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Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes. PLoS Comput Biol 2018; 14:e1006556. [PMID: 30444863 PMCID: PMC6283598 DOI: 10.1371/journal.pcbi.1006556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 12/06/2018] [Accepted: 10/09/2018] [Indexed: 01/13/2023] Open
Abstract
Essential metabolic reactions are shaping constituents of metabolic networks, enabling viable and distinct phenotypes across diverse life forms. Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes. Simulations of 15 manually curated genome-scale metabolic models were integrated with 36 large-scale gene essentiality datasets encompassing a wide variety of species of bacteria and archaea. Conservation of metabolic genes was estimated by analysing 79 representative genomes from all the branches of the prokaryotic tree of life. We find that essentiality patterns reflect phylogenetic relations both for modelling and experimental data, which correlate highly at the pathway level. Genes that are essential for several species tend to be highly conserved as opposed to non-essential genes which may be conserved or not. The tRNA-charging module is highlighted as ancestral and with high centrality in the networks, followed closely by cofactor metabolism, pointing to an early information processing system supplied by organic cofactors. The results, which point to model improvements and also indicate faults in the experimental data, should be relevant to the study of centrality in metabolic networks and ancient metabolism but also to metabolic engineering with prokaryotes. If we tried to list every known chemical reaction within an organism–human, plant or even bacteria–we would get quite a long and confusing read. But when this information is represented in so-called genome-scale metabolic networks, we have the means to access computationally each of those reactions and their interconnections. Some parts of the network have alternatives, while others are unique and therefore can be essential for growth. Here, we simulate growth and compare essential reactions and genes for the simplest type of unicellular species–prokaryotes–to understand which parts of their metabolism are universally essential and potentially ancestral. We show that similar patterns of essential reactions echo phylogenetic relationships (this makes sense, as the genome provides the building plan for the enzymes that perform those reactions). Our computational predictions correlate strongly with experimental essentiality data. Finally, we show that a crucial step of protein synthesis (tRNA charging) and the synthesis and transformation of small molecules that enzymes require (cofactors) are the most essential and conserved parts of metabolism in prokaryotes. Our results are a step further in understanding the biology and evolution of prokaryotes but can also be relevant in applied studies including metabolic engineering and antibiotic design.
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Antibiotics Resistance Genes Screening and Comparative Genomics Analysis of Commensal Escherichia coli Isolated from Poultry Farms between China and Sudan. BIOMED RESEARCH INTERNATIONAL 2018; 2018:5327450. [PMID: 30225258 PMCID: PMC6129349 DOI: 10.1155/2018/5327450] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/26/2018] [Accepted: 08/09/2018] [Indexed: 12/02/2022]
Abstract
Escherichia coli (E. coli) strains, from the gut of animals and humans, harbor wide range of drug resistance genes. A comparative study is conducted on the intestinal E. coli from fecal samples of healthy chicken from China and Sudan in order to monitor the antimicrobial sensitivity pattern. A number of 250 E. coli isolates from chicken farms, including 120 from China and 130 from Sudan, were isolated and identified. All isolates were subjected to susceptibility tests against 10 antibiotics and the distribution of antibiotic resistant genes was confirmed by PCR amplification, involving genes such as ampC, tetA, pKD13, acrA, ermA, ermB, ermC, tetB, mphA, aadA14, aadA1, aac3-1, and aac3- III. Many isolates were found to exhibit resistance against more than one antibiotic. However, the Chinese isolates showed more antibiotics resistance and resistance genes compared to the Sudanese isolates. For better understanding of the multidrug resistance factors, we conducted whole genome analyses of E. coli D107 isolated from China, which revealed that the genome possesses multiple resistance genes including tetracycline, erythromycin, and kanamycin. Furthermore, E. coli D4 isolate from Sudan was more sensitive to antibiotics such as erythromycin, tetracycline, and gentamicin. After analysis by RAST and MAUVE, the two strains showed 89% average nucleotide identity. However, the genomes mostly differed at the number of antibiotics-related genes, as the genome of D107 revealed a considerable number of antibiotics resistance genes such as ermA and mphD which were found to be absent in D4 genome. These outcomes provided confirmation that the poultry farms environment in different countries (China and Sudan) may serve as a potential reservoir of antimicrobial resistance genes and also indicated the evolutionary differences of strains in terms of resistant genes expression.
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Identification and manipulation of a novel locus to improve cell tolerance to short-chain alcohols in Escherichia coli. ACTA ACUST UNITED AC 2018; 45:589-598. [DOI: 10.1007/s10295-017-1996-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/09/2017] [Indexed: 12/30/2022]
Abstract
Abstract
Escherichia coli KO11 is a popular ethanologenic strain, but is more sensitive to ethanol than other producers. Here, an ethanol-tolerant mutant EM was isolated from ultraviolet mutagenesis library of KO11. Comparative genomic analysis added by piecewise knockout strategy and complementation assay revealed EKO11_3023 (espA) within the 36.6-kb deletion from KO11 was the only locus responsible for ethanol sensitivity. Interestingly, when espA was deleted in strain W (the parent strain of KO11), ethanol tolerance was dramatically elevated to the level of espA-free hosts [e.g., MG1655 and BL21(DE3)]. And overexpression of espA in strains MG1655 and BL21(DE3) led to significantly enhanced ethanol sensitivity. In addition to ethanol, deletion of espA also improved cell tolerance to other short-chain (C2–C4) alcohols, including methanol, isopropanol, n-butanol, isobutanol and 2-butanol. Therefore, espA was responsible for short-chain alcohol sensitivity of W-strains compared to other cells, which provides a potential engineering target for alcohols production.
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Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes. PLoS One 2018; 13:e0198584. [PMID: 29879172 PMCID: PMC6012718 DOI: 10.1371/journal.pone.0198584] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/22/2018] [Indexed: 01/06/2023] Open
Abstract
Listeria monocytogenes is a microorganism of great concern for the food industry and the cause of human foodborne disease. Therefore, novel methods of control are needed, and systems biology is one such approach to identify them. Using a combination of computational techniques and laboratory methods, genome-scale metabolic models (GEMs) can be created, validated, and used to simulate growth environments and discern metabolic capabilities of microbes of interest, including L. monocytogenes. The objective of the work presented here was to generate GEMs for six different strains of L. monocytogenes, and to both qualitatively and quantitatively validate these GEMs with experimental data to examine the diversity of metabolic capabilities of numerous strains from the three different serovar groups most associated with foodborne outbreaks and human disease. Following qualitative validation, 57 of the 95 carbon sources tested experimentally were present in the GEMs, and; therefore, these were the compounds from which comparisons could be drawn. Of these 57 compounds, agreement between in silico predictions and in vitro results for carbon source utilization ranged from 80.7% to 91.2% between strains. Nutrient utilization agreement between in silico predictions and in vitro results were also conducted for numerous nitrogen, phosphorous, and sulfur sources. Additionally, quantitative validation showed that the L. monocytogenes GEMs were able to generate in silico predictions for growth rate and growth yield that were strongly and significantly (p < 0.0013 and p < 0.0015, respectively) correlated with experimental results. These findings are significant because they show that these GEMs for L. monocytogenes are comparable to published GEMs of other organisms for agreement between in silico predictions and in vitro results. Therefore, as with the other GEMs, namely those for Escherichia coli, Staphylococcus aureus, Vibrio vulnificus, and Salmonella spp., they can be used to determine new methods of growth control and disease treatment.
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Biosynthesis of D-glucaric acid from sucrose with routed carbon distribution in metabolically engineered Escherichia coli. Metab Eng 2018; 47:393-400. [DOI: 10.1016/j.ymben.2018.04.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 04/25/2018] [Accepted: 04/27/2018] [Indexed: 01/09/2023]
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McCloskey D, Xu J, Schrübbers L, Christensen HB, Herrgård MJ. RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli. Metab Eng 2018; 47:383-392. [PMID: 29702276 DOI: 10.1016/j.ymben.2018.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 11/20/2022]
Abstract
Fast metabolite quantification methods are required for high throughput screening of microbial strains obtained by combinatorial or evolutionary engineering approaches. In this study, a rapid RIP-LC-MS/MS (RapidRIP) method for high-throughput quantitative metabolomics was developed and validated that was capable of quantifying 102 metabolites from central, amino acid, energy, nucleotide, and cofactor metabolism in less than 5 minutes. The method was shown to have comparable sensitivity and resolving capability as compared to a full length RIP-LC-MS/MS method (FullRIP). The RapidRIP method was used to quantify the metabolome of seven industrial strains of E. coli revealing significant differences in glycolytic, pentose phosphate, TCA cycle, amino acid, and energy and cofactor metabolites were found. These differences translated to statistically and biologically significant differences in thermodynamics of biochemical reactions between strains that could have implications when choosing a host for bioprocessing.
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Affiliation(s)
- Douglas McCloskey
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Julia Xu
- Department of Bioengineering, University of California - San Diego, La Jolla, CA 92093, USA
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Hanne B Christensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Markus J Herrgård
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark.
