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Gu P, Ma Q, Zhao S, Li Q, Gao J. Alanine dehydrogenases from four different microorganisms: characterization and their application in L-alanine production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:123. [PMID: 37537629 PMCID: PMC10401832 DOI: 10.1186/s13068-023-02373-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023]
Abstract
BACKGROUND Alanine dehydrogenase (AlaDH) belongs to oxidoreductases, and it exists in several different bacteria species and plays a key role in microbial carbon and nitrogen metabolism, spore formation and photosynthesis. In addition, AlaDH can also be applied in biosynthesis of L-alanine from cheap carbon source, such as glucose. RESULTS To achieve a better performance of L-alanine accumulation, system evaluation and comparison of different AlaDH with potential application value are essential. In this study, enzymatic properties of AlaDH from Bacillus subtilis 168 (BsAlaDH), Bacillus cereus (BcAlaDH), Mycobacterium smegmatis MC2 155 (MsAlaDH) and Geobacillus stearothermophilus (GsAlaDH) were firstly carefully investigated. Four different AlaDHs have few similarities in optimum temperature and optimum pH, while they also exhibited significant differences in enzyme activity, substrate affinity and enzymatic reaction rate. The wild E. coli BL21 with these four AlaDHs could produce 7.19 g/L, 7.81 g/L, 6.39 g/L and 6.52 g/L of L-alanine from 20 g/L glucose, respectively. To further increase the L-alanine titer, competitive pathways for L-alanine synthesis were completely blocked in E. coli. The final strain M-6 could produce 80.46 g/L of L-alanine with a yield of 1.02 g/g glucose after 63 h fed-batch fermentation, representing the highest yield for microbial L-alanine production. CONCLUSIONS Enzyme assay, biochemical characterization and structure analysis of BsAlaDH, BcAlaDH, MsAlaDH and GsAlaDH were carried out. In addition, application potential of these four AlaDHs in L-alanine productions were explored. The strategies here can be applied for developing L-alanine producing strains with high titers.
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Affiliation(s)
- Pengfei Gu
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
| | - Qianqian Ma
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Shuo Zhao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China
| | - Juan Gao
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, People's Republic of China.
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2
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Croitoru DO, Piguet V. Methylglyoxal Autoimmunity: A Hidden Link in HS and Associated Diseases? J Invest Dermatol 2023; 143:183-185. [PMID: 36681420 DOI: 10.1016/j.jid.2022.09.649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/22/2022] [Accepted: 09/22/2022] [Indexed: 01/21/2023]
Affiliation(s)
- David O Croitoru
- Division of Dermatology, Department of Medicine, University of Toronto, Toronto, Canada; Division of Dermatology, Department of Medicine, Women's College Hospital, Toronto, Canada
| | - Vincent Piguet
- Division of Dermatology, Department of Medicine, University of Toronto, Toronto, Canada; Division of Dermatology, Department of Medicine, Women's College Hospital, Toronto, Canada.
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3
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El-Mansi M. Control of central metabolism’s architecture in Escherichia coli: An overview. Microbiol Res 2023; 266:127224. [DOI: 10.1016/j.micres.2022.127224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
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Goodman AZ, Papudeshi B, Doane MP, Mora M, Kerr E, Torres M, Nero Moffatt J, Lima L, Nosal AP, Dinsdale E. Epidermal Microbiomes of Leopard Sharks ( Triakis semifasciata) Are Consistent across Captive and Wild Environments. Microorganisms 2022; 10:microorganisms10102081. [PMID: 36296361 PMCID: PMC9610875 DOI: 10.3390/microorganisms10102081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 01/24/2023] Open
Abstract
Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for <1 year in duration and scheduled for release; Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients.
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Affiliation(s)
- Asha Z. Goodman
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- Correspondence: (A.Z.G.); (E.D.)
| | - Bhavya Papudeshi
- College of Science and Engineering, Flinders University, Bedford Park, SA 3929, Australia
| | - Michael P. Doane
- College of Science and Engineering, Flinders University, Bedford Park, SA 3929, Australia
| | - Maria Mora
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Emma Kerr
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Melissa Torres
- Scripps Institution of Oceanography, Universtity of California, San Diego, CA 92093, USA
| | - Jennifer Nero Moffatt
- Scripps Institution of Oceanography, Universtity of California, San Diego, CA 92093, USA
| | - Lais Lima
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Andrew P. Nosal
- Department of Biology, Point Loma Nazarene University, San Diego, CA 92106, USA
| | - Elizabeth Dinsdale
- College of Science and Engineering, Flinders University, Bedford Park, SA 3929, Australia
- Correspondence: (A.Z.G.); (E.D.)
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Schoppel K, Trachtmann N, Korzin EJ, Tzanavari A, Sprenger GA, Weuster-Botz D. Metabolic control analysis enables rational improvement of E. coli L-tryptophan producers but methylglyoxal formation limits glycerol-based production. Microb Cell Fact 2022; 21:201. [PMID: 36195869 PMCID: PMC9531422 DOI: 10.1186/s12934-022-01930-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/24/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Although efficient L-tryptophan production using engineered Escherichia coli is established from glucose, the use of alternative carbon sources is still very limited. Through the application of glycerol as an alternate, a more sustainable substrate (by-product of biodiesel preparation), the well-studied intracellular glycolytic pathways are rerouted, resulting in the activity of different intracellular control sites and regulations, which are not fully understood in detail. Metabolic analysis was applied to well-known engineered E. coli cells with 10 genetic modifications. Cells were withdrawn from a fed-batch production process with glycerol as a carbon source, followed by metabolic control analysis (MCA). This resulted in the identification of several additional enzymes controlling the carbon flux to L-tryptophan. RESULTS These controlling enzyme activities were addressed stepwise by the targeted overexpression of 4 additional enzymes (trpC, trpB, serB, aroB). Their efficacy regarding L-tryptophan productivity was evaluated under consistent fed-batch cultivation conditions. Although process comparability was impeded by process variances related to a temporal, unpredictable break-off in L-tryptophan production, process improvements of up to 28% with respect to the L-tryptophan produced were observed using the new producer strains. The intracellular effects of these targeted genetic modifications were revealed by metabolic analysis in combination with MCA and expression analysis. Furthermore, it was discovered that the E. coli cells produced the highly toxic metabolite methylglyoxal (MGO) during the fed-batch process. A closer look at the MGO production and detoxification on the metabolome, fluxome, and transcriptome level of the engineered E. coli indicated that the highly toxic metabolite plays a critical role in the production of aromatic amino acids with glycerol as a carbon source. CONCLUSIONS A detailed process analysis of a new L-tryptophan producer strain revealed that several of the 4 targeted genetic modifications of the E. coli L-tryptophan producer strain proved to be effective, and, for others, new engineering approaches could be derived from the results. As a starting point for further strain and process optimization, the up-regulation of MGO detoxifying enzymes and a lowering of the feeding rate during the last third of the cultivation seems reasonable.
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Affiliation(s)
- Kristin Schoppel
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Natalia Trachtmann
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Emil J Korzin
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Angelina Tzanavari
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Georg A Sprenger
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany.
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Smith DA, Nakamoto BJ, Suess MK, Fogel ML. Central Metabolism and Growth Rate Impacts on Hydrogen and Carbon Isotope Fractionation During Amino Acid Synthesis in E. coli. Front Microbiol 2022; 13:840167. [PMID: 35910622 PMCID: PMC9335129 DOI: 10.3389/fmicb.2022.840167] [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: 12/20/2021] [Accepted: 06/22/2022] [Indexed: 11/20/2022] Open
Abstract
Compound specific stable isotope analysis (CSIA) of amino acids from bacterial biomass is a newly emerging powerful tool for exploring central carbon metabolism pathways and fluxes. By comparing isotopic values and fractionations relative to water and growth substrate, the impact of variable flow path for metabolites through different central metabolic pathways, perturbations of these paths, and their resultant consequences on intracellular pools and resultant biomass may be elucidated. Here, we explore the effects that central carbon metabolism and growth rate can have on stable hydrogen (δ2H) and carbon (δ13C) compound specific isotopic values of amino acids, and whether diagnostic isotopic fingerprints are revealed by these paired analyses. We measured δ2H and δ13C in amino acids in the wild type Escherichia coli (MG1655) across a range of growth rates in chemostat cultures to address the unknown isotopic consequences as metabolic fluxes are shuffled between catabolic and anabolic metabolisms. Additionally, two E. coli knockout mutants, one with deficiency in glycolysis –pgi (LC1888) and another inhibiting the oxidative pentose phosphate pathway (OPPP) –zwf (LC1889), were grown on glucose and used as a comparison against the wild type E. coli (MG1655) to address the isotopic changes of amino acids produced in these perturbed metabolic pathways. Amino acid δ2H values, which collectively vary in composition by more than 400‰, are altered along with δ13C values demonstrating fundamental shifts in central metabolic pathways and/or fluxes. Within our linear discriminant analysis with a simple model organism to examine potential amino acid fingerprinting, our knockout strains and variable growth rate samples plot across a wider array of organism classification than merely within the boundaries of other bacterial data.
