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Raza S, Sarkar D, Chan LJG, Mae J, Sutter M, Petzold CJ, Kerfeld CA, Ralston CY, Gupta S, Vermaas JV. Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells. bioRxiv 2024:2024.03.12.584231. [PMID: 38559214 PMCID: PMC10980050 DOI: 10.1101/2024.03.12.584231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Bacterial microcompartments (BMCs) are protein-bound organelles found in some bacteria which encapsulate enzymes for enhanced catalytic activity. These compartments spatially sequester enzymes within semi-permeable shell proteins, analogous to many membrane-bound organelles. The shell proteins assemble into multimeric tiles; hexamers, trimers, and pentamers, and these tiles self-assemble into larger assemblies with icosahedral symmetry. While icosahedral shells are the predominant form in vivo, the tiles can also form nanoscale cylinders or sheets. The individual multimeric tiles feature central pores that are key to regulating transport across the protein shell. Our primary interest is to quantify pore shape changes in response to alternative component morphologies at the nanoscale. We use molecular modeling tools to develop atomically detailed models for both planar sheets of tiles and curved structures representative of the complete shells found in vivo. Subsequently, these models were animated using classical molecular dynamics simulations. From the resulting trajectories, we analyzed overall structural stability, water accessibility to individual residues, water residence time, and pore geometry for the hexameric and trimeric protein tiles from the Haliangium ochraceum model BMC shell. These exhaustive analyses suggest no substantial variation in pore structure or solvent accessibility between the flat and curved shell geometries. We additionally compare our analysis to hydroxyl radical footprinting data to serve as a check against our simulation results, highlighting specific residues where water molecules are bound for a long time. Although with little variation in morphology or water interaction, we propose that the planar and capsular morphology can be used interchangeably when studying permeability through BMC pores.
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Affiliation(s)
- Saad Raza
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Daipayan Sarkar
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Leanne Jade G Chan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Current address: Calico Life Sciences LLC, South San Francisco, CA 94080
| | - Joshua Mae
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Department Of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Corie Y Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley CA 94720
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing MI 48824
- Department Of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824
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2
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van Munster JM, Daly P, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Arvas M, Raulo R, Pullan ST, Delmas S, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose. Biotechnol Biofuels 2020; 13:69. [PMID: 32313551 PMCID: PMC7155255 DOI: 10.1186/s13068-020-01702-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/24/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding how fungi degrade lignocellulose is a cornerstone of improving renewables-based biotechnology, in particular for the production of hydrolytic enzymes. Considerable progress has been made in investigating fungal degradation during time-points where CAZyme expression peaks. However, a robust understanding of the fungal survival strategies over its life time on lignocellulose is thereby missed. Here we aimed to uncover the physiological responses of the biotechnological workhorse and enzyme producer Aspergillus niger over its life time to six substrates important for biofuel production. RESULTS We analysed the response of A. niger to the feedstock Miscanthus and compared it with our previous study on wheat straw, alone or in combination with hydrothermal or ionic liquid feedstock pretreatments. Conserved (substrate-independent) metabolic responses as well as those affected by pretreatment and feedstock were identified via multivariate analysis of genome-wide transcriptomics combined with targeted transcript and protein analyses and mapping to a metabolic model. Initial exposure to all substrates increased fatty acid beta-oxidation and lipid metabolism transcripts. In a strain carrying a deletion of the ortholog of the Aspergillus nidulans fatty acid beta-oxidation transcriptional regulator farA, there was a reduction in expression of selected lignocellulose degradative CAZyme-encoding genes suggesting that beta-oxidation contributes to adaptation to lignocellulose. Mannan degradation expression was wheat straw feedstock-dependent and pectin degradation was higher on the untreated substrates. In the later life stages, known and novel secondary metabolite gene clusters were activated, which are of high interest due to their potential to synthesize bioactive compounds. CONCLUSION In this study, which includes the first transcriptional response of Aspergilli to Miscanthus, we highlighted that life time as well as substrate composition and structure (via variations in pretreatment and feedstock) influence the fungal responses to lignocellulose. We also demonstrated that the fungal response contains physiological stages that are conserved across substrates and are typically found outside of the conditions with high CAZyme expression, as exemplified by the stages that are dominated by lipid and secondary metabolism.
