1
|
Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
Collapse
Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department
of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| |
Collapse
|
2
|
Cacace C, Cocozza C, Traversa A, Coda R, Rizzello CG, Pontonio E, De Mastro F, Brunetti G, Verni M. Potential of native and bioprocessed brewers' spent grains as organic soil amendments. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1010890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
IntroductionThe use of novel soil amendments and the exploitation of plant growth-promoting microorganisms are considered promising tools for developing a more sustainable agriculture in times when ensuring high-yield productions with limited resources is essential.MethodsIn this study, the potential of brewers' spent grain (BSG), the major by-product of the brewing industry, as organic soil amendment, was investigated. Bioprocessed BSG, obtained by an enzymatic treatment coupled with fermentation, together with native BSG, were used as amendments in a pot-trial. An integrated analytical approach aimed at assessing the modification of the physicochemical properties of a typical Mediterranean alkaline agricultural soil, and the plant growth-promoting effect on escarole (Cichorium endivia var. Cuartana), was carried out.ResultsThe use of biomasses led to soil organic content and total nitrogen content up to 72 and 42% higher, compared to the unamended soils. Moreover, the lower pH and the higher organic acids content doubled phosphorus availability. Although the number of leaves per plant in escaroles from pots amended with native and bioprocessed BSG did not show any difference compared to plants cultivated on unamended pots, the average fresh weight per escarole head, was higher in pots amended with bioprocessed BSG.DiscussionHence, the results collected so far encourage BSG application for agricultural purpose, while solving the problem of disposing of such abundant side stream.
Collapse
|
3
|
Davis RW, Muse CG, Eggleston H, Hill M, Panizzi P. Sugar Shock: Probing Streptococcus pyogenes Metabolism Through Bioluminescence Imaging. Front Microbiol 2022; 13:864014. [PMID: 35722335 PMCID: PMC9203041 DOI: 10.3389/fmicb.2022.864014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
Streptococcus pyogenes (S. pyogenes) can thrive in its host during an infection, and, as a result, it must be able to respond to external stimuli and available carbon sources. The preclinical use of engineered pathogens capable of constitutive light production may provide real-time information on microbial-specific metabolic processes. In this study, we mapped the central metabolism of a luxABCDE-modified S. pyogenes Xen20 (Strep. Xen20) to its de novo synthesis of luciferase substrates as assessed by the rate of light production in response to different environmental triggers. Previous characterization predicted that the lux operon was under the myo-inositol iolE promotor. In this study, we revealed that supplementation with myo-inositol generated increased Strep. Xen20 luminescence. Surprisingly, when supplemented with infection-relevant carbon sources, such as glucose or glycine, light production was diminished. This was presumably due to the scavenging of pyruvate by L-lactate dehydrogenase (LDH). Inhibition of LDH by its inhibitor, oxamate, partially restored luminescent signal in the presence of glucose, presumably by allowing the resulting pyruvate to proceed to acetyl-coenzyme A (CoA). This phenomenon appeared specific to the lactic acid bacterial metabolism as glucose or glycine did not reduce signal in an analogous luxABCDE-modified Gram-positive pathogen, Staph. Xen29. The Strep. Xen20 cells produced light in a concentration-dependent manner, inversely related to the amount of glucose present. Taken together, our measures of microbial response could provide new information regarding the responsiveness of S. pyogenes metabolism to acute changes in its local environments and cellular health.