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Affiliation(s)
- Derek A. Smith
- Department of Biology, Case Western Reserve University, Cleveland, OH, United States
- *Correspondence: Derek A. Smith
| | - Bobby James Nakamoto
- Department of Biology, University of New Brunswick Fredericton, Fredericton, NB, Canada
- Department of Earth and Planetary Sciences, EDGE Institute, University of California, Riverside, Riverside, CA, United States
| | - Melanie K. Suess
- Department of Earth and Planetary Sciences, Washington University in St. Louis, St. Louis, MO, United States
| | - Marilyn L. Fogel
- Department of Earth and Planetary Sciences, EDGE Institute, University of California, Riverside, Riverside, CA, United States
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Li Z, Nees M, Bettenbrock K, Rinas U. Is energy excess the initial trigger of carbon overflow metabolism? Transcriptional network response of carbon-limited Escherichia coli to transient carbon excess. Microb Cell Fact 2022; 21:67. [PMID: 35449049 PMCID: PMC9027384 DOI: 10.1186/s12934-022-01787-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/26/2022] [Indexed: 12/20/2022] Open
Abstract
Background Escherichia coli adapted to carbon-limiting conditions is generally geared for energy-efficient carbon utilization. This includes also the efficient utilization of glucose, which serves as a source for cellular building blocks as well as energy. Thus, catabolic and anabolic functions are balanced under these conditions to minimize wasteful carbon utilization. Exposure to glucose excess interferes with the fine-tuned coupling of anabolism and catabolism leading to the so-called carbon overflow metabolism noticeable through acetate formation and eventually growth inhibition. Results Cellular adaptations towards sudden but timely limited carbon excess conditions were analyzed by exposing slow-growing cells in steady state glucose-limited continuous culture to a single glucose pulse. Concentrations of metabolites as well as time-dependent transcriptome alterations were analyzed and a transcriptional network analysis performed to determine the most relevant transcription and sigma factor combinations which govern these adaptations. Down-regulation of genes related to carbon catabolism is observed mainly at the level of substrate uptake and downstream of pyruvate and not in between in the glycolytic pathway. It is mainly accomplished through the reduced activity of CRP-cAMP and through an increased influence of phosphorylated ArcA. The initiated transcriptomic change is directed towards down-regulation of genes, which contribute to active movement, carbon uptake and catabolic carbon processing, in particular to down-regulation of genes which contribute to efficient energy generation. Long-term changes persisting after glucose depletion and consumption of acetete encompassed reduced expression of genes related to active cell movement and enhanced expression of genes related to acid resistance, in particular acid resistance system 2 (GABA shunt) which can be also considered as an inefficient bypass of the TCA cycle. Conclusions Our analysis revealed that the major part of the trancriptomic response towards the glucose pulse is not directed towards enhanced cell proliferation but towards protection against excessive intracellular accumulation of potentially harmful concentration of metabolites including among others energy rich compounds such as ATP. Thus, resources are mainly utilized to cope with “overfeeding” and not for growth including long-lasting changes which may compromise the cells future ability to perform optimally under carbon-limiting conditions (reduced motility and ineffective substrate utilization). Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01787-4.
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Affiliation(s)
- Zhaopeng Li
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany.,Technical Chemistry - Life Science, Leibniz University of Hannover, Callinstr. 5, 30167, Hannover, Germany
| | - Markus Nees
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Katja Bettenbrock
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Brunswick, Germany. .,Technical Chemistry - Life Science, Leibniz University of Hannover, Callinstr. 5, 30167, Hannover, Germany.
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8
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Weber J, Li Z, Rinas U. Recombinant protein production provoked accumulation of ATP, fructose-1,6-bisphosphate and pyruvate in E. coli K12 strain TG1. Microb Cell Fact 2021; 20:169. [PMID: 34446023 PMCID: PMC8394631 DOI: 10.1186/s12934-021-01661-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/16/2021] [Indexed: 12/03/2022] Open
Abstract
Background Recently it was shown that production of recombinant proteins in E. coli BL21(DE3) using pET based expression vectors leads to metabolic stress comparable to a carbon overfeeding response. Opposite to original expectations generation of energy as well as catabolic provision of precursor metabolites were excluded as limiting factors for growth and protein production. On the contrary, accumulation of ATP and precursor metabolites revealed their ample formation but insufficient withdrawal as a result of protein production mediated constraints in anabolic pathways. Thus, not limitation but excess of energy and precursor metabolites were identified as being connected to the protein production associated metabolic burden. Results Here we show that the protein production associated accumulation of energy and catabolic precursor metabolites is not unique to E. coli BL21(DE3) but also occurs in E. coli K12. Most notably, it was demonstrated that the IPTG-induced production of hFGF-2 using a tac-promoter based expression vector in the E. coli K12 strain TG1 was leading to persistent accumulation of key regulatory molecules such as ATP, fructose-1,6-bisphosphate and pyruvate. Conclusions Excessive energy generation, respectively, accumulation of ATP during recombinant protein production is not unique to the BL21(DE3)/T7 promoter based expression system but also observed in the E. coli K12 strain TG1 using another promoter/vector combination. These findings confirm that energy is not a limiting factor for recombinant protein production. Moreover, the data also show that an accelerated glycolytic pathway flux aggravates the protein production associated “metabolic burden”. Under conditions of compromised anabolic capacities cells are not able to reorganize their metabolic enzyme repertoire as required for reduced carbon processing.
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Affiliation(s)
- Jan Weber
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Zhaopeng Li
- Technical Chemistry-Life Science, Leibniz University of Hannover, Hannover, Germany
| | - Ursula Rinas
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany. .,Technical Chemistry-Life Science, Leibniz University of Hannover, Hannover, Germany.
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Kumar CMS, Chugh K, Dutta A, Mahamkali V, Bose T, Mande SS, Mande SC, Lund PA. Chaperonin Abundance Enhances Bacterial Fitness. Front Mol Biosci 2021; 8:669996. [PMID: 34381811 PMCID: PMC8350394 DOI: 10.3389/fmolb.2021.669996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/01/2021] [Indexed: 12/12/2022] Open
Abstract
The ability of chaperonins to buffer mutations that affect protein folding pathways suggests that their abundance should be evolutionarily advantageous. Here, we investigate the effect of chaperonin overproduction on cellular fitness in Escherichia coli. We demonstrate that chaperonin abundance confers 1) an ability to tolerate higher temperatures, 2) improved cellular fitness, and 3) enhanced folding of metabolic enzymes, which is expected to lead to enhanced energy harvesting potential.
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Affiliation(s)
- C M Santosh Kumar
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Kritika Chugh
- Department of Biotechnology and Bioinformatics, University of Rajasthan, Jaipur, India
| | - Anirban Dutta
- TCS Research, Tata Consultancy Services Ltd., Pune, India
| | - Vishnuvardhan Mahamkali
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia
| | - Tungadri Bose
- TCS Research, Tata Consultancy Services Ltd., Pune, India
| | | | - Shekhar C Mande
- Laboratory of Structural Biology, National Centre for Cell Science (NCCS), Pune, India
| | - Peter A Lund
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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Shanmugam KT, Ingram LO. Principles and practice of designing microbial biocatalysts for fuel and chemical production. J Ind Microbiol Biotechnol 2021; 49:6158391. [PMID: 33686428 PMCID: PMC9118985 DOI: 10.1093/jimb/kuab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/03/2021] [Indexed: 11/14/2022]
Abstract
The finite nature of fossil fuels and the environmental impact of its use have raised interest in alternate renewable energy sources. Specifically, non-food carbohydrates, such as lignocellulosic biomass, can be used to produce next generation biofuels, including cellulosic ethanol and other non-ethanol fuels like butanol. However, currently there is no native microorganism that can ferment all lignocellulosic sugars to fuel molecules. Thus, research is focused on engineering improved microbial biocatalysts for production of liquid fuels at high productivity, titer and yield. A clear understanding and application of the basic principles of microbial physiology and biochemistry are crucial to achieve this goal. In this review, we present and discuss the construction of microbial biocatalysts that integrate these principles with ethanol-producing Escherichia coli as an example of metabolic engineering. These principles also apply to fermentation of lignocellulosic sugars to other chemicals that are currently produced from petroleum.
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Affiliation(s)
- K 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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Spirulina-in Silico-Mutations and Their Comparative Analyses in the Metabolomics Scale by Using Proteome-Based Flux Balance Analysis. Cells 2020; 9:cells9092097. [PMID: 32942547 PMCID: PMC7563286 DOI: 10.3390/cells9092097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/28/2020] [Accepted: 09/05/2020] [Indexed: 11/17/2022] Open
Abstract
This study used an in silico metabolic engineering strategy for modifying the metabolic capabilities of Spirulina under specific conditions as an approach to modifying culture conditions in order to generate the intended outputs. In metabolic models, the basic metabolic fluxes in steady-state metabolic networks have generally been controlled by stoichiometric reactions; however, this approach does not consider the regulatory mechanism of the proteins responsible for the metabolic reactions. The protein regulatory network plays a critical role in the response to stresses, including environmental stress, encountered by an organism. Thus, the integration of the response mechanism of Spirulina to growth temperature stresses was investigated via simulation of a proteome-based GSMM, in which the boundaries were established by using protein expression levels obtained from quantitative proteomic analysis. The proteome-based flux balance analysis (FBA) under an optimal growth temperature (35 °C), a low growth temperature (22 °C) and a high growth temperature (40 °C) showed biomass yields that closely fit the experimental data obtained in previous research. Moreover, the response mechanism was analyzed by the integration of the proteome and protein-protein interaction (PPI) network, and those data were used to support in silico knockout/overexpression of selected proteins involved in the PPI network. The Spirulina, wild-type, proteome fluxes under different growth temperatures and those of mutants were compared, and the proteins/enzymes catalyzing the different flux levels were mapped onto their designated pathways for biological interpretation.
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Liu EJ, Tseng IT, Chen YL, Pang JJ, Shen ZX, Li SY. The Physiological Responses of Escherichia coli Triggered by Phosphoribulokinase (PrkA) and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco). Microorganisms 2020; 8:microorganisms8081187. [PMID: 32759862 PMCID: PMC7463662 DOI: 10.3390/microorganisms8081187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 11/20/2022] Open
Abstract
Phosphoribulokinase (PrkA) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been proposed to create a heterologous Rubisco-based engineered pathway in Escherichia coli for in situ CO2 recycling. While the feasibility of a Rubisco-based engineered pathway has been shown, heterologous expressions of PrkA and Rubisco also induced physiological responses in E. coli that may compete with CO2 recycling. In this study, the metabolic shifts caused by PrkA and Rubisco were investigated in recombinant strains where ppc and pta genes (encodes phosphoenolpyruvate carboxylase and phosphate acetyltransferase, respectively) were deleted from E. coli MZLF (E. coli BL21(DE3) Δzwf, ΔldhA, Δfrd). It has been shown that the demand for ATP created by the expression of PrkA significantly enhanced the glucose consumptions of E. coli CC (MZLF Δppc) and E. coli CA (MZLF Δppc, Δpta). The accompanying metabolic shift is suggested to be the mgsA route (the methylglyoxal pathway) which results in the lactate production for reaching the redox balance. The overexpression of Rubisco not only enhanced glucose consumption but also bacterial growth. Instead of the mgsA route, the overproduction of the reducing power was balanced by the ethanol production. It is suggested that Rubisco induces a high demand for acetyl-CoA which is subsequently used by the glyoxylate shunt. Therefore, Rubisco can enhance bacterial growth. This study suggests that responses induced by the expression of PrkA and Rubisco will reach a new energy balance profile inside the cell. The new profile results in a new distribution of the carbon flow and thus carbons cannot be majorly directed to the Rubisco-based engineered pathway.
