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Poust S, Yoon I, Adams PD, Katz L, Petzold CJ, Keasling JD. Understanding the role of histidine in the GHSxG acyltransferase active site motif: evidence for histidine stabilization of the malonyl-enzyme intermediate. PLoS One 2014; 9:e109421. [PMID: 25286165 PMCID: PMC4186864 DOI: 10.1371/journal.pone.0109421] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 08/30/2014] [Indexed: 11/18/2022] Open
Abstract
Acyltransferases determine which extender units are incorporated into polyketide and fatty acid products. The ping-pong acyltransferase mechanism utilizes a serine in a conserved GHSxG motif. However, the role of the conserved histidine in this motif is poorly understood. We observed that a histidine to alanine mutation (H640A) in the GHSxG motif of the malonyl-CoA specific yersiniabactin acyltransferase results in an approximately seven-fold higher hydrolysis rate over the wildtype enzyme, while retaining transacylation activity. We propose two possibilities for the reduction in hydrolysis rate: either H640 structurally stabilizes the protein by hydrogen bonding with a conserved asparagine in the ferredoxin-like subdomain of the protein, or a water-mediated hydrogen bond between H640 and the malonyl moiety stabilizes the malonyl-O-AT ester intermediate.
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202
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Haushalter RW, Kim W, Chavkin TA, The L, Garber ME, Nhan M, Adams PD, Petzold CJ, Katz L, Keasling JD. Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties. Metab Eng 2014; 26:111-118. [PMID: 25250846 DOI: 10.1016/j.ymben.2014.09.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 08/09/2014] [Accepted: 09/08/2014] [Indexed: 01/28/2023]
Abstract
Microbial fermentation is emerging as an increasingly important resource for the production of fatty acids to serve as precursors for renewable diesel as well as detergents, lubricants and other industrial chemicals, as an alternative to traditional sources of reduced carbon such as petroleum. A major disadvantage of fuels derived from biological sources is their undesirable physical properties such as high cloud and pour points, and high viscosity. Here we report the development of an Escherichia coli strain that efficiently produces anteiso-branched fatty acids, which can be converted into downstream products with lower cloud and pour points than the mixtures of compounds produced via the native metabolism of the cell. This work addresses a serious limitation that must be overcome in order to produce renewable biodiesel and oleochemicals that perform as well as their petroleum-based counterparts.
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203
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Hagen A, Poust S, de Rond T, Yuzawa S, Katz L, Adams PD, Petzold CJ, Keasling JD. In Vitro Analysis of Carboxyacyl Substrate Tolerance in the Loading and First Extension Modules of Borrelidin Polyketide Synthase. Biochemistry 2014; 53:5975-7. [DOI: 10.1021/bi500951c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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204
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Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, Martín HG. A peptide-based method for 13C Metabolic Flux Analysis in microbial communities. PLoS Comput Biol 2014; 10:e1003827. [PMID: 25188426 PMCID: PMC4154649 DOI: 10.1371/journal.pcbi.1003827] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 07/23/2014] [Indexed: 01/08/2023] Open
Abstract
The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, 13C Metabolic Flux Analysis (13C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during 13C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based 13C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species. Microbial communities underlie a variety of important biochemical processes ranging from underground cave formation to gold mining or the onset of obesity. Metabolic fluxes describe how carbon and energy flow through the microbial community and therefore provide insights that are rarely captured by other techniques, such as metatranscriptomics or metaproteomics. The most authoritative method to measure fluxes for pure cultures consists of feeding the cells a labeled carbon source and deriving the fluxes from the ensuing metabolite labeling pattern (typically amino acids). Since we cannot easily separate cells of metabolite for each species in a community, this approach is not generally applicable to microbial communities. Here we present a method to derive fluxes from the labeling of peptides, instead of amino acids. This approach has the advantage that peptides can be assigned to each species in a community in a high-throughput fashion through modern proteomic methods. We show that, by using this method, it is theoretically possible to recover the same amount of information as through the standard approach, if enough peptides are used. We computationally tested this method with a well-characterized simple microbial community consisting of two species.