Collapse
|
4
|
Isar J, Jain D, Joshi H, Dhoot S, Rangaswamy V. MICROBIAL isoprene production: an overview. World J Microbiol Biotechnol 2022; 38:122. [PMID: 35637362 DOI: 10.1007/s11274-022-03306-4] [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: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 11/28/2022]
Abstract
Isoprene, a volatile C5 hydrocarbon, is a precursor of synthetic rubber and an important building block for a variety of natural products, solely being produced by petrochemical routes. To mitigate the ever-increasing contribution of petrochemical industry to global warming through significant carbon (CO2) evolution, bio-based process for isoprene production using microbial cell factories have been explored. Highly efficient fermentation-based processes have been studied for little over a decade now with extensive research on the rational strain development for creating robust strains for commercial isoprene production. Most of these studies involved sugars as feedstocks and using naturally occurring isoprene pathways viz., mevalonate and methyl erythritol pathway in E. coli. Recent advances, driven by efforts in reducing environmental pollution, have focused on utilization of inorganic CO2 by cyanobacteria or syngas from waste gases by acetogens for isoprene production. This review endeavors to capture the latest relevant progress made in rational strain development, metabolic engineering and synthetic biology strategies used, challenges in fermentation process development at lab and commercial scale production of isoprene along with a future perspective pertaining to this area of research.
Collapse
Affiliation(s)
- Jasmine Isar
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Dharmendra Jain
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Harshvardhan Joshi
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Shrikant Dhoot
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India
| | - Vidhya Rangaswamy
- High Value Chemicals, Reliance Industries Limited, Reliance Corporate Park, Ghansoli, Navi Mumbai, 400701, India.
| |
Collapse
|
5
|
Eisenberg P, Albert L, Teuffel J, Zitzow E, Michaelis C, Jarick J, Sehlke C, Große L, Bader N, Nunes-Alves A, Kreikemeyer B, Schindelin H, Wade RC, Fiedler T. The Non-phosphorylating Glyceraldehyde-3-Phosphate Dehydrogenase GapN Is a Potential New Drug Target in Streptococcus pyogenes. Front Microbiol 2022; 13:802427. [PMID: 35242116 PMCID: PMC8886048 DOI: 10.3389/fmicb.2022.802427] [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: 10/27/2021] [Accepted: 01/14/2022] [Indexed: 01/01/2023] Open
Abstract
The strict human pathogen Streptococcus pyogenes causes infections of varying severity, ranging from self-limiting suppurative infections to life-threatening diseases like necrotizing fasciitis or streptococcal toxic shock syndrome. Here, we show that the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase GapN is an essential enzyme for S. pyogenes. GapN converts glyceraldehyde 3-phosphate into 3-phosphoglycerate coupled to the reduction of NADP to NADPH. The knock-down of gapN by antisense peptide nucleic acids (asPNA) significantly reduces viable bacterial counts of S. pyogenes laboratory and macrolide-resistant clinical strains in vitro. As S. pyogenes lacks the oxidative part of the pentose phosphate pathway, GapN appears to be the major NADPH source for the bacterium. Accordingly, other streptococci that carry a complete pentose phosphate pathway are not prone to asPNA-based gapN knock-down. Determination of the crystal structure of the S. pyogenes GapN apo-enzyme revealed an unusual cis-peptide in proximity to the catalytic binding site. Furthermore, using a structural modeling approach, we correctly predicted competitive inhibition of S. pyogenes GapN by erythrose 4-phosphate, indicating that our structural model can be used for in silico screening of specific GapN inhibitors. In conclusion, the data provided here reveal that GapN is a potential target for antimicrobial substances that selectively kill S. pyogenes and other streptococci that lack the oxidative part of the pentose phosphate pathway.