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Affiliation(s)
- En-Jung Liu
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - I-Ting Tseng
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - Yi-Ling Chen
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - Ju-Jiun Pang
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - Zhi-Xuan Shen
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung City 40227, Taiwan
- Correspondence: ; Tel.: +886-4-2284-0510 (ext. #509)
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Mahamkali V, Valgepea K, de Souza Pinto Lemgruber R, Plan M, Tappel R, Köpke M, Simpson SD, Nielsen LK, Marcellin E. Redox controls metabolic robustness in the gas-fermenting acetogen Clostridium autoethanogenum. Proc Natl Acad Sci U S A 2020; 117:13168-13175. [PMID: 32471945 PMCID: PMC7293625 DOI: 10.1073/pnas.1919531117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Living biological systems display a fascinating ability to self-organize their metabolism. This ability ultimately determines the metabolic robustness that is fundamental to controlling cellular behavior. However, fluctuations in metabolism can affect cellular homeostasis through transient oscillations. For example, yeast cultures exhibit rhythmic oscillatory behavior in high cell-density continuous cultures. Oscillatory behavior provides a unique opportunity for quantitating the robustness of metabolism, as cells respond to changes by inherently compromising metabolic efficiency. Here, we quantify the limits of metabolic robustness in self-oscillating autotrophic continuous cultures of the gas-fermenting acetogen Clostridium autoethanogenum Online gas analysis and high-resolution temporal metabolomics showed oscillations in gas uptake rates and extracellular byproducts synchronized with biomass levels. The data show initial growth on CO, followed by growth on CO and H2 Growth on CO and H2 results in an accelerated growth phase, after which a downcycle is observed in synchrony with a loss in H2 uptake. Intriguingly, oscillations are not linked to translational control, as no differences were observed in protein expression during oscillations. Intracellular metabolomics analysis revealed decreasing levels of redox ratios in synchrony with the cycles. We then developed a thermodynamic metabolic flux analysis model to investigate whether regulation in acetogens is controlled at the thermodynamic level. We used endo- and exo-metabolomics data to show that the thermodynamic driving force of critical reactions collapsed as H2 uptake is lost. The oscillations are coordinated with redox. The data indicate that metabolic oscillations in acetogen gas fermentation are controlled at the thermodynamic level.
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Affiliation(s)
- Vishnuvardhan Mahamkali
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia
| | - Kaspar Valgepea
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia
- ERA Chair in Gas Fermentation Technologies, Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | | | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, 4072 Brisbane, Australia
| | | | | | | | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, 4072 Brisbane, Australia
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, 4072 Brisbane, Australia;
- Queensland Node of Metabolomics Australia, The University of Queensland, 4072 Brisbane, Australia
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14
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Effect of Delays on the Response of Microalgae When Exposed to Dynamic Environmental Conditions. Processes (Basel) 2020. [DOI: 10.3390/pr8010087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
During mathematical representation of microbial cultures, it is normally assumed that changes in the environment produce instantaneous effects on growth. However, reports are available indicating that sometimes this may not be the case. This work studied the existence of delays on the response of a population of microalgae when subjected to changes in energy and carbon sources, and when exposed to a growth inhibitor. Results show that no appreciable delays exist when microalgae undergo changes in the incident light intensity. For changes in carbon source concentration (inorganic carbon), a small delay in the range of minutes was detected. Finally, when exposing microalgae to inhibitory concentrations of ammonia, a significant delay of several hours was observed.
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15
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Giovannini G, Gubala V, Hall AJ. ‘Off–on’ switchable fluorescent probe for prompt and cost-efficient detection of bacteria. NEW J CHEM 2019. [DOI: 10.1039/c9nj03110c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The rapid and straightforward detection of bacteria in food and human samples is becoming important, particularly in view of the development of point-of-care devices and lab-on-a-chip tools for prevention and treatment of bacterial infections.
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Affiliation(s)
- Giorgia Giovannini
- Medway School of Pharmacy
- University of Kent
- Central Avenue
- Chatham Maritime
- Kent
| | - Vladimir Gubala
- Medway School of Pharmacy
- University of Kent
- Central Avenue
- Chatham Maritime
- Kent
| | - Andrew J. Hall
- Medway School of Pharmacy
- University of Kent
- Central Avenue
- Chatham Maritime
- Kent
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16
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Zhou Z, Pan J, Wang F, Gu JD, Li M. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiol Rev 2018; 42:639-655. [PMID: 29790926 DOI: 10.1093/femsre/fuy023] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/18/2018] [Indexed: 11/12/2022] Open
Abstract
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. These results have not only demonstrated multiple and important ecological functions of this archaeal phylum, but also paved the way for a detailed understanding of the evolution and metabolism of archaea as such. This review summarizes the recent findings pertaining to the ecological, physiological and genomic aspects of Bathyarchaeota, highlighting the vital role of this phylum in global carbon cycling.
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Affiliation(s)
- Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.,Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
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17
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Gandhi NN, Barrett-Wilt G, Steele JL, Rankin SA. Lactobacillus casei expressing methylglyoxal synthase causes browning and heterocyclic amine formation in Parmesan cheese extract. J Dairy Sci 2018; 102:100-112. [PMID: 30415846 DOI: 10.3168/jds.2018-15042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022]
Abstract
Undesired browning of Parmesan cheese can occur during the latter period of ripening and cold storage despite the relative absence of reducing sugars and high temperatures typically associated with Maillard browning. Highly reactive α-dicarbonyls such as methylglyoxal (MG) are products and accelerants of Maillard browning chemistry and can result from the microbial metabolism of sugars and AA by lactic acid bacteria. We demonstrate the effects of microbially produced MG in a model Parmesan cheese extract using a strain of Lactobacillus casei 12A engineered for inducible overexpression of MG synthase (mgsA) from Thermoanaerobacterium thermosaccharolyticum HG-8. Maximum induction of plasmid-born mgsA led to 1.6 mM MG formation in Parmesan cheese extract and its distinct discoloration. The accumulation of heterocyclic amines including β-carboline derivatives arising from mgsA expression were determined by mass spectrometry. Potential MG-contributing reaction mechanisms for the formation of heterocyclic amines are proposed. These findings implicate nonstarter lactic acid bacteria may cause browning and influence nutritional aspects of Parmesan by enzymatic conversion of triosephosphates to MG. Moreover, these findings indicate that the microbial production of MG can lead to the formation of late-stage Maillard reaction products such as melanoidin and β-carbolines, effectively circumventing the thermal requirement of the early- and intermediate- stage Maillard reaction. Therefore, the identification and control of offending microbiota may prevent late-stage browning of Parmesan. The gene mgsA may serve as a genetic biomarker for cheeses with a propensity to undergo MG-mediated browning.
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Affiliation(s)
- N N Gandhi
- Department of Food Science, Madison 53706
| | - G Barrett-Wilt
- Biotechnology Center, University of Wisconsin, Madison 53706
| | - J L Steele
- Department of Food Science, Madison 53706
| | - S A Rankin
- Department of Food Science, Madison 53706.
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18
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Luna-Flores CH, Stowers CC, Cox BM, Nielsen LK, Marcellin E. Linking genotype and phenotype in an economically viable propionic acid biosynthesis process. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:224. [PMID: 30123322 PMCID: PMC6090647 DOI: 10.1186/s13068-018-1222-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Propionic acid (PA) is used as a food preservative and increasingly, as a precursor for the synthesis of monomers. PA is produced mainly through hydrocarboxylation of ethylene, also known as the 'oxo-process'; however, Propionibacterium species are promising biological PA producers natively producing PA as their main fermentation product. However, for fermentation to be competitive, a PA yield of at least 0.6 g/g is required. RESULTS A new strain able to reach the required yield was obtained using genome shuffling. To gain insight into the changes leading to the improved phenotype, the genome of the new strain was sequenced, and metabolomics and transcriptomics data were obtained. In combination, the data revealed three key mutations: (i) a mutation in the promoter region of a sugar transporter which enables an increase in the uptake rate of sucrose; (ii) a mutation in a polar amino acid transporter which improves consumption of amino acids and acid tolerance; and (iii) a mutation in a gene annotated as a cytochrome C biogenesis gene, which is likely responsible for the coupling of the Wood-Werkman cycle to ATP production were responsible for the phenotype. The bioprocess was further enhanced with a feeding strategy that achieved 70 g/L of product. The proposed bioprocess is expected to outperform the economics of the current 'oxo-process' by 2020. CONCLUSIONS In this study, using genome shuffling, we obtained a strain capable of producing PA exceeding the commercial needs. The multiomics comparison between the novel strain and the wild type revealed overexpression of amino acid pathways, changes in sucrose transporters and an increased activity in the methylglyoxal and the glucuronate interconversion pathways. The analysis also suggests that a mutation in the cytochrome C biogenesis gene, coupled with ATP production through the Wood-Werkman cycle, may be responsible for the increased PA production.
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Affiliation(s)
- Carlos H. Luna-Flores
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Chris C. Stowers
- BioEngineering and Bioprocessing R&D, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Brad M. Cox
- BioEngineering and Bioprocessing R&D, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072 Australia
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19
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Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes. Metab Eng 2018; 48:82-93. [PMID: 29842925 DOI: 10.1016/j.ymben.2018.05.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/03/2018] [Accepted: 05/23/2018] [Indexed: 11/21/2022]
Abstract
Methylglyoxal is a highly toxic metabolite that can be produced in all living organisms. Methylglyoxal was artificially elevated by removal of the tpiA gene from a growth optimized Escherichia coli strain. The initial response to elevated methylglyoxal and its toxicity was characterized, and detoxification mechanisms were studied using adaptive laboratory evolution. We found that: 1) Multi-omics analysis revealed biological consequences of methylglyoxal toxicity, which included attack on macromolecules including DNA and RNA and perturbation of nucleotide levels; 2) Counter-intuitive cross-talk between carbon starvation and inorganic phosphate signalling was revealed in the tpiA deletion strain that required mutations in inorganic phosphate signalling mechanisms to alleviate; and 3) The split flux through lower glycolysis depleted glycolytic intermediates requiring a host of synchronized and coordinated mutations in non-intuitive network locations in order to re-adjust the metabolic flux map to achieve optimal growth. Such mutations included a systematic inactivation of the Phosphotransferase System (PTS) and alterations in cell wall biosynthesis enzyme activity. This study demonstrated that deletion of major metabolic genes followed by ALE was a productive approach to gain novel insight into the systems biology underlying optimal phenotypic states.