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Affiliation(s)
- Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Manchester Institute of Biotechnology (MIB) & School of Chemistry, The University of Manchester, Manchester, M1 7DN UK
| | - Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present Address: Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, People’s Republic of China
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | | | | | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box FI-1000, 02044 VTT Espoo, Finland
| | - Roxane Raulo
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Public Health England, National Infection Service, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Present Address: Laboratory of Computational and Quantitative Biology, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, 75005 Paris, France
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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3
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Blake-Hedges JM, Pereira JH, Cruz-Morales P, Thompson MG, Barajas JF, Chen J, Krishna RN, Chan LJG, Nimlos D, Alonso-Martinez C, Baidoo EEK, Chen Y, Gin JW, Katz L, Petzold CJ, Adams PD, Keasling JD. Structural Mechanism of Regioselectivity in an Unusual Bacterial Acyl-CoA Dehydrogenase. J Am Chem Soc 2020; 142:835-846. [PMID: 31793780 DOI: 10.1021/jacs.9b09187] [Citation(s) in RCA: 9] [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: 12/23/2022]
Abstract
Terminal alkenes are easily derivatized, making them desirable functional group targets for polyketide synthase (PKS) engineering. However, they are rarely encountered in natural PKS systems. One mechanism for terminal alkene formation in PKSs is through the activity of an acyl-CoA dehydrogenase (ACAD). Herein, we use biochemical and structural analysis to understand the mechanism of terminal alkene formation catalyzed by an γ,δ-ACAD from the biosynthesis of the polyketide natural product FK506, TcsD. While TcsD is homologous to canonical α,β-ACADs, it acts regioselectively at the γ,δ-position and only on α,β-unsaturated substrates. Furthermore, this regioselectivity is controlled by a combination of bulky residues in the active site and a lateral shift in the positioning of the FAD cofactor within the enzyme. Substrate modeling suggests that TcsD utilizes a novel set of hydrogen bond donors for substrate activation and positioning, preventing dehydrogenation at the α,β position of substrates. From the structural and biochemical characterization of TcsD, key residues that contribute to regioselectivity and are unique to the protein family were determined and used to identify other putative γ,δ-ACADs that belong to diverse natural product biosynthetic gene clusters. These predictions are supported by the demonstration that a phylogenetically distant homologue of TcsD also regioselectively oxidizes α,β-unsaturated substrates. This work exemplifies a powerful approach to understand unique enzymatic reactions and will facilitate future enzyme discovery, inform enzyme engineering, and aid natural product characterization efforts.
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Affiliation(s)
- Jacquelyn M Blake-Hedges
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Jose Henrique Pereira
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Mitchell G Thompson
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Plant and Microbial Biology , University of California-Berkeley , Berkeley , California 94720 , United States
| | - Jesus F Barajas
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Plant and Microbial Biology , University of California-Berkeley , Berkeley , California 94720 , United States
| | - Jeffrey Chen
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Rohith N Krishna
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Leanne Jade G Chan
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Danika Nimlos
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Catalina Alonso-Martinez
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Edward E K Baidoo
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Yan Chen
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Energy Agile BioFoundry , Emeryville , California 94608 , United States
| | - Jennifer W Gin
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Energy Agile BioFoundry , Emeryville , California 94608 , United States
| | - Leonard Katz
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,QB3 Institute , University of California-Berkeley , Emeryville , California 94608 , United States
| | - Christopher J Petzold
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Department of Energy Agile BioFoundry , Emeryville , California 94608 , United States
| | - Paul D Adams
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Jay D Keasling
- Joint BioEnergy Institute , Emeryville , California 94608 , United States.,Biological Systems and Engineering Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,QB3 Institute , University of California-Berkeley , Emeryville , California 94608 , United States.,Department of Chemical & Biomolecular Engineering, Department of Bioengineering , University of California-Berkeley , Berkeley , California 94720 , United States.,Novo Nordisk Foundation Center for Biosustainability , Technical University Denmark , DK2970 Horsholm , Denmark.,Center for Synthetic Biochemistry , Shenzhen Institutes for Advanced Technologies , Shenzhen 518055 , P. R. China
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4
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Chen Y, Guenther JM, Gin JW, Chan LJG, Costello Z, Ogorzalek TL, Tran HM, Blake-Hedges JM, Keasling JD, Adams PD, García Martín H, Hillson NJ, Petzold CJ. Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes. J Proteome Res 2019; 18:3752-3761. [DOI: 10.1021/acs.jproteome.9b00455] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
| | - Joel M. Guenther
- Sandia National Laboratories (NTESS), Livermore, California 94551, United States
| | | | | | | | | | - Huu M. Tran
- Sandia National Laboratories (NTESS), Livermore, California 94551, United States
| | | | - Jay D. Keasling
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720-1460, United States
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby 2800, Denmark
- Center for Synthetic Biochemistry, Synthetic Biology Institute, Shenzhen Institutes for Advanced Technologies, Shenzhen 518000, China
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5
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Chen Y, Vu J, Thompson MG, Sharpless WA, Chan LJG, Gin JW, Keasling JD, Adams PD, Petzold CJ. A rapid methods development workflow for high-throughput quantitative proteomic applications. PLoS One 2019; 14:e0211582. [PMID: 30763335 PMCID: PMC6375547 DOI: 10.1371/journal.pone.0211582] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 10/11/2018] [Accepted: 01/16/2019] [Indexed: 12/13/2022] Open
Abstract
Recent improvements in the speed and sensitivity of liquid chromatography-mass spectrometry systems have driven significant progress toward system-wide characterization of the proteome of many species. These efforts create large proteomic datasets that provide insight into biological processes and identify diagnostic proteins whose abundance changes significantly under different experimental conditions. Yet, these system-wide experiments are typically the starting point for hypothesis-driven, follow-up experiments to elucidate the extent of the phenomenon or the utility of the diagnostic marker, wherein many samples must be analyzed. Transitioning from a few discovery experiments to quantitative analyses on hundreds of samples requires significant resources both to develop sensitive and specific methods as well as analyze them in a high-throughput manner. To aid these efforts, we developed a workflow using data acquired from discovery proteomic experiments, retention time prediction, and standard-flow chromatography to rapidly develop targeted proteomic assays. We demonstrated this workflow by developing MRM assays to quantify proteins of multiple metabolic pathways from multiple microbes under different experimental conditions. With this workflow, one can also target peptides in scheduled/dynamic acquisition methods from a shotgun proteomic dataset downloaded from online repositories, validate with appropriate control samples or standard peptides, and begin analyzing hundreds of samples in only a few minutes.
