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Singh V, Finke-Isami J, Hopper-Chidlaw AC, Schwerk P, Thompson A, Tedin K. Salmonella Co-opts Host Cell Chaperone-mediated Autophagy for Intracellular Growth. J Biol Chem 2017; 292:1847-1864. [PMID: 27932462 PMCID: PMC5290957 DOI: 10.1074/jbc.m116.759456] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/01/2016] [Indexed: 01/05/2023] Open
Abstract
Salmonella enterica are invasive intracellular pathogens that replicate within a membrane-bound compartment inside infected host cells known as the Salmonella-containing vacuole. How Salmonella obtains nutrients for growth within this intracellular niche despite the apparent isolation is currently not known. Recent studies have indicated the importance of glucose and related carbon sources for tissue colonization and intracellular proliferation within host cells during Salmonella infections, although none have been found to be essential. We found that wild-type Salmonella are capable of replicating within infected host cells in the absence of both exogenous sugars and/or amino acids. Furthermore, mutants defective in glucose uptake or dependent upon peptides for growth also showed no significant loss in intracellular replication, suggesting host-derived peptides can supply both carbon units and amino acids. Here, we show that intracellular Salmonella recruit the host proteins LAMP-2A and Hsc73, key components of the host protein turnover pathway known as chaperone-mediated autophagy involved in transport of cytosolic proteins to the lysosome for degradation. Host-derived peptides are shown to provide a significant contribution toward the intracellular growth of Salmonella The results reveal a means whereby intracellular Salmonella gain access to the host cell cytosol from within its membrane-bound compartment to acquire nutrients. Furthermore, this study provides an explanation as to how Salmonella evades activation of autophagy mechanisms as part of the innate immune response.
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Affiliation(s)
- Vikash Singh
- From the Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany
| | - Johannes Finke-Isami
- From the Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany
| | | | - Peter Schwerk
- From the Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany
| | - Arthur Thompson
- the Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom
| | - Karsten Tedin
- From the Centre for Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany.
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Antonovsky N, Gleizer S, Noor E, Zohar Y, Herz E, Barenholz U, Zelcbuch L, Amram S, Wides A, Tepper N, Davidi D, Bar-On Y, Bareia T, Wernick DG, Shani I, Malitsky S, Jona G, Bar-Even A, Milo R. Sugar Synthesis from CO2 in Escherichia coli. Cell 2016; 166:115-25. [PMID: 27345370 PMCID: PMC4930481 DOI: 10.1016/j.cell.2016.05.064] [Citation(s) in RCA: 208] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/02/2016] [Accepted: 05/17/2016] [Indexed: 11/29/2022]
Abstract
Can a heterotrophic organism be evolved to synthesize biomass from CO2 directly? So far, non-native carbon fixation in which biomass precursors are synthesized solely from CO2 has remained an elusive grand challenge. Here, we demonstrate how a combination of rational metabolic rewiring, recombinant expression, and laboratory evolution has led to the biosynthesis of sugars and other major biomass constituents by a fully functional Calvin-Benson-Bassham (CBB) cycle in E. coli. In the evolved bacteria, carbon fixation is performed via a non-native CBB cycle, while reducing power and energy are obtained by oxidizing a supplied organic compound (e.g., pyruvate). Genome sequencing reveals that mutations in flux branchpoints, connecting the non-native CBB cycle to biosynthetic pathways, are essential for this phenotype. The successful evolution of a non-native carbon fixation pathway, though not yet resulting in net carbon gain, strikingly demonstrates the capacity for rapid trophic-mode evolution of metabolism applicable to biotechnology. PaperClip
Non-native Calvin-Benson cycle allows for sugar synthesis from CO2 in E. coli Metabolic cutoff allows for the decoupling of energy harvesting from biomass synthesis Chemostat-based directed evolution led to the emergence of sugar synthesis from CO2 Mutations in flux branchpoints are essential for the CBB cycle stable operation
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Affiliation(s)
- Niv Antonovsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shmuel Gleizer
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Noor
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yehudit Zohar
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Elad Herz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Uri Barenholz
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Lior Zelcbuch
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shira Amram
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Aryeh Wides
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Tepper
- Department of Computer Science, Technion, Israel Institute of Technology, Haifa 3200003, Israel
| | - Dan Davidi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yinon Bar-On
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tasneem Bareia
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David G Wernick
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ido Shani
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Malitsky
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ghil Jona