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20
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Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches. ISME JOURNAL 2017; 11:1118-1129. [PMID: 28085154 DOI: 10.1038/ismej.2016.189] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 11/10/2016] [Accepted: 11/19/2016] [Indexed: 01/14/2023]
Abstract
Genomic bins belonging to multiple archaeal lineages were recovered from distinct redox regimes in sediments of the White Oak River estuary. The reconstructed archaeal genomes were identified as belonging to the rice cluster subgroups III and V (RC-III, RC-V), the Marine Benthic Group D (MBG-D), and a newly described archaeal class, the Theionarchaea. The metabolic capabilities of these uncultured archaea were inferred and indicated a common capability for extracellular protein degradation, supplemented by other pathways. The multiple genomic bins within the MBG-D archaea shared a nearly complete reductive acetyl-CoA pathway suggesting acetogenic capabilities. In contrast, the RC-III metabolism appeared centered on the degradation of detrital proteins and production of H2, whereas the RC-V archaea lacked capabilities for protein degradation and uptake, and appeared to be specialized on carbohydrate fermentation. The Theionarchaea appeared as complex metabolic hybrids; encoding a complete tricarboxylic acid cycle permitting carbon (acetyl-CoA) oxidation, together with a complete reductive acetyl-CoA pathway and sulfur reduction by a sulfhydrogenase. The differentiated inferred capabilities of these uncultured archaeal lineages indicated lineage-specific linkages with the nitrogen, carbon and sulfur cycles. The predicted metabolisms of these archaea suggest preferences for distinct geochemical niches within the estuarine sedimentary environment.
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21
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Role of O2 in the Growth of Rhizobium leguminosarum bv. viciae 3841 on Glucose and Succinate. J Bacteriol 2016; 199:JB.00572-16. [PMID: 27795326 DOI: 10.1128/jb.00572-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/01/2016] [Indexed: 12/12/2022] Open
Abstract
Insertion sequencing (INSeq) analysis of Rhizobium leguminosarum bv. viciae 3841 (Rlv3841) grown on glucose or succinate at both 21% and 1% O2 was used to understand how O2 concentration alters metabolism. Two transcriptional regulators were required for growth on glucose (pRL120207 [eryD] and RL0547 [phoB]), five were required on succinate (pRL100388, RL1641, RL1642, RL3427, and RL4524 [ecfL]), and three were required on 1% O2 (pRL110072, RL0545 [phoU], and RL4042). A novel toxin-antitoxin system was identified that could be important for generation of new plasmidless rhizobial strains. Rlv3841 appears to use the methylglyoxal pathway alongside the Entner-Doudoroff (ED) pathway and tricarboxylic acid (TCA) cycle for optimal growth on glucose. Surprisingly, the ED pathway was required for growth on succinate, suggesting that sugars made by gluconeogenesis must undergo recycling. Altered amino acid metabolism was specifically needed for growth on glucose, including RL2082 (gatB) and pRL120419 (opaA, encoding omega-amino acid:pyruvate transaminase). Growth on succinate specifically required enzymes of nucleobase synthesis, including ribose-phosphate pyrophosphokinase (RL3468 [prs]) and a cytosine deaminase (pRL90208 [codA]). Succinate growth was particularly dependent on cell surface factors, including the PrsD-PrsE type I secretion system and UDP-galactose production. Only RL2393 (glnB, encoding nitrogen regulatory protein PII) was specifically essential for growth on succinate at 1% O2, conditions similar to those experienced by N2-fixing bacteroids. Glutamate synthesis is constitutively activated in glnB mutants, suggesting that consumption of 2-ketoglutarate may increase flux through the TCA cycle, leading to excess reductant that cannot be reoxidized at 1% O2 and cell death. IMPORTANCE Rhizobium leguminosarum, a soil bacterium that forms N2-fixing symbioses with several agriculturally important leguminous plants (including pea, vetch, and lentil), has been widely utilized as a model to study Rhizobium-legume symbioses. Insertion sequencing (INSeq) has been used to identify factors needed for its growth on different carbon sources and O2 levels. Identification of these factors is fundamental to a better understanding of the cell physiology and core metabolism of this bacterium, which adapts to a variety of different carbon sources and O2 tensions during growth in soil and N2 fixation in symbiosis with legumes.
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22
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Kosmachevskaya OV, Shumaev KB, Topunov AF. Carbonyl Stress in Bacteria: Causes and Consequences. BIOCHEMISTRY (MOSCOW) 2016; 80:1655-71. [PMID: 26878572 DOI: 10.1134/s0006297915130039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Pathways of synthesis of the α-reactive carbonyl compound methylglyoxal (MG) in prokaryotes are described in this review. Accumulation of MG leads to development of carbonyl stress. Some pathways of MG formation are similar for both pro- and eukaryotes, but there are reactions specific for prokaryotes, e.g. the methylglyoxal synthase reaction. This reaction and the glyoxalase system constitute an alternative pathway of glucose catabolism - the MG shunt not associated with the synthesis of ATP. In violation of the regulation of metabolism, the cell uses MG shunt as well as other glycolysis shunting pathways and futile cycles enabling stabilization of its energetic status. MG was first examined as a biologically active metabolic factor participating in the formation of phenotypic polymorphism and hyperpersistent potential of bacterial populations. The study of carbonyl stress is interesting for evolutionary biology and can be useful for constructing highly effective producer strains.
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Affiliation(s)
- O V Kosmachevskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia.
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23
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Youngquist JT, Korosh TC, Pfleger BF. Functional genomics analysis of free fatty acid production under continuous phosphate limiting conditions. J Ind Microbiol Biotechnol 2016; 44:759-772. [PMID: 27738839 DOI: 10.1007/s10295-016-1846-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/28/2016] [Indexed: 12/19/2022]
Abstract
Free fatty acids (FFA) are an attractive platform chemical that serves as a functional intermediate in metabolic pathways for producing oleochemicals. Many groups have established strains of Escherichia coli capable of producing various chain-length mixtures of FFA by heterologous expression of acyl-ACP thioesterases. For example, high levels of dodecanoic acid are produced by an E. coli strain expressing the Umbellularia californica FatB2 thioesterase, BTE. Prior studies achieved high dodecanoic acid yields and productivities under phosphate-limiting media conditions. In an effort to understand the metabolic and physiological changes that led to increased FFA production, the transcriptome of this strain was assessed as a function of nutrient limitation and growth rate. FFA generation under phosphate limitation led to consistent changes in transporter expression, osmoregulation, and central metabolism. Guided by these results, targeted knockouts led to a further ~11 % in yield in FFA.
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Affiliation(s)
- J Tyler Youngquist
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI, USA
| | - Travis C Korosh
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI, USA.,Graduate Program in Environmental Chemistry and Technology, University of Wisconsin-Madison, Madison, WI, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI, USA. .,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
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24
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Orlenko A, Teufel AI, Chi PB, Liberles DA. Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biol Direct 2016; 11:31. [PMID: 27393343 PMCID: PMC4938953 DOI: 10.1186/s13062-016-0133-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 07/02/2016] [Indexed: 11/15/2022] Open
Abstract
Background While commonly assumed in the biochemistry community that the control of metabolic pathways is thought to be critical to cellular function, it is unclear if metabolic pathways generally have evolutionarily stable rate limiting (flux controlling) steps. Results A set of evolutionary simulations using a kinetic model of a metabolic pathway was performed under different conditions to evaluate the evolutionary stability of rate limiting steps. Simulations used combinations of selection for steady state flux, selection against the cost of molecular biosynthesis, and selection against the accumulation of high concentrations of a deleterious intermediate. Two mutational regimes were used, one with mutations that on average were neutral to molecular phenotype and a second with a preponderance of activity-destroying mutations. The evolutionary stability of rate limiting steps was low in all simulations with non-neutral mutational processes. Clustering of parameter co-evolution showed divergent inter-molecular evolutionary patterns under different evolutionary regimes. Conclusions This study provides a null model for pathway evolution when compensatory processes dominate with potential applications to predicting pathway functional change. This result also suggests a possible mechanism in which studies in statistical genetics that aim to associate a genotype to a phenotype assuming independent action of variants may be mis-specified through a mis-characterization of the link between individual gene function and pathway function. A better understanding of the genotype-phenotype map has potential applications in differentiating between compensatory changes and directional selection on pathways as well as detecting SNPs and fixed differences that might have phenotypic effects. Reviewers This article was reviewed by Arne Elofsson, David Ardell, and Shamil Sunyaev. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0133-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alena Orlenko
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Ashley I Teufel
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
| | - Peter B Chi
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA.,Department of Mathematics and Computer Science, Ursinus College, Collegeville, PA, 19426, USA
| | - David A Liberles
- Center for Computational Genetics and Genomics and Department of Biology, Temple University, Bio-Life Building, 1900 N. 12th Street, Philadelphia, PA, 19122-1801, USA. .,Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA.
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25
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Lazar CS, Baker BJ, Seitz K, Hyde AS, Dick GJ, Hinrichs KU, Teske AP. Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments. Environ Microbiol 2016; 18:1200-11. [PMID: 26626228 DOI: 10.1111/1462-2920.13142] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/19/2015] [Accepted: 11/19/2015] [Indexed: 11/28/2022]
Abstract
Investigations of the biogeochemical roles of benthic Archaea in marine sediments are hampered by the scarcity of cultured representatives. In order to determine their metabolic capacity, we reconstructed the genomic content of four widespread uncultured benthic Archaea recovered from estuary sediments at 48% to 95% completeness. Four genomic bins were found to belong to different subgroups of the former Miscellaneous Crenarcheota Group (MCG) now called Bathyarchaeota: MCG-6, MCG-1, MCG-7/17 and MCG-15. Metabolic predictions based on gene content of the different genome bins indicate that subgroup 6 has the ability to hydrolyse extracellular plant-derived carbohydrates, and that all four subgroups can degrade detrital proteins. Genes encoding enzymes involved in acetate production as well as in the reductive acetyl-CoA pathway were detected in all four genomes inferring that these Archaea are organo-heterotrophic and autotrophic acetogens. Genes involved in nitrite reduction were detected in all Bathyarchaeota subgroups and indicate a potential for dissimilatory nitrite reduction to ammonium. Comparing the genome content of the different Bathyarchaeota subgroups indicated preferences for distinct types of carbohydrate substrates and implicitly, for different niches within the sedimentary environment.
