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Ha NS, Onley JR, Deng K, Andeer P, Bowen BP, Gupta K, Kim PW, Kuch N, Kutschke M, Parker A, Song F, Fox B, Adams PD, de Raad M, Northen TR. A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening. Lab Chip 2023; 23:3361-3369. [PMID: 37401915 PMCID: PMC10484474 DOI: 10.1039/d2lc00980c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Mass spectrometry (MS) enables detection of different chemical species with a very high specificity; however, it can be limited by its throughput. Integrating MS with microfluidics has a tremendous potential to improve throughput and accelerate biochemical research. In this work, we introduce Drop-NIMS, a combination of a passive droplet loading microfluidic device and a matrix-free MS laser desorption ionization technique called nanostructure-initiator mass spectrometry (NIMS). This platform combines different droplets at random to generate a combinatorial library of enzymatic reactions that are deposited directly on the NIMS surface without requiring additional sample handling. The enzyme reaction products are then detected with MS. Drop-NIMS was used to rapidly screen enzymatic reactions containing low (on the order of nL) volumes of glycoside reactants and glycoside hydrolase enzymes per reaction. MS "barcodes" (small compounds with unique masses) were added to the droplets to identify different combinations of substrates and enzymes created by the device. We assigned xylanase activities to several putative glycoside hydrolases, making them relevant to food and biofuel industrial applications. Overall, Drop-NIMS is simple to fabricate, assemble, and operate and it has potential to be used with many other small molecule metabolites.
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Affiliation(s)
- Noel S Ha
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenny R Onley
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Peter Andeer
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Kshitiz Gupta
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter W Kim
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Nathaniel Kuch
- University of Wisconsin - Madison, Madison, WI, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | | | - Alex Parker
- University of Wisconsin - Madison, Madison, WI, USA
| | - Fangchao Song
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brian Fox
- University of Wisconsin - Madison, Madison, WI, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | - Markus de Raad
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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2
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Chen Y, Gin JW, Wang Y, de Raad M, Tan S, Hillson NJ, Northen TR, Adams PD, Petzold CJ. Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format. PLoS One 2023; 18:e0288102. [PMID: 37418444 DOI: 10.1371/journal.pone.0288102] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/20/2023] [Indexed: 07/09/2023] Open
Abstract
Plate-based proteomic sample preparation offers a solution to the large sample throughput demands in the biotechnology field where hundreds or thousands of engineered microbes are constructed for testing is routine. Meanwhile, sample preparation methods that work efficiently on broader microbial groups are desirable for new applications of proteomics in other fields, such as microbial communities. Here, we detail a step-by-step protocol that consists of cell lysis in an alkaline chemical buffer (NaOH/SDS) followed by protein precipitation with high-ionic strength acetone in 96-well format. The protocol works for a broad range of microbes (e.g., Gram-negative bacteria, Gram-positive bacteria, non-filamentous fungi) and the resulting proteins are ready for tryptic digestion for bottom-up quantitative proteomic analysis without the need for desalting column cleanup. The yield of protein using this protocol increases linearly with respect to the amount of starting biomass from 0.5-2.0 OD*mL of cells. By using a bench-top automated liquid dispenser, a cost-effective and environmentally-friendly option to eliminating pipette tips and reducing reagent waste, the protocol takes approximately 30 minutes to extract protein from 96 samples. Tests on mock mixtures showed expected results that the biomass composition structure is in close agreement with the experimental design. Lastly, we applied the protocol for the composition analysis of a synthetic community of environmental isolates grown on two different media. This protocol has been developed to facilitate rapid, low-variance sample preparation of hundreds of samples and allow flexibility for future protocol development.
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Affiliation(s)
- Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Jennifer W Gin
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Ying Wang
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Stephen Tan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Nathan J Hillson
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
| | - Trent R Northen
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Paul D Adams
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- Department of Bioengineering, University of California Berkeley, Berkeley, California, United States of America
- Molecular Biophysics and Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- DOE Joint BioEnergy Institute, Emeryville, California, United States of America
- DOE Agile BioFoundry, Emeryville, California, United States of America
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3
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Deng K, Wang X, Ing N, Opgenorth P, de Raad M, Kim J, Simmons BA, Adams PD, Singh AK, Lee TS, Northen TR. Rapid quantification of alcohol production in microorganisms based on nanostructure-initiator mass spectrometry (NIMS). Anal Biochem 2023; 662:114997. [PMID: 36435200 DOI: 10.1016/j.ab.2022.114997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022]
Abstract
We described a mass spectrometry-based assay to rapidly quantify the production of primary alcohols directly from cell cultures. This novel assay used the combination of TEMPO-based oxidation chemistry and oxime ligation, followed by product analysis based on Nanostructure-Initiator Mass Spectrometry. This assay enables quantitative monitor both C5 to C18 alcohols as well as glucose and gluconate in the growth medium to support strain characterization and optimization. We find that this assay yields similar results to gas chromatography for isoprenol production but required much less acquisition time per sample. We applied this assay to gain new insights into P. Putida's utilization of alcohols and find that this strain largely could not grow on heptanol and octanol.