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205
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Weaver LJ, Sousa MML, Wang G, Baidoo E, Petzold CJ, Keasling JD. A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli. Biotechnol Bioeng 2014; 112:111-9. [PMID: 24981116 DOI: 10.1002/bit.25323] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/17/2014] [Accepted: 06/25/2014] [Indexed: 01/12/2023]
Abstract
To aid in debugging efforts to increase yield, titer, and productivity of engineered metabolic pathways, computational models are increasingly needed to predict how changes in experimentally manipulable variables such as enzyme expression map to changes in pathway flux. Here, an ordinary differential equation model is developed for a heterologous mevalonate pathway in E. coli using kinetic parameters culled from literature and enzyme concentrations derived from Selective Reaction Monitoring Mass Spectrometry (SRM-MS). To identify parameters most important to further experimental investigation, a global sensitivity analysis was performed, which pointed to amorphadiene synthase activity as the main limiting factor for amorphadiene production. Furthermore, the model predicted that in this local enzyme expression regime, the overall pathway flux is insensitive to farnesyl pyrophosphate (FPP)-mediated inhibition of mevalonate kinase, not supporting a hypothesis that had previously been posited to be limiting amorphadiene production. To test these predictions experimentally, two strains were constructed: (1) a strain containing a homologous mevalonate kinase with weaker feedback inhibition, and (2) a strain with greater amorphadiene synthase expression. The experimental results validate the qualitative model hypotheses and accurately match the predicted productivities for the two strains, particularly when an in vivo-derived kcat for amorphadiene synthase was substituted for the literature value. These results demonstrate the utility of using kinetic representations of engineered metabolic pathways parameterized with experimentally derived protein concentrations and enzyme kinetic constants to predict productivities and test hypotheses about engineering strategies.
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206
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Linshiz G, Stawski N, Goyal G, Bi C, Poust S, Sharma M, Mutalik V, Keasling JD, Hillson NJ. PR-PR: cross-platform laboratory automation system. ACS Synth Biol 2014; 3:515-24. [PMID: 25126893 DOI: 10.1021/sb4001728] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To enable protocol standardization, sharing, and efficient implementation across laboratory automation platforms, we have further developed the PR-PR open-source high-level biology-friendly robot programming language as a cross-platform laboratory automation system. Beyond liquid-handling robotics, PR-PR now supports microfluidic and microscopy platforms, as well as protocol translation into human languages, such as English. While the same set of basic PR-PR commands and features are available for each supported platform, the underlying optimization and translation modules vary from platform to platform. Here, we describe these further developments to PR-PR, and demonstrate the experimental implementation and validation of PR-PR protocols for combinatorial modified Golden Gate DNA assembly across liquid-handling robotic, microfluidic, and manual platforms. To further test PR-PR cross-platform performance, we then implement and assess PR-PR protocols for Kunkel DNA mutagenesis and hierarchical Gibson DNA assembly for microfluidic and manual platforms.
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207
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Kyrpides NC, Hugenholtz P, Eisen JA, Woyke T, Göker M, Parker CT, Amann R, Beck BJ, Chain PSG, Chun J, Colwell RR, Danchin A, Dawyndt P, Dedeurwaerdere T, DeLong EF, Detter JC, De Vos P, Donohue TJ, Dong XZ, Ehrlich DS, Fraser C, Gibbs R, Gilbert J, Gilna P, Glöckner FO, Jansson JK, Keasling JD, Knight R, Labeda D, Lapidus A, Lee JS, Li WJ, MA J, Markowitz V, Moore ERB, Morrison M, Meyer F, Nelson KE, Ohkuma M, Ouzounis CA, Pace N, Parkhill J, Qin N, Rossello-Mora R, Sikorski J, Smith D, Sogin M, Stevens R, Stingl U, Suzuki KI, Taylor D, Tiedje JM, Tindall B, Wagner M, Weinstock G, Weissenbach J, White O, Wang J, Zhang L, Zhou YG, Field D, Whitman WB, Garrity GM, Klenk HP. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains. PLoS Biol 2014; 12:e1001920. [PMID: 25093819 PMCID: PMC4122341 DOI: 10.1371/journal.pbio.1001920] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
This manuscript calls for an international effort to generate a comprehensive catalog from genome sequences of all the archaeal and bacterial type strains. Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.