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Affiliation(s)
- Cassandre Sara Lazar
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA.,Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany.,Institute of Ecology, Friedrich Schiller University Jena, Dornburger Straße 159, 07743, Jena, Germany
| | - Brett J Baker
- University of Texas Austin, Department of Marine Science, Marine Science Institute, Port Aransas, TX, 78383, USA
| | - Kiley Seitz
- University of Texas Austin, Department of Marine Science, Marine Science Institute, Port Aransas, TX, 78383, USA
| | - Andrew S Hyde
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA
| | - Gregory J Dick
- University of Michigan, Earth and Environmental Sciences, Ann Arbor, MI, 48109, USA
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, Bremen, Germany
| | - Andreas P Teske
- University of North Carolina Chapel Hill, Marine Sciences, Chapel Hill, NC, USA
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26
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De la Fuente IM. Elements of the cellular metabolic structure. Front Mol Biosci 2015; 2:16. [PMID: 25988183 PMCID: PMC4428431 DOI: 10.3389/fmolb.2015.00016] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/12/2015] [Indexed: 12/19/2022] Open
Abstract
A large number of studies have demonstrated the existence of metabolic covalent modifications in different molecular structures, which are able to store biochemical information that is not encoded by DNA. Some of these covalent mark patterns can be transmitted across generations (epigenetic changes). Recently, the emergence of Hopfield-like attractor dynamics has been observed in self-organized enzymatic networks, which have the capacity to store functional catalytic patterns that can be correctly recovered by specific input stimuli. Hopfield-like metabolic dynamics are stable and can be maintained as a long-term biochemical memory. In addition, specific molecular information can be transferred from the functional dynamics of the metabolic networks to the enzymatic activity involved in covalent post-translational modulation, so that determined functional memory can be embedded in multiple stable molecular marks. The metabolic dynamics governed by Hopfield-type attractors (functional processes), as well as the enzymatic covalent modifications of specific molecules (structural dynamic processes) seem to represent the two stages of the dynamical memory of cellular metabolism (metabolic memory). Epigenetic processes appear to be the structural manifestation of this cellular metabolic memory. Here, a new framework for molecular information storage in the cell is presented, which is characterized by two functionally and molecularly interrelated systems: a dynamic, flexible and adaptive system (metabolic memory) and an essentially conservative system (genetic memory). The molecular information of both systems seems to coordinate the physiological development of the whole cell.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine “López-Neyra,” Consejo Superior de Investigaciones CientíficasGranada, Spain
- Department of Mathematics, University of the Basque Country, UPV/Euskal Herriko UnibertsitateaLeioa, Spain
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27
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Abstract
Trans-aconitate methyltransferase regulator (TamR) is a member of the ligand-responsive multiple antibiotic resistance regulator (MarR) family of transcription factors. In Streptomyces coelicolor, TamR regulates transcription of tamR (encoding TamR), tam (encoding trans-aconitate methyltransferase) and sacA (encoding aconitase); up-regulation of these genes promotes metabolic flux through the citric acid cycle. DNA binding by TamR is attenuated and transcriptional derepression is achieved on binding of ligands such as citrate and trans-aconitate to TamR. In the present study, we show that three additional genes are regulated by S. coelicolor TamR. Genes encoding malate synthase (aceB1; SCO6243), malate dehydrogenase (mdh; SCO4827) and isocitrate dehydrogenase (idh; SCO7000) are up-regulated in vivo when citrate and trans-aconitate accumulate, and TamR binds the corresponding gene promoters in vitro, a DNA binding that is attenuated by cognate ligands. Mutations to the TamR binding site attenuate DNA binding in vitro and result in constitutive promoter activity in vivo. The predicted TamR binding sites are highly conserved in the promoters of these genes in Streptomyces species that encode divergent tam-tamR gene pairs, suggesting evolutionary conservation. Like aconitase and trans-aconitate methyltransferase, malate dehydrogenase, isocitrate dehydrogenase and malate synthase are closely related to the citric acid cycle, either catalysing individual reaction steps or, in the case of malate synthase, participating in the glyoxylate cycle to produce malate that enters the citric acid cycle to replenish the intermediate pool. Taken together, our data suggest that TamR plays an important and conserved role in promoting metabolic flux through the citric acid cycle.
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28
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Illeghems K, Weckx S, De Vuyst L. Applying meta-pathway analyses through metagenomics to identify the functional properties of the major bacterial communities of a single spontaneous cocoa bean fermentation process sample. Food Microbiol 2015; 50:54-63. [PMID: 25998815 DOI: 10.1016/j.fm.2015.03.005] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 03/01/2015] [Accepted: 03/24/2015] [Indexed: 11/15/2022]
Abstract
A high-resolution functional metagenomic analysis of a representative single sample of a Brazilian spontaneous cocoa bean fermentation process was carried out to gain insight into its bacterial community functioning. By reconstruction of microbial meta-pathways based on metagenomic data, the current knowledge about the metabolic capabilities of bacterial members involved in the cocoa bean fermentation ecosystem was extended. Functional meta-pathway analysis revealed the distribution of the metabolic pathways between the bacterial members involved. The metabolic capabilities of the lactic acid bacteria present were most associated with the heterolactic fermentation and citrate assimilation pathways. The role of Enterobacteriaceae in the conversion of substrates was shown through the use of the mixed-acid fermentation and methylglyoxal detoxification pathways. Furthermore, several other potential functional roles for Enterobacteriaceae were indicated, such as pectinolysis and citrate assimilation. Concerning acetic acid bacteria, metabolic pathways were partially reconstructed, in particular those related to responses toward stress, explaining their metabolic activities during cocoa bean fermentation processes. Further, the in-depth metagenomic analysis unveiled functionalities involved in bacterial competitiveness, such as the occurrence of CRISPRs and potential bacteriocin production. Finally, comparative analysis of the metagenomic data with bacterial genomes of cocoa bean fermentation isolates revealed the applicability of the selected strains as functional starter cultures.
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Affiliation(s)
- Koen Illeghems
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
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29
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De la Fuente IM, Cortés JM, Valero E, Desroches M, Rodrigues S, Malaina I, Martínez L. On the dynamics of the adenylate energy system: homeorhesis vs homeostasis. PLoS One 2014; 9:e108676. [PMID: 25303477 PMCID: PMC4193753 DOI: 10.1371/journal.pone.0108676] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 09/03/2014] [Indexed: 11/20/2022] Open
Abstract
Biochemical energy is the fundamental element that maintains both the adequate turnover of the biomolecular structures and the functional metabolic viability of unicellular organisms. The levels of ATP, ADP and AMP reflect roughly the energetic status of the cell, and a precise ratio relating them was proposed by Atkinson as the adenylate energy charge (AEC). Under growth-phase conditions, cells maintain the AEC within narrow physiological values, despite extremely large fluctuations in the adenine nucleotides concentration. Intensive experimental studies have shown that these AEC values are preserved in a wide variety of organisms, both eukaryotes and prokaryotes. Here, to understand some of the functional elements involved in the cellular energy status, we present a computational model conformed by some key essential parts of the adenylate energy system. Specifically, we have considered (I) the main synthesis process of ATP from ADP, (II) the main catalyzed phosphotransfer reaction for interconversion of ATP, ADP and AMP, (III) the enzymatic hydrolysis of ATP yielding ADP, and (IV) the enzymatic hydrolysis of ATP providing AMP. This leads to a dynamic metabolic model (with the form of a delayed differential system) in which the enzymatic rate equations and all the physiological kinetic parameters have been explicitly considered and experimentally tested in vitro. Our central hypothesis is that cells are characterized by changing energy dynamics (homeorhesis). The results show that the AEC presents stable transitions between steady states and periodic oscillations and, in agreement with experimental data these oscillations range within the narrow AEC window. Furthermore, the model shows sustained oscillations in the Gibbs free energy and in the total nucleotide pool. The present study provides a step forward towards the understanding of the fundamental principles and quantitative laws governing the adenylate energy system, which is a fundamental element for unveiling the dynamics of cellular life.
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Affiliation(s)
- Ildefonso M. De la Fuente
- Institute of Parasitology and Biomedicine “López-Neyra”, CSIC, Granada, Spain
- Department of Mathematics, University of the Basque Country UPV/EHU, Leioa, Spain
- Unit of Biophysics (CSIC, UPV/EHU), and Department of Biochemistry and Molecular Biology University of the Basque Country, Bilbao, Spain
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
| | - Jesús M. Cortés
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
- Ikerbasque: The Basque Foundation for Science, Bilbao, Basque Country, Spain
| | - Edelmira Valero
- Department of Physical Chemistry, School of Industrial Engineering, University of Castilla-La Mancha, Albacete, Spain
| | | | - Serafim Rodrigues
- School of Computing and Mathematics, University of Plymouth, Plymouth, United Kingdom
| | - Iker Malaina
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
- Department of Physiology, University of the Basque Country UPV/EHU, Bilbao, Spain
| | - Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, Leioa, Spain
- Biocruces Health Research Institute, Hospital Universitario de Cruces, Barakaldo, Spain
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30
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Morshedi D, Aliakbari F, Nouri HR, Lotfinia M, Fallahi J. Using small molecules as a new challenge to redirect metabolic pathway. 3 Biotech 2014; 4:513-522. [PMID: 28324386 PMCID: PMC4162896 DOI: 10.1007/s13205-013-0185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/09/2013] [Indexed: 11/26/2022] Open
Abstract
The presence of acetate in the bacterial medium leads to a reduction in the growth rate of cells and recombinant protein production. In this study, three compounds including propionic acid, lithium chloride and butyric acid were added to the medium which decreased acetate levels and enhanced recombinant protein production (alpha-synuclein). In fact, propionic acid and lithium chloride are both known as acetate kinase inhibitors. The results obtained in the case of butyric acid were similar to those of the two other compounds indicating that butyric acid may act through a mechanism similar to propionic acid and lithium chloride. Consequently, it was shown that the presence of each of these supplements (5–200 μM) increased recombinant alpha-synuclein production and cell density by approximately 10–15 %. HPLC analysis showed that the levels of acetate in the media containing the supplements were considerably less than those of the control. Furthermore, pH values remained almost constant in the supplemented cultures. Growing the bacteria at lower temperatures (25 °C) indicated that the positive effects of these supplements were not as effective as at higher temperatures (37 °C), presumably due to the adequate balance between oxygen and carbon consumption. This study can confirm the viewpoint regarding the harmful effects of acetate on the recombinant protein production and cell density. Besides, such methods represent easy and complementary ways to increase target recombinant protein production without negatively affecting host cell density, and requiring complex genetic manipulation.