- Department of Biological Services, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Arren Bar-Even
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ron Milo
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Vargas-Tah A, Martínez LM, Hernández-Chávez G, Rocha M, Martínez A, Bolívar F, Gosset G. Production of cinnamic and p-hydroxycinnamic acid from sugar mixtures with engineered Escherichia coli. Microb Cell Fact 2015; 14:6. [PMID: 25592545 PMCID: PMC4305220 DOI: 10.1186/s12934-014-0185-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/20/2014] [Indexed: 11/15/2022] Open
Abstract
Background The aromatic compounds cinnamic acid (CA) and p-hydroxycinnamic acid (pHCA) are used as flavoring agents as well as precursors of chemicals. These compounds are present in plants at low concentrations, therefore, complex purification processes are usually required to extract the product. An alternative production method for these aromatic acids is based on the use of microbial strains modified by metabolic engineering. These biotechnological processes are usually based on the use of simple sugars like glucose as a raw material. However, sustainable production processes should preferably be based on the use of waste material such as lignocellulosic hydrolysates. Results In this study, E. coli strains with active (W3110) and inactive phosphoenolpyruvate:sugar phosphotransferase system (PTS) (VH33) were engineered for CA and pHCA production by transforming them with plasmids expressing genes encoding phenylalanine/tyrosine ammonia lyase (PAL/TAL) enzymes from Rhodotorula glutinis or Arabidopsis thaliana as well as genes aroGfbr and tktA, encoding a feedback inhibition resistant version of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase and transketolase, respectively. The generated strains were evaluated in cultures with glucose, xylose or arabinose, as well as a simulated lignocellulosic hydrolysate containing a mixture of these three sugars plus acetate. Production of CA was detected in strains expressing PAL/TAL from A. thaliana, whereas both CA and pHCA accumulated in strains expressing the enzyme from R. glutinis. These experiments identified arabinose and W3110 expressing PAL/TAL from A. thaliana, aroGfbr and tktA as the carbon source/strain combination resulting in the best CA specific productivity and titer. To improve pHCA production, a mutant with inactive pheA gene was generated, causing an 8-fold increase in the yield of this aromatic acid from the sugars in a simulated hydrolysate. Conclusions In this study the quantitative contribution of active or inactive PTS as well as expression of PAL/TAL from R. glutinis or A. thaliana were determined for production performance of CA and pHCA when growing on carbon sources derived from lignocellulosic hydrolysates. These data will be a useful resource in efforts towards the development of sustainable technologies for the production of aromatic acids. Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0185-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alejandra Vargas-Tah
- Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos, 62210, México.
| | - Luz María Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos, 62210, México.
| | - Georgina Hernández-Chávez
- Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos, 62210, México.
| | - Mario Rocha
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos, 62210, México.
| | - Alfredo Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos, 62210, México.
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos, 62210, México.
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos, 62210, México.
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Wang K, Wang X, Ge X, Tian P. Heterologous Expression of Aldehyde Dehydrogenase from Saccharomyces cerevisiae in Klebsiella pneumoniae for 3-Hydroxypropionic Acid Production from Glycerol. Indian J Microbiol 2012; 52:478-83. [PMID: 23997342 DOI: 10.1007/s12088-012-0280-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 06/04/2012] [Indexed: 11/28/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) is a commercially valuable platform compound. Klebsiella pneumoniae has been concerned as an appropriate host for 3-HP production because of its robust capacity to metabolize glycerol. Glycerol conversion to 3-HP in K. pneumoniae comprises two successive reactions: glycerol dehydratase catalyzes glycerol to 3-hydroxypropionaldehyde (3-HPA); aldehyde dehydrogenase catalyzes 3-HPA to 3-HP. Previous studies focusing on inducible expression of aldehyde dehydrogenase have shown defects of high cost of inducer and low catalytic activity due to inclusion body. Here we show a different strategy that a native promoter in the host K. pneumoniae was used to drive the heterologous expression of aldehyde dehydrogenase gene ald4 from Saccharomyces cerevisiae. The 3-HP yield of the recombinant reached a peak of 4.23 g/L at log phase, but it decreased during later period of fermentation. Except the validation of high activity of ald4, particularly, the 3-HP formation was uncovered to be closely coupled with cell division, and the lacking of NAD and ATP at latter fermentation phase became the bottleneck for cell growth and 3-HP accumulation. Furthermore, 3-HP is postulated to be converted to 3-HPA via feedback inhibition or other metabolite via unknown mechanism. Since glycerol dissimilation is a common mechanism in a variety of bacteria, the expression strategy using native promoter and implications may provide significant insight into the metabolic engineering for 3-HP production.
