1
|
Bendig T, Ulmer A, Luzia L, Müller S, Sahle S, Bergmann FT, Lösch M, Erdemann F, Zeidan AA, Mendoza SN, Teusink B, Takors R, Kummer U, Figueiredo AS. The pH-dependent lactose metabolism of Lactobacillus delbrueckii subsp. bulgaricus: An integrative view through a mechanistic computational model. J Biotechnol 2023; 374:90-100. [PMID: 37572793 DOI: 10.1016/j.jbiotec.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/20/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The fermentation process of milk to yoghurt using Lactobacillus delbrueckii subsp. bulgaricus in co-culture with Streptococcus thermophilus is hallmarked by the breakdown of lactose to organic acids such as lactate. This leads to a substantial decrease in pH - both in the medium, as well as cytosolic. The latter impairs metabolic activities due to the pH-dependence of enzymes, which compromises microbial growth. To quantitatively elucidate the impact of the acidification on metabolism of L. bulgaricus in an integrated way, we have developed a proton-dependent computational model of lactose metabolism and casein degradation based on experimental data. The model accounts for the influence of pH on enzyme activities as well as cellular growth and proliferation of the bacterial population. We used a machine learning approach to quantify the cell volume throughout fermentation. Simulation results show a decrease in metabolic flux with acidification of the cytosol. Additionally, the validated model predicts a similar metabolic behaviour within a wide range of non-limiting substrate concentrations. This computational model provides a deeper understanding of the intricate relationships between metabolic activity and acidification and paves the way for further optimization of yoghurt production under industrial settings.
Collapse
Affiliation(s)
- Tamara Bendig
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Andreas Ulmer
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Laura Luzia
- Systems Biology Lab, Vrije Universiteit, Amsterdam, the Netherlands
| | - Susanne Müller
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Sven Sahle
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Frank T Bergmann
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Maren Lösch
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Florian Erdemann
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ahmad A Zeidan
- Systems Biology, R&D Discovery, Chr. Hansen A/S, Hørsholm, Denmark
| | | | - Bas Teusink
- Systems Biology Lab, Vrije Universiteit, Amsterdam, the Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Ursula Kummer
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
| | - Ana Sofia Figueiredo
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany.
| |
Collapse
|
2
|
Sato R, Ikeda M, Tanaka T, Ohara H, Aso Y. Production of R- and S-1,2-propanediol in engineered Lactococcus lactis. AMB Express 2021; 11:117. [PMID: 34398341 PMCID: PMC8368392 DOI: 10.1186/s13568-021-01276-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/11/2022] Open
Abstract
1,2-propanediol (1,2-PDO) is a versatile chemical used in multiple manufacturing processes. To date, some engineered and non-engineered microbes, such as Escherichia coli, Lactobacillus buchneri, and Clostridium thermosaccharolyticum, have been used to produce 1,2-PDO. In this study, we demonstrated the production of R- and S-1,2-PDO using engineered Lactococcus lactis. The L- and D-lactic acid-producing L. lactis strains NZ9000 and AH1 were transformed with the plasmid pNZ8048-ppy harboring pct, pduP, and yahK genes for 1,2-PDO biosynthesis, resulting in L. lactis LL1 and LL2, respectively. These engineered L. lactis produced S- and R-1,2-PDO at concentrations of 0.69 and 0.50 g/L with 94.4 and 78.0% ee optical purities, respectively, from 1% glucose after 72 h of cultivation. Both 1% mannitol and 1% gluconate were added instead of glucose to the culture of L. lactis LL1 to supply NADH and NADPH to the 1,2-PDO production pathway, resulting in 75% enhancement of S-1,2-PDO production. Production of S-1,2-PDO from 5% mannitol and 5% gluconate was demonstrated using L. lactis LL1 with a pH-stat approach. This resulted in S-1,2-PDO production at a concentration of 1.88 g/L after 96 h of cultivation. To our knowledge, this is the first report on the production of R- and S-1,2-PDO using engineered lactic acid bacteria.
Collapse
Affiliation(s)
- Rintaro Sato
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
- JST-Mirai Program, Japan Science and Technology Agency, Saitama, Japan
| | - Motoyuki Ikeda
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
| | - Tomonari Tanaka
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
| | - Hitomi Ohara
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan
| | - Yuji Aso
- Department of Biobased Materials Science, Kyoto Institute of Technology, Kyoto, Japan.
- JST-Mirai Program, Japan Science and Technology Agency, Saitama, Japan.
| |
Collapse
|
3
|
Holzheu P, Krebs M, Larasati C, Schumacher K, Kummer U. An integrative view on vacuolar pH homeostasis in Arabidopsis thaliana: Combining mathematical modeling and experimentation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1541-1556. [PMID: 33780094 DOI: 10.1111/tpj.15251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/27/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
The acidification of plant vacuoles is of great importance for various physiological processes, as a multitude of secondary active transporters utilize the proton gradient established across the vacuolar membrane. Vacuolar-type H+ -translocating ATPases and a pyrophosphatase are thought to enable vacuoles to accumulate protons against their electrochemical potential. However, recent studies pointed to the ATPase located at the trans-Golgi network/early endosome (TGN/EE) to contribute to vacuolar acidification in a manner not understood as of now. Here, we combined experimental data and computational modeling to test different hypotheses for vacuolar acidification mechanisms. For this, we analyzed different models with respect to their ability to describe existing experimental data. To better differentiate between alternative acidification mechanisms, new experimental data have been generated. By fitting the models to the experimental data, we were able to prioritize the hypothesis in which vesicular trafficking of Ca2+ /H+ -antiporters from the TGN/EE to the vacuolar membrane and the activity of ATP-dependent Ca2+ -pumps at the tonoplast might explain the residual acidification observed in Arabidopsis mutants defective in vacuolar proton pump activity. The presented modeling approach provides an integrative perspective on vacuolar pH regulation in Arabidopsis and holds potential to guide further experimental work.