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Affiliation(s)
- Dina Morshedi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran.
| | - Farhang Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
- Department of Biotechnology, Semnan University of Medical Sciences, Semnan, Iran
| | - Hamid Reza Nouri
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
| | - Majid Lotfinia
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran
| | - Jafar Fallahi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Shahrak-e Pajoohesh, km 15, Tehran-Karaj Highway, P. O. Box: 14965/161, Tehran, Iran
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31
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Collins T, Barroca M, Branca F, Padrão J, Machado R, Casal M. High Level Biosynthesis of a Silk-Elastin-like Protein in E. coli. Biomacromolecules 2014; 15:2701-8. [DOI: 10.1021/bm5005564] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tony Collins
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Mário Barroca
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Fernando Branca
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Jorge Padrão
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Raul Machado
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Margarida Casal
- Centre
of Molecular and Environmental
Biology (CBMA), Department of Biology, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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32
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Suarez-Mendez CA, Sousa A, Heijnen JJ, Wahl A. Fast "Feast/Famine" Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae. Metabolites 2014; 4:347-72. [PMID: 24957030 PMCID: PMC4101510 DOI: 10.3390/metabo4020347] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 05/01/2014] [Accepted: 05/06/2014] [Indexed: 01/24/2023] Open
Abstract
Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes in substrate availability in an aerobic glucose cultivation of Saccharomyces cerevisiae. After a few cycles, the feast/famine produced a stable and repetitive pattern with a reproducible metabolic response in time, thus providing a robust platform for studying the microorganism's physiology under dynamic conditions. We found that the biomass yield was slightly reduced (-5%) under the feast/famine regime, while the averaged substrate and oxygen consumption as well as the carbon dioxide production rates were comparable. The dynamic response of the intracellular metabolites showed specific differences in comparison to other dynamic experiments (especially stimulus-response experiments, SRE). Remarkably, the frequently reported ATP paradox observed in single pulse experiments was not present during the repetitive perturbations applied here. We found that intracellular dynamic accumulations led to an uncoupling of the substrate uptake rate (up to 9-fold change at 20 s.) Moreover, the dynamic profiles of the intracellular metabolites obtained with the feast/famine suggest the presence of regulatory mechanisms that resulted in a delayed response. With the feast famine setup many cellular states can be measured at high frequency given the feature of reproducible cycles. The feast/famine regime is thus a versatile platform for systems biology approaches, which can help us to identify and investigate metabolite regulations under realistic conditions (e.g., large-scale bioreactors or natural environments).
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Affiliation(s)
- Camilo A Suarez-Mendez
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Andre Sousa
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Joseph J Heijnen
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
| | - Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands.
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33
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Serrano H, Blanchard JS. Kinetic and isotopic characterization of L-proline dehydrogenase from Mycobacterium tuberculosis. Biochemistry 2013; 52:5009-15. [PMID: 23834473 DOI: 10.1021/bi400338f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The monofunctional proline dehydrogenase (ProDH) from Mycobacterium tuberculosis performs the flavin-dependent oxidation of l-proline to Δ(1)-pyrroline-5-carboxylate in the proline catabolic pathway. The ProDH gene, prub, was cloned into the pYUB1062 vector, and the C-terminal His-tagged 37 kDa protein was expressed and purified by nickel affinity chromatography. A steady-state kinetic analysis revealed a ping-pong mechanism with an overall kcat of 33 ± 2 s(-1) and Km values of 5.7 ± 0.8 mM and 3.4 ± 0.3 μM for l-proline and 2,6-dichlorophenolindophenol (DCPIP), respectively. The pH dependence of kcat revealed that one enzyme group exhibiting a pK value of 6.8 must be deprotonated for optimal catalytic activity. Site-directed mutagenesis suggests that this group is Lys110. The primary kinetic isotope effects on V/KPro and V of 5.5 and 1.1, respectively, suggest that the transfer of hydride from l-proline to FAD is rate-limiting for the reductive half-reaction, but that FAD reoxidation is the rate-limiting step in the overall reaction. Solvent and multiple kinetic isotope effects suggest that l-proline oxidation occurs in a stepwise rather than concerted mechanism. Pre-steady-state kinetics reveal an overall kred of 88.5 ± 0.7 s(-1), and this rate is subject to a primary kinetic isotope effect of 5.2. These data confirm that the overall reaction is limited by reduced flavin reoxidation in the second half-reaction.
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Affiliation(s)
- Hector Serrano
- Department of Biochemistry, Albert Einstein College of Medicine , 1300 Morris Park Avenue, Bronx, New York 10461, United States
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34
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Kremling A, Goehler A, Jahreis K, Nees M, Auerbach B, Schmidt-Heck W, Kökpinar O, Geffers R, Rinas U, Bettenbrock K. Analysis and Design of Stimulus Response Curves of E. coli. Metabolites 2012; 2:844-71. [PMID: 24957765 PMCID: PMC3901224 DOI: 10.3390/metabo2040844] [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: 10/17/2012] [Accepted: 10/29/2012] [Indexed: 11/16/2022] Open
Abstract
Metabolism and signalling are tightly coupled in bacteria. Combining several theoretical approaches, a core model is presented that describes transcriptional and allosteric control of glycolysis in Escherichia coli. Experimental data based on microarrays, signaling components and extracellular metabolites are used to estimate kinetic parameters. A newly designed strain was used that adjusts the incoming glucose flux into the system and allows a kinetic analysis. Based on the results, prediction for intracelluar metabolite concentrations over a broad range of the growth rate could be performed and compared with data from literature.
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Affiliation(s)
- Andreas Kremling
- Systems Biotechnology, Technische Universität München, Boltzmannstr. 15, Garching b. München, Germany.
| | - Anna Goehler
- University Osnabrück, Barbarastrasse 11, Osnabrück, Germany.
| | - Knut Jahreis
- University Osnabrück, Barbarastrasse 11, Osnabrück, Germany.
| | - Markus Nees
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
| | - Benedikt Auerbach
- Systems Biotechnology, Technische Universität München, Boltzmannstr. 15, Garching b. München, Germany.
| | | | - Oznur Kökpinar
- Helmholtz Center for Infection Research, Inhoffenstr. 7, Braunschweig, Germany.
| | - Robert Geffers
- Helmholtz Center for Infection Research, Inhoffenstr. 7, Braunschweig, Germany.
| | - Ursula Rinas
- Helmholtz Center for Infection Research, Inhoffenstr. 7, Braunschweig, Germany.
| | - Katja Bettenbrock
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
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35
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Carneiro S, Villas-Bôas SG, Ferreira EC, Rocha I. Influence of the RelA Activity on E. coli Metabolism by Metabolite Profiling of Glucose-Limited Chemostat Cultures. Metabolites 2012; 2:717-32. [PMID: 24957759 PMCID: PMC3901239 DOI: 10.3390/metabo2040717] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/13/2012] [Accepted: 09/28/2012] [Indexed: 11/24/2022] Open
Abstract
Metabolite profiling of E. coli W3110 and the isogenic ΔrelA mutant cells was used to characterize the RelA-dependent stringent control of metabolism under different growth conditions. Metabolic profiles were obtained by gas chromatography–mass spectrometry (GC-MS) analysis and revealed significant differences between E. coli strains grown at different conditions. Major differences between the two strains were assessed in the levels of amino acids and fatty acids and their precursor metabolites, especially when growing at the lower dilution rates, demonstrating differences in their metabolic behavior. Despite the fatty acid biosynthesis being the most affected due to the lack of the RelA activity, other metabolic pathways involving succinate, lactate and threonine were also affected. Overall, metabolite profiles indicate that under nutrient-limiting conditions the RelA-dependent stringent response may be elicited and promotes key changes in the E. coli metabolism.
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Affiliation(s)
- Sónia Carneiro
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Silas G Villas-Bôas
- Centre for Microbial Innovation, School of Biological Sciences, The University of Auckland, 3A Symonds Street, Auckland 1142, New Zealand.
| | - Eugénio C Ferreira
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
| | - Isabel Rocha
- Institute for Biotechnology and Bioengineering (IBB), Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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36
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Azevedo NF, Bragança SM, Simões LC, Cerqueira L, Almeida C, Keevil CW, Vieira MJ. Proposal for a method to estimate nutrient shock effects in bacteria. BMC Res Notes 2012; 5:422. [PMID: 22873690 PMCID: PMC3490807 DOI: 10.1186/1756-0500-5-422] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 07/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plating methods are still the golden standard in microbiology; however, some studies have shown that these techniques can underestimate the microbial concentrations and diversity. A nutrient shock is one of the mechanisms proposed to explain this phenomenon. In this study, a tentative method to assess nutrient shock effects was tested. FINDINGS To estimate the extent of nutrient shock effects, two strains isolated from tap water (Sphingomonas capsulata and Methylobacterium sp.) and two culture collection strains (E. coli CECT 434 and Pseudomonas fluorescens ATCC 13525) were exposed both to low and high nutrient conditions for different times and then placed in low nutrient medium (R2A) and rich nutrient medium (TSA).The average improvement (A.I.) of recovery between R2A and TSA for the different times was calculated to more simply assess the difference obtained in culturability between each medium. As expected, A.I. was higher when cells were plated after the exposition to water than when they were recovered from high-nutrient medium showing the existence of a nutrient shock for the diverse bacteria used. S. capsulata was the species most affected by this phenomenon. CONCLUSIONS This work provides a method to consistently determine the extent of nutrient shock effects on different microorganisms and hence quantify the ability of each species to deal with sudden increases in substrate concentration.
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Affiliation(s)
- Nuno F Azevedo
- LEPAE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Roberto Frias, 4200-465, Porto, Portugal
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sofia M Bragança
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Lúcia C Simões
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Laura Cerqueira
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Carina Almeida
- LEPAE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Roberto Frias, 4200-465, Porto, Portugal
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Charles W Keevil
- Environmental Healthcare Unit, Microbiology Group, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton, SO16 7PX, United Kingdom
| | - Maria J Vieira
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
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37
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Srivastava RK, Maiti SK, Das D, Bapat PM, Batta K, Bhushan M, Wangikar PP. Metabolic flexibility of d-ribose producer strain of Bacillus pumilus under environmental perturbations. ACTA ACUST UNITED AC 2012; 39:1227-43. [DOI: 10.1007/s10295-012-1115-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Accepted: 02/27/2012] [Indexed: 02/07/2023]
Abstract
Abstract
The metabolic reaction rate vector is a bridge that links gene and protein expression alterations to the phenotypic endpoint. We present a simple approach for the estimation of flux distribution at key branch points in the metabolic network by using substrate uptake, metabolite secretion rate, and biomass growth rate for transketolase (tkt) deficient Bacillus pumilus ATCC 21951. We find that the glucose-6-phosphate (G6P) and pseudo catabolic/anabolic branch points are flexible in the d-ribose-producing tkt deficient strain of B. pumilus. The normalized flux through the pentose phosphate pathway (PPP) varied from 1.5 to 86 % under different growth conditions, thereby enabling substantial extracellular accumulation of d-ribose under certain conditions. Interestingly, the flux through PPP was affected by the extracellular phosphate concentration and dissolved oxygen concentration. This metabolic flexibility may have been the underlying reason for this strain being selected from thousands of others in a screening for d-ribose producers conducted in the 1970s.