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Affiliation(s)
- Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Jonathan Vu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Mitchell G. Thompson
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - William A. Sharpless
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Leanne Jade G. Chan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Jennifer W. Gin
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Jay D. Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, United States of America
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, United States of America
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Paul D. Adams
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, United States of America
- Molecular Biophysics and Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, United States of America
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- * E-mail:
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6
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Budin I, de Rond T, Chen Y, Chan LJG, Petzold CJ, Keasling JD. Viscous control of cellular respiration by membrane lipid composition. Science 2018; 362:1186-1189. [PMID: 30361388 DOI: 10.1126/science.aat7925] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/11/2018] [Indexed: 12/15/2022]
Abstract
Lipid composition determines the physical properties of biological membranes and can vary substantially between and within organisms. We describe a specific role for the viscosity of energy-transducing membranes in cellular respiration. Engineering of fatty acid biosynthesis in Escherichia coli allowed us to titrate inner membrane viscosity across a 10-fold range by controlling the abundance of unsaturated or branched lipids. These fluidizing lipids tightly controlled respiratory metabolism, an effect that can be explained with a quantitative model of the electron transport chain (ETC) that features diffusion-coupled reactions between enzymes and electron carriers (quinones). Lipid unsaturation also modulated mitochondrial respiration in engineered budding yeast strains. Thus, diffusion in the ETC may serve as an evolutionary constraint for lipid composition in respiratory membranes.
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Affiliation(s)
- Itay Budin
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA. .,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tristan de Rond
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.,Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.,Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.,Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA. .,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.,QB3 Institute, University of California, Berkeley, Berkeley, CA 94270, USA.,The Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, Denmark.,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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7
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Curran SC, Hagen A, Poust S, Chan LJG, Garabedian BM, de Rond T, Baluyot MJ, Vu JT, Lau AK, Yuzawa S, Petzold CJ, Katz L, Keasling JD. Probing the Flexibility of an Iterative Modular Polyketide Synthase with Non-Native Substrates in Vitro. ACS Chem Biol 2018; 13:2261-2268. [PMID: 29912551 DOI: 10.1021/acschembio.8b00422] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the search for molecular machinery for custom biosynthesis of valuable compounds, the modular type I polyketide synthases (PKSs) offer great potential. In this study, we investigate the flexibility of BorM5, the iterative fifth module of the borrelidin synthase, with a panel of non-native priming substrates in vitro. BorM5 differentially extends various aliphatic and substituted substrates. Depending on substrate size and substitution BorM5 can exceed the three iterations it natively performs. To probe the effect of methyl branching on chain length regulation, we engineered a BorM5 variant capable of incorporating methylmalonyl- and malonyl-CoA into its intermediates. Intermediate methylation did not affect overall chain length, indicating that the enzyme does not to count methyl branches to specify the number of iterations. In addition to providing regulatory insight about BorM5, we produced dozens of novel methylated intermediates that might be used for production of various hydrocarbons or pharmaceuticals. These findings enable rational engineering and recombination of BorM5 and inform the study of other iterative modules.