Collapse
Affiliation(s)
- Pascal Holzheu
- Department of Modeling of Biological Processes, COS Heidelberg/Bioquant, Heidelberg University, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany
| | - Melanie Krebs
- Department of Cell Biology, COS Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Catharina Larasati
- Department of Cell Biology, COS Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Karin Schumacher
- Department of Cell Biology, COS Heidelberg, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Ursula Kummer
- Department of Modeling of Biological Processes, COS Heidelberg/Bioquant, Heidelberg University, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany
| |
Collapse
|
4
|
Jung J, Kim S, Lee JY, Yoon S, You S, Kim SH. Multifunctional properties of Lactobacillus plantarum strains WiKim83 and WiKim87 as a starter culture for fermented food. Food Sci Nutr 2019; 7:2505-2516. [PMID: 31428338 PMCID: PMC6694436 DOI: 10.1002/fsn3.1075] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/04/2023] Open
Abstract
This study aimed to evaluate the safety (hemolysis and enzyme activity), probiotic properties (gastrointestinal tract tolerance, adhesion, hydrophobicity, and auto-aggregation), and functional characteristics (antimicrobial, antioxidant, and β-galactosidase activities) of lactic acid bacteria (LAB), isolated from kimchi, in order to select a multifunctional LAB strain for starter culture in fermented food. The five isolated strains included Lactobacillus plantarum WiKim83, L. plantarum WiKim84, Pediococcus pentosaceus WiKim85, P. pentosaceus WiKim86, and L. plantarum WiKim87, as identified by 16S rRNA gene sequence analysis; they were confirmed to be nonhemolytic and not able to produce β-glucuronidase, a carcinogenic enzyme. Probiotic properties of the five LAB strains were evaluated relative to those of commercial Lactobacillus rhamnosus GG, and results revealed probiotic potential of three strains (L. plantarum WiKim83, L. plantarum WiKim84, and L. plantarum WiKim87) to be superior. L. plantarum WiKim84 showed high antimicrobial activity against pathogens, and L. plantarum WiKim83 exhibited the highest antioxidant and β-galactosidase activities. Based on the probiotic and functional properties, the main characteristics of each strain were highlighted and two of them, L. plantarum WiKim83 and L. plantarum WiKim87, were selected as the most potent by principal component analysis. These strains showed antimicrobial, β-galactosidase, and antioxidant activities, which recommend their suitability as starter culture in various fermented foods.
Collapse
Affiliation(s)
- Ji‐Hye Jung
- Hygienic Safety and Analysis CenterWorld Institute of KimchiGwangjuKorea
| | - Su‐Ji Kim
- Hygienic Safety and Analysis CenterWorld Institute of KimchiGwangjuKorea
| | - Jae Yong Lee
- Hygienic Safety and Analysis CenterWorld Institute of KimchiGwangjuKorea
| | - So‐Ra Yoon
- Hygienic Safety and Analysis CenterWorld Institute of KimchiGwangjuKorea
| | - Su‐Yeon You
- Hygienic Safety and Analysis CenterWorld Institute of KimchiGwangjuKorea
| | - Sung Hyun Kim
- Hygienic Safety and Analysis CenterWorld Institute of KimchiGwangjuKorea
| |
Collapse
|
5
|
Gallagher D, Parker D, Allen DJ, Tsesmetzis N. Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production. BIORESOURCE TECHNOLOGY 2018; 264:163-173. [PMID: 29803086 DOI: 10.1016/j.biortech.2018.05.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/11/2018] [Accepted: 05/12/2018] [Indexed: 05/03/2023]
Abstract
Significant low-cost biofuel production volumes could be achieved from commercial-scale silage by redirecting lactic acid fermentation to ethanol production. A temporal metagenomic analysis on ensiled sweet sorghum inoculated with an ethanologenic yeast has been conducted to understand the underlying microbial processes during bioethanol production. Individual silage buckets approximating silage piles were prepared with freshly harvested material and supplemented with ethanologenic yeast, sulfuric acid or both. The ensiling progress was assessed using high performance liquid chromatography, microbial taxonomic identification and abundance. The combined treatment with Saccharomyces and acid led to a steady reduction of bacterial abundance and microbial diversity with Lactobacillus becoming the dominant genus during the late timepoints. Furthermore, the addition of acid to inhibit bacterial growth hindered Saccharomyces ability to compete with native yeasts like Candida. Knowledge of the response of the in-situ microbial community to the various treatments during ensiling will help improve current methodologies for bioethanol production.