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Chu HY, Sprouffske K, Wagner A. Assessing the benefits of horizontal gene transfer by laboratory evolution and genome sequencing. BMC Evol Biol 2018; 18:54. [PMID: 29673327 PMCID: PMC5909237 DOI: 10.1186/s12862-018-1164-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/22/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recombination is widespread across the tree of life, because it helps purge deleterious mutations and creates novel adaptive traits. In prokaryotes, it often takes the form of horizontal gene transfer from a donor to a recipient bacterium. While such transfer is widespread in natural communities, its immediate fitness benefits are usually unknown. We asked whether any such benefits depend on the environment, and on the identity of donor and recipient strains. To this end, we adapted Escherichia coli to two novel carbon sources over several hundred generations of laboratory evolution, exposing evolving populations to various DNA donors. RESULTS At the end of these experiments, we measured fitness and sequenced the genomes of 65 clones from 34 replicate populations to study the genetic changes associated with adaptive evolution. Furthermore, we identified candidate de novo beneficial mutations. During adaptive evolution on the first carbon source, 4-Hydroxyphenylacetic acid (HPA), recombining populations adapted better, which was likely mediated by acquiring the hpa operon from the donor. In contrast, recombining populations did not adapt better to the second carbon source, butyric acid, even though they suffered fewer extinctions than non-recombining populations. The amount of DNA transferred, but not its benefit, strongly depended on the donor-recipient strain combination. CONCLUSIONS To our knowledge, our study is the first to investigate the genomic consequences of prokaryotic recombination and horizontal gene transfer during laboratory evolution. It shows that the benefits of recombination strongly depend on the environment and the foreign DNA donor.
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Affiliation(s)
- Hoi Yee Chu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Kathleen Sprouffske
- The Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, 1015 Lausanne, Switzerland
| | - Andreas Wagner
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- The Swiss Institute of Bioinformatics, Quartier Sorge – Batiment Genopode, 1015 Lausanne, Switzerland
- Santa Fe Institute, Santa Fe, New Mexico USA
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Balikó G, Vernyik V, Karcagi I, Györfy Z, Draskovits G, Fehér T, Pósfai G. Rational Efforts to Streamline the Escherichia coliGenome. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Gabriella Balikó
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Viktor Vernyik
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Ildikó Karcagi
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Zsuzsanna Györfy
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Gábor Draskovits
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - Tamás Fehér
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
| | - György Pósfai
- Biological Research Centre of the Hungarian Academy of Sciences; Institute of Biochemistry, Synthetic and Systems Biology Unit; Temesvari krt. 62 Szeged 6726 Hungary
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Alonso‐Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS. Toward industrial production of isoprenoids in
Escherichia coli
: Lessons learned from CRISPR‐Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnol Bioeng 2018; 115:1000-1013. [DOI: 10.1002/bit.26530] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 12/22/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Jorge Alonso‐Gutierrez
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Daisuke Koma
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- Osaka Municipal Technical Research InstituteOsakaJapan
| | - Qijun Hu
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Yuchen Yang
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Leanne J. G. Chan
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Paul D. Adams
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Jay D. Keasling
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkHorsholmDenmark
- Department of Chemical and Biomolecular EngineeringUniversity of CaliforniaBerkeleyCalifornia
- Department of BioengineeringUniversity of CaliforniaBerkeleyCalifornia
| | - Taek S. Lee
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
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Bhat SV, Kamencic B, Körnig A, Shahina Z, Dahms TES. Exposure to Sub-lethal 2,4-Dichlorophenoxyacetic Acid Arrests Cell Division and Alters Cell Surface Properties in Escherichia coli. Front Microbiol 2018; 9:44. [PMID: 29472899 PMCID: PMC5810288 DOI: 10.3389/fmicb.2018.00044] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/09/2018] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is a robust, easily adaptable and culturable bacterium in vitro, and a model bacterium for studying the impact of xenobiotics in the environment. We have used correlative atomic force – laser scanning confocal microscopy (AFM-LSCM) to characterize the mechanisms of cellular response to the herbicide 2,4-dichlorophenoxyacetic acid (2,4-D). One of the most extensively used herbicides world-wide, 2,4-D is known to cause hazardous effects in diverse non-target organisms. Sub-lethal concentrations of 2,4-D caused DNA damage in E. coli WM1074 during short exposure periods which increased significantly over time. In response to 2,4-D, FtsZ and FtsA relocalized within seconds, coinciding with the complete inhibition of cell septation and cell elongation. Exposure to 2,4-D also resulted in increased activation of the SOS response. Changes to cell division were accompanied by concomitant changes to surface roughness, elasticity and adhesion in a time-dependent manner. This is the first study describing the mechanistic details of 2,4-D at sub-lethal levels in bacteria. Our study suggests that 2,4-D arrests E. coli cell division within seconds after exposure by disrupting the divisome complex, facilitated by dissipation of membrane potential. Over longer exposures, 2,4-D causes filamentation as a result of an SOS response to oxidative stress induced DNA damage.
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Affiliation(s)
- Supriya V Bhat
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Belma Kamencic
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | | | - Zinnat Shahina
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
| | - Tanya E S Dahms
- Department of Chemistry and Biochemistry, University of Regina, Regina, SK, Canada
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Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. J Biotechnol 2018; 268:40-52. [DOI: 10.1016/j.jbiotec.2018.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/10/2018] [Accepted: 01/13/2018] [Indexed: 10/18/2022]
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The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification. mSphere 2018; 3:mSphere00553-17. [PMID: 29404421 PMCID: PMC5793043 DOI: 10.1128/msphere.00553-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/05/2018] [Indexed: 01/19/2023] Open
Abstract
More than a century ago, Theodor Escherich isolated the bacterium that was to become Escherichia coli, one of the most studied organisms. Not long after, the strain began an odyssey and landed in many laboratories across the world. As laboratory culture conditions could be responsible for major changes in bacterial strains, we conducted a genome analysis of isolates of this emblematic strain from different culture collections (England, France, the United States, Germany). Strikingly, many discrepancies between the isolates were observed, as revealed by multilocus sequence typing (MLST), the presence of virulence-associated genes, core genome MLST, and single nucleotide polymorphism/indel analyses. These differences are correlated with the phylogeographic history of the strain and were due to an unprecedented number of mutations in coding DNA repair functions such as mismatch repair (MutL) and oxidized guanine nucleotide pool cleaning (MutT), conferring a specific mutational spectrum and leading to a mutator phenotype. The mutator phenotype was probably acquired during subculturing and corresponded to second-order selection. Furthermore, all of the isolates exhibited hypersusceptibility to antibiotics due to mutations in efflux pump- and porin-encoding genes, as well as a specific mutation in the sigma factor-encoding gene rpoS. These defects reflect a self-preservation and nutritional competence tradeoff allowing survival under the starvation conditions imposed by storage. From a clinical point of view, dealing with such mutator strains can lead microbiologists to draw false conclusions about isolate relatedness and may impact therapeutic effectiveness. IMPORTANCE Mutator phenotypes have been described in laboratory-evolved bacteria, as well as in natural isolates. Several genes can be impacted, each of them being associated with a typical mutational spectrum. By studying one of the oldest strains available, the ancestral Escherich strain, we were able to identify its mutator status leading to tremendous genetic diversity among the isolates from various collections and allowing us to reconstruct the phylogeographic history of the strain. This mutator phenotype was probably acquired during the storage of the strain, promoting adaptation to a specific environment. Other mutations in rpoS and efflux pump- and porin-encoding genes highlight the acclimatization of the strain through self-preservation and nutritional competence regulation. This strain history can be viewed as unintentional experimental evolution in culture collections all over the word since 1885, mimicking the long-term experimental evolution of E. coli of Lenski et al. (O. Tenaillon, J. E. Barrick, N. Ribeck, D. E. Deatherage, J. L. Blanchard, A. Dasgupta, G. C. Wu, S. Wielgoss, S. Cruveiller, C. Médigue, D. Schneider, and R. E. Lenski, Nature 536:165-170, 2016, https://doi.org/10.1038/nature18959) that shares numerous molecular features.
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Miño GL, Baabour M, Chertcoff R, Gutkind G, Clément E, Auradou H, Ippolito I. <i>E coli</i> Accumulation behind an Obstacle. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/aim.2018.86030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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64
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Ettelt V, Ekat K, Kämmerer PW, Kreikemeyer B, Epple M, Veith M. Streptavidin-coated surfaces suppress bacterial colonization by inhibiting non-specific protein adsorption. J Biomed Mater Res A 2017; 106:758-768. [DOI: 10.1002/jbm.a.36276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/10/2017] [Accepted: 10/16/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Volker Ettelt
- Laboratory of Biophysics, Faculty of Applied Natural Sciences; Westphalian University of Applied Sciences; Recklinghausen D-45665 Germany
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), Faculty of Chemistry; University of Duisburg-Essen; Essen D-45141 Germany
| | - Katharina Ekat
- Department Cell Biology; University Medical Center Rostock; Rostock D-18057 Germany
- Department of Operative Dentistry and Periodontology; University Medical Center Rostock; Rostock D-18057 Germany
| | - Peer W. Kämmerer
- Department of Oral, Maxillofacial and Plastic Surgery; University Medical Center Rostock; Rostock D-18057 Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, University Medical Center Rostock; Rostock D-18057 Germany
| | - Matthias Epple
- Inorganic Chemistry and Center for Nanointegration Duisburg-Essen (CeNIDE), Faculty of Chemistry; University of Duisburg-Essen; Essen D-45141 Germany
| | - Michael Veith
- Laboratory of Biophysics, Faculty of Applied Natural Sciences; Westphalian University of Applied Sciences; Recklinghausen D-45665 Germany
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Abstract
The type VI secretion system (T6SS) is a multiprotein complex widespread in Proteobacteria and dedicated to the delivery of toxins into both prokaryotic and eukaryotic cells. It thus participates in interbacterial competition as well as pathogenesis. The T6SS is a contractile weapon, related to the injection apparatus of contractile tailed bacteriophages. Basically, it assembles an inner tube wrapped by a sheath-like structure and anchored to the cell envelope via a membrane complex. The energy released by the contraction of the sheath propels the inner tube through the membrane channel and toward the target cell. Although the assembly and the mechanism of action are conserved across species, the repertoire of secreted toxins and the diversity of the regulatory mechanisms and of target cells make the T6SS a highly versatile secretion system. The T6SS is particularly represented in Escherichia coli pathotypes and Salmonella serotypes. In this review we summarize the current knowledge regarding the prevalence, the assembly, the regulation, and the roles of the T6SS in E. coli, Salmonella, and related species.