Collapse
Affiliation(s)
- Philip Eisenberg
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Leon Albert
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Jonathan Teuffel
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Eric Zitzow
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Claudia Michaelis
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Jane Jarick
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Clemens Sehlke
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Lisa Große
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Nicole Bader
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Ariane Nunes-Alves
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Hermann Schindelin
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Würzburg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical Centre, Rostock, Germany
| |
Collapse
|
6
|
Pázmándi M, Kovács Z, Maráz A. Potential of Lactobacillus strains for the production of fermented functional beverages enriched in galacto-oligosaccharides. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111097] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
7
|
Joshi H, Isar J, Jain DA, Badle SS, Dhoot SB, Rangaswamy V. C/N Ratio and Specific Growth Rate Plays Important Role on Enhancing Isoprene Production in Recombinant Escherichia coli. Appl Biochem Biotechnol 2021; 193:2403-2419. [PMID: 33689123 DOI: 10.1007/s12010-021-03545-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/26/2021] [Indexed: 11/24/2022]
Abstract
Effect of fermentation parameters such as C/N ratio, specific growth rate, phosphate limitation, and plasmid instability on enhancing isoprene production is the focus of the current study. Isoprene productivity in the recombinant Escherichia coli K12_MVA strain showed a bell-shaped relationship with specific growth rate in bioreactor studies with isoprene volumetric productivity peaking at 0.35/h. This behavior was depicted by a production inhibition kinetic model which envisaged a serious competition between the cellular growth, acetic acid production, and isoprene biosynthesis. The model equation derived showed a reasonable fit with the experimental values. Judicious control of the growth rates and acetate accumulation by optimizing C/N ratio, phosphate concentration, and intermittent feeding strategy resulted in maximizing the carbon flux towards isoprene. Plasmid instability caused by metabolic burden posed by the presence of dual plasmids on the bacteria was simulated using first-order degradation kinetics. The experimental plasmid loss trend was in accordance with the model simulated trend, where higher plasmid loss correlated with higher specific growth rates. Modulating the growth rate, acetate accumulation, and plasmid instability resulted in achieving maximum isoprene volumetric productivity of 1.125 g/l/h with 46.67% of carbon flux towards isoprene and a isoprene titre of 18 g/l in 16 h fermentation run.
Collapse
Affiliation(s)
- Harshvardhan Joshi
- High Value Chemicals, Reliance Industries Limited, Ghansoli, Navi Mumbai, Maharashtra, 400701, India
| | - Jasmine Isar
- High Value Chemicals, Reliance Industries Limited, Ghansoli, Navi Mumbai, Maharashtra, 400701, India
| | - Dharmendra A Jain
- High Value Chemicals, Reliance Industries Limited, Ghansoli, Navi Mumbai, Maharashtra, 400701, India
| | - Sneh S Badle
- High Value Chemicals, Reliance Industries Limited, Ghansoli, Navi Mumbai, Maharashtra, 400701, India
| | - Shrikant B Dhoot
- High Value Chemicals, Reliance Industries Limited, Ghansoli, Navi Mumbai, Maharashtra, 400701, India
| | - Vidhya Rangaswamy
- High Value Chemicals, Reliance Industries Limited, Ghansoli, Navi Mumbai, Maharashtra, 400701, India.
| |
Collapse
|
8
|
Mbye M, Baig MA, AbuQamar SF, El-Tarabily KA, Obaid RS, Osaili TM, Al-Nabulsi AA, Turner MS, Shah NP, Ayyash MM. Updates on understanding of probiotic lactic acid bacteria responses to environmental stresses and highlights on proteomic analyses. Compr Rev Food Sci Food Saf 2020; 19:1110-1124. [PMID: 33331686 DOI: 10.1111/1541-4337.12554] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/15/2022]
Abstract
Probiotics are defined as live microorganisms that improve the health of the host when administered in adequate quantities. Nonetheless, probiotics encounter extreme environmental conditions during food processing or along the gastrointestinal tract. This review discusses different environmental stresses that affect probiotics during food preparation, storage, and along the alimentary canal, including high temperature, low temperature, low and alkaline pH, oxidative stress, high hydrostatic pressure, osmotic pressure, and starvation. The understanding of how probiotics deal with environmental stress and thrive provides useful information to guide the selection of the strains with enhanced performance in specific situations, in food processing or during gastrointestinal transit. In most cases, multiple biological functions are affected upon exposure of the cell to environmental stress. Sensing of sublethal environmental stress can allow for adaptation processes to occur, which can include alterations in the expression of specific proteins.