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Affiliation(s)
- Rajesh K Srivastava
- grid.417971.d 0000000121987527 Department of Biosciences and Bioengineering Indian Institute of Technology Bombay 400076 Powai Mumbai India
| | - Soumen K Maiti
- grid.417971.d 0000000121987527 Department of Chemical Engineering Indian Institute of Technology Bombay 400076 Powai Mumbai India
| | - Debasish Das
- grid.417971.d 0000000121987527 Department of Chemical Engineering Indian Institute of Technology Bombay 400076 Powai Mumbai India
| | - Prashant M Bapat
- grid.417971.d 0000000121987527 Department of Chemical Engineering Indian Institute of Technology Bombay 400076 Powai Mumbai India
- grid.5170.3 0000000121818870 Center for Mikrobiel Bioteknologi, BioCentrum-DTU Danmarks Tekniske Universitet Bygning 223 2800 Kgs. Lyngby Denmark
| | - Kritika Batta
- grid.417971.d 0000000121987527 Department of Chemical Engineering Indian Institute of Technology Bombay 400076 Powai Mumbai India
| | - Mani Bhushan
- grid.417971.d 0000000121987527 Department of Chemical Engineering Indian Institute of Technology Bombay 400076 Powai Mumbai India
| | - Pramod P Wangikar
- grid.417971.d 0000000121987527 Department of Chemical Engineering Indian Institute of Technology Bombay 400076 Powai Mumbai India
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38
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Uncoupling of substrate-level phosphorylation in Escherichia coli during glucose-limited growth. Appl Environ Microbiol 2012; 78:6908-13. [PMID: 22843529 DOI: 10.1128/aem.01507-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The respiratory chain of Escherichia coli contains three different cytochrome oxidases. Whereas the cytochrome bo oxidase and the cytochrome bd-I oxidase are well characterized and have been shown to contribute to proton translocation, physiological data suggested a nonelectrogenic functioning of the cytochrome bd-II oxidase. Recently, however, this view was challenged by an in vitro biochemical analysis that showed that the activity of cytochrome bd-II oxidase does contribute to proton translocation with an H(+)/e(-) stoichiometry of 1. Here, we propose that this apparent discrepancy is due to the activities of two alternative catabolic pathways: the pyruvate oxidase pathway for acetate production and a pathway with methylglyoxal as an intermediate for the production of lactate. The ATP yields of these pathways are lower than those of the pathways that have so far always been assumed to catalyze the main catabolic flux under energy-limited growth conditions (i.e., pyruvate dehydrogenase and lactate dehydrogenase). Inclusion of these alternative pathways in the flux analysis of growing E. coli strains for the calculation of the catabolic ATP synthesis rate indicates an electrogenic function of the cytochrome bd-II oxidase, compatible with an H(+)/e(-) ratio of 1. This analysis shows for the first time the extent of bypassing of substrate-level phosphorylation in E. coli under energy-limited growth conditions.
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Martínez-Gómez K, Flores N, Castañeda HM, Martínez-Batallar G, Hernández-Chávez G, Ramírez OT, Gosset G, Encarnación S, Bolivar F. New insights into Escherichia coli metabolism: carbon scavenging, acetate metabolism and carbon recycling responses during growth on glycerol. Microb Cell Fact 2012; 11:46. [PMID: 22513097 PMCID: PMC3390287 DOI: 10.1186/1475-2859-11-46] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 04/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycerol has enhanced its biotechnological importance since it is a byproduct of biodiesel synthesis. A study of Escherichia coli physiology during growth on glycerol was performed combining transcriptional-proteomic analysis as well as kinetic and stoichiometric evaluations in the strain JM101 and certain derivatives with important inactivated genes. RESULTS Transcriptional and proteomic analysis of metabolic central genes of strain JM101 growing on glycerol, revealed important changes not only in the synthesis of MglB, LamB and MalE proteins, but also in the overexpression of carbon scavenging genes: lamB, malE, mglB, mglC, galP and glk and some members of the RpoS regulon (pfkA, pfkB, fbaA, fbaB, pgi, poxB, acs, actP and acnA). Inactivation of rpoS had an important effect on stoichiometric parameters and growth adaptation on glycerol. The observed overexpression of poxB, pta, acs genes, glyoxylate shunt genes (aceA, aceB, glcB and glcC) and actP, suggested a possible carbon flux deviation into the PoxB, Acs and glyoxylate shunt. In this scenario acetate synthesized from pyruvate with PoxB was apparently reutilized via Acs and the glyoxylate shunt enzymes. In agreement, no acetate was detected when growing on glycerol, this strain was also capable of glycerol and acetate coutilization when growing in mineral media and derivatives carrying inactivated poxB or pckA genes, accumulated acetate. Tryptophanase A (TnaA) was synthesized at high levels and indole was produced by this enzyme, in strain JM101 growing on glycerol. Additionally, in the isogenic derivative with the inactivated tnaA gene, no indole was detected and acetate and lactate were accumulated. A high efficiency aromatic compounds production capability was detected in JM101 carrying pJLBaroG(fbr)tktA, when growing on glycerol, as compared to glucose. CONCLUSIONS The overexpression of several carbon scavenging, acetate metabolism genes and the absence of acetate accumulation occurred in JM101 cultures growing on glycerol. To explain these results it is proposed that in addition to the glycolytic metabolism, a gluconeogenic carbon recycling process that involves acetate is occurring simultaneously in this strain when growing on glycerol. Carbon flux from glycerol can be efficiently redirected in JM101 strain into the aromatic pathway using appropriate tools.
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Affiliation(s)
- Karla Martínez-Gómez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 510-3, Cuernavaca, Morelos, CP 62250, Mexico
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 510-3, Cuernavaca, Morelos, CP 62250, Mexico
| | - Héctor M Castañeda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 510-3, Cuernavaca, Morelos, CP 62250, Mexico
| | - Gabriel Martínez-Batallar
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 565-A, Cuernavaca, Morelos, CP 62210, Mexico
| | - Georgina Hernández-Chávez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 510-3, Cuernavaca, Morelos, CP 62250, Mexico
| | - Octavio T Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 510-3, Cuernavaca, Morelos, CP 62250, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 510-3, Cuernavaca, Morelos, CP 62250, Mexico
| | - Sergio Encarnación
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 565-A, Cuernavaca, Morelos, CP 62210, Mexico
| | - Francisco Bolivar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Apdo. Postal 510-3, Cuernavaca, Morelos, CP 62250, Mexico
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Abstract
A metabolism is a complex network of chemical reactions that converts sources of energy and chemical elements into biomass and other molecules. To design a metabolism from scratch and to implement it in a synthetic genome is almost within technological reach. Ideally, a synthetic metabolism should be able to synthesize a desired spectrum of molecules at a high rate, from multiple different nutrients, while using few chemical reactions, and producing little or no waste. Not all of these properties are achievable simultaneously. We here use a recently developed technique to create random metabolic networks with pre-specified properties to quantify trade-offs between these and other properties. We find that for every additional molecule to be synthesized a network needs on average three additional reactions. For every additional carbon source to be utilized, it needs on average two additional reactions. Networks able to synthesize 20 biomass molecules from each of 20 alternative sole carbon sources need to have at least 260 reactions. This number increases to 518 reactions for networks that can synthesize more than 60 molecules from each of 80 carbon sources. The maximally achievable rate of biosynthesis decreases by approximately 5 percent for every additional molecule to be synthesized. Biochemically related molecules can be synthesized at higher rates, because their synthesis produces less waste. Overall, the variables we study can explain 87 percent of variation in network size and 84 percent of the variation in synthesis rate. The constraints we identify prescribe broad boundary conditions that can help to guide synthetic metabolism design.
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Affiliation(s)
- Tugce Bilgin
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Zürich, Switzerland.
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Abstract
The cytosol of a cell is a concentrated milieu of a variety of different molecules, including small molecules (salts and metabolites) and macromolecules such as nucleic acids, polysaccharides, proteins and large macromolecular complexes. Macromolecular crowding in the cytosolic environment is proposed to influence various properties of proteins, including substrate binding affinity and enzymatic activity. Here we chose to use the synthetic crowding agent Ficoll, which is commonly used to mimic cytosolic crowding conditions to study the crowding effect on the catalytic properties of glycolytic enzymes, namely phosphoglycerate kinase, glyceraldehyde 3-phosphate dehydrogenase, and acylphosphatase. We determined the kinetic parameters of these enzymes in the absence and in the presence of the crowding agent. We found that the Michaelis constant, K(m), and the catalytic turnover number, k(cat), of these enzymes are not perturbed by the presence of the crowding agent Ficoll. Our results support earlier findings which suggested that the Michaelis constant of certain enzymes evolved in consonance with the substrate concentration in the cell to allow effective enzyme function in bidirectional pathways. This conclusion is further supported by the analysis of nine other enzymes for which the K(m) values in the presence and absence of crowding agents have been measured.
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Affiliation(s)
- Tobias Vöpel
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
| | - George I. Makhatadze
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
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Narawongsanont R, Kabinpong S, Auiyawong B, Tantitadapitak C. Cloning and characterization of AKR4C14, a rice aldo-keto reductase, from Thai Jasmine rice. Protein J 2012; 31:35-42. [PMID: 22101802 DOI: 10.1007/s10930-011-9371-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aldo-keto reductase (AKR) is an enzyme superfamily whose members are involved in the metabolism of aldehydes/ketones. The AKR4 subfamily C (AKR4C) is a group of aldo-keto reductases that are found in plants. Some AKR4C(s) in dicot plants are capable of metabolizing reactive aldehydes whereas, such activities have not been reported for AKR4C(s) from monocot species. In this study, we have screened Indica rice genome for genes with significant homology to dicot AKR4C(s) and identified a cluster of putative AKR4C(s) located on the Indica rice chromosome I. The genes including OsI_04426, OsI_04428 and OsI_04429 were successfully cloned and sequenced by qRT-PCR from leaves of Thai Jasmine rice (KDML105). OsI_04428, later named AKR4C14, was chosen for further studies because it shares highest homology to the dicot AKR4C(s). The bacterially expressed recombinant protein of AKR4C14 was successfully produced as a MBP fusion protein and his-tagged protein. The recombinant AKR4C14 were capable of metabolizing sugars and reactive aldehydes i.e. methylglyoxal, a toxic by-product of the glycolysis pathway, glutaraldehyde, and trans-2-hexenal, a natural reactive 2-alkenal. AKR4C14 was highly expressed in green tissues, i.e. leaf sheets and stems, whereas flowers and roots had a significantly lower level of expression. These findings indicated that monocot AKR4C(s) can metabolize reactive aldehydes like the dicot AKR4C(s) and possibly play a role in detoxification mechanism of reactive aldehydes.