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Affiliation(s)
- Samuel C. Curran
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew Hagen
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Sean Poust
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Leanne Jade G. Chan
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Brett M. Garabedian
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Tristan de Rond
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Marian-Joy Baluyot
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jonathan T. Vu
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Andrew K. Lau
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
| | - Satoshi Yuzawa
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leonard Katz
- Joint Bioenergy Institute, 5885 Hollis Street, Emeryville California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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8
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George KW, Thompson MG, Kim J, Baidoo EE, Wang G, Benites VT, Petzold CJ, Chan LJG, Yilmaz S, Turhanen P, Adams PD, Keasling JD, Lee TS. Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli. Metab Eng 2018. [DOI: 10.1016/j.ymben.2018.03.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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Denby CM, Li RA, Vu VT, Costello Z, Lin W, Chan LJG, Williams J, Donaldson B, Bamforth CW, Petzold CJ, Scheller HV, Martin HG, Keasling JD. Industrial brewing yeast engineered for the production of primary flavor determinants in hopped beer. Nat Commun 2018; 9:965. [PMID: 29559655 PMCID: PMC5861129 DOI: 10.1038/s41467-018-03293-x] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [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: 08/09/2017] [Accepted: 02/02/2018] [Indexed: 12/04/2022] Open
Abstract
Flowers of the hop plant provide both bitterness and “hoppy” flavor to beer. Hops are, however, both a water and energy intensive crop and vary considerably in essential oil content, making it challenging to achieve a consistent hoppy taste in beer. Here, we report that brewer’s yeast can be engineered to biosynthesize aromatic monoterpene molecules that impart hoppy flavor to beer by incorporating recombinant DNA derived from yeast, mint, and basil. Whereas metabolic engineering of biosynthetic pathways is commonly enlisted to maximize product titers, tuning expression of pathway enzymes to affect target production levels of multiple commercially important metabolites without major collateral metabolic changes represents a unique challenge. By applying state-of-the-art engineering techniques and a framework to guide iterative improvement, strains are generated with target performance characteristics. Beers produced using these strains are perceived as hoppier than traditionally hopped beers by a sensory panel in a double-blind tasting. Production of aromatic monoterpene molecules in hop flowers is affected by genetic, environmental, and processing factors. Here, the authors engineer brewer’s yeast for the production of linalool and geraniol, and show pilot-scale beer produced by engineered strains reconstitutes some qualities of hop flavor.
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Affiliation(s)
- Charles M Denby
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA. .,Joint BioEnergy Institute, Emeryville, CA, 94608, USA.
| | - Rachel A Li
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.,Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Van T Vu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
| | - Zak Costello
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA.,DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Weiyin Lin
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA.,Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Joseph Williams
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | | | - Charles W Bamforth
- Department of Food Science and Technology, University of California Davis, Davis, CA, 95616, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.,Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, 94720, USA
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA.,DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Jay D Keasling
- California Institute of Quantitative Biosciences (QB3), University of California, Berkeley, CA, 94720, USA. .,Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA. .,Department of Bioengineering, University of California, Berkeley, CA, 94720, USA. .,Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA. .,Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, 2900, Hellerup, Denmark.
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10
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Kolinko S, Wu YW, Tachea F, Denzel E, Hiras J, Gabriel R, Bäcker N, Chan LJG, Eichorst SA, Frey D, Chen Q, Azadi P, Adams PD, Pray TR, Tanjore D, Petzold CJ, Gladden JM, Simmons BA, Singer SW. A bacterial pioneer produces cellulase complexes that persist through community succession. Nat Microbiol 2017; 3:99-107. [PMID: 29109478 PMCID: PMC6794216 DOI: 10.1038/s41564-017-0052-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 01/26/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022]
Abstract
Cultivation of microbial consortia provides low-complexity communities that can serve as tractable models to understand community dynamics. Time-resolved metagenomics demonstrated that an aerobic cellulolytic consortium cultivated from compost exhibited community dynamics consistent with the definition of an endogenous heterotrophic succession. The genome of the proposed pioneer population, ‘Candidatus Reconcilibacillus cellulovorans’, possessed a gene cluster containing multidomain glycoside hydrolases (GHs). Purification of the soluble cellulase activity from a 300litre cultivation of this consortium revealed that ~70% of the activity arose from the ‘Ca. Reconcilibacillus cellulovorans’ multidomain GHs assembled into cellulase complexes through glycosylation. These remarkably stable complexes have supramolecular structures for enzymatic cellulose hydrolysis that are distinct from cellulosomes. The persistence of these complexes during cultivation indicates that they may be active through multiple cultivations of this consortium and act as public goods that sustain the community. The provision of extracellular GHs as public goods may influence microbial community dynamics in native biomass-deconstructing communities relevant to agriculture, human health and biotechnology. Cultivation of a cellulolytic consortium reveals successional community dynamics and the presence of multidomain glycoside hydrolases assembled into stable complexes distinct from cellulosomes, which are produced by a potential pioneer population.
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Affiliation(s)
- Sebastian Kolinko
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yu-Wei Wu
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Firehiwot Tachea
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Evelyn Denzel
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Jennifer Hiras
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Corning Incorporated, Corning, NY, USA
| | - Raphael Gabriel
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Institut für Genetik, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Bäcker
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephanie A Eichorst
- Joint BioEnergy Institute, Emeryville, CA, USA.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Research network "Chemistry meets Microbiology", University of Vienna, Vienna, Austria
| | - Dario Frey
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Faculty of Biotechnology, University of Applied Sciences, Mannheim, Germany
| | - Qiushi Chen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Todd R Pray
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological and Materials Science Center, Sandia National Laboratories, Livermore, CA, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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11
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de Rond T, Stow P, Eigl I, Johnson RE, Chan LJG, Goyal G, Baidoo EEK, Hillson NJ, Petzold CJ, Sarpong R, Keasling JD. Oxidative cyclization of prodigiosin by an alkylglycerol monooxygenase-like enzyme. Nat Chem Biol 2017; 13:1155-1157. [PMID: 28892091 PMCID: PMC5677514 DOI: 10.1038/nchembio.2471] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/26/2017] [Indexed: 11/08/2022]
Abstract
Prodiginines, which are tripyrrole alkaloids displaying a wide array of bioactivities, occur as linear and cyclic congeners. Identification of an unclustered biosynthetic gene led to the discovery of the enzyme responsible for catalyzing the regiospecific C-H activation and cyclization of prodigiosin to cycloprodigiosin in Pseudoalteromonas rubra. This enzyme is related to alkylglycerol monooxygenase and unrelated to RedG, the Rieske oxygenase that produces cyclized prodiginines in Streptomyces, implying convergent evolution.