Collapse
Affiliation(s)
- Daniella Gallagher
- Shell International Exploration and Production Inc., Houston, TX, USA; Biosciences, The University of Exeter, Exeter, UK
| | - David Parker
- Shell International Exploration and Production Inc., Houston, TX, USA; Biosciences, The University of Exeter, Exeter, UK
| | - Damian J Allen
- Shell International Exploration and Production Inc., Houston, TX, USA; Agronomy, Purdue University, West Lafayette, IN, USA
| | - Nicolas Tsesmetzis
- Shell International Exploration and Production Inc., Houston, TX, USA; Natural and Environmental Sciences, Newcastle University, Newcastle, UK.
| |
Collapse
|
6
|
Roth A, Govaerts C. LmrP from Lactoccoccus lactis: a tractable model to understand secondary multidrug transport in MFS. Res Microbiol 2018; 169:468-477. [PMID: 30145366 DOI: 10.1016/j.resmic.2018.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 06/25/2018] [Accepted: 07/26/2018] [Indexed: 10/28/2022]
Abstract
The secondary transporter LmrP from Lactoccoccus lactis is a remarkable model to study the molecular basis of secondary multidrug transport. This review article addresses more than twenty years of research about transport activity, substrates range, conformational dynamics and mechanistic models of drug export for LmrP. Several studies have shown that the transporter alternates between inward-open and outward-open conformations and that the transition is regulated by the protonation state of key acidic residues and is further modulated by the lipid environment.
Collapse
Affiliation(s)
- Aurélie Roth
- SFMB, Université Libre de Bruxelles (ULB) CP206/02, Boulevard du Triomphe, Building BC, B-1050 Brussels, Belgium
| | - Cedric Govaerts
- SFMB, Université Libre de Bruxelles (ULB) CP206/02, Boulevard du Triomphe, Building BC, B-1050 Brussels, Belgium.
| |
Collapse
|
7
|
Effects of the probiotics Lactococcus lacttis (MTCC-440) on Salmonella enteric serovar Typhi in co-culture study. Microb Pathog 2018; 120:42-46. [PMID: 29704985 DOI: 10.1016/j.micpath.2018.04.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 11/22/2022]
Abstract
Lactococcus lactis (L. lactis)a probiotics microorganism having wide range of benefits on human health, and also protects the body from pathogenic microorganism. This study was conducted to determine the co-culture effect with the probiotic strain L. lactis (MTCC440) on Salmonella enterica serovar Typhi (S.Typhi). The existing problem was to determine the individual growth of both strains during co-culture. Growth kinetics study was performed and observed for 28 h and used to determine specific growth rate of S. Typhi under co-culture study. In growth kinetics study maximum specific growth rate (μ) of S. Typhi under monoculture and co-culture study was achieved 0.695 h-1 and 0.35 h-1 respectively. The maximum cell mass of L. lactis and S. Typhi was obtained 0.15 g/L and 0.18 g/L respectively. In co-culture study, L. lactis was found effective for the inhibition of 73% growth of S. Typhi due to lactic acid production.
Collapse
|
8
|
Rupprecht C, Wingen M, Potzkei J, Gensch T, Jaeger KE, Drepper T. A novel FbFP-based biosensor toolbox for sensitive in vivo determination of intracellular pH. J Biotechnol 2017; 258:25-32. [PMID: 28501596 DOI: 10.1016/j.jbiotec.2017.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/05/2017] [Accepted: 05/07/2017] [Indexed: 02/07/2023]
Abstract
The intracellular pH is an important modulator of various bio(techno)logical processes such as enzymatic conversion of metabolites or transport across the cell membrane. Changes of intracellular pH due to altered proton distribution can thus cause dysfunction of cellular processes. Consequently, accurate monitoring of intracellular pH allows elucidating the pH-dependency of (patho)physiological and biotechnological processes. In this context, genetically encoded biosensors represent a powerful tool to determine intracellular pH values non-invasively and with high spatiotemporal resolution. We have constructed a toolbox of novel genetically encoded FRET-based pH biosensors (named Fluorescence Biosensors for pH or FluBpH) that utilizes the FMN-binding fluorescent protein EcFbFP as donor domain. In contrast to many fluorescent proteins of the GFP family, EcFbFP exhibits a remarkable tolerance towards acidic pH (pKa∼3.2). To cover the broad range of physiologically relevant pH values, three EYFP variants exhibiting pKa values of 5.7, 6.1 and 7.5 were used as pH-sensing FRET acceptor domains. The resulting biosensors FluBpH 5.7, FluBpH 6.1 and FluBpH 7.5 were calibrated in vitro and in vivo to accurately evaluate their pH indicator properties. To demonstrate the in vivo applicability of FluBpH, changes of intracellular pH were ratiometrically measured in E. coli cells during acid stress.