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Antimutagenic activity of vitamin B1 against damages induced by chemical and physical mutagens in Salmonella typhimurium and Escherichia coli. Toxicol In Vitro 2017; 45:202-206. [PMID: 28927723 DOI: 10.1016/j.tiv.2017.09.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/14/2017] [Accepted: 09/15/2017] [Indexed: 11/22/2022]
Abstract
Thiamine (vitamin B1) is an essential nutrient acting mainly as an enzymatic cofactor on diverse cell processes. It has been reported that vitamin B1 has a significant role in the signaling pathways related to the response to adverse environmental conditions (chemical and physical). The objectives of this study were to evaluate the antimutagenic potential of vitamin B1 in front of DNA-alkylating agents in the presence/absence of ogt and ada repairing genes in Salmonella typhimurium strains and against damage induced by ultraviolet light type C in Escherichia coli strains mutated at the uvrABC system and recBCD enzymes. For S. typhimurium, an antimutagenesis test (Ames test) was performed using strains deficient in one or both genes (YG7100 ada-/ogt+, YG7104 ada+/ogt-, YG7108 ada-/ogt-). For E. coli, mutated strains (K-12 derived strains Hfr H180 uvrB+/recA+, W3110 uvrB+/recA- and ATCC®8739 uvrB-/recA+) were exposed to UV-C light at different time intervals, with and without vitamin B1. Our results showed that thiamine is an antimutagen against methyl-N-nitro-N-nitrosoguanidine or ethyl-N-nitro-N-nitrosoguanidine only when the ogt gene is present. While for E. coli, the presence of vitamin B1 increased the survival rate, implying an antimutagenesis independent of uvrABC repairing system and recBCD enzymes.
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Pasotti L, Zucca S, Casanova M, Micoli G, Cusella De Angelis MG, Magni P. Fermentation of lactose to ethanol in cheese whey permeate and concentrated permeate by engineered Escherichia coli. BMC Biotechnol 2017; 17:48. [PMID: 28577554 PMCID: PMC5457738 DOI: 10.1186/s12896-017-0369-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 05/22/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Whey permeate is a lactose-rich effluent remaining after protein extraction from milk-resulting cheese whey, an abundant dairy waste. The lactose to ethanol fermentation can complete whey valorization chain by decreasing dairy waste polluting potential, due to its nutritional load, and producing a biofuel from renewable source at the same time. Wild type and engineered microorganisms have been proposed as fermentation biocatalysts. However, they present different drawbacks (e.g., nutritional supplements requirement, high transcriptional demand of recombinant genes, precise oxygen level, and substrate inhibition) which limit the industrial attractiveness of such conversion process. In this work, we aim to engineer a new bacterial biocatalyst, specific for dairy waste fermentation. RESULTS We metabolically engineered eight Escherichia coli strains via a new expression plasmid with the pyruvate-to-ethanol conversion genes, and we carried out the selection of the best strain among the candidates, in terms of growth in permeate, lactose consumption and ethanol formation. We finally showed that the selected engineered microbe (W strain) is able to efficiently ferment permeate and concentrated permeate, without nutritional supplements, in pH-controlled bioreactor. In the conditions tested in this work, the selected biocatalyst could complete the fermentation of permeate and concentrated permeate in about 50 and 85 h on average, producing up to 17 and 40 g/l of ethanol, respectively. CONCLUSIONS To our knowledge, this is the first report showing efficient ethanol production from the lactose contained in whey permeate with engineered E. coli. The selected strain is amenable to further metabolic optimization and represents an advance towards efficient biofuel production from industrial waste stream.
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Affiliation(s)
- Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, 27100, Pavia, Italy
| | - Susanna Zucca
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, 27100, Pavia, Italy
| | - Michela Casanova
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100, Pavia, Italy.,Centre for Health Technologies, University of Pavia, 27100, Pavia, Italy
| | - Giuseppina Micoli
- Centro di Ricerche Ambientali, IRCCS Fondazione Salvatore Maugeri, via Salvatore Maugeri 10, 27100, Pavia, Italy
| | | | - Paolo Magni
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100, Pavia, Italy. .,Centre for Health Technologies, University of Pavia, 27100, Pavia, Italy.
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68
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Jeong H, Sim YM, Kim HJ, Lee SJ. Unveiling the Hybrid Genome Structure of Escherichia coli RR1 (HB101 RecA +). Front Microbiol 2017; 8:585. [PMID: 28421066 PMCID: PMC5379014 DOI: 10.3389/fmicb.2017.00585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 03/21/2017] [Indexed: 01/26/2023] Open
Abstract
There have been extensive genome sequencing studies for Escherichia coli strains, particularly for pathogenic isolates, because fast determination of pathogenic potential and/or drug resistance and their propagation routes is crucial. For laboratory E. coli strains, however, genome sequence information is limited except for several well-known strains. We determined the complete genome sequence of laboratory E. coli strain RR1 (HB101 RecA+), which has long been used as a general cloning host. A hybrid genome sequence of K-12 MG1655 and B BL21(DE3) was constructed based on the initial mapping of Illumina HiSeq reads to each reference, and iterative rounds of read mapping, variant detection, and consensus extraction were carried out. Finally, PCR and Sanger sequencing-based finishing were applied to resolve non-single nucleotide variant regions with aberrant read depths and breakpoints, most of them resulting from prophages and insertion sequence transpositions that are not present in the reference genome sequence. We found that 96.9% of the RR1 genome is derived from K-12, and identified exact crossover junctions between K-12 and B genomic fragments. However, because RR1 has experienced a series of genetic manipulations since branching from the common ancestor, it has a set of mutations different from those found in K-12 MG1655. As well as identifying all known genotypes of RR1 on the basis of genomic context, we found novel mutations. Our results extend current knowledge of the genotype of RR1 and its relatives, and provide insights into the pedigree, genomic background, and physiology of common laboratory strains.
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Affiliation(s)
- Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea.,Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Young Mi Sim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and BiotechnologyDaejeon, South Korea
| | - Hyun Ju Kim
- Biosystems and Bioengineering Program, University of Science and TechnologyDaejeon, South Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang UniversityAnseong, South Korea
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69
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Peng B, Plan MR, Carpenter A, Nielsen LK, Vickers CE. Coupling gene regulatory patterns to bioprocess conditions to optimize synthetic metabolic modules for improved sesquiterpene production in yeast. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:43. [PMID: 28239415 PMCID: PMC5320780 DOI: 10.1186/s13068-017-0728-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/09/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Assembly of heterologous metabolic pathways is commonly required to generate microbial cell factories for industrial production of both commodity chemicals (including biofuels) and high-value chemicals. Promoter-mediated transcriptional regulation coordinates the expression of the individual components of these heterologous pathways. Expression patterns vary during culture as conditions change, and this can influence yeast physiology and productivity in both positive and negative ways. Well-characterized strategies are required for matching transcriptional regulation with desired output across changing culture conditions. RESULTS Here, constitutive and inducible regulatory mechanisms were examined to optimize synthetic isoprenoid metabolic pathway modules for production of trans-nerolidol, an acyclic sesquiterpene alcohol, in yeast. The choice of regulatory system significantly affected physiological features (growth and productivity) over batch cultivation. Use of constitutive promoters resulted in poor growth during the exponential phase. Delaying expression of the assembled metabolic modules using the copper-inducible CUP1 promoter resulted in a 1.6-fold increase in the exponential-phase growth rate and a twofold increase in productivity in the post-exponential phase. However, repeated use of the CUP1 promoter in multiple expression cassettes resulted in genetic instability. A diauxie-inducible expression system, based on an engineered GAL regulatory circuit and a set of four different GAL promoters, was characterized and employed to assemble nerolidol synthetic metabolic modules. Nerolidol production was further improved by 60% to 392 mg L-1 using this approach. Various carbon source systems were investigated in batch/fed-batch cultivation to regulate induction through the GAL system; final nerolidol titres of 4-5.5 g L-1 were achieved, depending on the conditions. CONCLUSION Direct comparison of different transcriptional regulatory mechanisms clearly demonstrated that coupling the output strength to the fermentation stage is important to optimize the growth fitness and overall productivities of engineered cells in industrially relevant processes. Applying different well-characterized promoters with the same induction behaviour mitigates against the risks of homologous sequence-mediated genetic instability. Using these approaches, we significantly improved sesquiterpene production in yeast.