Collapse
Affiliation(s)
- Mustapha Mbye
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, 15551, UAE
| | - Mohd Affan Baig
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, 15551, UAE
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University (UAEU), Al Ain, UAE
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University (UAEU), Al Ain, UAE.,Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University (UAEU), Al-Ain, UAE.,College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Reyad S Obaid
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, UAE
| | - Tareq M Osaili
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, UAE.,Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas A Al-Nabulsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid, Jordan
| | - Mark S Turner
- School of Agriculture and Food Sciences, the University of Queensland (UQ), Brisbane, Queensland, Australia
| | - Nagendra P Shah
- Food and Nutritional Science, School of Biological Sciences, the University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Mutamed M Ayyash
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, 15551, UAE
| |
Collapse
|
9
|
Christensen CD, Hofmeyr JHS, Rohwer JM. Delving deeper: Relating the behaviour of a metabolic system to the properties of its components using symbolic metabolic control analysis. PLoS One 2018; 13:e0207983. [PMID: 30485345 PMCID: PMC6261606 DOI: 10.1371/journal.pone.0207983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/11/2018] [Indexed: 11/22/2022] Open
Abstract
High-level behaviour of metabolic systems results from the properties of, and interactions between, numerous molecular components. Reaching a complete understanding of metabolic behaviour based on the system’s components is therefore a difficult task. This problem can be tackled by constructing and subsequently analysing kinetic models of metabolic pathways since such models aim to capture all the relevant properties of the system components and their interactions. Symbolic control analysis is a framework for analysing pathway models in order to reach a mechanistic understanding of their behaviour. By providing algebraic expressions for the sensitivities of system properties, such as metabolic flux or steady-state concentrations, in terms of the properties of individual reactions it allows one to trace the high level behaviour back to these low level components. Here we apply this method to a model of pyruvate branch metabolism in Lactococcus lactis in order to explain a previously observed negative flux response towards an increase in substrate concentration. With this method we are able to show, first, that the sensitivity of flux towards changes in reaction rates (represented by flux control coefficients) is determined by the individual metabolic branches of the pathway, and second, how the sensitivities of individual reaction rates towards their substrates (represented by elasticity coefficients) contribute to this flux control. We also quantify the contributions of enzyme binding and mass-action to enzyme elasticity separately, which allows for an even finer-grained understanding of flux control. These analytical tools allow us to analyse the control properties of a metabolic model and to arrive at a mechanistic understanding of the quantitative contributions of each of the enzymes to this control. Our analysis provides an example of the descriptive power of the general principles of symbolic control analysis.
Collapse
Affiliation(s)
- Carl D. Christensen
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Jan-Hendrik S. Hofmeyr
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
- Centre for Complex Systems in Transition, Stellenbosch University, Stellenbosch, South Africa
| | - Johann M. Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
- * E-mail:
| |
Collapse
|
10
|
Production of a highly concentrated probiotic culture of Lactococcus lactis CECT 539 containing high amounts of nisin. 3 Biotech 2018; 8:292. [PMID: 29963352 DOI: 10.1007/s13205-018-1318-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/18/2018] [Indexed: 10/28/2022] Open
Abstract
In this study, probiotic biomass and nisin productions by Lactococcus lactis CECT 539 were followed in two realkalized fed-batch cultures in diluted whey (DW) supplemented with KH2PO4 up to a total phosphorus concentration of 0.459 g/L. Increased biomass (5.12 g/L, 2.18 × 1010 CFU/mL) and nisin (235.23 BU/mL) concentrations were obtained in the culture fed concentrated whey and concentrated mussel processing waste (CMPW) medium supplemented with glucose up to a concentration of 400 g/L (CMPW + G medium) compared with similar fed-batch fermentations in DW medium. In the second fed-batch fermentation, the feeding medium CMPW + G was supplemented with KH2PO4 up to a TP concentration of 3.21 g/L. With this approach, increased production of biomass (5.49 g/L, 2.33 × 1010 CFU/mL) and nisin (257.59 BU/mL) was obtained. Considering the substantial availability of these wastes at very low prices from local dairy and mussel processing plants in Galicia, their use as culture media could offer an attractive alternative for a low-cost production of probiotic biomass and nisin at a high scale.