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Affiliation(s)
- Tristan de Rond
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Parker Stow
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Ian Eigl
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Rebecca E Johnson
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Leanne Jade G Chan
- DOE Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, California, USA
| | - Garima Goyal
- DOE Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, California, USA
| | - Edward E K Baidoo
- DOE Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, California, USA
| | - Nathan J Hillson
- DOE Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, California, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Christopher J Petzold
- DOE Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, California, USA
| | - Richmond Sarpong
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Jay D Keasling
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- DOE Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Lab, Berkeley, California, USA
- Department of Bioengineering and California Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
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12
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Fukushima T, Gupta S, Rad B, Cornejo JA, Petzold CJ, Chan LJG, Mizrahi RA, Ralston CY, Ajo-Franklin CM. The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface. J Am Chem Soc 2017; 139:12647-12654. [DOI: 10.1021/jacs.7b06560] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Tatsuya Fukushima
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Sayan Gupta
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Behzad Rad
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jose A. Cornejo
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leanne Jade G. Chan
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rena A. Mizrahi
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Corie Y. Ralston
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Caroline M. Ajo-Franklin
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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13
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Venturelli OS, Tei M, Bauer S, Chan LJG, Petzold CJ, Arkin AP. Programming mRNA decay to modulate synthetic circuit resource allocation. Nat Commun 2017; 8:15128. [PMID: 28443619 PMCID: PMC5414051 DOI: 10.1038/ncomms15128] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [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: 10/08/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic circuits embedded in host cells compete with cellular processes for limited intracellular resources. Here we show how funnelling of cellular resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence. The expression of a protected fluorescent reporter and flux of a high-value metabolite are significantly enhanced using this genome-scale control strategy. Proteomics measurements discover a host factor in need of protection to improve resource redistribution activity. A computational model demonstrates that the MazF mRNA-decay feedback loop enables proportional control of MazF in an optimal operating regime. Transcriptional profiling of MazF-induced cells elucidates the dynamic shifts in transcript abundance and discovers regulatory design elements. Altogether, our results suggest that manipulation of cellular resource allocation is a key control parameter for synthetic circuit design. Synthetic circuits in host cells compete with endogenous processes for limited resources. Here the authors use MazF to funnel cellular resources to a synthetic circuit to increase product production and demonstrate how resource allocation can be manipulated.
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Affiliation(s)
- Ophelia S Venturelli
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94158, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, USA
| | - Mika Tei
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94158, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, USA
| | - Stefan Bauer
- Energy Biosciences Institute, University of California Berkeley, Berkeley, California 94704, USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Adam P Arkin
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94158, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, USA.,Energy Biosciences Institute, University of California Berkeley, Berkeley, California 94704, USA.,Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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14
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Daly P, van Munster JM, Blythe MJ, Ibbett R, Kokolski M, Gaddipati S, Lindquist E, Singan VR, Barry KW, Lipzen A, Ngan CY, Petzold CJ, Chan LJG, Pullan ST, Delmas S, Waldron PR, Grigoriev IV, Tucker GA, Simmons BA, Archer DB. Expression of Aspergillus niger CAZymes is determined by compositional changes in wheat straw generated by hydrothermal or ionic liquid pretreatments. Biotechnol Biofuels 2017; 10:35. [PMID: 28184248 PMCID: PMC5294722 DOI: 10.1186/s13068-017-0700-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/05/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND The capacity of fungi, such as Aspergillus niger, to degrade lignocellulose is harnessed in biotechnology to generate biofuels and high-value compounds from renewable feedstocks. Most feedstocks are currently pretreated to increase enzymatic digestibility: improving our understanding of the transcriptomic responses of fungi to pretreated lignocellulosic substrates could help to improve the mix of activities and reduce the production costs of commercial lignocellulose saccharifying cocktails. RESULTS We investigated the responses of A. niger to untreated, ionic liquid and hydrothermally pretreated wheat straw over a 5-day time course using RNA-seq and targeted proteomics. The ionic liquid pretreatment altered the cellulose crystallinity while retaining more of the hemicellulosic sugars than the hydrothermal pretreatment. Ionic liquid pretreatment of straw led to a dynamic induction and repression of genes, which was correlated with the higher levels of pentose sugars saccharified from the ionic liquid-pretreated straw. Hydrothermal pretreatment of straw led to reduced levels of transcripts of genes encoding carbohydrate-active enzymes as well as the derived proteins and enzyme activities. Both pretreatments abolished the expression of a large set of genes encoding pectinolytic enzymes. These reduced levels could be explained by the removal of parts of the lignocellulose by the hydrothermal pretreatment. The time course also facilitated identification of temporally limited gene induction patterns. CONCLUSIONS The presented transcriptomic and biochemical datasets demonstrate that pretreatments caused modifications of the lignocellulose, to both specific structural features as well as the organisation of the overall lignocellulosic structure, that determined A. niger transcript levels. The experimental setup allowed reliable detection of substrate-specific gene expression patterns as well as hitherto non-expressed genes. Our data suggest beneficial effects of using untreated and IL-pretreated straw, but not HT-pretreated straw, as feedstock for CAZyme production.