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Affiliation(s)
- Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Sandia National Laboratories, Livermore, CA, 94551, USA.
| | - Xi Wang
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nicole Ing
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Paul Opgenorth
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Markus de Raad
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jinho Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; University of California, Berkeley, CA, 94720, USA
| | - Anup K Singh
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Livermore National Laboratory, Livermore, 94550, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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4
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de Raad M, Koper K, Deng K, Bowen BP, Maeda HA, Northen TR. Mass spectrometry imaging-based assays for aminotransferase activity reveal a broad substrate spectrum for a previously uncharacterized enzyme. J Biol Chem 2023; 299:102939. [PMID: 36702250 PMCID: PMC9957770 DOI: 10.1016/j.jbc.2023.102939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/25/2023] Open
Abstract
Aminotransferases (ATs) catalyze pyridoxal 5'-phosphate-dependent transamination reactions between amino donor and keto acceptor substrates and play central roles in nitrogen metabolism of all organisms. ATs are involved in the biosynthesis and degradation of both proteinogenic and nonproteinogenic amino acids and also carry out a wide variety of functions in photorespiration, detoxification, and secondary metabolism. Despite the importance of ATs, their functionality is poorly understood as only a small fraction of putative ATs, predicted from DNA sequences, are associated with experimental data. Even for characterized ATs, the full spectrum of substrate specificity, among many potential substrates, has not been explored in most cases. This is largely due to the lack of suitable high-throughput assays that can screen for AT activity and specificity at scale. Here we present a new high-throughput platform for screening AT activity using bioconjugate chemistry and mass spectrometry imaging-based analysis. Detection of AT reaction products is achieved by forming an oxime linkage between the ketone groups of transaminated amino donors and a probe molecule that facilitates mass spectrometry-based analysis using nanostructure-initiator mass spectrometry or MALDI-mass spectrometry. As a proof-of-principle, we applied the newly established method and found that a previously uncharacterized Arabidopsis thaliana tryptophan AT-related protein 1 is a highly promiscuous enzyme that can utilize 13 amino acid donors and three keto acid acceptors. These results demonstrate that this oxime-mass spectrometry imaging AT assay enables high-throughput discovery and comprehensive characterization of AT enzymes, leading to an accurate understanding of the nitrogen metabolic network.
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Affiliation(s)
- Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
| | - Kaan Koper
- Department of Botany, University of Wisconsin-Madison; Madison, Wisconsin, USA
| | - Kai Deng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison; Madison, Wisconsin, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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5
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de Raad M, Li YV, Kuehl JV, Andeer PF, Kosina SM, Hendrickson A, Saichek NR, Golini AN, Han LZ, Wang Y, Bowen BP, Deutschbauer AM, Arkin AP, Chakraborty R, Northen TR. A Defined Medium for Cultivation and Exometabolite Profiling of Soil Bacteria. Front Microbiol 2022; 13:855331. [PMID: 35694313 PMCID: PMC9174792 DOI: 10.3389/fmicb.2022.855331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Exometabolomics is an approach to assess how microorganisms alter, or react to their environments through the depletion and production of metabolites. It allows the examination of how soil microbes transform the small molecule metabolites within their environment, which can be used to study resource competition and cross-feeding. This approach is most powerful when used with defined media that enable tracking of all metabolites. However, microbial growth media have traditionally been developed for the isolation and growth of microorganisms but not metabolite utilization profiling through Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). Here, we describe the construction of a defined medium, the Northen Lab Defined Medium (NLDM), that not only supports the growth of diverse soil bacteria but also is defined and therefore suited for exometabolomic experiments. Metabolites included in NLDM were selected based on their presence in R2A medium and soil, elemental stoichiometry requirements, as well as knowledge of metabolite usage by different bacteria. We found that NLDM supported the growth of 108 of the 110 phylogenetically diverse (spanning 36 different families) soil bacterial isolates tested and all of its metabolites were trackable through LC–MS/MS analysis. These results demonstrate the viability and utility of the constructed NLDM medium for growing and characterizing diverse microbial isolates and communities.
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Affiliation(s)
- Markus de Raad
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Yifan V. Li
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jennifer V. Kuehl
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Peter F. Andeer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Suzanne M. Kosina
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Andrew Hendrickson
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Nicholas R. Saichek
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Amber N. Golini
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - La Zhen Han
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Ying Wang
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - Adam P. Arkin
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States
| | - Romy Chakraborty
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
- *Correspondence: Trent R. Northen,
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6
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Kosina SM, Rademacher P, Wetmore KM, de Raad M, Zemla M, Zane GM, Zulovich JJ, Chakraborty R, Bowen BP, Wall JD, Auer M, Arkin AP, Deutschbauer AM, Northen TR. Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms. Front Microbiol 2021; 12:757856. [PMID: 34956122 PMCID: PMC8696352 DOI: 10.3389/fmicb.2021.757856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.