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Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Manuel R. Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Alexander Carpenter
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
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70
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Hays SG, Yan LLW, Silver PA, Ducat DC. Synthetic photosynthetic consortia define interactions leading to robustness and photoproduction. J Biol Eng 2017; 11:4. [PMID: 28127397 PMCID: PMC5259876 DOI: 10.1186/s13036-017-0048-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/05/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Microbial consortia composed of autotrophic and heterotrophic species abound in nature, yet examples of synthetic communities with mixed metabolism are limited in the laboratory. We previously engineered a model cyanobacterium, Synechococcus elongatus PCC 7942, to secrete the bulk of the carbon it fixes as sucrose, a carbohydrate that can be utilized by many other microbes. Here, we tested the capability of sucrose-secreting cyanobacteria to act as a flexible platform for the construction of synthetic, light-driven consortia by pairing them with three disparate heterotrophs: Bacillus subtilis, Escherichia coli, or Saccharomyces cerevisiae. The comparison of these different co-culture dyads reveals general design principles for the construction of robust autotroph/heterotroph consortia. RESULTS We observed heterotrophic growth dependent upon cyanobacterial photosynthate in each co-culture pair. Furthermore, these synthetic consortia could be stabilized over the long-term (weeks to months) and both species could persist when challenged with specific perturbations. Stability and productivity of autotroph/heterotroph co-cultures was dependent on heterotroph sucrose utilization, as well as other species-independent interactions that we observed across all dyads. One destabilizing interaction we observed was that non-sucrose byproducts of oxygenic photosynthesis negatively impacted heterotroph growth. Conversely, inoculation of each heterotrophic species enhanced cyanobacterial growth in comparison to axenic cultures. Finally, these consortia can be flexibly programmed for photoproduction of target compounds and proteins; by changing the heterotroph in co-culture to specialized strains of B. subtilis or E. coli we demonstrate production of alpha-amylase and polyhydroxybutyrate, respectively. CONCLUSIONS Enabled by the unprecedented flexibility of this consortia design, we uncover species-independent design principles that influence cyanobacteria/heterotroph consortia robustness. The modular nature of these communities and their unusual robustness exhibits promise as a platform for highly-versatile photoproduction strategies that capitalize on multi-species interactions and could be utilized as a tool for the study of nascent symbioses. Further consortia improvements via engineered interventions beyond those we show here (i.e., increased efficiency growing on sucrose) could improve these communities as production platforms.
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Affiliation(s)
- Stephanie G Hays
- Department of Systems Biology, Harvard Medical School, Boston, MA USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA USA
| | - Leo L W Yan
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI USA.,Department of Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA USA
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI USA.,Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI USA
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71
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Uropathogenic Escherichia coli: An Ideal Resource for DNA Microarray Probe Designing. BIOINFORMATICS AND BIOMEDICAL ENGINEERING 2017. [DOI: 10.1007/978-3-319-56154-7_2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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72
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Anderhuber N, Fladischer P, Gruber-Khadjawi M, Mairhofer J, Striedner G, Wiltschi B. High-level biosynthesis of norleucine in E. coli for the economic labeling of proteins. J Biotechnol 2016; 235:100-11. [PMID: 27107466 DOI: 10.1016/j.jbiotec.2016.04.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/14/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
Abstract
The residue-specific labeling of proteins with non-canonical amino acids (ncAA) is well established in shake flask cultures. A key aspect for the transfer of the methodology to larger scales for biotechnological applications is the cost of the supplemented ncAAs. Therefore, we established a scalable bioprocess using an engineered host strain for the biosynthesis of the methionine analog norleucine at titers appropriate for the efficient and economic labeling of proteins. To enhance the biosynthesis of norleucine, which is a side-product of the branched chain amino acid pathway, we deleted all three acetolactate synthase isoforms of the methionine auxotrophic Escherichia coli expression strain B834(DE3). Additionally, we overexpressed leuABCD to boost the biosynthesis of norleucine. We systematically analyzed the production of norleucine under the conditions for its residue-specific incorporation in bioreactor cultures that had a 30-fold higher cell density than shake flask cultures. Under optimized conditions, 5g/L norleucine was biosynthesized. This titer is two times higher than the standard supplementation with norleucine of a culture with comparable cell density. We expect that our metabolically engineered strain for the improved biosynthesis of norleucine in combination with the proposed bioprocess will facilitate the efficient residue-specific labeling of proteins at a reasonable price in scales beyond the shake flask.
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Affiliation(s)
- Niklaus Anderhuber
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria
| | - Patrik Fladischer
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, A-8010 Graz, Austria
| | - Mandana Gruber-Khadjawi
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Department of Organic Chemistry, Graz University of Technology, Stremayrgasse 9/4, A-8010 Graz, Austria
| | - Juergen Mairhofer
- Department of Biotechnology, University of Natural Resources and Life Sciences, and Department of Biotechnology, Muthgasse 18, A-1190 Vienna, Austria; enGenes Biotech GmbH, Mooslackengasse 17, A-1190 Vienna, Austria
| | - Gerald Striedner
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria; Department of Biotechnology, University of Natural Resources and Life Sciences, and Department of Biotechnology, Muthgasse 18, A-1190 Vienna, Austria
| | - Birgit Wiltschi
- acib-Austrian Centre of Industrial Biotechnology, Petersgasse 14, A-8010 Graz, Austria.
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73
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Juhas M, Ajioka JW. Lambda Red recombinase-mediated integration of the high molecular weight DNA into the Escherichia coli chromosome. Microb Cell Fact 2016; 15:172. [PMID: 27716307 PMCID: PMC5050610 DOI: 10.1186/s12934-016-0571-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/28/2016] [Indexed: 01/15/2023] Open
Abstract
Background Escherichia coli K-12 is a frequently used host for a number of synthetic biology and biotechnology applications and chassis for the development of the minimal cell factories. Novel approaches for integrating high molecular weight DNA into the E. coli chromosome would therefore greatly facilitate engineering efforts in this bacterium. Results We developed a reliable and flexible lambda Red recombinase-based system, which utilizes overlapping DNA fragments for integration of the high molecular weight DNA into the E. coli chromosome. Our chromosomal integration strategy can be used to integrate high molecular weight DNA of variable length into any non-essential locus in the E. coli chromosome. Using this approach we integrated 15 kb DNA encoding sucrose catabolism and lactose metabolism and transport operons into the fliK locus of the flagellar region 3b in the E. coli K12 MG1655 chromosome. Furthermore, with this system we integrated 50 kb of Bacillus subtilis 168 DNA into two target sites in the E. coli K12 MG1655 chromosome. The chromosomal integrations into the fliK locus occurred with high efficiency, inhibited motility, and did not have a negative effect on the growth of E. coli. Conclusions In addition to the rational design of synthetic biology devices, our high molecular weight DNA chromosomal integration system will facilitate metabolic and genome-scale engineering of E. coli. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0571-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mario Juhas
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK.
| | - James W Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
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74
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Loaces I, Rodríguez C, Amarelle V, Fabiano E, Noya F. Improved glycerol to ethanol conversion by E. coli using a metagenomic fragment isolated from an anaerobic reactor. ACTA ACUST UNITED AC 2016; 43:1405-16. [DOI: 10.1007/s10295-016-1818-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/30/2016] [Indexed: 01/22/2023]
Abstract
Abstract
Crude glycerol obtained as a by-product of biodiesel production is a reliable feedstock with the potential to be converted into reduced chemicals with high yields. It has been previously shown that ethanol is the primary product of glycerol fermentation by Escherichia coli. However, few efforts were made to enhance this conversion by means of the expression of heterologous genes with the potential to improve glycerol transport or metabolism. In this study, a fosmid-based metagenomic library constructed from an anaerobic reactor purge sludge was screened for genetic elements that promote the use and fermentation of crude glycerol by E. coli. One clone was selected based on its improved growth rate on this feedstock. The corresponding fosmid, named G1, was fully sequenced (41 kbp long) and the gene responsible for the observed phenotype was pinpointed by in vitro insertion mutagenesis. Ethanol production from both pure and crude glycerol was evaluated using the parental G1 clone harboring the ethanologenic plasmid pLOI297 or the industrial strain LY180 complemented with G1. In mineral salts media containing 50 % (v/v) pure glycerol, ethanol concentrations increased two-fold on average when G1 was present in the cells reaching up to 20 g/L after 24 h fermentation. Similar fermentation experiments were done using crude instead of pure glycerol. With an initial OD620 of 8.0, final ethanol concentrations after 24 h were much higher reaching 67 and 75 g/L with LY180 cells carrying the control fosmid or the G1 fosmid, respectively. This translates into a specific ethanol production rate of 0.39 g h−1 OD−1 L−1.
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Affiliation(s)
- Inés Loaces
- grid.419088.c 0000000406140469 Departamento de Bioquímica y Genómica Microbianas Instituto de Investigaciones Biológicas Clemente Estable Av. Italia 3318 11600 Montevideo Uruguay
| | - Cecilia Rodríguez
- grid.419088.c 0000000406140469 Departamento de Bioquímica y Genómica Microbianas Instituto de Investigaciones Biológicas Clemente Estable Av. Italia 3318 11600 Montevideo Uruguay
| | - Vanesa Amarelle
- grid.419088.c 0000000406140469 Departamento de Bioquímica y Genómica Microbianas Instituto de Investigaciones Biológicas Clemente Estable Av. Italia 3318 11600 Montevideo Uruguay
| | - Elena Fabiano
- grid.419088.c 0000000406140469 Departamento de Bioquímica y Genómica Microbianas Instituto de Investigaciones Biológicas Clemente Estable Av. Italia 3318 11600 Montevideo Uruguay
| | - Francisco Noya
- grid.419088.c 0000000406140469 Departamento de Bioquímica y Genómica Microbianas Instituto de Investigaciones Biológicas Clemente Estable Av. Italia 3318 11600 Montevideo Uruguay
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75
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Monk JM, Koza A, Campodonico MA, Machado D, Seoane JM, Palsson BO, Herrgård MJ, Feist AM. Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes. Cell Syst 2016; 3:238-251.e12. [PMID: 27667363 DOI: 10.1016/j.cels.2016.08.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/25/2016] [Accepted: 08/19/2016] [Indexed: 11/16/2022]
Abstract
Escherichia coli strains are widely used in academic research and biotechnology. New technologies for quantifying strain-specific differences and their underlying contributing factors promise greater understanding of how these differences significantly impact physiology, synthetic biology, metabolic engineering, and process design. Here, we quantified strain-specific differences in seven widely used strains of E. coli (BL21, C, Crooks, DH5a, K-12 MG1655, K-12 W3110, and W) using genomics, phenomics, transcriptomics, and genome-scale modeling. Metabolic physiology and gene expression varied widely with downstream implications for productivity, product yield, and titer. These differences could be linked to differential regulatory structure. Analyzing high-flux reactions and expression of encoding genes resulted in a correlated and quantitative link between these sets, with strain-specific caveats. Integrated modeling revealed that certain strains are better suited to produce given compounds or express desired constructs considering native expression states of pathways that enable high-production phenotypes. This study yields a framework for quantitatively comparing strains in a species with implications for strain selection.