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Affiliation(s)
- Rawint Narawongsanont
- Department of Biochemistry, Faculty of Science, Kasetsart University, Pahonyothin Rd, Bangkok, 10903, Thailand
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Sunya S, Gorret N, Delvigne F, Uribelarrea JL, Molina-Jouve C. Real-time monitoring of metabolic shift and transcriptional induction of yciG::luxCDABE E. coli reporter strain to a glucose pulse of different concentrations. J Biotechnol 2011; 157:379-90. [PMID: 22209969 DOI: 10.1016/j.jbiotec.2011.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 11/20/2011] [Accepted: 12/12/2011] [Indexed: 10/14/2022]
Abstract
Ineffective mixing entailing heterogeneity issue within industrial bioreactors has been reported to affect microbial physiology and consequently bioprocess performances. Alteration of these performances results from microorganism ability to modulate their physiology at metabolic and/or transcriptional levels in order to survive in a given environment. Until now, dynamics of both metabolic and transcriptional microbial response to external stimuli have been investigated using mainly ex situ measurements with sampling and/or quenching constraints. This work showed an in situ bioluminescence approach for real-time monitoring of characteristic stress responses of Escherichia coli containing yciG::luxCDABE reporter to glucose pulses in well-controlled steady-state chemostat cultures. Reproducibility of in situ bioluminescence profiles was assessed. A dramatic transient increase in the bioluminescence intensity (sharp peak) was observed for a complete depletion of sugars and for a sudden decrease in the dilution rate. This response was connected to a sudden change of the metabolic activity. On the contrary a bell curve of bioluminescence intensity, dose-dependent, was related to an induction of transcriptional activity. Real-time monitoring of the bioluminescence signal with time-span less than a second gave access to the characteristic times of the metabolic shift and transcriptional induction of the stress response.
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Affiliation(s)
- Sirichai Sunya
- Université de Toulouse, INSA, UPS, INP, LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
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Global transcriptomic and proteomic responses of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation. Appl Environ Microbiol 2011; 78:1424-36. [PMID: 22179257 DOI: 10.1128/aem.06792-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Bacteria of the genus Dehalococcoides play an important role in the reductive dechlorination of chlorinated ethenes. A systems-level approach was taken in this study to examine the global transcriptomic and proteomic responses of exponentially growing cells of Dehalococcoides ethenogenes strain 195 to fixed nitrogen limitation (FNL), as dechlorination activity and cell yield both decrease during FNL. As expected, the nitrogen-fixing (nif) genes were differentially upregulated in the transcriptome and proteome of strain 195 during FNL. Aside from the nif operon, a putative methylglyoxal synthase-encoding gene (DET1576), the product of which is predicted to catalyze the formation of the toxic electrophile methylglyoxal and is implicated in the uncoupling of anabolism from catabolism in bacteria, was strongly upregulated in the transcriptome and could potentially play a role in the observed growth inhibition during FNL. Carbon catabolism genes were generally downregulated in response to FNL, and a number of transporters were differentially regulated in response to nitrogen limitation, with some playing apparent roles in nitrogen acquisition, while others were associated with general stress responses. A number of genes related to the functions of nucleotide synthesis, replication, transcription, translation, and posttranslational modifications were also differentially expressed. One gene coding for a putative reductive dehalogenase (DET1545) and a number of genes coding for oxidoreductases, which have implications in energy generation and redox reactions, were also differentially regulated. Interestingly, most of the genes within the multiple integrated elements were not differentially expressed. Overall, this study elucidates the molecular responses of strain 195 to FNL and identifies differentially expressed genes that are potential biomarkers to evaluate environmental cellular nitrogen status.
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Landmann JJ, Werner S, Hillen W, Stülke J, Görke B. Carbon source control of the phosphorylation state of the Bacillus subtilis carbon-flux regulator Crh in vivo. FEMS Microbiol Lett 2011; 327:47-53. [PMID: 22092971 DOI: 10.1111/j.1574-6968.2011.02456.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 10/31/2011] [Accepted: 11/07/2011] [Indexed: 11/29/2022] Open
Abstract
Bacillus subtilis possesses carbon-flux regulating histidine protein (Crh), a paralog of the histidine protein (HPr) of the phosphotransferase system (PTS). Like HPr, Crh becomes (de)phosphorylated in vitro at residue Ser46 by the metabolite-controlled HPr kinase/phosphorylase HPrK/P. Depending on its phosphorylation state, Crh exerts regulatory functions in connection with carbohydrate metabolism. So far, knowledge on phosphorylation of Crh in vivo has been limited and derived from indirect evidence. Here, we studied the dynamics of Crh phosphorylation directly by non-denaturing gel electrophoresis followed by Western analysis. The results confirm that HPrK/P is the single kinase catalyzing phosphorylation of Crh in vivo. Accordingly, phosphorylation of Crh is triggered by the carbon source as observed previously for HPr, but with some differences. Phosphorylation of both proteins occurred during exponential growth and disappeared upon exhaustion of the carbon source. During exponential growth, ~80% of the Crh molecules were phosphorylated when cells utilized a preferred carbon source. The reverse distribution, i.e. around 20% of Crh molecules phosphorylated, was obtained upon utilization of less favorable substrates. This clear-cut classification of the substrates into two groups has not previously been observed for HPr(Ser)~P formation. The likely reason for this difference is the additional PTS-dependent phosphorylation of HPr at His15, which limits accumulation of HPr(Ser)~P.
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Affiliation(s)
- Jens J Landmann
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany
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Landmann JJ, Busse RA, Latz JH, Singh KD, Stülke J, Görke B. Crh, the paralogue of the phosphocarrier protein HPr, controls the methylglyoxal bypass of glycolysis in Bacillus subtilis. Mol Microbiol 2011; 82:770-87. [PMID: 21992469 DOI: 10.1111/j.1365-2958.2011.07857.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The histidine protein HPr has a key role in regulation of carbohydrate utilization in low-GC Gram-positive bacteria. Bacilli possess the paralogue Crh. Like HPr, Crh becomes phosphorylated by kinase HPrK/P in response to high fructose-1,6-bisphosphate concentrations. However, Crh can only partially substitute for the regulatory functions of HPr leaving its role mysterious. Using protein co-purification, we identified enzyme methylglyoxal synthase MgsA as interaction partner of Crh in Bacillus subtilis. MgsA converts dihydroxyacetone-phosphate to methylglyoxal and thereby initiates a glycolytic bypass that prevents the deleterious accumulation of phospho-sugars under carbon overflow conditions. However, methylgyloxal is toxic and its production requires control. We show here that exclusively the non-phosphorylated form of Crh interacts with MgsA in vivo and inhibits MgsA activity in vitro. Accordingly, Crh inhibits methylglyoxal formation in vivo under nutritional famine conditions that favour a low HPr kinase activity. Thus, Crh senses the metabolic state of the cell, as reflected by its phosphorylation state, and accordingly controls flux through the harmful methylglyoxal pathway. Interestingly, HPr is unable to bind and regulate MgsA, making this a bona fide function of Crh. Four residues that differ in the interaction surfaces of HPr and Crh may account for this difference.
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Affiliation(s)
- Jens J Landmann
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-University, Grisebachstrasse 8, 37077 Göttingen, Germany
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McLeod A, Snipen L, Naterstad K, Axelsson L. Global transcriptome response in Lactobacillus sakei during growth on ribose. BMC Microbiol 2011; 11:145. [PMID: 21702908 PMCID: PMC3146418 DOI: 10.1186/1471-2180-11-145] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 06/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Lactobacillus sakei is valuable in the fermentation of meat products and exhibits properties that allow for better preservation of meat and fish. On these substrates, glucose and ribose are the main carbon sources available for growth. We used a whole-genome microarray based on the genome sequence of L. sakei strain 23K to investigate the global transcriptome response of three L. sakei strains when grown on ribose compared with glucose. RESULTS The function of the common regulated genes was mostly related to carbohydrate metabolism and transport. Decreased transcription of genes encoding enzymes involved in glucose metabolism and the L-lactate dehydrogenase was observed, but most of the genes showing differential expression were up-regulated. Especially transcription of genes directly involved in ribose catabolism, the phosphoketolase pathway, and in alternative fates of pyruvate increased. Interestingly, the methylglyoxal synthase gene, which encodes an enzyme unique for L. sakei among lactobacilli, was up-regulated. Ribose catabolism seems closely linked with catabolism of nucleosides. The deoxyribonucleoside synthesis operon transcriptional regulator gene was strongly up-regulated, as well as two gene clusters involved in nucleoside catabolism. One of the clusters included a ribokinase gene. Moreover, hprK encoding the HPr kinase/phosphatase, which plays a major role in the regulation of carbon metabolism and sugar transport, was up-regulated, as were genes encoding the general PTS enzyme I and the mannose-specific enzyme II complex (EIIman). Putative catabolite-responsive element (cre) sites were found in proximity to the promoter of several genes and operons affected by the change of carbon source. This could indicate regulation by a catabolite control protein A (CcpA)-mediated carbon catabolite repression (CCR) mechanism, possibly with the EIIman being indirectly involved. CONCLUSIONS Our data shows that the ribose uptake and catabolic machinery in L. sakei is highly regulated at the transcription level. A global regulation mechanism seems to permit a fine tuning of the expression of enzymes that control efficient exploitation of available carbon sources.
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Affiliation(s)
- Anette McLeod
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, Ås, NO-1430, Norway
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, Ås, NO-1432, Norway
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, Ås, NO-1432, Norway
| | - Kristine Naterstad
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, Ås, NO-1430, Norway
| | - Lars Axelsson
- Nofima Mat AS, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, Ås, NO-1430, Norway
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Experimental and theoretical analysis of poly(β-hydroxybutyrate) formation and consumption in Ralstonia eutropha. Biochem Eng J 2011. [DOI: 10.1016/j.bej.2011.03.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Ammonium and phosphate limitation in 1,3-propanediol production by Klebsiella pneumoniae. Biotechnol Lett 2009; 32:289-94. [DOI: 10.1007/s10529-009-0150-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 09/25/2009] [Accepted: 09/30/2009] [Indexed: 10/20/2022]
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50
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Xu H, Dou W, Xu H, Zhang X, Rao Z, Shi Z, Xu Z. A two-stage oxygen supply strategy for enhanced l-arginine production by Corynebacterium crenatum based on metabolic fluxes analysis. Biochem Eng J 2009. [DOI: 10.1016/j.bej.2008.08.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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