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Affiliation(s)
- Paul Daly
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Fungal Physiology, CBS-KNAW Fungal Biodiversity Centre, Utrecht University, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - Jolanda M. van Munster
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Martin J. Blythe
- Deep Seq, Faculty of Medicine and Health Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, NG7 2UH UK
| | - Roger Ibbett
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Matt Kokolski
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Sanyasi Gaddipati
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Vasanth R. Singan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Kerrie W. Barry
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | | | - Steven T. Pullan
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- TB Programme, Microbiology Services, Public Health England, Salisbury, UK
| | - Stéphane Delmas
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- UPMC, Univ. Paris 06, CNRS UMR7238, Sorbonne Universités, 15 rue de l’Ecole de Médecine, 75270 Paris, France
| | - Paul R. Waldron
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Gregory A. Tucker
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | | | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
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15
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Gupta S, Feng J, Chan LJG, Petzold CJ, Ralston CY. Synchrotron X-ray footprinting as a method to visualize water in proteins. J Synchrotron Radiat 2016; 23:1056-69. [PMID: 27577756 PMCID: PMC5006651 DOI: 10.1107/s1600577516009024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/03/2016] [Indexed: 05/23/2023]
Abstract
The vast majority of biomolecular processes are controlled or facilitated by water interactions. In enzymes, regulatory proteins, membrane-bound receptors and ion-channels, water bound to functionally important residues creates hydrogen-bonding networks that underlie the mechanism of action of the macromolecule. High-resolution X-ray structures are often difficult to obtain with many of these classes of proteins because sample conditions, such as the necessity of detergents, often impede crystallization. Other biophysical techniques such as neutron scattering, nuclear magnetic resonance and Fourier transform infrared spectroscopy are useful for studying internal water, though each has its own advantages and drawbacks, and often a hybrid approach is required to address important biological problems associated with protein-water interactions. One major area requiring more investigation is the study of bound water molecules which reside in cavities and channels and which are often involved in both the structural and functional aspects of receptor, transporter and ion channel proteins. In recent years, significant progress has been made in synchrotron-based radiolytic labeling and mass spectroscopy techniques for both the identification of bound waters and for characterizing the role of water in protein conformational changes at a high degree of spatial and temporal resolution. Here the latest developments and future capabilities of this method for investigating water-protein interactions and its synergy with other synchrotron-based methods are discussed.
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Affiliation(s)
- Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jun Feng
- Experimental Systems, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Leanne Jade G. Chan
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Christopher J. Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Corie Y. Ralston
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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16
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Schwessinger B, Li X, Ellinghaus TL, Chan LJG, Wei T, Joe A, Thomas N, Pruitt R, Adams PD, Chern MS, Petzold CJ, Liu CC, Ronald PC. A second-generation expression system for tyrosine-sulfated proteins and its application in crop protection. Integr Biol (Camb) 2015; 8:542-5. [PMID: 26611838 DOI: 10.1039/c5ib00232j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Posttranslational modification (PTM) of proteins and peptides is important for diverse biological processes in plants and animals. The paucity of heterologous expression systems for PTMs and the technical challenges associated with chemical synthesis of these modified proteins has limited detailed molecular characterization and therapeutic applications. Here we describe an optimized system for expression of tyrosine-sulfated proteins in Escherichia coli and its application in a bio-based crop protection strategy in rice.
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Affiliation(s)
- Benjamin Schwessinger
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA.
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17
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Abstract
Realizing the promise of metabolic engineering has been slowed by challenges related to moving beyond proof-of-concept examples to robust and economically viable systems. Key to advancing metabolic engineering beyond trial-and-error research is access to parts with well-defined performance metrics that can be readily applied in vastly different contexts with predictable effects. As the field now stands, research depends greatly on analytical tools that assay target molecules, transcripts, proteins, and metabolites across different hosts and pathways. Screening technologies yield specific information for many thousands of strain variants, while deep omics analysis provides a systems-level view of the cell factory. Efforts focused on a combination of these analyses yield quantitative information of dynamic processes between parts and the host chassis that drive the next engineering steps. Overall, the data generated from these types of assays aid better decision-making at the design and strain construction stages to speed progress in metabolic engineering research.
