shandong Microbial Engineering, QILU University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, P. R. China
| |
Collapse
|
3
|
Latimer LN, Russ ZN, Lucas J, Dueber JE. Exploration of Acetylation as a Base-Labile Protecting Group in Escherichia coli for an Indigo Precursor. ACS Synth Biol 2020; 9:2775-2783. [PMID: 32886882 DOI: 10.1021/acssynbio.0c00297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Biochemical protecting groups are observed in natural metabolic pathways to control reactivity and properties of chemical intermediates; similarly, they hold promise as a tool for metabolic engineers to achieve the same goals. Protecting groups come with costs: lower yields from carbon, metabolic load to the production host, deprotection catalyst costs and kinetics limitations, and wastewater treatment of the group. Compared to glycosyl biochemical protection, such as glucosyl groups, acetylation can mitigate each of these costs. As an example application where these benefits could be valuable, we explored acetylation protection of indoxyl, the reactive precursor to the clothing dye, indigo. First, we demonstrated denim dyeing with chemically sourced indoxyl acetate by deprotection with base, showing results comparable to industry-standard denim dyeing. Second, we modified an Escherichia coli production host for improved indoxyl acetate stability by the knockout of 14 endogenous hydrolases. Cumulatively, these knockouts yielded a 67% reduction in the indoxyl acetate hydrolysis rate from 0.22 mmol/g DCW/h to 0.07 mmol/g DCW/h. To biosynthesize indoxyl acetate, we identified three promiscuous acetyltransferases which acetylate indoxyl in vivo. Indoxyl acetate titer, while low, was improved 50%, from 43 μM to 67 μM, in the hydrolase knockout strain compared to wild-type E. coli. Unfortunately, low millimolar concentrations of indoxyl acetate proved to be toxic to the E. coli production host; however, the principle of acetylation as a readily cleavable and low impact biochemical protecting group and the engineered hydrolase knockout production host should prove useful for other metabolic products.
Collapse
Affiliation(s)
- Luke N. Latimer
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
| | - Zachary N. Russ
- The UC Berkeley & UCSF Graduate Program in Bioengineering, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - James Lucas
- The UC Berkeley & UCSF Graduate Program in Bioengineering, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| |
Collapse
|
4
|
Swarbrick CMD, Nanson JD, Patterson EI, Forwood JK. Structure, function, and regulation of thioesterases. Prog Lipid Res 2020; 79:101036. [PMID: 32416211 DOI: 10.1016/j.plipres.2020.101036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/15/2023]
Abstract
Thioesterases are present in all living cells and perform a wide range of important biological functions by catalysing the cleavage of thioester bonds present in a diverse array of cellular substrates. Thioesterases are organised into 25 families based on their sequence conservation, tertiary and quaternary structure, active site configuration, and substrate specificity. Recent structural and functional characterisation of thioesterases has led to significant changes in our understanding of the regulatory mechanisms that govern enzyme activity and their respective cellular roles. The resulting dogma changes in thioesterase regulation include mechanistic insights into ATP and GDP-mediated regulation by oligomerisation, the role of new key regulatory regions, and new insights into a conserved quaternary structure within TE4 family members. Here we provide a current and comparative snapshot of our understanding of thioesterase structure, function, and regulation across the different thioesterase families.
Collapse
Affiliation(s)
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward I Patterson
- Centre for Neglected Tropical Diseases, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales, Australia.