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208
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Rajeev L, Luning EG, Altenburg S, Zane GM, Baidoo EEK, Catena M, Keasling JD, Wall JD, Fields MW, Mukhopadhyay A. Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. Front Microbiol 2014; 5:382. [PMID: 25120537 PMCID: PMC4114195 DOI: 10.3389/fmicb.2014.00382] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/09/2014] [Indexed: 01/02/2023] Open
Abstract
We surveyed the eight putative cyclic-di-GMP-modulating response regulators (RRs) in Desulfovibrio vulgaris Hildenborough that are predicted to function via two-component signaling. Using purified proteins, we examined cyclic-di-GMP (c-di-GMP) production or turnover in vitro of all eight proteins. The two RRs containing only GGDEF domains (DVU2067, DVU0636) demonstrated c-di-GMP production activity in vitro. Of the remaining proteins, three RRs with HD-GYP domains (DVU0722, DVUA0086, and DVU2933) were confirmed to be Mn2+-dependent phosphodiesterases (PDEs) in vitro and converted c-di-GMP to its linear form, pGpG. DVU0408, containing both c-di-GMP production (GGDEF) and degradation domains (EAL), showed c-di-GMP turnover activity in vitro also with production of pGpG. No c-di-GMP related activity could be assigned to the RR DVU0330, containing a metal-dependent phosphohydrolase HD-OD domain, or to the HD-GYP domain RR, DVU1181. Studies included examining the impact of overexpressed cyclic-di-GMP-modulating RRs in the heterologous host E. coli and led to the identification of one RR, DVU0636, with increased cellulose production. Evaluation of a transposon mutant in DVU0636 indicated that the strain was impaired in biofilm formation and demonstrated an altered carbohydrate:protein ratio relative to the D. vulgaris wild type biofilms. However, grown in liquid lactate/sulfate medium, the DVU0636 transposon mutant showed no growth impairment relative to the wild-type strain. Among the eight candidates, only the transposon disruption mutant in the DVU2067 RR presented a growth defect in liquid culture. Our results indicate that, of the two diguanylate cyclases (DGCs) that function as part of two-component signaling, DVU0636 plays an important role in biofilm formation while the function of DVU2067 has pertinence in planktonic growth.
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209
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Rodriguez S, Kirby J, Denby CM, Keasling JD. Production and quantification of sesquiterpenes in Saccharomyces cerevisiae, including extraction, detection and quantification of terpene products and key related metabolites. Nat Protoc 2014; 9:1980-96. [DOI: 10.1038/nprot.2014.132] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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210
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Sarria S, Wong B, Martín HG, Keasling JD, Peralta-Yahya P. Microbial synthesis of pinene. ACS Synth Biol 2014; 3:466-75. [PMID: 24679043 DOI: 10.1021/sb4001382] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The volumetric heating values of today's biofuels are too low to power energy-intensive aircraft, rockets, and missiles. Recently, pinene dimers were shown to have a volumetric heating value similar to that of the tactical fuel JP-10. To provide a sustainable source of pinene, we engineered Escherichia coli for pinene production. We combinatorially expressed three pinene synthases (PS) and three geranyl diphosphate synthases (GPPS), with the best combination achieving ~28 mg/L of pinene. We speculated that pinene toxicity was limiting production; however, toxicity should not be limiting at current titers. Because GPPS is inhibited by geranyl diphosphate (GPP) and to increase flux through the pathway, we combinatorially constructed GPPS-PS protein fusions. The Abies grandis GPPS-PS fusion produced 32 mg/L of pinene, a 6-fold improvement over the highest titer previously reported in engineered E. coli. Finally, we investigated the pinene isomer ratio of our pinene-producing microbe and discovered that the isomer profile is determined not only by the identity of the PS used but also by the identity of the GPPS with which the PS is paired. We demonstrated that the GPP concentration available to PS for cyclization alters the pinene isomer ratio.
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211
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Frederix M, Hütter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch HW, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A. Development of a native Escherichia coli induction system for ionic liquid tolerance. PLoS One 2014; 9:e101115. [PMID: 24983352 PMCID: PMC4077768 DOI: 10.1371/journal.pone.0101115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 06/03/2014] [Indexed: 01/15/2023] Open
Abstract
The ability to solubilize lignocellulose makes certain ionic liquids (ILs) very effective reagents for pretreating biomass prior to its saccharification for biofuel fermentation. However, residual IL in the aqueous sugar solution can inhibit the growth and function of biofuel-producing microorganisms. In E. coli this toxicity can be partially overcome by the heterologous expression of an IL efflux pump encoded by eilA from Enterobacter lignolyticus. In the present work, we used microarray analysis to identify native E. coli IL-inducible promoters and develop control systems for regulating eilA gene expression. Three candidate promoters, PmarR', PydfO', and PydfA', were selected and compared to the IPTG-inducible PlacUV5 system for controlling expression of eilA. The PydfA' and PmarR' based systems are as effective as PlacUV5 in their ability to rescue E. coli from typically toxic levels of IL, thereby eliminating the need to use an IPTG-based system for such tolerance engineering. We present a mechanistic model indicating that inducible control systems reduce target gene expression when IL levels are low. Selected-reaction monitoring mass spectrometry analysis revealed that at high IL concentrations EilA protein levels were significantly elevated under the control of PydfA' and PmarR' in comparison to the other promoters. Further, in a pooled culture competition designed to determine fitness, the strain containing pPmarR'-eilA outcompeted strains with other promoter constructs, most significantly at IL concentrations above 150 mM. These results indicate that native promoters such as PmarR' can provide effective systems for regulating the expression of heterologous genes in host engineering and simplify the development of industrially useful strains.