Collapse
Affiliation(s)
- Christian Rupprecht
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Marcus Wingen
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Janko Potzkei
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany; GO-Bio Projekt SenseUP, Forschungszentrum Jülich, D-52425 Jülich GmbH, Germany
| | - Thomas Gensch
- Institute of Complex Systems ICS-4: Cellular Biophysics, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany; Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Düsseldorf, Forschungszentrum Jülich, D-52425 Jülich, Germany.
| |
Collapse
|
9
|
Hu D, Zhou Z, Niu T, Wei H, Dou W, Jiang LM, Lv Y. Co-treatment of reject water from sludge dewatering and supernatant from sludge lime stabilization process for nutrient removal: A cost-effective approach. Sep Purif Technol 2017. [DOI: 10.1016/j.seppur.2016.08.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
10
|
Sudarsan S, Blank LM, Dietrich A, Vielhauer O, Takors R, Schmid A, Reuss M. Dynamics of benzoate metabolism in Pseudomonas putida KT2440. Metab Eng Commun 2016; 3:97-110. [PMID: 29468117 PMCID: PMC5779716 DOI: 10.1016/j.meteno.2016.03.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/29/2016] [Accepted: 03/14/2016] [Indexed: 12/26/2022] Open
Abstract
Soil microorganisms mineralize lignin-derived aromatic carbon sources using oxidative catabolic pathways, such as the β-ketoadipate pathway. Although this aromatic pathway is one of the best-studied pathways in biochemistry, the complete pathway, including its regulation by aromatic carbon sources, has not been integrated into the metabolic network. In particular, information about the in vivo operation (e.g., kinetics and flux capacity) of the pathway is lacking. In this contribution, we use kinetic modeling and thermodynamic analysis to evaluate the in vivo operation of this key aromatic multi-step pathway. The resulting ab initio deterministic model of benzoate degradation via the β-ketoadipate (ortho-cleavage) pathway in Pseudomonas putida KT2440 is presented. The kinetic model includes mechanistic rate expressions for the enzymes and transport processes. The design and experimental validation of the model are driven by data generated from short-term perturbation experiments in a benzoate-limited continuous culture. The results of rigorous modeling of the in vivo dynamics provide strong support for flux regulation by the benzoate transporter and the enzymes forming and cleaving catechol. Revisiting the β-ketoadipate pathway might be valuable for applications in different fields, such as biochemistry and metabolic engineering, that use lignin monomers as a carbon source. We describe a kinetic model for the β-ketoadipate pathway. Short term metabolic responses were tracked on metabolite level by rapid sampling. The model captures steady state and dynamic conditions of the β-ketoadipate pathway. Thermodynamic analysis revealed regulation points of the pathway. The results are discussed in the context of metabolic network operation.
Collapse
Affiliation(s)
- Suresh Sudarsan
- Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology Department, RWTH Aachen University, 52074 Aachen, Germany
| | - Lars M. Blank
- Institute of Applied Microbiology, ABBt – Aachen Biology and Biotechnology Department, RWTH Aachen University, 52074 Aachen, Germany
| | - Alexander Dietrich
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Oliver Vielhauer
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Andreas Schmid
- Department Solar Materials, Helmholtz Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany
| | - Matthias Reuss
- Stuttgart Research Center Systems Biology, University of Stuttgart, Nobelstrasse 15, 70569 Stuttgart, Germany
- Corresponding author.
| |
Collapse
|
11
|
Murabito E, Verma M, Bekker M, Bellomo D, Westerhoff HV, Teusink B, Steuer R. Monte-Carlo modeling of the central carbon metabolism of Lactococcus lactis: insights into metabolic regulation. PLoS One 2014; 9:e106453. [PMID: 25268481 PMCID: PMC4182131 DOI: 10.1371/journal.pone.0106453] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 08/07/2014] [Indexed: 11/18/2022] Open
Abstract
Metabolic pathways are complex dynamic systems whose response to perturbations and environmental challenges are governed by multiple interdependencies between enzyme properties, reactions rates, and substrate levels. Understanding the dynamics arising from such a network can be greatly enhanced by the construction of a computational model that embodies the properties of the respective system. Such models aim to incorporate mechanistic details of cellular interactions to mimic the temporal behavior of the biochemical reaction system and usually require substantial knowledge of kinetic parameters to allow meaningful conclusions. Several approaches have been suggested to overcome the severe data requirements of kinetic modeling, including the use of approximative kinetics and Monte-Carlo sampling of reaction parameters. In this work, we employ a probabilistic approach to study the response of a complex metabolic system, the central metabolism of the lactic acid bacterium Lactococcus lactis, subject to perturbations and brief periods of starvation. Supplementing existing methodologies, we show that it is possible to acquire a detailed understanding of the control properties of a corresponding metabolic pathway model that is directly based on experimental observations. In particular, we delineate the role of enzymatic regulation to maintain metabolic stability and metabolic recovery after periods of starvation. It is shown that the feedforward activation of the pyruvate kinase by fructose-1,6-bisphosphate qualitatively alters the bifurcation structure of the corresponding pathway model, indicating a crucial role of enzymatic regulation to prevent metabolic collapse for low external concentrations of glucose. We argue that similar probabilistic methodologies will help our understanding of dynamic properties of small-, medium- and large-scale metabolic networks models.