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Affiliation(s)
- Suzanne M. Kosina
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter Rademacher
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kelly M. Wetmore
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcin Zemla
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Grant M. Zane
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | | | - Romy Chakraborty
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
| | - Judy D. Wall
- Department of Biochemistry, University of Missouri, Columbia, MO, United States
| | - Manfred Auer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam P. Arkin
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Adam M. Deutschbauer
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Lawrence Berkeley National Laboratory, Joint Genome Institute, Berkeley, CA, United States
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7
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Ha NS, de Raad M, Han LZ, Golini A, Petzold CJ, Northen TR. Faster, better, and cheaper: harnessing microfluidics and mass spectrometry for biotechnology. RSC Chem Biol 2021; 2:1331-1351. [PMID: 34704041 PMCID: PMC8496484 DOI: 10.1039/d1cb00112d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
High-throughput screening technologies are widely used for elucidating biological activities. These typically require trade-offs in assay specificity and sensitivity to achieve higher throughput. Microfluidic approaches enable rapid manipulation of small volumes and have found a wide range of applications in biotechnology providing improved control of reaction conditions, faster assays, and reduced reagent consumption. The integration of mass spectrometry with microfluidics has the potential to create high-throughput, sensitivity, and specificity assays. This review introduces the widely-used mass spectrometry ionization techniques that have been successfully integrated with microfluidics approaches such as continuous-flow system, microchip electrophoresis, droplet microfluidics, digital microfluidics, centrifugal microfluidics, and paper microfluidics. In addition, we discuss recent applications of microfluidics integrated with mass spectrometry in single-cell analysis, compound screening, and the study of microorganisms. Lastly, we provide future outlooks towards online coupling, improving the sensitivity and integration of multi-omics into a single platform.
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Affiliation(s)
- Noel S Ha
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Markus de Raad
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
| | - La Zhen Han
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Amber Golini
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
| | - Trent R Northen
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint BioEnergy Institute Emeryville CA USA
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory Berkeley CA USA
- US Department of Energy Joint Genome Institute Berkeley CA USA
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8
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Sasse J, Kosina SM, de Raad M, Jordan JS, Whiting K, Zhalnina K, Northen TR. Root morphology and exudate availability are shaped by particle size and chemistry in Brachypodium distachyon. Plant Direct 2020; 4:e00207. [PMID: 32642632 PMCID: PMC7330624 DOI: 10.1002/pld3.207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 02/04/2020] [Accepted: 02/11/2020] [Indexed: 05/26/2023]
Abstract
Root morphology and exudation define a plants' sphere of influence in soils. In turn, soil characteristics influence plant growth, morphology, root microbiome, and rhizosphere chemistry. Collectively, all these parameters have significant implications on the major biogeochemical cycles, crop yield, and ecosystem health. However, how plants are shaped by the physiochemistry of soil particles is still not well understood. We explored how particle size and chemistry of growth substrates affect root morphology and exudation of a model grass. We grew Brachypodium distachyon in glass beads with various sizes (0.5, 1, 2, 3 mm), as well as in sand (0.005, 0.25, 4 mm) and in clay (4 mm) particles and in particle-free hydroponic medium. Plant morphology, root weight, and shoot weight were measured. We found that particle size significantly influenced root fresh weight and root length, whereas root number and shoot weight remained constant. Next, plant exudation profiles were analyzed with mass spectrometry imaging and liquid chromatography-mass spectrometry. Mass spectrometry imaging suggested that both, root length and number shape root exudation. Exudate profiles were comparable for plants growing in glass beads or sand with various particles sizes, but distinct for plants growing in clay for in situ exudate collection. Clay particles were found to sorb 20% of compounds exuded by clay-grown plants, and 70% of compounds from a defined exudate medium. The sorbed compounds belonged to a range of chemical classes, among them nucleosides, organic acids, sugars, and amino acids. Some of the sorbed compounds could be desorbed by a rhizobacterium (Pseudomonas fluorescens WCS415), supporting its growth. This study demonstrates the effect of different characteristics of particles on root morphology, plant exudation and availability of nutrients to microorganisms. These findings further support the critical importance of the physiochemical properties of soils when investigating plant morphology, plant chemistry, and plant-microbe interactions.
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Affiliation(s)
- Joelle Sasse
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Department of Plant and Microbial BiologyUniversity of ZurichZurichSwitzerland
| | - Suzanne M. Kosina
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Markus de Raad
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Jacob S. Jordan
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Katherine Whiting
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Kateryna Zhalnina
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Trent R. Northen
- Environmental Genomics and Systems BiologyLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Joint Genome InstituteLawrence Berkeley National LaboratoryBerkeleyCAUSA
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9
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Opgenorth P, Costello Z, Okada T, Goyal G, Chen Y, Gin J, Benites V, de Raad M, Northen TR, Deng K, Deutsch S, Baidoo EEK, Petzold CJ, Hillson NJ, Garcia Martin H, Beller HR. Lessons from Two Design-Build-Test-Learn Cycles of Dodecanol Production in Escherichia coli Aided by Machine Learning. ACS Synth Biol 2019; 8:1337-1351. [PMID: 31072100 DOI: 10.1021/acssynbio.9b00020] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The Design-Build-Test-Learn (DBTL) cycle, facilitated by exponentially improving capabilities in synthetic biology, is an increasingly adopted metabolic engineering framework that represents a more systematic and efficient approach to strain development than historical efforts in biofuels and biobased products. Here, we report on implementation of two DBTL cycles to optimize 1-dodecanol production from glucose using 60 engineered Escherichia coli MG1655 strains. The first DBTL cycle employed a simple strategy to learn efficiently from a relatively small number of strains (36), wherein only the choice of ribosome-binding sites and an acyl-ACP/acyl-CoA reductase were modulated in a single pathway operon including genes encoding a thioesterase (UcFatB1), an acyl-ACP/acyl-CoA reductase (Maqu_2507, Maqu_2220, or Acr1), and an acyl-CoA synthetase (FadD). Measured variables included concentrations of dodecanol and all proteins in the engineered pathway. We used the data produced in the first DBTL cycle to train several machine-learning algorithms and to suggest protein profiles for the second DBTL cycle that would increase production. These strategies resulted in a 21% increase in dodecanol titer in Cycle 2 (up to 0.83 g/L, which is more than 6-fold greater than previously reported batch values for minimal medium). Beyond specific lessons learned about optimizing dodecanol titer in E. coli, this study had findings of broader relevance across synthetic biology applications, such as the importance of sequencing checks on plasmids in production strains as well as in cloning strains, and the critical need for more accurate protein expression predictive tools.