| |
Collapse
|
5
|
Hickman TWP, Baud D, Benhamou L, Hailes HC, Ward JM. Characterisation of four hotdog-fold thioesterases for their implementation in a novel organic acid production system. Appl Microbiol Biotechnol 2020; 104:4397-4406. [PMID: 32193574 PMCID: PMC7190597 DOI: 10.1007/s00253-020-10519-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 02/23/2020] [Accepted: 03/03/2020] [Indexed: 11/24/2022]
Abstract
With increasing interest in the diverse properties of organic acids and their application in synthetic pathways, developing biological tools for producing known and novel organic acids would be very valuable. In such a system, organic acids may be activated as coenzyme A (CoA) esters, then modified by CoA-dependent enzymes, followed by CoA liberation by a broad-acting thioesterase. This study has focused on the identification of suitable thioesterases (TE) for utilisation in such a pathway. Four recombinant hotdog-fold TEs were screened with a range of CoA esters in order to identify a highly active, broad spectrum TE. The TesB-like TE, RpaL, from Rhodopseudomonas palustris was found to be able to use aromatic, alicyclic and both long and short aliphatic CoA esters. Size exclusion chromatography, revealed RpaL to be a monomer of fused hotdog domains, in contrast to the complex quaternary structures found with similar TesB-like TEs. Nonetheless, sequence alignments showed a conserved catalytic triad despite the variation in quaternary arrangement. Kinetic analysis revealed a preference towards short-branched chain CoA esters with the highest specificity towards DL-β-hydroxybutyryl CoA (1.6 × 104 M−1 s−1), which was found to decrease as the acyl chain became longer and more functionalised. Substrate inhibition was observed with the fatty acyl n-heptadecanoyl CoA at concentrations exceeding 0.3 mM; however, this was attributed to its micellar aggregation properties. As a result of the broad activity observed with RpaL, it is a strong candidate for implementation in CoA ester pathways to generate modified or novel organic acids.
Collapse
Affiliation(s)
- T W P Hickman
- Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - D Baud
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - L Benhamou
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - H C Hailes
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK
| | - J M Ward
- Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
6
|
Abstract
Prenylquinones are isoprenoid compounds with a characteristic quinone structure and isoprenyl tail that are ubiquitous in almost all living organisms. There are four major prenylquinone classes: ubiquinone (UQ), menaquinone (MK), plastoquinone (PQ), and rhodoquinone (RQ). The quinone structure and isoprenyl tail length differ among organisms. UQ, PQ, and RQ contain benzoquinone, while MK contains naphthoquinone. UQ, MK, and RQ are involved in oxidative phosphorylation, while PQ functions in photosynthetic electron transfer. Some organisms possess two types of prenylquinones; Escherichia coli has UQ8 and MK8, and Caenorhabditis elegans has UQ9 and RQ9. Crystal structures of most of the enzymes involved in MK synthesis have been solved. Studies on the biosynthesis and functions of quinones have advanced recently, including for phylloquinone (PhQ), which has a phytyl moiety instead of an isoprenyl tail. Herein, the synthesis and applications of prenylquinones are reviewed.
Collapse
Affiliation(s)
- Makoto Kawamukai
- a Department of Life Science and Biotechnology, Faculty of Life and Environmental Science , Shimane University , Matsue , Japan
| |
Collapse
|
7
|
Latham JA, Ji T, Matthews K, Mariano PS, Allen KN, Dunaway-Mariano D. Catalytic Mechanism of the Hotdog-Fold Thioesterase PA1618 Revealed by X-ray Structure Determination of a Substrate-Bound Oxygen Ester Analogue Complex. Chembiochem 2017; 18:1935-1943. [DOI: 10.1002/cbic.201700322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Indexed: 11/11/2022]
Affiliation(s)
- John A. Latham
- Department of Chemistry and Biochemistry; University of Denver; Denver CO 80208-0183 USA
| | - Tianyang Ji
- Department of Chemistry; Boston University; 590 Commonwealth Avenue Room 299 Boston MA 02215 USA
| | - Kaila Matthews
- Department of Chemistry and Chemical Biology; University of New Mexico; Albuquerque NM 87131 USA
| | - Patrick S. Mariano
- Department of Chemistry and Chemical Biology; University of New Mexico; Albuquerque NM 87131 USA
| | - Karen N. Allen
- Department of Chemistry; Boston University; 590 Commonwealth Avenue Room 299 Boston MA 02215 USA
| | - Debra Dunaway-Mariano
- Department of Chemistry and Chemical Biology; University of New Mexico; Albuquerque NM 87131 USA