Collapse
Affiliation(s)
- Ettore Murabito
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Sciences (CEAS), Manchester Centre for Integrative Systems Biology (MCISB), The University of Manchester, Manchester, United Kingdom
- * E-mail: (EM); (RS)
| | - Malkhey Verma
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Sciences (CEAS), Manchester Centre for Integrative Systems Biology (MCISB), The University of Manchester, Manchester, United Kingdom
| | - Martijn Bekker
- Molecular Microbial Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Domenico Bellomo
- Systems Bioinformatics IBIVU and Netherlands Institute for Systems Biology (NISB), VU University Amsterdam, Amsterdam, The Netherlands
| | - Hans V. Westerhoff
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Sciences (CEAS), Manchester Centre for Integrative Systems Biology (MCISB), The University of Manchester, Manchester, United Kingdom
- Synthetic Systems Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Molecular Cell Physiology, FALW, VU University Amsterdam, Amsterdam, The Netherlands
| | - Bas Teusink
- Systems Bioinformatics IBIVU and Netherlands Institute for Systems Biology (NISB), VU University Amsterdam, Amsterdam, The Netherlands
| | - Ralf Steuer
- CzechGlobe - Global Change Research Center, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Humboldt-University Berlin, Institute for Theoretical Biology, Berlin, Germany
- * E-mail: (EM); (RS)
| |
Collapse
|
12
|
Masureel M, Martens C, Stein RA, Mishra S, Ruysschaert JM, Mchaourab HS, Govaerts C. Protonation drives the conformational switch in the multidrug transporter LmrP. Nat Chem Biol 2014; 10:149-55. [PMID: 24316739 PMCID: PMC4749020 DOI: 10.1038/nchembio.1408] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 10/18/2013] [Indexed: 02/07/2023]
Abstract
Multidrug antiporters of the major facilitator superfamily couple proton translocation to the extrusion of cytotoxic molecules. The conformational changes that underlie the transport cycle and the structural basis of coupling of these transporters have not been elucidated. Here we used extensive double electron-electron resonance measurements to uncover the conformational equilibrium of LmrP, a multidrug transporter from Lactococcus lactis, and to investigate how protons and ligands shift this equilibrium to enable transport. We find that the transporter switches between outward-open and outward-closed conformations, depending on the protonation states of specific acidic residues forming a transmembrane protonation relay. Our data can be framed in a model of transport wherein substrate binding initiates the transport cycle by opening the extracellular side. Subsequent protonation of membrane-embedded acidic residues induces substrate release to the extracellular side and triggers a cascade of conformational changes that concludes in proton release to the intracellular side.
Collapse
Affiliation(s)
- Matthieu Masureel
- 1] Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium. [2]
| | - Chloé Martens
- 1] Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium. [2]
| | - Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Smriti Mishra
- Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jean-Marie Ruysschaert
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Hassane S Mchaourab
- 1] Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, Tennessee, USA. [2]
| | - Cédric Govaerts
- 1] Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium. [2]
| |
Collapse
|
13
|
Costa RS, Hartmann A, Gaspar P, Neves AR, Vinga S. An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production. MOLECULAR BIOSYSTEMS 2014; 10:628-39. [PMID: 24413179 DOI: 10.1039/c3mb70265k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Biomedical research and biotechnological production are greatly benefiting from the results provided by the development of dynamic models of microbial metabolism. Although several kinetic models of Lactococcus lactis (a Lactic Acid Bacterium (LAB) commonly used in the dairy industry) have been developed so far, most of them are simplified and focus only on specific metabolic pathways. Therefore, the application of mathematical models in the design of an engineering strategy for the production of industrially important products by L. lactis has been very limited. In this work, we extend the existing kinetic model of L. lactis central metabolism to include industrially relevant production pathways such as mannitol and 2,3-butanediol. In this way, we expect to study the dynamics of metabolite production and make predictive simulations in L. lactis. We used a system of ordinary differential equations (ODEs) with approximate Michaelis-Menten-like kinetics for each reaction, where the parameters were estimated from multivariate time-series metabolite concentrations obtained by our team through in vivo Nuclear Magnetic Resonance (NMR). The results show that the model captures observed transient dynamics when validated under a wide range of experimental conditions. Furthermore, we analyzed the model using global perturbations, which corroborate experimental evidence about metabolic responses upon enzymatic changes. These include that mannitol production is very sensitive to lactate dehydrogenase (LDH) in the wild type (W.T.) strain, and to mannitol phosphoenolpyruvate: a phosphotransferase system (PTS(Mtl)) in a LDH mutant strain. LDH reduction has also a positive control on 2,3-butanediol levels. Furthermore, it was found that overproduction of mannitol-1-phosphate dehydrogenase (MPD) in a LDH/PTS(Mtl) deficient strain can increase the mannitol levels. The results show that this model has prediction capability over new experimental conditions and offers promising possibilities to elucidate the effect of alterations in the main metabolism of L. lactis, with application in strain optimization.