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Affiliation(s)
- Kang Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029 People's Republic of China
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Jäckel C, Hilvert D. Biocatalysts by evolution. Curr Opin Biotechnol 2010; 21:753-9. [DOI: 10.1016/j.copbio.2010.08.008] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2010] [Revised: 08/15/2010] [Accepted: 08/19/2010] [Indexed: 11/28/2022]
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Van Vleet J, Kleeb A, Kast P, Hilvert D, Cleland WW. 13C isotope effect on the reaction catalyzed by prephenate dehydratase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:752-4. [PMID: 19948253 DOI: 10.1016/j.bbapap.2009.11.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 11/12/2009] [Accepted: 11/19/2009] [Indexed: 01/28/2023]
Abstract
The (13)C isotope effect for the conversion of prephenate to phenylpyruvate by the enzyme prephenate dehydratase from Methanocaldococcus jannaschii is 1.0334+/-0.0006. The size of this isotope effect suggests that the reaction is concerted. From the X-ray structure of a related enzyme, it appears that the only residue capable of acting as the general acid needed for removal of the hydroxyl group is threonine-172, which is contained in a conserved TRF motif. The more favorable entropy of activation for the enzyme-catalyzed process (25 eu larger than for the acid-catalyzed reaction) has been explained by a preorganized microenvironment that obviates the need for extensive solvent reorganization. This is consistent with forced planarity of the ring and side chain, which would place the leaving carboxyl and hydroxyl out of plane. Such distortion of the substrate may be a major contributor to catalysis.
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Affiliation(s)
- Jeremy Van Vleet
- Institute for Enzyme Research and Department of Biochemistry, University of Wisconsin, Madison, WI, USA
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Affiliation(s)
- Christian Jäckel
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland; ,
| | - Peter Kast
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland; ,
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, CH-8093 Zurich, Switzerland; ,
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Metabolic engineering of Escherichia coli for L-tyrosine production by expression of genes coding for the chorismate mutase domain of the native chorismate mutase-prephenate dehydratase and a cyclohexadienyl dehydrogenase from Zymomonas mobilis. Appl Environ Microbiol 2008; 74:3284-90. [PMID: 18344329 DOI: 10.1128/aem.02456-07] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The expression of the feedback inhibition-insensitive enzyme cyclohexadienyl dehydrogenase (TyrC) from Zymomonas mobilis and the chorismate mutase domain from native chorismate mutase-prephenate dehydratase (PheA(CM)) from Escherichia coli was compared to the expression of native feedback inhibition-sensitive chorismate mutase-prephenate dehydrogenase (CM-TyrA(p)) with regard to the capacity to produce l-tyrosine in E. coli strains modified to increase the carbon flow to chorismate. Shake flask experiments showed that TyrC increased the yield of l-tyrosine from glucose (Y(l-Tyr/Glc)) by 6.8-fold compared to the yield obtained with CM-TyrA(p). In bioreactor experiments, a strain expressing both TyrC and PheA(CM) produced 3 g/liter of l-tyrosine with a Y(l-Tyr/Glc) of 66 mg/g. These values are 46 and 48% higher than the values for a strain expressing only TyrC. The results show that the feedback inhibition-insensitive enzymes can be employed for strain development as part of a metabolic engineering strategy for l-tyrosine production.
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Bershtein S, Tawfik DS. Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 2008; 12:151-8. [PMID: 18284924 DOI: 10.1016/j.cbpa.2008.01.027] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/17/2008] [Accepted: 01/24/2008] [Indexed: 11/19/2022]
Abstract
We address recent developments in the area of laboratory, or directed evolution, with a focus on enzymes and on new methodologies of generic potential. We survey three main areas: (i) library making techniques, including the application of computational and rational methods for library design; (ii) screening and selection techniques, including recent applications of enzyme screening by FACS (fluorescence activated cell sorter); (iii) new approaches for performing directed evolution, and in particular, the application of 'neutral drifts' (libraries generated by rounds of mutation and selection for the enzyme's original function) and of consensus mutations to generate highly evolvable starting points for directed evolution.
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Affiliation(s)
- Shimon Bershtein
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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News in brief. Nat Methods 2007. [DOI: 10.1038/nmeth1007-773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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