Collapse
|
11
|
Zuo S, Xiao J, Zhang Y, Zhang X, Nomura CT, Chen S, Wang Q. Rational design and medium optimization for shikimate production in recombinant Bacillus licheniformis strains. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
12
|
Oehmcke-Hecht S, Nass LE, Wichura JB, Mikkat S, Kreikemeyer B, Fiedler T. Deletion of the L-Lactate Dehydrogenase Gene ldh in Streptococcus pyogenes Leads to a Loss of SpeB Activity and a Hypovirulent Phenotype. Front Microbiol 2017; 8:1841. [PMID: 28983299 PMCID: PMC5613712 DOI: 10.3389/fmicb.2017.01841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/08/2017] [Indexed: 01/19/2023] Open
Abstract
Streptococcus pyogenes uses lactic acid fermentation for the generation of ATP. Here, we analyzed the impact of a deletion of the L-lactate dehydrogenase gene ldh on the virulence of S. pyogenes M49. While the ldh deletion does not cause a general growth deficiency in laboratory media, the growth in human blood and plasma is significantly hampered. The ldh deletion strain is furthermore less virulent in a Galleria mellonella infection model. We show that the ldh deletion leads to a decrease in the activity of the cysteine protease SpeB, an important secreted virulence factor of S. pyogenes. The reduced SpeB activity is caused by a hampered autocatalytic activation of the SpeB zymogen into the mature SpeB. The missing SpeB activity furthermore leads to increased plasmin activation and a reduced activation of the contact system on the surface of S. pyogenes. All these effects can be reversed when ldh is reintroduced into the mutant via a plasmid. The results demonstrate a previously unappreciated role for LDH in modulation of SpeB maturation.
Collapse
Affiliation(s)
- Sonja Oehmcke-Hecht
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| | - Leif E Nass
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| | - Jan B Wichura
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| | - Stefan Mikkat
- Core Facility Proteome Analysis, Rostock University Medical CentreRostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology, and Hygiene, Rostock University Medical CentreRostock, Germany
| |
Collapse
|
13
|
Azizan KA, Ressom HW, Mendoza ER, Baharum SN. 13C based proteinogenic amino acid (PAA) and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP) pathway in response to agitation and temperature related stresses. PeerJ 2017; 5:e3451. [PMID: 28695065 PMCID: PMC5501154 DOI: 10.7717/peerj.3451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/19/2017] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis subsp. cremoris MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, L. lactis is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of L. lactis to several stresses has been described, the adaptation mechanisms at the level of in vivo fluxes have seldom been described. To gain insights into cellular metabolism, 13C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS) were used to measure the flux ratios of active pathways in the central metabolism of L. lactis when subjected to three conditions varying in temperature (30°C, 37°C) and agitation (with and without agitation at 150 rpm). Collectively, the concentrations of proteinogenic amino acids (PAAs) and free fatty acids (FAAs) were compared, and Pearson correlation analysis (r) was calculated to measure the pairwise relationship between PAAs. Branched chain and aromatic amino acids, threonine, serine, lysine and histidine were correlated strongly, suggesting changes in flux regulation in glycolysis, the pentose phosphate (PP) pathway, malic enzyme and anaplerotic reaction catalysed by pyruvate carboxylase (pycA). Flux ratio analysis revealed that glucose was mainly converted by glycolysis, highlighting the stability of L. lactis’ central carbon metabolism despite different conditions. Higher flux ratios through oxaloacetate (OAA) from pyruvate (PYR) reaction in all conditions suggested the activation of pyruvate carboxylate (pycA) in L. lactis, in response to acid stress during exponential phase. Subsequently, more significant flux ratio differences were seen through the oxidative and non-oxidative pentose phosphate (PP) pathways, malic enzyme, and serine and C1 metabolism, suggesting NADPH requirements in response to environmental stimuli. These reactions could play an important role in optimization strategies for metabolic engineering in L. lactis. Overall, the integration of systematic analysis of amino acids and flux ratio analysis provides a systems-level understanding of how L. lactis regulates central metabolism under various conditions.