Collapse
Affiliation(s)
- Rafael S Costa
- Instituto de Engenharia de Sistemas e Computadores, Investigacão e Desenvolvimento (INESC-ID), R Alves Redol 9, 1000-029 Lisboa, Portugal.
| | | | | | | | | |
Collapse
|
14
|
Yang X, Lai Z, Lai C, Zhu M, Li S, Wang J, Wang X. Efficient production of l-lactic acid by an engineered Thermoanaerobacterium aotearoense with broad substrate specificity. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:124. [PMID: 23985133 PMCID: PMC3766646 DOI: 10.1186/1754-6834-6-124] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 08/22/2013] [Indexed: 05/25/2023]
Abstract
BACKGROUND Efficient conversion of lignocellulosic biomass to optically pure lactic acid is a key challenge for the economical production of biodegradable poly-lactic acid. A recently isolated strain, Thermoanaerobacterium aotearoense SCUT27, is promising as an efficient lactic acid production bacterium from biomass due to its broad substrate specificity. Additionally, its strictly anaerobic and thermophilic characteristics suppress contamination from other microoragnisms. Herein, we report the significant improvements of concentration and yield in lactic acid production from various lignocellulosic derived sugars, achieved by the carbon flux redirection through homologous recombination in T. aotearoense SCUT27. RESULTS T. aotearoense SCUT27 was engineered to block the acetic acid formation pathway to improve the lactic acid production. The genetic manipulation resulted in 1.8 and 2.1 fold increase of the lactic acid yield using 10 g/L of glucose or 10 g/L of xylose as substrate, respectively. The maximum l-lactic acid yield of 0.93 g/g glucose with an optical purity of 99.3% was obtained by the engineered strain, designated as LA1002, from 50 g/L of substrate, which is very close to the theoretical value (1.0 g/g of glucose). In particular, LA1002 produced lactic acid at an unprecedented concentration up to 3.20 g/L using 10 g/L xylan as the single substrate without any pretreatment after 48 h fermentation. The non-sterilized fermentative production of l-lactic acid was also carried out, achieving values of 44.89 g/L and 0.89 g/g mixed sugar for lactic acid concentration and yield, respectively. CONCLUSIONS Blocking acetic acid formation pathway in T. aotearoense SCUT27 increased l-lactic acid production and yield dramatically. To our best knowledge, this is the best performance of fermentation on lactic acid production using xylan as the sole carbon source, considering the final concentration, yield and fermentation time. In addition, it should be mentioned that the performance of non-sterilized simultaneous fermentation from glucose and xylose was very close to that of normal sterilized cultivation. All these results used the mutant strain, LA1002, indicated that it is a new promising candidate for the effective production of optically pure l-lactic acid from lignocellulosic biomass.
Collapse
Affiliation(s)
- Xiaofeng Yang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Zhicheng Lai
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Chaofeng Lai
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Muzi Zhu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Shuang Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou 510640, China
| | - Jufang Wang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, China
| | - Xiaoning Wang
- State Key Laboratory of Kidney, the Institute of Life Sciences, Chinese PLA General Hospital, Beijing 100853, China
| |
Collapse
|
15
|
Levering J, Kummer U, Becker K, Sahle S. Glycolytic oscillations in a model of a lactic acid bacterium metabolism. Biophys Chem 2012; 172:53-60. [PMID: 23357412 DOI: 10.1016/j.bpc.2012.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 11/12/2012] [Accepted: 11/12/2012] [Indexed: 11/16/2022]
Abstract
Glycolytic oscillations in yeast have been extensively studied. It is still unclear, if these oscillations are caused by the allosteric enzyme phosphofructokinase or the stoichiometry of glycolysis which contains an autocatalysis with respect to ATP. Bacterial glycolysis shows a different stoichiometry, however, also containing a stoichiometric autocatalysis. For Escherichia coli, the regulation of the enzyme phosphofructokinase is also assumed to be a major reason for oscillations to occur. We investigated glycolytic oscillations in a quantitative kinetic model for Streptococcus pyogenes set-up on the basis of experimental data. We found oscillations within physiologically feasible parameter ranges. We investigated the origin of these oscillations and conclude that, again, both the stoichiometry of the system, as well as its allosterically regulated enzymes can give rise to these oscillations. For the analysis we employed established and new optimization methods for finding oscillatory regimes and present these in the context of this study.
Collapse
Affiliation(s)
- Jennifer Levering
- Department of Modeling of Biological Processes, COS Heidelberg/BioQuant, University Heidelberg, 69120 Heidelberg, Germany.
| | | | | | | |
Collapse
|
16
|
Branco dos Santos F, de Vos WM, Teusink B. Towards metagenome-scale models for industrial applications--the case of Lactic Acid Bacteria. Curr Opin Biotechnol 2012. [PMID: 23200025 DOI: 10.1016/j.copbio.2012.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We review the uses and limitations of modelling approaches that are in use in the field of Lactic Acid Bacteria (LAB). We describe recent developments in model construction and computational methods, starting from application of such models to monocultures. However, since most applications in food biotechnology involve complex nutrient environments and mixed cultures, we extend the scope to discuss developments in modelling such complex systems. With metagenomics and meta-functional genomics data becoming available, the developments in genome-scale community models are discussed. We conclude that exploratory tools are available and useful, but truly predictive mechanistic models will remain a major challenge in the field.