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Affiliation(s)
- Jonathan M Monk
- Department of NanoEngineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Miguel A Campodonico
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA; Centre for Biotechnology and Bioengineering, CeBiB, University of Chile, Beauchef 850, Santiago, Chile
| | - Daniel Machado
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Jose Miguel Seoane
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Bernhard O Palsson
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark
| | - Adam M Feist
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Hørsholm, Denmark; Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0412, USA.
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76
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Bernal V, Castaño-Cerezo S, Cánovas M. Acetate metabolism regulation in Escherichia coli: carbon overflow, pathogenicity, and beyond. Appl Microbiol Biotechnol 2016; 100:8985-9001. [DOI: 10.1007/s00253-016-7832-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 12/11/2022]
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77
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Han MJ. Exploring the proteomic characteristics of the Escherichia coli B and K-12 strains in different cellular compartments. J Biosci Bioeng 2016; 122:1-9. [DOI: 10.1016/j.jbiosc.2015.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/24/2015] [Accepted: 12/03/2015] [Indexed: 11/26/2022]
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78
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Tummler K, Kühn C, Klipp E. Dynamic metabolic models in context: biomass backtracking. Integr Biol (Camb) 2016; 7:940-51. [PMID: 26189715 DOI: 10.1039/c5ib00050e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mathematical modeling has proven to be a powerful tool to understand and predict functional and regulatory properties of metabolic processes. High accuracy dynamic modeling of individual pathways is thereby opposed by simplified but genome scale constraint based approaches. A method that links these two powerful techniques would greatly enhance predictive power but is so far lacking. We present biomass backtracking, a workflow that integrates the cellular context in existing dynamic metabolic models via stoichiometrically exact drain reactions based on a genome scale metabolic model. With comprehensive examples, for different species and environmental contexts, we show the importance and scope of applications and highlight the improvement compared to common boundary formulations in existing metabolic models. Our method allows for the contextualization of dynamic metabolic models based on all available information. We anticipate this to greatly increase their accuracy and predictive power for basic research and also for drug development and industrial applications.
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Affiliation(s)
- Katja Tummler
- Theoretische Biophysik, Humboldt-Universität zu Berlin, Germany.
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79
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Restriction Profiling of 23S Microheterogenic Ribosomal Repeats for Detection and Characterizing of E. coli and Their Clonal, Pathogenic, and Phylogroups. J Pathog 2016; 2015:562136. [PMID: 26885397 PMCID: PMC4738725 DOI: 10.1155/2015/562136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 10/31/2015] [Accepted: 11/02/2015] [Indexed: 11/17/2022] Open
Abstract
Correlating ribosomal microheterogenicity with unique restriction profiles can prove to be an efficacious and cost-effective approach compared with sequencing for microbial identification. An attempt to peruse restriction profiling of 23S ribosomal assemblage was ventured; digestion patterns with Bfa I discriminated E. coli from its colony morphovars, while Hae III profiles assisted in establishing distinct clonal groups. Among the gene pool of 399 ribosomal sequences extrapolated from 57 E. coli genomes, varying degree of predominance (I > III > IV > II) of Hae III pattern was observed. This was also corroborated in samples collected from clinical, commensal, and environmental origin. K-12 and its descendants showed type I pattern whereas E. coli-B and its descendants exhibited type IV, both of these patterns being exclusively present in E. coli. A near-possible association between phylogroups and Hae III profiles with presumable correlation between the clonal groups and different pathovars was established. The generic nature, conservation, and barcode gap of 23S rRNA gene make it an ideal choice and substitute to 16S rRNA gene, the most preferred region for molecular diagnostics in bacteria.
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80
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Casanova M, Pasotti L, Zucca S, Politi N, Massaiu I, Calvio C, Cusella De Angelis MG, Magni P. A BioBrick™-Compatible Vector for Allelic Replacement Using the XylE Gene as Selection Marker. Biol Proced Online 2016; 18:6. [PMID: 26877712 PMCID: PMC4752771 DOI: 10.1186/s12575-016-0036-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 02/08/2016] [Indexed: 01/10/2023] Open
Abstract
Background Circular plasmid-mediated homologous recombination is commonly used for marker-less allelic replacement, exploiting the endogenous recombination machinery of the host. Common limitations of existing methods include high false positive rates due to mutations in counter-selection genes, and limited applicability to specific strains or growth media. Finally, solutions compatible with physical standards, such as the BioBrick™, are not currently available, although they proved to be successful in the design of other replicative or integrative plasmids. Findings We illustrate pBBknock, a novel BioBrick™-compatible vector for allelic replacement in Escherichia coli. It includes a temperature-sensitive replication origin and enables marker-less genome engineering via two homologous recombination events. Chloramphenicol resistance allows positive selection of clones after the first event, whereas a colorimetric assay based on the xylE gene provides a simple way to screen clones in which the second recombination event occurs. Here we successfully use pBBknock to delete the lactate dehydrogenase gene in E. coli W, a popular host used in metabolic engineering. Conclusions Compared with other plasmid-based solutions, pBBknock has a broader application range, not being limited to specific strains or media. We expect that pBBknock will represent a versatile solution both for practitioners, also among the iGEM competition teams, and for research laboratories that use BioBrick™-based assembly procedures. Electronic supplementary material The online version of this article (doi:10.1186/s12575-016-0036-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michela Casanova
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Lorenzo Pasotti
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Susanna Zucca
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Nicolò Politi
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Ilaria Massaiu
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | - Cinzia Calvio
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
| | | | - Paolo Magni
- Department of Electrical, Computer and Biomedical Engineering, Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, University of Pavia, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, 27100 Pavia, Italy
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81
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PSAMM: A Portable System for the Analysis of Metabolic Models. PLoS Comput Biol 2016; 12:e1004732. [PMID: 26828591 PMCID: PMC4734835 DOI: 10.1371/journal.pcbi.1004732] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 01/05/2016] [Indexed: 11/19/2022] Open
Abstract
The genome-scale models of metabolic networks have been broadly applied in phenotype prediction, evolutionary reconstruction, community functional analysis, and metabolic engineering. Despite the development of tools that support individual steps along the modeling procedure, it is still difficult to associate mathematical simulation results with the annotation and biological interpretation of metabolic models. In order to solve this problem, here we developed a Portable System for the Analysis of Metabolic Models (PSAMM), a new open-source software package that supports the integration of heterogeneous metadata in model annotations and provides a user-friendly interface for the analysis of metabolic models. PSAMM is independent of paid software environments like MATLAB, and all its dependencies are freely available for academic users. Compared to existing tools, PSAMM significantly reduced the running time of constraint-based analysis and enabled flexible settings of simulation parameters using simple one-line commands. The integration of heterogeneous, model-specific annotation information in PSAMM is achieved with a novel format of YAML-based model representation, which has several advantages, such as providing a modular organization of model components and simulation settings, enabling model version tracking, and permitting the integration of multiple simulation problems. PSAMM also includes a number of quality checking procedures to examine stoichiometric balance and to identify blocked reactions. Applying PSAMM to 57 models collected from current literature, we demonstrated how the software can be used for managing and simulating metabolic models. We identified a number of common inconsistencies in existing models and constructed an updated model repository to document the resolution of these inconsistencies. The broad application of genome-scale metabolic modeling has made it a useful technique for tackling fundamental questions in biological research and engineering. Today over 100 models have been constructed for organisms that carry out a diverse array of metabolic activities spanning all three kingdoms of life. These models, however, have been curated independently following different conventions. The maintenance of model consistency has been challenging due to the lack of consensus in model representation and the absence of integrated modeling software for associating mathematical simulations with the annotation and biological interpretation of metabolic models. To solve this problem, we developed a new software package, PSAMM, and a new model format that incorporates heterogeneous, model-specific annotation information into modular representations of model definitions and simulation settings. PSAMM provides significant advances in standardizing the workflow of model annotation and consistency checking. Compared to existing tools, PSAMM supports more flexible configurations and is more efficient in running constraint-based simulations. All functions of PSAMM are freely available for academic users and can be downloaded from a public Git repository (https://zhanglab.github.io/psamm/) under the GNU General Public License.