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Affiliation(s)
- Christopher J Petzold
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Leanne Jade G Chan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Melissa Nhan
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA
| | - Paul D Adams
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, CA , USA ; Department of Bioengineering, University of California Berkeley , Berkeley, CA , USA
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18
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Pruitt RN, Schwessinger B, Joe A, Thomas N, Liu F, Albert M, Robinson MR, Chan LJG, Luu DD, Chen H, Bahar O, Daudi A, De Vleesschauwer D, Caddell D, Zhang W, Zhao X, Li X, Heazlewood JL, Ruan D, Majumder D, Chern M, Kalbacher H, Midha S, Patil PB, Sonti RV, Petzold CJ, Liu CC, Brodbelt JS, Felix G, Ronald PC. The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium. Sci Adv 2015; 1:e1500245. [PMID: 26601222 PMCID: PMC4646787 DOI: 10.1126/sciadv.1500245] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/14/2015] [Indexed: 05/18/2023]
Abstract
Surveillance of the extracellular environment by immune receptors is of central importance to eukaryotic survival. The rice receptor kinase XA21, which confers robust resistance to most strains of the Gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is representative of a large class of cell surface immune receptors in plants and animals. We report the identification of a previously undescribed Xoo protein, called RaxX, which is required for activation of XA21-mediated immunity. Xoo strains that lack RaxX, or carry mutations in the single RaxX tyrosine residue (Y41), are able to evade XA21-mediated immunity. Y41 of RaxX is sulfated by the prokaryotic tyrosine sulfotransferase RaxST. Sulfated, but not nonsulfated, RaxX triggers hallmarks of the plant immune response in an XA21-dependent manner. A sulfated, 21-amino acid synthetic RaxX peptide (RaxX21-sY) is sufficient for this activity. Xoo field isolates that overcome XA21-mediated immunity encode an alternate raxX allele, suggesting that coevolutionary interactions between host and pathogen contribute to RaxX diversification. RaxX is highly conserved in many plant pathogenic Xanthomonas species. The new insights gained from the discovery and characterization of the sulfated protein, RaxX, can be applied to the development of resistant crop varieties and therapeutic reagents that have the potential to block microbial infection of both plants and animals.
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Affiliation(s)
- Rory N. Pruitt
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Benjamin Schwessinger
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The Australian National University, Research School of Biology, Acton ACT 2601, Australia
- Corresponding author. E-mail: (B.S.); (P.C.R.)
| | - Anna Joe
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas Thomas
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Furong Liu
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Markus Albert
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
| | - Michelle R. Robinson
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
| | - Leanne Jade G. Chan
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dee Dee Luu
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Huamin Chen
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Ofir Bahar
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Arsalan Daudi
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - David De Vleesschauwer
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Daniel Caddell
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Weiguo Zhang
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Xiuxiang Zhao
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Xiang Li
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Deling Ruan
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dipali Majumder
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tübingen, 72074 Tübingen, Germany
| | - Samriti Midha
- Council of Scientific & Industrial Research (CSIR)–Institute of Microbial Technology, Chandigarh 160036, India
| | - Prabhu B. Patil
- Council of Scientific & Industrial Research (CSIR)–Institute of Microbial Technology, Chandigarh 160036, India
| | - Ramesh V. Sonti
- CSIR–Centre for Cellular and Molecular Biology, Hyderabad 500007, India
| | - Christopher J. Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chang C. Liu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Georg Felix
- Centre for Plant Molecular Biology, University of Tübingen, 72074 Tübingen, Germany
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, Davis, CA 95616, USA
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Corresponding author. E-mail: (B.S.); (P.C.R.)
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19
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Ebert B, Rautengarten C, Guo X, Xiong G, Stonebloom S, Smith-Moritz AM, Herter T, Chan LJG, Adams PD, Petzold CJ, Pauly M, Willats WGT, Heazlewood JL, Scheller HV. Identification and Characterization of a Golgi-Localized UDP-Xylose Transporter Family from Arabidopsis. Plant Cell 2015; 27:1218-27. [PMID: 25804536 PMCID: PMC4558686 DOI: 10.1105/tpc.114.133827] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 03/05/2015] [Indexed: 05/02/2023]
Abstract
Most glycosylation reactions require activated glycosyl donors in the form of nucleotide sugars to drive processes such as posttranslational modifications and polysaccharide biosynthesis. Most plant cell wall polysaccharides are biosynthesized in the Golgi apparatus from cytosolic-derived nucleotide sugars, which are actively transferred into the Golgi lumen by nucleotide sugar transporters (NSTs). An exception is UDP-xylose, which is biosynthesized in both the cytosol and the Golgi lumen by a family of UDP-xylose synthases. The NST-based transport of UDP-xylose into the Golgi lumen would appear to be redundant. However, employing a recently developed approach, we identified three UDP-xylose transporters in the Arabidopsis thaliana NST family and designated them UDP-XYLOSE TRANSPORTER1 (UXT1) to UXT3. All three transporters localize to the Golgi apparatus, and UXT1 also localizes to the endoplasmic reticulum. Mutants in UXT1 exhibit ∼30% reduction in xylose in stem cell walls. These findings support the importance of the cytosolic UDP-xylose pool and UDP-xylose transporters in cell wall biosynthesis.