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Affiliation(s)
- Paul Opgenorth
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Zak Costello
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Takuya Okada
- Research Institute for Bioscience Product & Fine Chemicals, Ajinomoto Co., Inc., Kawasaki 210-8680, Japan
| | - Garima Goyal
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Yan Chen
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Jennifer Gin
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Veronica Benites
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Trent R. Northen
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Kai Deng
- Sandia National Laboratories, Livermore, California 94550, United States
| | - Samuel Deutsch
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
| | - Nathan J. Hillson
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- DOE Joint Genome Institute, Walnut Creek, California 94598, United States
| | - Hector Garcia Martin
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- DOE Agile BioFoundry, Emeryville, California 94608, United States
- BCAM, Basque Center for Applied Mathematics, 48009 Bilbao, Spain
| | - Harry R. Beller
- Joint BioEnergy Institute (JBEI), Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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10
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de Rond T, Gao J, Zargar A, de Raad M, Cunha J, Northen TR, Keasling JD. A High-Throughput Mass Spectrometric Enzyme Activity Assay Enabling the Discovery of Cytochrome P450 Biocatalysts. Angew Chem Int Ed Engl 2019; 58:10114-10119. [PMID: 31140688 DOI: 10.1002/anie.201901782] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/29/2019] [Indexed: 12/21/2022]
Abstract
Assaying for enzymatic activity is a persistent bottleneck in biocatalyst and drug development. Existing high-throughput assays for enzyme activity tend to be applicable only to a narrow range of biochemical transformations, whereas universal enzyme characterization methods usually require chromatography to determine substrate turnover, greatly diminishing throughput. We present an enzyme activity assay that allows the high-throughput mass-spectrometric detection of enzyme activity in complex matrices without the need for a chromatographic step. This technology, which we call probing enzymes with click-assisted NIMS (PECAN), can detect the activity of medically and biocatalytically significant cytochrome P450s in cell lysate, microsomes, and bacteria. Using this approach, a cytochrome P450BM3 mutant library was successfully screened for the ability to catalyze the oxidation of the sesquiterpene valencene.
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Affiliation(s)
- Tristan de Rond
- College of Chemistry, University of California, Berkeley, Berkeley, CA, 94270, USA.,Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Current address: Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Jian Gao
- Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory, USA
| | - Amin Zargar
- Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Markus de Raad
- Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, USA
| | - Jack Cunha
- Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Trent R Northen
- Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Department of Energy Joint Genome Institute (DOE JGI), Lawrence Berkeley National Laboratory, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, USA
| | - Jay D Keasling
- College of Chemistry, University of California, Berkeley, Berkeley, CA, 94270, USA.,Joint Bioenergy Institute (JBEI), Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, USA.,Center for Biosustainability, Danish Technical University, Lyngby, Denmark.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Shenzhen, China
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11
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Erbilgin O, Rübel O, Louie KB, Trinh M, Raad MD, Wildish T, Udwary D, Hoover C, Deutsch S, Northen TR, Bowen BP. MAGI: A Method for Metabolite Annotation and Gene Integration. ACS Chem Biol 2019; 14:704-714. [PMID: 30896917 DOI: 10.1021/acschembio.8b01107] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metabolomics is a widely used technology for obtaining direct measures of metabolic activities from diverse biological systems. However, ambiguous metabolite identifications are a common challenge and biochemical interpretation is often limited by incomplete and inaccurate genome-based predictions of enzyme activities (that is, gene annotations). Metabolite Annotation and Gene Integration (MAGI) generates a metabolite-gene association score using a biochemical reaction network. This is calculated by a method that emphasizes consensus between metabolites and genes via biochemical reactions. To demonstrate the potential of this method, we applied MAGI to integrate sequence data and metabolomics data collected from Streptomyces coelicolor A3(2), an extensively characterized bacterium that produces diverse secondary metabolites. Our findings suggest that coupling metabolomics and genomics data by scoring consensus between the two increases the quality of both metabolite identifications and gene annotations in this organism. MAGI also made biochemical predictions for poorly annotated genes that were consistent with the extensive literature on this important organism. This limited analysis suggests that using metabolomics data has the potential to improve annotations in sequenced organisms and also provides testable hypotheses for specific biochemical functions. MAGI is freely available for academic use both as an online tool at https://magi.nersc.gov and with source code available at https://github.com/biorack/magi .