| |
Collapse
|
8
|
Wang J, Mahajani M, Jackson SL, Yang Y, Chen M, Ferreira EM, Lin Y, Yan Y. Engineering a bacterial platform for total biosynthesis of caffeic acid derived phenethyl esters and amides. Metab Eng 2017; 44:89-99. [PMID: 28943460 DOI: 10.1016/j.ymben.2017.09.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 08/29/2017] [Accepted: 09/18/2017] [Indexed: 12/19/2022]
Abstract
Caffeic acid has been widely recognized as a versatile pharmacophore for synthesis of new chemical entities, among which caffeic acid derived phenethyl esters and amides are the most extensively-investigated bioactive compounds with potential therapeutical applications. However, the natural biosynthetic routes for caffeic acid derived phenethyl esters or amides remain enigmatic, limiting their bio-based production. Herein, product-directed design of biosynthetic schemes allowed the development of thermodynamically favorable pathways for these compounds via acyltransferase (ATF) mediated trans-esterification. Production based screening identified a microbial O-ATF from Saccharomyces cerevisiae and a plant N-ATF from Capsicum annuum capable of forming caffeic acid derived esters and amides, respectively. Subsequent combinatorial incorporation of caffeic acid with various aromatic alcohol or amine biosynthetic pathways permitted the de novo bacterial production of a panel of caffeic acid derived phenethyl esters or amides in Escherichia coli for the first time. Particularly, host strain engineering via systematic knocking out endogenous caffeoyl-CoA degrading thioesterase and pathway optimization via titrating co-substrates enabled production enhancement of five caffeic acid derived phenethyl esters and amides, with titers ranging from 9.2 to 369.1mg/L. This platform expanded the capabilities of bacterial production of high-value natural aromatic esters and amides from renewable carbon source via tailoring non-natural biosynthetic pathways.
Collapse
Affiliation(s)
- Jian Wang
- College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | | | - Sheneika L Jackson
- Department of Chemistry, The University of Georgia, Athens, GA 30602, USA
| | - Yaping Yang
- College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Mengyin Chen
- BiotecEra Inc., 220 Riverbend Rd., Athens, GA 30602, USA
| | - Eric M Ferreira
- Department of Chemistry, The University of Georgia, Athens, GA 30602, USA
| | - Yuheng Lin
- BiotecEra Inc., 220 Riverbend Rd., Athens, GA 30602, USA.
| | - Yajun Yan
- College of Engineering, The University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
9
|
Shen X, Mahajani M, Wang J, Yang Y, Yuan Q, Yan Y, Lin Y. Elevating 4-hydroxycoumarin production through alleviating thioesterase-mediated salicoyl-CoA degradation. Metab Eng 2017; 42:59-65. [PMID: 28587908 DOI: 10.1016/j.ymben.2017.05.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/15/2017] [Accepted: 05/31/2017] [Indexed: 12/23/2022]
Abstract
Acyl-CoAs are essential intermediates in the biosynthetic pathways of a number of industrially and pharmaceutically important molecules. When these pathways are reconstituted in a heterologous microbial host for metabolic engineering purposes, the acyl-CoAs may be subject to undesirable hydrolysis by the host's native thioesterases, resulting in a waste of cellular energy and decreased intermediate availability, thus impairing bioconversion efficiency. 4-hydroxycoumarin (4HC) is a direct synthetic precursor to the commonly used oral anticoagulants (e.g. warfarin) and rodenticides. In our previous study, we have established an artificial pathway for 4HC biosynthesis in Escherichia coli, which involves the thioester intermediate salicoyl-CoA. Here, we utilized the 4HC pathway as a demonstration to examine the negative effect of salicoyl-CoA degradaton, identify and inactivate the responsible thioesterase, and eventually improve the 4HC production. We screened a total of 16 E. coli thioesterases and tested their hydrolytic activity towards salicoyl-CoA in vitro. Among all the tested candidate enzymes, YdiI was found to be the dominant contributor to the salicoyl-CoA degradation in E. coli. Remarkably, the ydiI knockout strain carrying the 4HC pathway exhibited an up to 300% increase in 4HC production. An optimized 4HC pathway construct introduced in the ydiI knockout strain led to the accumulation of 935mg/L of 4HC in shake flasks, which is about 1.5 folds higher than the wild-type strain. This study demonstrates a systematic strategy to alleviate the undesirable hydrolysis of thioester intermediates, allowing production enhancement for other biosynthetic pathways with similar issues.