Collapse
Affiliation(s)
- Filipe Branco dos Santos
- Systems Bioinformatics/NISB, Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | | | | |
Collapse
|
17
|
Levering J, Musters MWJM, Bekker M, Bellomo D, Fiedler T, de Vos WM, Hugenholtz J, Kreikemeyer B, Kummer U, Teusink B. Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach. FEBS J 2012; 279:1274-90. [DOI: 10.1111/j.1742-4658.2012.08523.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
18
|
Ytting CK, Fuglsang AT, Hiltunen JK, Kastaniotis AJ, Özalp VC, Nielsen LJ, Olsen LF. Measurements of intracellular ATP provide new insight into the regulation of glycolysis in the yeast Saccharomyces cerevisiae. Integr Biol (Camb) 2011; 4:99-107. [PMID: 22134619 DOI: 10.1039/c1ib00108f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Glycolysis in the yeast Saccharomyces cerevisiae exhibits temporal oscillation under anaerobic or semianaerobic conditions. Previous evidence indicated that at least two membrane-bound ATPases, the mitochondrial F(0)F(1) ATPase and the plasma membrane P-type ATPase (Pma1p), were important in regulating the glycolytic oscillation. Measurements of intracellular ATP provide a unique tool to understand the role of these membrane ATPases and how their activities are regulated. We have constructed a new nanobiosensor that can perform time-resolved measurements of intracellular ATP in intact cells. Measurements of the temporal behaviour of intracellular ATP in a yeast strain with oscillating glycolysis showed that, in addition to oscillation in intracellular ATP, there is an overall slow decrease in intracellular ATP because the ATP consumption rate exceeds the ATP production in glycolysis. Measurements of the temporal behaviour of intracellular ATP in yeast strains lacking either of the two membrane bound ATPases have confirmed that F(0)F(1) ATPase and Pma1p contribute significantly to the ATP consumption in the cell and to the regulation of glycolytic oscillation. Furthermore, our measurements also demonstrate that ATPase activity is under strict control. In the absence of glucose ATPase activity is switched off, and the intracellular ATP concentration is high. When glucose is added to the cells the ATP concentration starts to decrease, because ATP consumption exceeds ATP production by glycolysis. Finally, when glucose is used up, the ATP consumption stops immediately. Thus, glucose or some compound derived from glucose must be involved in controlling the activity of these two ATPases.
Collapse
Affiliation(s)
- Cecilie K Ytting
- The Centre for Membrane Pumps in Cells and Diseases - PUMPkin, Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | | | | | | | | | | | | |
Collapse
|
19
|
Standardized assay medium to measure Lactococcus lactis enzyme activities while mimicking intracellular conditions. Appl Environ Microbiol 2011; 78:134-43. [PMID: 22020503 DOI: 10.1128/aem.05276-11] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Knowledge of how the activity of enzymes is affected under in vivo conditions is essential for analyzing their regulation and constructing models that yield an integrated understanding of cell behavior. Current kinetic parameters for Lactococcus lactis are scattered through different studies and performed under different assay conditions. Furthermore, assay conditions often diverge from conditions prevailing in the intracellular environment. To establish uniform assay conditions that resemble intracellular conditions, we analyzed the intracellular composition of anaerobic glucose-limited chemostat cultures of L. lactis subsp. cremoris MG 1363. Based on this, we designed a new assay medium for enzyme activity measurements of growing cells of L. lactis, mimicking as closely as practically possible its intracellular environment. Procedures were optimized to be carried out in 96-well plates, and the reproducibility and dynamic range were checked for all enzyme activity measurements. The effects of freezing and the carryover of ammonium sulfate from the addition of coupling enzymes were also established. Activities of all 10 glycolytic and 4 fermentative enzymes were measured. Remarkably, most in vivo-like activities were lower than previously published data. Yet, the ratios of V(max) over measured in vivo fluxes were above 1. With this work, we have developed and extensively validated standard protocols for enzyme activity measurements for L. lactis.
Collapse
|
20
|
Teusink B, Bachmann H, Molenaar D. Systems biology of lactic acid bacteria: a critical review. Microb Cell Fact 2011; 10 Suppl 1:S11. [PMID: 21995498 PMCID: PMC3231918 DOI: 10.1186/1475-2859-10-s1-s11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Understanding the properties of a system as emerging from the interaction of well described parts is the most important goal of Systems Biology. Although in the practice of Lactic Acid Bacteria (LAB) physiology we most often think of the parts as the proteins and metabolites, a wider interpretation of what a part is can be useful. For example, different strains or species can be the parts of a community, or we could study only the chemical reactions as the parts of metabolism (and forgetting about the enzymes that catalyze them), as is done in flux balance analysis. As long as we have some understanding of the properties of these parts, we can investigate whether their interaction leads to novel or unanticipated behaviour of the system that they constitute. There has been a tendency in the Systems Biology community to think that the collection and integration of data should continue ad infinitum, or that we will otherwise not be able to understand the systems that we study in their details. However, it may sometimes be useful to take a step back and consider whether the knowledge that we already have may not explain the system behaviour that we find so intriguing. Reasoning about systems can be difficult, and may require the application of mathematical techniques. The reward is sometimes the realization of unexpected conclusions, or in the worst case, that we still do not know enough details of the parts, or of the interactions between them. We will discuss a number of cases, with a focus on LAB-related work, where a typical systems approach has brought new knowledge or perspective, often counterintuitive, and clashing with conclusions from simpler approaches. Also novel types of testable hypotheses may be generated by the systems approach, which we will illustrate. Finally we will give an outlook on the fields of research where the systems approach may point the way for the near future.