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Affiliation(s)
- Onur Erbilgin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Oliver Rübel
- Data Analytics and Visualization Group, Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Katherine B. Louie
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Matthew Trinh
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tony Wildish
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel Udwary
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Cindi Hoover
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Samuel Deutsch
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Trent R. Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Benjamin P. Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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12
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Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM. Enzyme promiscuity shapes adaptation to novel growth substrates. Mol Syst Biol 2019; 15:e8462. [PMID: 30962359 PMCID: PMC6452873 DOI: 10.15252/msb.20188462] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Evidence suggests that novel enzyme functions evolved from low‐level promiscuous activities in ancestral enzymes. Yet, the evolutionary dynamics and physiological mechanisms of how such side activities contribute to systems‐level adaptations are not well characterized. Furthermore, it remains untested whether knowledge of an organism's promiscuous reaction set, or underground metabolism, can aid in forecasting the genetic basis of metabolic adaptations. Here, we employ a computational model of underground metabolism and laboratory evolution experiments to examine the role of enzyme promiscuity in the acquisition and optimization of growth on predicted non‐native substrates in Escherichia coli K‐12 MG1655. After as few as approximately 20 generations, evolved populations repeatedly acquired the capacity to grow on five predicted non‐native substrates—D‐lyxose, D‐2‐deoxyribose, D‐arabinose, m‐tartrate, and monomethyl succinate. Altered promiscuous activities were shown to be directly involved in establishing high‐efficiency pathways. Structural mutations shifted enzyme substrate turnover rates toward the new substrate while retaining a preference for the primary substrate. Finally, genes underlying the phenotypic innovations were accurately predicted by genome‐scale model simulations of metabolism with enzyme promiscuity.
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Affiliation(s)
- Gabriela I Guzmán
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ryan A LaCroix
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ákos Nyerges
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Henrietta Papp
- Virological Research Group, Szentágothai Research Centre University of Pécs, Pécs, Hungary
| | - Markus de Raad
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Zachary A King
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, CA, USA
| | - Richard A Notebaart
- Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Csaba Pál
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Balázs Papp
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
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13
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Gao J, Louie KB, Steinke P, Bowen BP, Raad MD, Zuckermann RN, Siuzdak G, Northen TR. Morphology-Driven Control of Metabolite Selectivity Using Nanostructure-Initiator Mass Spectrometry. Anal Chem 2017; 89:6521-6526. [PMID: 28520405 DOI: 10.1021/acs.analchem.7b00599] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Nanostructure-initiator mass spectrometry (NIMS) is a laser desorption/ionization analysis technique based on the vaporization of a nanostructure-trapped liquid "initiator" phase. Here we report an intriguing relationship between NIMS surface morphology and analyte selectivity. Scanning electron microscopy and spectroscopic ellipsometry were used to characterize the surface morphologies of a series of NIMS substrates generated by anodic electrochemical etching. Mass spectrometry imaging was applied to compare NIMS sensitivity of these various surfaces toward the analysis of diverse analytes. The porosity of NIMS surfaces was found to increase linearly with etching time where the pore size ranged from 4 to 12 nm with corresponding porosities estimated to be 7-70%. Surface morphology was found to significantly and selectively alter NIMS sensitivity. The small molecule (<2k Da) sensitivity was found to increase with increased porosity, whereas low porosity had the highest sensitivity for the largest molecules examined. Estimation of molecular sizes showed that this transition occurs when the pore size is <3× the maximum of molecular dimensions. While the origins of selectivity are unclear, increased signal from small molecules with increased surface area is consistent with a surface area restructuring-driven desorption/ionization process where signal intensity increases with porosity. In contrast, large molecules show highest signal for the low-porosity and small-pore-size surfaces. We attribute this to strong interactions between the initiator-coated pore structures and large molecules that hinder desorption/ionization by trapping large molecules. This finding may enable us to design NIMS surfaces with increased specificity to molecules of interest.
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Affiliation(s)
- Jian Gao
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Katherine B Louie
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Philipp Steinke
- Fraunhofer Institute for Photonic Microsystems IPMS - Center Nanoelectronic Technologies (CNT), Königsbrücker Strasse 178, 01099 Dresden, Germany
| | - Benjamin P Bowen
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Markus de Raad
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | | | - Gary Siuzdak
- Scripps Center for Metabolomics & Departments of Chemistry, Molecular and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Trent R Northen
- Joint Genome Institute, Department of Energy , 2800 Mitchell Drive, Walnut Creek, California 94598, United States
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14
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de Raad M, de Rond T, Rübel O, Keasling JD, Northen TR, Bowen BP. OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging. Anal Chem 2017; 89:5818-5823. [PMID: 28467051 DOI: 10.1021/acs.analchem.6b05004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mass spectrometry imaging (MSI) has primarily been applied in localizing biomolecules within biological matrices. Although well-suited, the application of MSI for comparing thousands of spatially defined spotted samples has been limited. One reason for this is a lack of suitable and accessible data processing tools for the analysis of large arrayed MSI sample sets. The OpenMSI Arrayed Analysis Toolkit (OMAAT) is a software package that addresses the challenges of analyzing spatially defined samples in MSI data sets. OMAAT is written in Python and is integrated with OpenMSI ( http://openmsi.nersc.gov ), a platform for storing, sharing, and analyzing MSI data. By using a web-based python notebook (Jupyter), OMAAT is accessible to anyone without programming experience yet allows experienced users to leverage all features. OMAAT was evaluated by analyzing an MSI data set of a high-throughput glycoside hydrolase activity screen comprising 384 samples arrayed onto a NIMS surface at a 450 μm spacing, decreasing analysis time >100-fold while maintaining robust spot-finding. The utility of OMAAT was demonstrated for screening metabolic activities of different sized soil particles, including hydrolysis of sugars, revealing a pattern of size dependent activities. These results introduce OMAAT as an effective toolkit for analyzing spatially defined samples in MSI. OMAAT runs on all major operating systems, and the source code can be obtained from the following GitHub repository: https://github.com/biorack/omaat .