Collapse
Affiliation(s)
- Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | | | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yaping Yang
- College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yajun Yan
- College of Engineering, The University of Georgia, Athens, GA 30602, USA.
| | | |
Collapse
|
10
|
Sánchez-Reyez A, Batista-García RA, Valdés-García G, Ortiz E, Perezgasga L, Zárate-Romero A, Pastor N, Folch-Mallol JL. A family 13 thioesterase isolated from an activated sludge metagenome: Insights into aromatic compounds metabolism. Proteins 2017; 85:1222-1237. [DOI: 10.1002/prot.25282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/21/2017] [Accepted: 02/27/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Ayixon Sánchez-Reyez
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
- Centro de Investigación en Biotecnología UAEM; CP 62209 Cuernavaca Morelos Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | - Gilberto Valdés-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | - Ernesto Ortiz
- Instituto de Biotecnología. Universidad Nacional Autónoma de México; CP 62210 Cuernavaca Morelos Mexico
| | - Lucía Perezgasga
- Instituto de Biotecnología. Universidad Nacional Autónoma de México; CP 62210 Cuernavaca Morelos Mexico
| | - Andrés Zárate-Romero
- Centro de Investigación en Biotecnología UAEM; CP 62209 Cuernavaca Morelos Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos (UAEM), Colonia Chamilpa; CP 62209 Cuernavaca, Morelos Mexico
| | | |
Collapse
|
11
|
Cattò C, Grazioso G, Dell'Orto S, Gelain A, Villa S, Marzano V, Vitali A, Villa F, Cappitelli F, Forlani F. The response of Escherichia coli biofilm to salicylic acid. BIOFOULING 2017; 33:235-251. [PMID: 28270055 DOI: 10.1080/08927014.2017.1286649] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
In this research, salicylic acid is proposed as an alternative biocide-free agent suitable for a preventive or integrative anti-biofilm approach. Salicylic acid has been proved to: (1) reduce bacterial adhesion up to 68.1 ± 5.6%; (2) affect biofilm structural development, reducing viable biomass by 97.0 ± 0.7% and extracellular proteins and polysaccharides by 83.9 ± 2.5% and 49.5 ± 5.5% respectively; and (3) promote biofilm detachment 3.4 ± 0.6-fold. Moreover, salicylic acid treated biofilm showed an increased amount of intracellular (2.3 ± 0.2-fold) and extracellular (2.1 ± 0.3-fold) reactive oxygen species, and resulted in increased production of the quorum sensing signal indole (7.6 ± 1.4-fold). For the first time, experiments revealed that salicylic acid interacts with proteins that play a role in quorum sensing, reactive oxygen species accumulation, motility, extracellular polymeric matrix components, transport and metabolism.
Collapse
Affiliation(s)
- Cristina Cattò
- a Department of Food Environmental and Nutritional Sciences , Università degli Studi di Milano , Milan , Italy
| | - Giovanni Grazioso
- b Department of Pharmaceutical Sciences , Università degli Studi di Milano , Milan , Italy
| | - Silvia Dell'Orto
- b Department of Pharmaceutical Sciences , Università degli Studi di Milano , Milan , Italy
| | - Arianna Gelain
- b Department of Pharmaceutical Sciences , Università degli Studi di Milano , Milan , Italy
| | - Stefania Villa
- b Department of Pharmaceutical Sciences , Università degli Studi di Milano , Milan , Italy
| | - Valeria Marzano
- c Institute of Biochemistry and Clinical Biochemistry , Catholic University , Rome , Italy
| | - Alberto Vitali
- d Institute of Chemistry of Molecular Recognition-UOS Roma , CNR , Rome , Italy
| | - Federica Villa
- a Department of Food Environmental and Nutritional Sciences , Università degli Studi di Milano , Milan , Italy
| | - Francesca Cappitelli
- a Department of Food Environmental and Nutritional Sciences , Università degli Studi di Milano , Milan , Italy
| | - Fabio Forlani
- a Department of Food Environmental and Nutritional Sciences , Università degli Studi di Milano , Milan , Italy
| |
Collapse
|
12
|