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Song JY, Yoo YJ, Lim SK, Cha SH, Kim JE, Roe JH, Kim JF, Yoon YJ. Complete genome sequence of Streptomyces venezuelae ATCC 15439, a promising cell factory for production of secondary metabolites. J Biotechnol 2015; 219:57-8. [PMID: 26718561 DOI: 10.1016/j.jbiotec.2015.12.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 12/15/2015] [Indexed: 11/17/2022]
Abstract
Streptomyces venezuelae ATCC 15439, which produces 12- and 14-membered ring macrolide antibiotics, is a platform strain for heterologous expression of secondary metabolites. Its 9.05-Mb genome sequence revealed an abundance of genes involved in the biosynthesis of secondary metabolites and their precursors, which should be useful for the production of bioactive compounds.
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Affiliation(s)
- Ju Yeon Song
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Young Ji Yoo
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea
| | - Si-Kyu Lim
- GenoTech Corporation, 26-69 Gajeongbuk-ro, Daejeon 34113, Republic of Korea
| | - Sun Ho Cha
- GenoTech Corporation, 26-69 Gajeongbuk-ro, Daejeon 34113, Republic of Korea
| | - Ji-Eun Kim
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jung-Hye Roe
- School of Biological Sciences and Institute of Microbiology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology and Division of Life Sciences, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea; Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Yeo Joon Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Republic of Korea.
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83
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Bongers M, Chrysanthopoulos PK, Behrendorff JBYH, Hodson MP, Vickers CE, Nielsen LK. Systems analysis of methylerythritol-phosphate pathway flux in E. coli: insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite. Microb Cell Fact 2015; 14:193. [PMID: 26610700 PMCID: PMC4662018 DOI: 10.1186/s12934-015-0381-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/11/2015] [Indexed: 12/13/2022] Open
Abstract
Background High-throughput screening methods assume that the output measured is representative of changes in metabolic flux toward the desired product and is not affected by secondary phenotypes. However, metabolic engineering can result in unintended phenotypes that may go unnoticed in initial screening. The red pigment lycopene, a carotenoid with antioxidant properties, has been used as a reporter of isoprenoid pathway flux in metabolic engineering for over a decade. Lycopene production is known to vary between wild-type Escherichia coli hosts, but the reasons behind this variation have never been fully elucidated. Results In an examination of six E. coli strains we observed that strains also differ in their capacity for increased lycopene production in response to metabolic engineering. A combination of genetic complementation, quantitative SWATH proteomics, and biochemical analysis in closely-related strains was used to examine the mechanistic reasons for variation in lycopene accumulation. This study revealed that rpoS, a gene previously identified in lycopene production association studies, exerts its effect on lycopene accumulation not through modulation of pathway flux, but through alteration of cellular oxidative status. Specifically, absence of rpoS results in increased accumulation of reactive oxygen species during late log and stationary phases. This change in cellular redox has no effect on isoprenoid pathway flux, despite the presence of oxygen-sensitive iron-sulphur cluster enzymes and the heavy redox requirements of the methylerythritol phosphate pathway. Instead, decreased cellular lycopene in the ΔrpoS strain is caused by degradation of lycopene in the presence of excess reactive oxygen species. Conclusions Our results demonstrate that lycopene is not a reliable indicator of isoprenoid pathway flux in the presence of oxidative stress, and suggest that caution should be exercised when using lycopene as a screening tool in genome-wide metabolic engineering studies. More extensive use of systems biology for strain analysis will help elucidate such unpredictable side-effects in metabolic engineering projects. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0381-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mareike Bongers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Panagiotis K Chrysanthopoulos
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Metabolomics Australia (Queensland Node), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - James B Y H Behrendorff
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Mark P Hodson
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Metabolomics Australia (Queensland Node), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
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84
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Sawisit A, Jantama K, Zheng H, Yomano LP, York SW, Shanmugam KT, Ingram LO. Mutation in galP improved fermentation of mixed sugars to succinate using engineered Escherichia coli AS1600a and AM1 mineral salts medium. BIORESOURCE TECHNOLOGY 2015; 193:433-441. [PMID: 26159300 DOI: 10.1016/j.biortech.2015.06.108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 06/04/2023]
Abstract
Escherichia coli KJ122 was engineered to produce succinate from glucose using the wild type GalP for glucose uptake instead of the native phosphotransferase system (ptsI mutation). This strain now ferments 10% xylose poorly. Mutants were selected by serial transfers in AM1 mineral salts medium with 10% xylose. Clones from this population all exhibited a similar improvement, co-fermentation of an equal mixture of xylose and glucose. One of these, AS1600a, produced 84.26 ± 1.37 g/L succinate, equivalent to that produced by the parent (KJ122) from 10% glucose (85.46 ± 1.78 g/L). AS1600a was sequenced and found to contain a mutation in galactose permease (GalP, G236D). This mutation was shown to be responsible for the improvement in fermentation using KJΔgalP as the host and expression vectors with native galP and with mutant galP(∗). Strain AS1600a and KJΔgalP(pLOI5746; galP(∗)) also co-fermented a mixture of glucose, xylose, arabinose, and galactose in sugarcane bagasse hydrolysate using mineral salts medium.
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Affiliation(s)
- Apichai Sawisit
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kaemwich Jantama
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Huabao Zheng
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lorraine P Yomano
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Sean W York
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Keelnatham T Shanmugam
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lonnie O Ingram
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
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85
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Liu C, Zheng H, Yang M, Xu Z, Wang X, Wei L, Tang B, Liu F, Zhang Y, Ding Y, Tang X, Wu B, Johnson TJ, Chen H, Tan C. Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033. BMC Genomics 2015; 16:717. [PMID: 26391348 PMCID: PMC4578781 DOI: 10.1186/s12864-015-1890-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2015] [Accepted: 09/01/2015] [Indexed: 11/17/2022] Open
Abstract
Background Strains of extraintestinal pathogenic Escherichia coli (ExPEC) can invade and colonize extraintestinal sites and cause a wide range of infections. Genomic analysis of ExPEC has mainly focused on isolates of human and avian origins, with porcine ExPEC isolates yet to be sequenced. To better understand the genomic attributes underlying the pathogenicity of porcine ExPEC, we isolated two E. coli strains PCN033 and PCN061 from pigs, assessed their in vivo virulence, and completed and compared their genomes. Results Animal experiments demonstrated that strain PCN033, but not PCN061, was pathogenic in a pig model. The chromosome of PCN033 was 384 kb larger than that of PCN061. Among the PCN033-specific sequences, genes encoding adhesins, unique lipopolysaccharide, unique capsular polysaccharide, iron acquisition and transport systems, and metabolism were identified. Additionally, a large plasmid PCN033p3 harboring many typical ExPEC virulence factors was identified in PCN033. Based on the genetic variation between PCN033 and PCN061, corresponding phenotypic differences in flagellum-dependent swarming motility and metabolism were verified. Furthermore, the comparative genomic analyses showed that the PCN033 genome shared many similarities with genomic sequences of human ExPEC strains. Additionally, comparison of PCN033 genome with other nine characteristic E. coli genomes revealed 425 PCN033-special coding sequences. Genes of this subset included those encoding type I restriction-modification (R-M) system, type VI secretion system (T6SS) and membrane-associated proteins. Conclusions The genetic and phenotypic differences between PCN033 and PCN061 could partially explain their differences in virulence, and also provide insight towards the molecular mechanisms of porcine ExPEC infections. Additionally, the similarities between the genomes of PCN033 and human ExPEC strains suggest that some connections between porcine and human ExPEC strains exist. The first completed genomic sequence for porcine ExPEC and the genomic differences identified by comparative analyses provide a baseline understanding of porcine ExPEC genetics and lay the foundation for their further study. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1890-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Canying Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China. .,Department of Veterinary Medicine, Foshan University, Foshan, Guangdong, China.
| | - Huajun Zheng
- Shanghai-Most Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.
| | - Minjun Yang
- Shanghai-Most Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China.
| | - Zhuofei Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Xiangru Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Liuya Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Biao Tang
- Shanghai-Most Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. .,State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences, Fudan University, Shanghai, China.
| | - Feng Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Yanyan Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Yi Ding
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Xibiao Tang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Bin Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Timothy J Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota, USA.