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Affiliation(s)
- Markus de Raad
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Tristan de Rond
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Oliver Rübel
- Computational Research Division, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Jay D Keasling
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, and California Institute for Quantitative Biosciences, University of California , Berkeley, California 94720, United States.,DOE Joint BioEnergy Institute , Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Lab , Berkeley, California 94720, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark , Hørsholm 2970, Denmark
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States.,Joint Genome Institute , Department of Energy, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology, Biosciences, Lawrence Berkeley National Laboratory , 1 Cyclotron Road, Berkeley, California 94720, United States.,Joint Genome Institute , Department of Energy, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
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15
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Raad MD, Modavi C, Sukovich DJ, Anderson JC. Observing Biosynthetic Activity Utilizing Next Generation Sequencing and the DNA Linked Enzyme Coupled Assay. ACS Chem Biol 2017; 12:191-199. [PMID: 28103681 DOI: 10.1021/acschembio.6b00652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Currently, the identification of new genes drastically outpaces current experimental methods for determining their enzymatic function. This disparity necessitates the development of high-throughput techniques that operate with the same scalability as modern gene synthesis and sequencing technologies. In this paper, we demonstrate the versatility of the recently reported DNA-Linked Enzyme-Coupled Assay (DLEnCA) and its ability to support high-throughput data acquisition through next-generation sequencing (NGS). Utilizing methyltransferases, we highlight DLEnCA's ability to rapidly profile an enzyme's substrate specificity, determine relative enzyme kinetics, detect biosynthetic formation of a target molecule, and its potential to benefit from the scales and standardization afforded by NGS. This improved methodology minimizes the effort in acquiring biosynthetic knowledge by tying biochemical techniques to the rapidly evolving abilities in sequencing and synthesizing DNA.
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Affiliation(s)
- Markus de Raad
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Cyrus Modavi
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - David J. Sukovich
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - J. Christopher Anderson
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
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16
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Affiliation(s)
- Jian Gao
- Life
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
- Joint Genome Institute, Department of Energy, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Markus de Raad
- Life
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
- Joint Genome Institute, Department of Energy, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Benjamin P. Bowen
- Life
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
- Joint Genome Institute, Department of Energy, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
| | - Ronald N. Zuckermann
- The
Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
| | - Trent R. Northen
- Life
Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron
Road, Berkeley, California 94720, United States
- Joint Genome Institute, Department of Energy, 2800 Mitchell Drive, Walnut Creek, California 94598, United States
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17
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Abstract
Mass spectrometry has become a choice method for broad-spectrum metabolite analysis in both fundamental and applied research. This can range from comprehensive analysis achieved through time-consuming chromatography to the rapid analysis of a few target metabolites without chromatography. In this review article, we highlight current high-throughput MS-based platforms and their potential application in metabolomics. Although current MS platforms can reach throughputs up to 0.5 seconds per sample, the metabolite coverage of these platforms are low compared to low-throughput, separation-based MS methods. High-throughput comes at a cost, as it's a trade-off between sample throughput and metabolite coverage. As we will discuss, promising emerging technologies, including microfluidics and miniaturization of separation techniques, have the potential to achieve both rapid and more comprehensive metabolite analysis.
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Affiliation(s)
- Markus de Raad
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States
| | - Curt R Fischer
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States
| | - Trent R Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, United States.
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18
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Abstract
Traditional enzyme characterization methods are low-throughput and therefore limit engineering efforts in synthetic biology and biotechnology. Here, we propose a DNA-linked enzyme-coupled assay (DLEnCA) to monitor enzyme reactions in a high-throughput manner. Throughput is improved by removing the need for protein purification and by limiting the need for liquid chromatography mass spectrometry (LCMS) product detection by linking enzymatic function to DNA modification. We demonstrate the DLEnCA methodology using glucosyltransferases as an illustration. The assay utilizes cell free transcription/translation systems to produce enzymes of interest, while UDP-glucose and T4-β-glucosyltransferase are used to modify DNA, which is detected postreaction using qPCR or a similar means of DNA analysis. OleD and two glucosyltransferases from Arabidopsis were used to verify the assay's generality toward glucosyltransferases. We further show DLEnCA's utility by mapping out the substrate specificity for these enzymes.
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Affiliation(s)
- David J. Sukovich
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Cyrus Modavi
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Markus de Raad
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - Robin N. Prince
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
| | - J. Christopher Anderson
- Department of Biological
Engineering, Synthetic Biology Institute, University of California, Berkeley, Berkeley, California 94704, United States
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19
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Raad MD, Teunissen EA, Mastrobattista E. Peptide vectors for gene delivery: from single peptides to multifunctional peptide nanocarriers. Nanomedicine (Lond) 2014; 9:2217-32. [DOI: 10.2217/nnm.14.90] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The therapeutic use of nucleic acids relies on the availability of sophisticated delivery systems for targeted and intracellular delivery of these molecules. Such a gene delivery should possess essential characteristics to overcome several extracellular and intracellular barriers. Peptides offer an attractive platform for nonviral gene delivery, as several functional peptide classes exist capable of overcoming these barriers. However, none of these functional peptide classes contain all the essential characteristics required to overcome all of the barriers associated with successful gene delivery. Combining functional peptides into multifunctional peptide vectors will be pivotal for improving peptide-based gene delivery systems. By using combinatorial strategies and high-throughput screening, the identification of multifunctional peptide vectors will accelerate the optimization of peptide-based gene delivery systems.