Kim S, Cheong S, Gonzalez R. Engineering Escherichia coli for the synthesis of short- and medium-chain α,β-unsaturated carboxylic acids. Metab Eng 2016; 36:90-98. [DOI: 10.1016/j.ymben.2016.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 02/26/2016] [Accepted: 03/14/2016] [Indexed: 01/27/2023]
|
13
|
Kim S, Clomburg JM, Gonzalez R. Synthesis of medium-chain length (C6-C10) fuels and chemicals via β-oxidation reversal in Escherichia coli. J Ind Microbiol Biotechnol 2015; 42:465-75. [PMID: 25645093 DOI: 10.1007/s10295-015-1589-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/14/2015] [Indexed: 11/30/2022]
Abstract
The recently engineered reversal of the β-oxidation cycle has been proposed as a potential platform for the efficient synthesis of longer chain (C ≥ 4) fuels and chemicals. Here, we demonstrate the utility of this platform for the synthesis of medium-chain length (C6-C10) products through the manipulation of key components of the pathway. Deletion of endogenous thioesterases provided a clean background in which the expression of various thiolase and termination components, along with required core enzymes, resulted in the ability to alter the chain length distribution and functionality of target products. This approach enabled the synthesis of medium-chain length carboxylic acids and primary alcohols from glycerol, a low-value feedstock. The use of BktB as the thiolase component with thioesterase TesA' as the termination enzyme enabled the synthesis of about 1.3 g/L C6-C10 saturated carboxylic acids. Tailoring of product formation to primary alcohol synthesis was achieved with the use of various acyl-CoA reductases. The combination of AtoB and FadA as the thiolase components with the alcohol-forming acyl-CoA reductase Maqu2507 from M. aquaeolei resulted in the synthesis of nearly 0.3 g/L C6-C10 alcohols. These results further demonstrate the versatile nature of a β-oxidation reversal, and highlight several key aspects and control points that can be further manipulated to fine-tune the synthesis of various fuels and chemicals.
Collapse
Affiliation(s)
- Seohyoung Kim
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 Main Street, MS-362, Houston, TX, 77005, USA
| | | | | |
Collapse
|
14
|
Wu R, Latham JA, Chen D, Farelli J, Zhao H, Matthews K, Allen KN, Dunaway-Mariano D. Structure and catalysis in the Escherichia coli hotdog-fold thioesterase paralogs YdiI and YbdB. Biochemistry 2014; 53:4788-805. [PMID: 25010423 PMCID: PMC4116151 DOI: 10.1021/bi500334v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Herein,
the structural determinants for substrate recognition and
catalysis in two hotdog-fold thioesterase paralogs, YbdB and YdiI
from Escherichia coli, are identified and analyzed
to provide insight into the evolution of biological function in the
hotdog-fold enzyme superfamily. The X-ray crystal structures of YbdB
and YdiI, in complex with inert substrate analogs, determined in this
study revealed the locations of the respective thioester substrate
binding sites and the identity of the residues positioned for substrate
binding and catalysis. The importance of each of these residues was
assessed through amino acid replacements followed by steady-state
kinetic analyses of the corresponding site-directed mutants. Transient
kinetic and solvent 18O-labeling studies were then carried
out to provide insight into the role of Glu63 posited to function
as the nucleophile or general base in catalysis. Finally, the structure–function–mechanism
profiles of the two paralogs, along with that of a more distant homolog,
were compared to identify conserved elements of substrate recognition
and catalysis, which define the core traits of the hotdog-fold thioesterase
family, as well as structural features that are unique to each thioesterase.
Founded on the insight gained from this analysis, we conclude that
the promiscuity revealed by in vitro substrate activity
determinations, and posited to facilitate the evolution of new biological
function, is the product of intrinsic plasticity in substrate binding
as well as in the catalytic mechanism.
Collapse
Affiliation(s)
- Rui Wu
- Department of Chemistry, Boston University , Boston, Massachusetts 02215, United States
| | | | | | | | | | | | | | | |
Collapse
|