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213
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Way JC, Collins JJ, Keasling JD, Silver PA. Integrating biological redesign: where synthetic biology came from and where it needs to go. Cell 2014; 157:151-61. [PMID: 24679533 DOI: 10.1016/j.cell.2014.02.039] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/26/2013] [Accepted: 02/19/2014] [Indexed: 01/17/2023]
Abstract
Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering.
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214
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Saini A, Boutigny S, Baidoo EE, Yeung N, Keasling JD, Butland G. Physical and Functional Interactions of the E. coli Monothiol Glutaredoxin GrxD Suggest a Role in FeS Apoprotein Maturation (LB132). FASEB J 2014. [DOI: 10.1096/fasebj.28.1_supplement.lb132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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215
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Ruegg TL, Kim EM, Simmons BA, Keasling JD, Singer SW, Lee TS, Thelen MP. An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production. Nat Commun 2014; 5:3490. [PMID: 24667370 DOI: 10.1038/ncomms4490] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/21/2014] [Indexed: 01/16/2023] Open
Abstract
Ionic liquids (ILs) are emerging as superior solvents for numerous industrial applications, including the pretreatment of biomass for the microbial production of biofuels. However, some of the most effective ILs used to solubilize cellulose inhibit microbial growth, decreasing efficiency in the overall process. Here we identify an IL-resistance mechanism consisting of two adjacent genes from Enterobacter lignolyticus, a rain forest soil bacterium that is tolerant to an imidazolium-based IL. These genes retain their full functionality when transferred to an Escherichia coli biofuel host, with IL resistance established by an inner membrane transporter, regulated by an IL-inducible repressor. Expression of the transporter is dynamically adjusted in direct response to IL, enabling growth and biofuel production at levels of IL that are toxic to native strains. This natural auto-regulatory system provides the basis for engineering IL-tolerant microbes, which should accelerate progress towards effective conversion of lignocellulosic biomass to fuels and renewable chemicals.
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216
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Garcia DE, Keasling JD. Kinetics of phosphomevalonate kinase from Saccharomyces cerevisiae. PLoS One 2014; 9:e87112. [PMID: 24475236 PMCID: PMC3903622 DOI: 10.1371/journal.pone.0087112] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 12/21/2013] [Indexed: 01/08/2023] Open
Abstract
The mevalonate-based isoprenoid biosynthetic pathway is responsible for producing cholesterol in humans and is used commercially to produce drugs, chemicals, and fuels. Heterologous expression of this pathway in Escherichia coli has enabled high-level production of the antimalarial drug artemisinin and the proposed biofuel bisabolane. Understanding the kinetics of the enzymes in the biosynthetic pathway is critical to optimize the pathway for high flux. We have characterized the kinetic parameters of phosphomevalonate kinase (PMK, EC 2.7.4.2) from Saccharomyces cerevisiae, a previously unstudied enzyme. An E. coli codon-optimized version of the S. cerevisiae gene was cloned into pET-52b+, then the C-terminal 6X His-tagged protein was expressed in E. coli BL21(DE3) and purified on a Ni²⁺ column. The KM of the ATP binding site was determined to be 98.3 µM at 30°C, the optimal growth temperature for S. cerevisiae, and 74.3 µM at 37°C, the optimal growth temperature for E. coli. The K(M) of the mevalonate-5-phosphate binding site was determined to be 885 µM at 30°C and 880 µM at 37°C. The V(max) was determined to be 4.51 µmol/min/mg enzyme at 30°C and 5.33 µmol/min/mg enzyme at 37°C. PMK is Mg²⁺ dependent, with maximal activity achieved at concentrations of 10 mM or greater. Maximum activity was observed at pH = 7.2. PMK was not found to be substrate inhibited, nor feedback inhibited by FPP at concentrations up to 10 µM FPP.