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
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De Bruyn F, Van Brempt M, Maertens J, Van Bellegem W, Duchi D, De Mey M. Metabolic engineering of Escherichia coli into a versatile glycosylation platform: production of bio-active quercetin glycosides. Microb Cell Fact 2015; 14:138. [PMID: 26377568 PMCID: PMC4573293 DOI: 10.1186/s12934-015-0326-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 08/27/2015] [Indexed: 02/01/2023] Open
Abstract
Background Flavonoids are bio-active specialized plant metabolites which mainly occur as different glycosides. Due to the increasing market demand, various biotechnological approaches have been developed which use Escherichia coli as a microbial catalyst for the stereospecific glycosylation of flavonoids. Despite these efforts, most processes still display low production rates and titers, which render them unsuitable for large-scale applications. Results In this contribution, we expanded a previously developed in vivo glucosylation platform in E. coli W, into an efficient system for selective galactosylation and rhamnosylation. The rational of the novel metabolic engineering strategy constitutes of the introduction of an alternative sucrose metabolism in the form of a sucrose phosphorylase, which cleaves sucrose into fructose and glucose 1-phosphate as precursor for UDP-glucose. To preserve these intermediates for glycosylation purposes, metabolization reactions were knocked-out. Due to the pivotal role of UDP-glucose, overexpression of the interconverting enzymes galE and MUM4 ensured the formation of both UDP-galactose and UDP-rhamnose, respectively. By additionally supplying exogenously fed quercetin and overexpressing a flavonol galactosyltransferase (F3GT) or a rhamnosyltransferase (RhaGT), 0.94 g/L hyperoside (quercetin 3-O-galactoside) and 1.12 g/L quercitrin (quercetin 3-O-rhamnoside) could be produced, respectively. In addition, both strains showed activity towards other promising dietary flavonols like kaempferol, fisetin, morin and myricetin. Conclusions Two E. coli W mutants were engineered that could effectively produce the bio-active flavonol glycosides hyperoside and quercitrin starting from the cheap substrates sucrose and quercetin. This novel fermentation-based glycosylation strategy will allow the economically viable production of various glycosides. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0326-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Frederik De Bruyn
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Maarten Van Brempt
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Jo Maertens
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Wouter Van Bellegem
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Dries Duchi
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Marjan De Mey
- Department of Biochemical and Microbial Technology, Centre of Expertise-Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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87
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Genomic Comparison of Translocating and Non-Translocating Escherichia coli. PLoS One 2015; 10:e0137131. [PMID: 26317913 PMCID: PMC4552563 DOI: 10.1371/journal.pone.0137131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/12/2015] [Indexed: 11/19/2022] Open
Abstract
Translocation of E. coli across the gut epithelium can result in fatal sepsis in post-surgical patients. In vitro and in vivo experiments have identified the existence of a novel pathotype of translocating E. coli (TEC) that employs an unknown mechanism for translocating across epithelial cells to the mesenteric lymph nodes and the blood stream in both humans and animal models. In this study the genomes of four TEC strains isolated from the mesenteric lymph nodes of a fatal case of hospitalised patient (HMLN-1), blood of pigs after experimental shock (PC-1) and after non-lethal haemorrhage in rats (KIC-1 and KIC-2) were sequenced in order to identify the genes associated with their adhesion and/or translocation. To facilitate the comparison, the genomes of a non-adhering, non-translocating E. coli (46–4) and adhering but non-translocating E. coli (73–89) were also sequenced and compared. Whole genome comparison revealed that three (HMLN-1, PC-1 and KIC-2) of the four TEC strains carried a genomic island that encodes a Type 6 Secretion System that may contribute to adhesion of the bacteria to gut epithelial cells. The human TEC strain HMLN-1 also carried the invasion ibeA gene, which was absent in the animal TEC strains and is likely to be associated with host-specific translocation. Phylogenetic analysis revealed that the four TEC strains were distributed amongst three distinct E. coli phylogroups, which was supported by the presence of phylogroup specific fimbriae gene clusters. The genomic comparison has identified potential genes that can be targeted with knock-out experiments to further characterise the mechanisms of E. coli translocation.
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88
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Massaiu I, Pasotti L, Casanova M, Politi N, Zucca S, Cusella De Angelis MG, Magni P. Quantification of the gene silencing performances of rationally-designed synthetic small RNAs. SYSTEMS AND SYNTHETIC BIOLOGY 2015; 9:107-23. [PMID: 26279705 DOI: 10.1007/s11693-015-9177-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 06/12/2015] [Accepted: 07/27/2015] [Indexed: 11/30/2022]
Abstract
Small RNAs (sRNAs) are genetic tools for the efficient and specific tuning of target genes expression in bacteria. Inspired by naturally occurring sRNAs, recent works proposed the use of artificial sRNAs in synthetic biology for predictable repression of the desired genes. Their potential was demonstrated in several application fields, such as metabolic engineering and bacterial physiology studies. Guidelines for the rational design of novel sRNAs have been recently proposed. According to these guidelines, in this work synthetic sRNAs were designed, constructed and quantitatively characterized in Escherichia coli. An sRNA targeting the reporter gene RFP was tested by measuring the specific gene silencing when RFP was expressed at different transcription levels, under the control of different promoters, in different strains, and in single-gene or operon architecture. The sRNA level was tuned by using plasmids maintained at different copy numbers. Results demonstrated that RFP silencing worked as expected in an sRNA and mRNA expression-dependent fashion. A mathematical model was used to support sRNA characterization and to estimate an efficiency-related parameter that can be used to compare the performance of the designed sRNA. Gene silencing was also successful when RFP was placed in a two-gene synthetic operon, while the non-target gene (GFP) in the operon was not considerably affected. Finally, silencing was evaluated for another designed sRNA targeting the endogenous lactate dehydrogenase gene. The quantitative study performed in this work elucidated interesting performance-related and context-dependent features of synthetic sRNAs that will strongly support predictable gene silencing in disparate basic or applied research studies.
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Affiliation(s)
- Ilaria Massaiu
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Lorenzo Pasotti
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Michela Casanova
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Nicolò Politi
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | - Susanna Zucca
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
| | | | - Paolo Magni
- Laboratory of Bioinformatics, Mathematical Modelling and Synthetic Biology, Department of Electrical, Computer and Biomedical Engineering, University of Pavia, via Ferrata 5, 27100 Pavia, Italy ; Centre for Health Technologies, University of Pavia, via Ferrata 5, 27100 Pavia, Italy
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89
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Peng B, Williams TC, Henry M, Nielsen LK, Vickers CE. Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microb Cell Fact 2015; 14:91. [PMID: 26112740 PMCID: PMC4480987 DOI: 10.1186/s12934-015-0278-5] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/01/2015] [Indexed: 11/10/2022] Open
Abstract
Background Predictable control of gene expression is necessary for the rational design and optimization of cell factories. In the yeast Saccharomyces cerevisiae, the promoter is one of the most important tools available for controlling gene expression. However, the complex expression patterns of yeast promoters have not been fully characterised and compared on different carbon sources (glucose, sucrose, galactose and ethanol) and across the diauxic shift in glucose batch cultivation. These conditions are of importance to yeast cell factory design because they are commonly used and encountered in industrial processes. Here, the activities of a series of “constitutive” and inducible promoters were characterised in single cells throughout the fermentation using green fluorescent protein (GFP) as a reporter. Results The “constitutive” promoters, including glycolytic promoters, transcription elongation factor promoters and ribosomal promoters, differed in their response patterns to different carbon sources; however, in glucose batch cultivation, expression driven by these promoters decreased sharply as glucose was depleted and cells moved towards the diauxic shift. Promoters induced at low-glucose levels (PHXT7, PSSA1 and PADH2) varied in induction strength on non-glucose carbon sources (sucrose, galactose and ethanol); in contrast to the “constitutive” promoters, GFP expression increased as glucose decreased and cells moved towards the diauxic shift. While lower than several “constitutive” promoters during the exponential phase, expression from the SSA1 promoter was higher in the post-diauxic phase than the commonly-used TEF1 promoter. The galactose-inducible GAL1 promoter provided the highest GFP expression on galactose, and the copper-inducible CUP1 promoter provided the highest induced GFP expression following the diauxic shift. Conclusions The data provides a foundation for predictable and optimised control of gene expression levels on different carbon sources and throughout batch fermentation, including during and after the diauxic shift. This information can be applied for designing expression approaches to improve yields, rates and titres in yeast cell factories. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0278-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Thomas C Williams
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Matthew Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
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90
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De Bruyn F, De Paepe B, Maertens J, Beauprez J, De Cocker P, Mincke S, Stevens C, De Mey M. Development of an in vivo glucosylation platform by coupling production to growth: Production of phenolic glucosides by a glycosyltransferase of Vitis vinifera. Biotechnol Bioeng 2015; 112:1594-603. [PMID: 25728421 DOI: 10.1002/bit.25570] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/08/2015] [Accepted: 02/11/2015] [Indexed: 01/02/2023]
Abstract
Glycosylation of small molecules can significantly alter their properties such as solubility, stability, and/or bioactivity, making glycosides attractive and highly demanded compounds. Consequently, many biotechnological glycosylation approaches have been developed, with enzymatic synthesis and whole-cell biocatalysis as the most prominent techniques. However, most processes still suffer from low yields, production rates and inefficient UDP-sugar formation. To this end, a novel metabolic engineering strategy is presented for the in vivo glucosylation of small molecules in Escherichia coli W. This strategy focuses on the introduction of an alternative sucrose metabolism using sucrose phosphorylase for the direct and efficient generation of glucose 1-phosphate as precursor for UDP-glucose formation and fructose, which serves as a carbon source for growth. By targeted gene deletions, a split metabolism is created whereby glucose 1-phosphate is rerouted from the glycolysis to product formation (i.e., glucosylation). Further, the production pathway was enhanced by increasing and preserving the intracellular UDP-glucose pool. Expression of a versatile glucosyltransferase from Vitis vinifera (VvGT2) enabled the strain to efficiently produce 14 glucose esters of various hydroxycinnamates and hydroxybenzoates with conversion yields up to 100%. To our knowledge, this fast growing (and simultaneously producing) E. coli mutant is the first versatile host described for the glucosylation of phenolic acids in a fermentative way using only sucrose as a cheap and sustainable carbon source.