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Affiliation(s)
- Berit Ebert
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Carsten Rautengarten
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Xiaoyuan Guo
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark
| | - Guangyan Xiong
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Solomon Stonebloom
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Andreia M Smith-Moritz
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Thomas Herter
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Leanne Jade G Chan
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Paul D Adams
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Bioengineering, University of California, Berkeley, California 94720
| | - Christopher J Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Markus Pauly
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - William G T Willats
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, C 1871 Copenhagen, Denmark
| | - Joshua L Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Victoria 3010, Australia
| | - Henrik Vibe Scheller
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
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20
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González Fernández-Niño SM, Smith-Moritz AM, Chan LJG, Adams PD, Heazlewood JL, Petzold CJ. Standard flow liquid chromatography for shotgun proteomics in bioenergy research. Front Bioeng Biotechnol 2015; 3:44. [PMID: 25883932 PMCID: PMC4381839 DOI: 10.3389/fbioe.2015.00044] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [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: 02/11/2015] [Accepted: 03/18/2015] [Indexed: 11/18/2022] Open
Abstract
Over the past 10 years, the bioenergy field has realized significant achievements that have encouraged many follow on efforts centered on biosynthetic production of fuel-like compounds. Key to the success of these efforts has been transformational developments in feedstock characterization and metabolic engineering of biofuel-producing microbes. Lagging far behind these advancements are analytical methods to characterize and quantify systems of interest to the bioenergy field. In particular, the utilization of proteomics, while valuable for identifying novel enzymes and diagnosing problems associated with biofuel-producing microbes, is limited by a lack of robustness and limited throughput. Nano-flow liquid chromatography coupled to high-mass accuracy, high-resolution mass spectrometers has become the dominant approach for the analysis of complex proteomic samples, yet such assays still require dedicated experts for data acquisition, analysis, and instrument upkeep. The recent adoption of standard flow chromatography (ca. 0.5 mL/min) for targeted proteomics has highlighted the robust nature and increased throughput of this approach for sample analysis. Consequently, we assessed the applicability of standard flow liquid chromatography for shotgun proteomics using samples from Escherichia coli and Arabidopsis thaliana, organisms commonly used as model systems for lignocellulosic biofuels research. Employing 120 min gradients with standard flow chromatography, we were able to routinely identify nearly 800 proteins from E. coli samples; while for samples from Arabidopsis, over 1,000 proteins could be reliably identified. An examination of identified peptides indicated that the method was suitable for reproducible applications in shotgun proteomics. Standard flow liquid chromatography for shotgun proteomics provides a robust approach for the analysis of complex samples. To the best of our knowledge, this study represents the first attempt to validate the standard flow approach for shotgun proteomics.
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Affiliation(s)
| | - A. Michelle Smith-Moritz
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Leanne Jade G. Chan
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D. Adams
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Joshua L. Heazlewood
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Australian Research Council Centre of Excellence in Plant Cell Walls, School of Botany, The University of Melbourne, Melbourne, VIC, Australia
| | - Christopher J. Petzold
- Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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21
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Winger AM, Heazlewood JL, Chan LJG, Petzold CJ, Permaul K, Singh S. Secretome analysis of the thermophilic xylanase hyper-producer Thermomyces lanuginosus SSBP cultivated on corn cobs. J Ind Microbiol Biotechnol 2014; 41:1687-96. [PMID: 25223615 DOI: 10.1007/s10295-014-1509-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/03/2014] [Indexed: 12/27/2022]
Abstract
Thermomyces lanuginosus is a thermophilic fungus known for its ability to produce industrially important enzymes including large amounts of xylanase, the key enzyme in hemicellulose hydrolysis. The secretome of T. lanuginosus SSBP was profiled by shotgun proteomics to elucidate important enzymes involved in hemicellulose saccharification and to characterise the presence of other industrially interesting enzymes. This study reproducibly identified a total of 74 proteins in the supernatant following growth on corn cobs. An analysis of proteins revealed nine glycoside hydrolase (GH) enzymes including xylanase GH11, β-xylosidase GH43, β-glucosidase GH3, α-galactosidase GH36 and trehalose hydrolase GH65. Two commercially produced Thermomyces enzymes, lipase and amylase, were also identified. In addition, other industrially relevant enzymes not currently explored in Thermomyces were identified including glutaminase, fructose-bisphosphate aldolase and cyanate hydratase. Overall, these data provide insight into the novel ability of a cellulase-free fungus to utilise lignocellulosic material, ultimately producing a number of enzymes important to various industrial processes.
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Affiliation(s)
- A M Winger
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4001, South Africa
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