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217
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Eudes A, Juminaga D, Baidoo EEK, Collins FW, Keasling JD, Loqué D. Erratum to: Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli. Microb Cell Fact 2014. [PMCID: PMC3897996 DOI: 10.1186/1475-2859-13-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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218
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Baidoo EEK, Xiao Y, Dehesh K, Keasling JD. Metabolite profiling of plastidial deoxyxylulose-5-phosphate pathway intermediates by liquid chromatography and mass spectrometry. Methods Mol Biol 2014; 1153:57-76. [PMID: 24777790 PMCID: PMC4811599 DOI: 10.1007/978-1-4939-0606-2_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Metabolite profiling is a powerful tool that enhances our understanding of complex regulatory processes and extends to the comparative analysis of plant gene function. However, at present, there are relatively few examples of metabolite profiling being used to characterize the regulatory aspects of the plastidial deoxyxylulose-5-phosphate (DXP) pathway in plants. Since the DXP pathway is one of two pathways in plants that are essential for isoprenoid biosynthesis, it is imperative that robust analytical methods be employed for the characterization of this metabolic pathway. Recently, liquid chromatography-mass spectrometry (LC-MS), in conjunction with traditional molecular biology approaches, established that the DXP pathway metabolite, methylerythritol cyclodiphosphate (MEcPP), previously known solely as an intermediate in the isoprenoid biosynthetic pathway, is a stress sensor that communicates environmental perturbations sensed by plastids to the nucleus, a process referred to as retrograde signaling. In this chapter, we describe two LC-MS methods from this study that can be broadly used to characterize DXP pathway intermediates.
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Ito J, Herter T, Baidoo EEK, Lao J, Vega-Sánchez ME, Michelle Smith-Moritz A, Adams PD, Keasling JD, Usadel B, Petzold CJ, Heazlewood JL. Analysis of plant nucleotide sugars by hydrophilic interaction liquid chromatography and tandem mass spectrometry. Anal Biochem 2013; 448:14-22. [PMID: 24299991 DOI: 10.1016/j.ab.2013.11.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 11/11/2013] [Accepted: 11/22/2013] [Indexed: 12/22/2022]
Abstract
Understanding the intricate metabolic processes involved in plant cell wall biosynthesis is limited by difficulties in performing sensitive quantification of many involved compounds. Hydrophilic interaction liquid chromatography is a useful technique for the analysis of hydrophilic metabolites from complex biological extracts and forms the basis of this method to quantify plant cell wall precursors. A zwitterionic silica-based stationary phase has been used to separate hydrophilic nucleotide sugars involved in cell wall biosynthesis from milligram amounts of leaf tissue. A tandem mass spectrometry operating in selected reaction monitoring mode was used to quantify nucleotide sugars. This method was highly repeatable and quantified 12 nucleotide sugars at low femtomole quantities, with linear responses up to four orders of magnitude to several 100pmol. The method was also successfully applied to the analysis of purified leaf extracts from two model plant species with variations in their cell wall sugar compositions and indicated significant differences in the levels of 6 out of 12 nucleotide sugars. The plant nucleotide sugar extraction procedure was demonstrated to have good recovery rates with minimal matrix effects. The approach results in a significant improvement in sensitivity when applied to plant samples over currently employed techniques.
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220
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Nowroozi FF, Baidoo EEK, Ermakov S, Redding-Johanson AM, Batth TS, Petzold CJ, Keasling JD. Metabolic pathway optimization using ribosome binding site variants and combinatorial gene assembly. Appl Microbiol Biotechnol 2013; 98:1567-81. [DOI: 10.1007/s00253-013-5361-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/22/2013] [Accepted: 10/28/2013] [Indexed: 02/01/2023]
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221
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Colloms SD, Merrick CA, Olorunniji FJ, Stark WM, Smith MCM, Osbourn A, Keasling JD, Rosser SJ. Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination. Nucleic Acids Res 2013; 42:e23. [PMID: 24225316 PMCID: PMC3936721 DOI: 10.1093/nar/gkt1101] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by C31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. C31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
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Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD, Keasling JD. Engineering dynamic pathway regulation using stress-response promoters. Nat Biotechnol 2013; 31:1039-46. [DOI: 10.1038/nbt.2689] [Citation(s) in RCA: 352] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 08/09/2013] [Indexed: 12/20/2022]
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Szmidt-Middleton HL, Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A. Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.06.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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224
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Woo HM, Murray GW, Batth TS, Prasad N, Adams PD, Keasling JD, Petzold CJ, Lee TS. Application of targeted proteomics and biological parts assembly in E. coli to optimize the biosynthesis of an anti-malarial drug precursor, amorpha-4,11-diene. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2013.04.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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225
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Chou HH, Keasling JD. Programming adaptive control to evolve increased metabolite production. Nat Commun 2013; 4:2595. [DOI: 10.1038/ncomms3595] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 09/11/2013] [Indexed: 11/09/2022] Open
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