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Affiliation(s)
- Frederik De Bruyn
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, 9000, Ghent, Belgium.
| | - Brecht De Paepe
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Jo Maertens
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Joeri Beauprez
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Pieter De Cocker
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Stein Mincke
- Research Group SynBioC, Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Christian Stevens
- Research Group SynBioC, Department of Sustainable Organic Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium
| | - Marjan De Mey
- Centre of Expertise - Industrial Biotechnology and Biocatalysis, Department of Biochemical and Microbial Technology, Ghent University, Coupure links 653, 9000, Ghent, Belgium
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91
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Rocker A, Meinhart A. A
cis
‐acting antitoxin domain within the chromosomal toxin–antitoxin module
EzeT
of
E
scherichia coli
quenches toxin activity. Mol Microbiol 2015; 97:589-604. [DOI: 10.1111/mmi.13051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Andrea Rocker
- Department of Biomolecular Mechanisms Max Planck Institute for Medical Research Jahnstrasse 29 Heidelberg 69120 Germany
| | - Anton Meinhart
- Department of Biomolecular Mechanisms Max Planck Institute for Medical Research Jahnstrasse 29 Heidelberg 69120 Germany
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92
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Complete Genome Sequence of ER2796, a DNA Methyltransferase-Deficient Strain of Escherichia coli K-12. PLoS One 2015; 10:e0127446. [PMID: 26010885 PMCID: PMC4444293 DOI: 10.1371/journal.pone.0127446] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 04/14/2015] [Indexed: 11/19/2022] Open
Abstract
We report the complete sequence of ER2796, a laboratory strain of Escherichia coli K-12 that is completely defective in DNA methylation. Because of its lack of any native methylation, it is extremely useful as a host into which heterologous DNA methyltransferase genes can be cloned and the recognition sequences of their products deduced by Pacific Biosciences Single-Molecule Real Time (SMRT) sequencing. The genome was itself sequenced from a long-insert library using the SMRT platform, resulting in a single closed contig devoid of methylated bases. Comparison with K-12 MG1655, the first E. coli K-12 strain to be sequenced, shows an essentially co-linear relationship with no major rearrangements despite many generations of laboratory manipulation. The comparison revealed a total of 41 insertions and deletions, and 228 single base pair substitutions. In addition, the long-read approach facilitated the surprising discovery of four gene conversion events, three involving rRNA operons and one between two cryptic prophages. Such events thus contribute both to genomic homogenization and to bacteriophage diversification. As one of relatively few laboratory strains of E. coli to be sequenced, the genome also reveals the sequence changes underlying a number of classical mutant alleles including those affecting the various native DNA methylation systems.
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93
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Genome based phylogeny and comparative genomic analysis of intra-mammary pathogenic Escherichia coli. PLoS One 2015; 10:e0119799. [PMID: 25807497 PMCID: PMC4373696 DOI: 10.1371/journal.pone.0119799] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/22/2015] [Indexed: 12/25/2022] Open
Abstract
Escherichia coli is an important cause of bovine mastitis and can cause both severe inflammation with a short-term transient infection, as well as less severe, but more chronic inflammation and infection persistence. E. coli is a highly diverse organism that has been classified into a number of different pathotypes or pathovars, and mammary pathogenic E. coli (MPEC) has been proposed as a new such pathotype. The purpose of this study was to use genome sequence data derived from both transient and persistent MPEC isolates (two isolates of each phenotype) to construct a genome-based phylogeny that places MPEC in its phylogenetic context with other E. coli pathovars. A subsidiary goal was to conduct comparative genomic analyses of these MPEC isolates with other E. coli pathovars to provide a preliminary perspective on loci that might be correlated with the MPEC phenotype. Both concatenated and consensus tree phylogenies did not support MPEC monophyly or the monophyly of either transient or persistent phenotypes. Three of the MPEC isolates (ECA-727, ECC-Z, and ECA-O157) originated from within the predominately commensal clade of E. coli, referred to as phylogroup A. The fourth MPEC isolate, of the persistent phenotype (ECC-1470), was sister group to an isolate of ETEC, falling within the E. coli B1 clade. This suggests that the MPEC phenotype has arisen on numerous independent occasions and that this has often, although not invariably, occurred from commensal ancestry. Examination of the genes present in the MPEC strains relative to the commensal strains identified a consistent presence of the type VI secretion system (T6SS) in the MPEC strains, with only occasional representation in commensal strains, suggesting that T6SS may be associated with MPEC pathogenesis and/or as an inter-bacterial competitive attribute and therefore could represent a useful target to explore for the development of MPEC specific inhibitors.
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94
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Jeong J, Seo HN, Jung YK, Lee J, Ryu G, Lee W, Kwon E, Ryoo K, Kim J, Cho HY, Cho KM, Park JH, Bang D. Repetitive genomic insertion of gene-sized dsDNAs by targeting the promoter region of a counter-selectable marker. Sci Rep 2015; 5:8712. [PMID: 25736821 PMCID: PMC4348660 DOI: 10.1038/srep08712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/30/2015] [Indexed: 11/18/2022] Open
Abstract
Genome engineering can be used to produce bacterial strains with a wide range of desired phenotypes. However, the incorporation of gene-sized DNA fragments is often challenging due to the intricacy of the procedure, off-target effects, and low insertion efficiency. Here we report a genome engineering method enabling the continuous incorporation of gene-sized double-stranded DNAs (dsDNAs) into the Escherichia coli genome. DNA substrates are inserted without introducing additional marker genes, by synchronously turning an endogenous counter-selectable marker gene ON and OFF. To accomplish this, we utilized λ Red protein-mediated recombination to insert dsDNAs within the promoter region of a counter-selectable marker gene, tolC. By repeatedly switching the marker gene ON and OFF, a number of desired gene-sized dsDNAs can be inserted consecutively. With this method, we successfully inserted approximately 13 kb gene clusters to generate engineered E. coli strains producing 1,4-butanediol (1,4-BDO).
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Affiliation(s)
- Jaehwan Jeong
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Han Na Seo
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Yu Kyung Jung
- Samsung Advanced Institute of Technology, 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-803, Korea
| | - Jeewon Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Gyuri Ryu
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Wookjae Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Euijin Kwon
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Keunsoo Ryoo
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Jungyeon Kim
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, U.K
| | - Hwa-Young Cho
- Samsung Advanced Institute of Technology, 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-803, Korea
| | - Kwang Myung Cho
- Samsung Advanced Institute of Technology, 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-803, Korea
| | - Jin Hwan Park
- Samsung Advanced Institute of Technology, 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-803, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
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95
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Scientific Opinion on the safety and efficacy of L-valine produced by Escherichia coliNITE SD 00066 for all animal species. EFSA J 2015. [DOI: 10.2903/j.efsa.2015.3965] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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96
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Production of Industrially Relevant Isoprenoid Compounds in Engineered Microbes. MICROORGANISMS IN BIOREFINERIES 2015. [DOI: 10.1007/978-3-662-45209-7_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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97
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Draft Genome Sequence of Escherichia coli Strain VKPM B-10182, Producing the Enzyme for Synthesis of Cephalosporin Acids. GENOME ANNOUNCEMENTS 2014; 2:2/6/e01222-14. [PMID: 25414512 PMCID: PMC4239367 DOI: 10.1128/genomea.01222-14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Escherichia coli strain VKPM B-10182, obtained by chemical mutagenesis from E. coli strain ATCC 9637, produces cephalosporin acid synthetase employed in the synthesis of β-lactam antibiotics, such as cefazolin. The draft genome sequence of strain VKPM B-10182 revealed 32 indels and 1,780 point mutations that might account for the improvement in antibiotic synthesis that we observed.
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98
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The transport and mediation mechanisms of the common sugars in Escherichia coli. Biotechnol Adv 2014; 32:905-19. [DOI: 10.1016/j.biotechadv.2014.04.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/23/2014] [Accepted: 04/18/2014] [Indexed: 11/17/2022]
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99
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Bruschi M, Krömer JO, Steen JA, Nielsen LK. Production of the short peptide surfactant DAMP4 from glucose or sucrose in high cell density cultures of Escherichia coli BL21(DE3). Microb Cell Fact 2014; 13:99. [PMID: 25134850 PMCID: PMC4229601 DOI: 10.1186/s12934-014-0099-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/26/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Peptides are increasingly used in industry as highly functional materials. Bacterial production of recombinant peptides has the potential to provide large amounts of renewable and low cost peptides, however, achieving high product titers from Chemically Defined Media (CDM) supplemented with simple sugars remains challenging. RESULTS In this work, the short peptide surfactant, DAMP4, was used as a model peptide to investigate production in Escherichia coli BL21(DE3), a classical strain used for protein production. Under the same fermentation conditions, switching production of DAMP4 from rich complex media to CDM resulted in a reduction in yield that could be attributed to the reduction in final cell density more so than a significant reduction in specific productivity. To maximize product titer, cell density at induction was maximized using a fed-batch approach. In fed-batch DAMP4 product titer increased 9-fold compared to batch, while maintaining 60% specific productivity. Under the fed-batch conditions, the final product titer of DAMP4 reached more than 7 g/L which is the highest titer of DAMP4 reported to date. To investigate production from sucrose, sucrose metabolism was engineered into BL21(DE3) using a simple plasmid approach. Using this strain, growth and DAMP4 production characteristics obtained from CDM supplemented with sucrose were similar to those obtained when culturing the parent strain on CDM supplemented with glucose. CONCLUSIONS Production of a model peptide was increased to several grams per liter using a CDM medium with either glucose or sucrose feedstock. It is hoped that this work will contribute cost reduction for production of designer peptide surfactants to facilitate their commercial application.
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Affiliation(s)
| | - Jens O Krömer
- Centre for Microbial Electrosynthesis (CEMES), Advanced Water Management Centre (AWMC), Research Road (Bldg 60), The University of Queensland, St, Lucia 4072, QLD, Australia.
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100
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Arifin Y, Archer C, Lim S, Quek LE, Sugiarto H, Marcellin E, Vickers CE, Krömer JO, Nielsen LK. Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation. Appl Microbiol Biotechnol 2014; 98:9033-44. [DOI: 10.1007/s00253-014-5956-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
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