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Affiliation(s)
- Markus de Raad
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Erik A Teunissen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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20
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Teunissen EA, de Raad M, Mastrobattista E. Production and biomedical applications of virus-like particles derived from polyomaviruses. J Control Release 2013; 172:305-321. [PMID: 23999392 DOI: 10.1016/j.jconrel.2013.08.026] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 08/18/2013] [Accepted: 08/20/2013] [Indexed: 10/26/2022]
Abstract
Virus-like particles (VLPs), aggregates of capsid proteins devoid of viral genetic material, show great promise in the fields of vaccine development and gene therapy. These particles spontaneously self-assemble after heterologous expression of viral structural proteins. This review will focus on the use of virus-like particles derived from polyomavirus capsid proteins. Since their first recombinant production 27 years ago these particles have been investigated for a myriad of biomedical applications. These virus-like particles are safe, easy to produce, can be loaded with a broad range of diverse cargoes and can be tailored for specific delivery or epitope presentation. We will highlight the structural characteristics of polyomavirus-derived VLPs and give an overview of their applications in diagnostics, vaccine development and gene delivery.
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Affiliation(s)
- Erik A Teunissen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Markus de Raad
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands.
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21
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de Raad M, Kooijmans SAA, Teunissen EA, Mastrobattista E. A solid-phase platform for combinatorial and scarless multipart gene assembly. ACS Synth Biol 2013; 2:316-26. [PMID: 23654269 DOI: 10.1021/sb300122q] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the emergence of standardized genetic modules as part of the synthetic biology toolbox, the need for universal and automatable assembly protocols increases. Although several methods and standards have been developed, these all suffer from drawbacks such as the introduction of scar sequences during ligation or the need for specific flanking sequences or a priori knowledge of the final sequence to be obtained. We have developed a method for scarless ligation of multipart gene segments in a truly sequence-independent fashion. The big advantage of this approach is that it is combinatorial, allowing the generation of all combinations of several variants of two or more modules to be ligated in less than a day. This method is based on the ligation of single-stranded or double-stranded oligodeoxynucleotides (ODN) and PCR products immobilized on a solid support. Different settings were tested to optimize the solid-support ligation. Finally, to show proof of concept for this novel multipart gene assembly platform a small library of all possible combinations of 4 BioBrick modules was generated and tested.
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Affiliation(s)
- Markus de Raad
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Sander A. A. Kooijmans
- Department of Clinical Chemistry
and Haematology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Erik A. Teunissen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Enrico Mastrobattista
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical
Sciences, Faculty of Science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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de Raad M, Teunissen EA, Lelieveld D, Egan DA, Mastrobattista E. High-content screening of peptide-based non-viral gene delivery systems. J Control Release 2011; 158:433-42. [PMID: 21983020 DOI: 10.1016/j.jconrel.2011.09.078] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/15/2011] [Accepted: 09/18/2011] [Indexed: 01/13/2023]
Abstract
High-content screening (HCS) uses high-capacity automated fluorescence imaging for the quantitative analysis of single cells and cell populations. Here, we developed an HCS assay for rapid screening of non-viral gene delivery systems as exemplified by the screening of a small library of peptide-based transfectants. These peptides were simultaneously screened for transfection efficiency, cytotoxicity, induction of cell permeability and the capacity to transfect non-dividing cells. We demonstrated that HCS is a valuable extension to the already existing screening methods for the in vitro evaluation of non-viral gene delivery systems with the added value that multiple parameters can be screened in parallel thereby obtaining more information from a single screening event, which will accelerate the development of novel gene delivery systems.
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Affiliation(s)
- Markus de Raad
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Faculty of science, University of Utrecht, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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Amidi M, de Raad M, Crommelin DJA, Hennink WE, Mastrobattista E. Antigen-expressing immunostimulatory liposomes as a genetically programmable synthetic vaccine. Syst Synth Biol 2010; 5:21-31. [PMID: 21949673 PMCID: PMC3159695 DOI: 10.1007/s11693-010-9066-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/07/2010] [Indexed: 01/13/2023]
Abstract
Liposomes are versatile (sub)micron-sized membrane vesicles that can be used for a variety of applications, including drug delivery and in vivo imaging but they also represent excellent models for artificial membranes or cells. Several studies have demonstrated that in vitro transcription and translation can take place inside liposomes to obtain compartmentalized production of functional proteins within the liposomes (Kita et al. in Chembiochem 9(15):2403–2410, 2008; Moritani et al.in FEBS J, 2010; Kuruma et al. in Methods Mol Biol 607:161–171, 2010; Murtas et al. in Biochem Biophys Res Commun 363(1):12–17, 2007; Sunami et al. in Anal Biochem 357(1):128–136, 2006; Ishikawa et al. in FEBS Lett 576(3):387–390, 2004; Oberholzer et al. in Biochem Biophys Res Commun 261(2):238–241, 1999). Such a minimal artificial cell-based model is ideal for synthetic biology based applications. In this study, we propose the use of liposomes as artificial microbes for vaccination. These artificial microbes can be genetically programmed to produce specific antigens at will. To show proof-of-concept for this artificial cell-based platform, a bacterial in vitro transcription and translation system together with a gene construct encoding the model antigen β-galactosidase were entrapped inside multilamellar liposomes. Vaccination studies in mice showed that such antigen-expressing immunostimulatory liposomes (AnExILs) elicited higher specific humoral immune responses against the produced antigen (β-galactosidase) than control vaccines (i.e. AnExILs without genetic input, liposomal β-galactosidase or pDNA encoding β-galactosidase). In conclusion, AnExILs present a new platform for DNA-based vaccines which combines antigen production, adjuvanticity and delivery in one system and which offer several advantages over existing vaccine formulations.