Collapse
Affiliation(s)
- Bas Teusink
- Systems Bioinformatics/NISB, Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands.
| | | | | |
Collapse
|
21
|
Microcalorimetric study of the growth of bacterial colonies of Lactococcus lactis IL1403 in agar gels. Food Microbiol 2011; 29:67-79. [PMID: 22029920 DOI: 10.1016/j.fm.2011.08.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 08/01/2011] [Accepted: 08/16/2011] [Indexed: 11/20/2022]
Abstract
Growth of Lactococcus lactis IL1403 in solid agar gels and liquid cultures at different glucose concentrations of 2, 10 and 20 g/L and different inoculation rates from 10(0) to 10(6) cfu/mL with the 10-fold increment was studied using thermal activity monitor TAM III. In parallel to calorimetric measurements the changes of glucose and lactic acid concentrations and pH of culture media were measured in order to obtain additional information for the interpretation of calorimetric power-time curves. Maximal specific growth rates of heat evolution proportional to growth rates of biomass μ(max) (W/h), heat produced during different growth stages Q(TOT) (J/mL), Q(ExP) (J/mL) and duration of lag-phases λ (h) were obtained by processing calorimetric curves. The sizes of colonies were measured also at the end of growth using microscope. The data obtained together with calculated heat yield coefficient Y(Q) (J/cfu) allowed to analyze and describe quantitatively the growth of individual colonies and develop a model of multistage growth of a typical colony of L. lactis in 1% agar gel. Microcalorimetry used in combination with other relevant methods is a very powerful and precise tool in studying solid-state fermentations.
Collapse
|
22
|
Abstract
Systems biology has received an ever increasing interest during the last decade. A large amount of third-party funding is spent on this topic, which involves quantitative experimentation integrated with computational modeling. Industrial companies are also starting to use this approach more and more often, especially in pharmaceutical research and biotechnology. This leads to the question of whether such interest is wisely invested and whether there are success stories to be told for basic science and/or technology/biomedicine. In this review, we focus on the application of systems biology approaches that have been employed to shed light on both biochemical functions and previously unknown mechanisms. We point out which computational and experimental methods are employed most frequently and which trends in systems biology research can be observed. Finally, we discuss some problems that we have encountered in publications in the field.
Collapse
Affiliation(s)
- Katrin Hübner
- Department of Modeling of Biological Processes, COS Heidelberg/BioQuant, University of Heidelberg, Germany
| | | | | |
Collapse
|
23
|
Characterization of three lactic acid bacteria and their isogenic ldh deletion mutants shows optimization for YATP (cell mass produced per mole of ATP) at their physiological pHs. Appl Environ Microbiol 2010; 77:612-7. [PMID: 21097579 DOI: 10.1128/aem.01838-10] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Several lactic acid bacteria use homolactic acid fermentation for generation of ATP. Here we studied the role of the lactate dehydrogenase enzyme on the general physiology of the three homolactic acid bacteria Lactococcus lactis, Enterococcus faecalis, and Streptococcus pyogenes. Of note, deletion of the ldh genes hardly affected the growth rate in chemically defined medium under microaerophilic conditions. However, the growth rate was affected in rich medium. Furthermore, deletion of ldh affected the ability for utilization of various substrates as a carbon source. A switch to mixed acid fermentation was observed during glucose-limited continuous growth and was dependent on the growth rate for S. pyogenes and on the pH for E. faecalis. In S. pyogenes and L. lactis, a change in pH resulted in a clear change in Y(ATP) (cell mass produced per mole of ATP). The pH that showed the highest Y(ATP) corresponded to the pH of the natural habitat of the organisms.
Collapse
|
24
|
MILLS SUSAN, O’SULLIVAN ORLA, HILL COLIN, FITZGERALD GERALD, ROSS RPAUL. The changing face of dairy starter culture research: From genomics to economics. INT J DAIRY TECHNOL 2010. [DOI: 10.1111/j.1471-0307.2010.00563.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
25
|
Diskin CJ. Lessons From Single Cell Organisms: Insights Into the Antimicrobial and Toxic Effects of Peritoneal Dialysate Bases. Ther Apher Dial 2010; 14:127-35. [DOI: 10.1111/j.1744-9987.2009.00745.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
26
|
Kay E, Wren BW. Recent advances in systems microbiology. Curr Opin Microbiol 2009; 12:577-81. [PMID: 19748820 DOI: 10.1016/j.mib.2009.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2009] [Revised: 07/24/2009] [Accepted: 08/14/2009] [Indexed: 12/29/2022]
Abstract
Systems biology is a rapidly expanding field fuelled by the 'omics' era coupled to several new technological advances that have increased the precision of data obtainable, meaning that it is now feasible to obtain quantitative measurements from a single cell. The aim of systems biology is to understand the structure, dynamics and interactions of whole cells rather than the function of individual parts. The challenge now is to use these data in conjunction with modelling techniques to extend our knowledge of bacterial systems and to be able to experimentally verify in silico predictions.
Collapse
Affiliation(s)
- Emily Kay
- Department of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel St., London WC1E 7HT, United Kingdom
| | | |
Collapse
|