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Affiliation(s)
- Maryam Amidi
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, PO Box 80082, 3508 TB Utrecht, The Netherlands
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Amidi M, de Raad M, de Graauw H, van Ditmarsch D, Hennink WE, Crommelin DJA, Mastrobattista E. Optimization and quantification of protein synthesis inside liposomes. J Liposome Res 2010; 20:73-83. [PMID: 19941408 DOI: 10.3109/08982100903402954] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Synthetic biology aims at reprogramming existing, or creating new, biological systems, with the ultimate aim to obtain artificial cells whose functions can be tailored. For the latter, encapsulation of complex biochemical reactions into cell-sized compartments, such as liposomes, is required. Recently, several groups have demonstrated that proteins of interest can be produced de novo within liposomes by entrapping cell-free protein-synthesis systems and DNA templates inside liposomes. Although detectable, intraliposomal protein synthesis was generally poor. Here, we have optimized intraliposomal cell-free protein synthesis by changing several variables, including lipid composition as well as liposome, pyrophosphatase, and T7 RNA polymerase concentration. Further, by using an activity-based assay, we have quantified the amount of full-length protein that was produced from DNA templates inside liposomes before and after optimization of aforementioned variables. Based on the model protein beta-galactosidase, it is demonstrated that liposomal protein synthesis can yield microgram quantities of protein (30-40 microg/mL liposomes).
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Affiliation(s)
- Maryam Amidi
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands
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de Wolf HK, de Raad M, Snel C, van Steenbergen MJ, Fens MHAM, Storm G, Hennink WE. Biodegradable poly(2-dimethylamino ethylamino)phosphazene for in vivo gene delivery to tumor cells. Effect of polymer molecular weight. Pharm Res 2007; 24:1572-80. [PMID: 17435970 PMCID: PMC1915646 DOI: 10.1007/s11095-007-9299-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Accepted: 03/16/2007] [Indexed: 12/01/2022]
Abstract
PURPOSE Previously, we have shown that complexes of plasmid DNA with the biodegradable polymer poly(2-dimethylamino ethylamino)phosphazene (p(DMAEA)-ppz) mediated tumor selective gene expression after intravenous administration in mice. In this study, we investigated the effect of p(DMAEA)-ppz molecular weight on both in vitro and in vivo tumor transfection, as well as on complex induced toxicity. MATERIALS AND METHODS p(DMAEA)-ppz with a broad molar mass distribution was fractionated by preparative size exclusion chromatography. Polyplexes consisting of plasmid DNA and the collected polymer fractions were tested for biophysical properties, (cyto)toxicity and transfection activity. RESULTS Four p(DMAEA)-ppz fractions were collected with weight average molecular weights ranging from 130 to 950 kDa, and with narrow molecular mass distributions (Mw/Mn from 1.1 to 1.3). At polymer-to-DNA (N/P) ratios above 6, polyplexes based on these polymers were all positively charged (zeta potential 25-29 mV), and had a size of 80-90 nm. The in vitro cytotoxicity of the polyplexes positively correlated with polymer molecular weight. The in vitro transfection activity of the different polyplexes depended on their N/P ratio, and was affected by the degree of cytotoxicity, as well as the colloidal stability of the different polyplexes. Intravenous administration of polyplexes based on the high molecular weight polymers led to apparent toxicity, as a result of polyplex-induced erythrocyte aggregation. On the other hand, administration of polyplexes based on low molecular weight p(DMAEA)-ppz's (Mw 130 kDa) did not show signs of toxicity and resulted in tumor selective gene expression. CONCLUSION Polymer molecular weight fractionation enabled us to optimize the transfection efficiency/toxicity ratio of p(DMAEA)-ppz polyplexes for in vitro and in vivo tumor transfection.
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Affiliation(s)
- Holger K. de Wolf
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 80082, 3508 TB, Utrecht, The Netherlands
| | - Markus de Raad
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 80082, 3508 TB, Utrecht, The Netherlands
| | - Cor Snel
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 80082, 3508 TB, Utrecht, The Netherlands
| | - Mies J. van Steenbergen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 80082, 3508 TB, Utrecht, The Netherlands
| | - Marcel H. A. M. Fens
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 80082, 3508 TB, Utrecht, The Netherlands
| | - Gert Storm
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 80082, 3508 TB, Utrecht, The Netherlands
| | - Wim E. Hennink
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, 80082, 3508 TB, Utrecht, The Netherlands
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