Collapse
Affiliation(s)
- Kamalrul Azlan Azizan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Habtom W Ressom
- Departments of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Eduardo R Mendoza
- Institute of Mathematics, University of the Philippines Diliman, Quezon City, Metro Manila, Philippines.,Membrane Biochemistry Group, Max Planck Institute of Biochemistry, Planegg, Germany
| | - Syarul Nataqain Baharum
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| |
Collapse
|
14
|
Costas Malvido M, Alonso González E, Outeiriño D, Fajardo Bernárdez P, Pérez Guerra N. Combination of food wastes for an efficient production of nisin in realkalized fed-batch cultures. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2017.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
15
|
Bachmann H, Molenaar D, Branco dos Santos F, Teusink B. Experimental evolution and the adjustment of metabolic strategies in lactic acid bacteria. FEMS Microbiol Rev 2017. [DOI: 10.1093/femsre/fux024] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
16
|
Esteban-Torres M, Reverón I, Plaza-Vinuesa L, de las Rivas B, Muñoz R, López de Felipe F. Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge. Front Microbiol 2017; 8:244. [PMID: 28261192 PMCID: PMC5313477 DOI: 10.3389/fmicb.2017.00244] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/03/2017] [Indexed: 12/16/2022] Open
Abstract
Dietary fats may exert selective pressures on Lactobacillus species, however, knowledge on the mechanisms of adaptation to fat stress in these organisms is still fragmentary. This study was undertaken to gain insight into the mechanisms of adaptation of Lactobacillus plantarum WCFS1 to olive oil challenge by whole genome transcriptional profiling using DNA microarrays. A set of 230 genes were differentially expressed by L. plantarum WCFS1 to respond to this vegetable oil. This response involved elements typical of the stringent response, as indicated by the induction of genes involved in stress-related pathways and downregulation of genes related to processes associated with rapid growth. A set of genes involved in the transport and metabolism of compatible solutes were downregulated, indicating that this organism does not require osmoprotective mechanisms in presence of olive oil. The fatty acid biosynthetic pathway was thoroughly downregulated at the transcriptional level, which coincided with a diminished expression of genes controlled by this pathway in other organisms and that are required for the respiratory function, pyruvate dehydrogenase activity, RNA processing and cell size setting. Finally, a set of genes involved in host-cell signaling by L. plantarum were differentially regulated indicating that olive oil can influence the expression of metabolic traits involved in the crosstalk between this bacterium and the host.
Collapse
Affiliation(s)
| | | | | | | | | | - Félix López de Felipe
- Laboratorio de Biotecnología Bacteriana, Instituto de Ciencia y Tecnología de los Alimentos y Nutrición – Consejo Superior de Investigaciones CientificasMadrid, Spain
| |
Collapse
|
17
|
Großeholz R, Koh CC, Veith N, Fiedler T, Strauss M, Olivier B, Collins BC, Schubert OT, Bergmann F, Kreikemeyer B, Aebersold R, Kummer U. Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis. NPJ Syst Biol Appl 2016; 2:16017. [PMID: 28725473 PMCID: PMC5516852 DOI: 10.1038/npjsba.2016.17] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/10/2016] [Accepted: 06/17/2016] [Indexed: 01/19/2023] Open
Abstract
Genome-scale metabolic models represent the entirety of metabolic reactions of an organism based on the annotation of the respective genome. These models commonly allow all reactions to proceed concurrently, disregarding the fact that at no point all proteins will be present in a cell. The metabolic reaction space can be constrained to a more physiological state using experimentally obtained information on enzyme abundances. However, high-quality, genome-wide protein measurements have been challenging and typically transcript abundances have been used as a surrogate for protein measurements. With recent developments in mass spectrometry-based proteomics, exemplified by SWATH-MS, the acquisition of highly quantitative proteome-wide data at reasonable throughput has come within reach. Here we present methodology to integrate such proteome-wide data into genome-scale models. We applied this methodology to study cellular changes in Enterococcus faecalis during adaptation to low pH. Our results indicate reduced proton production in the central metabolism and decreased membrane permeability for protons due to different membrane composition. We conclude that proteomic data constrain genome-scale models to a physiological state and, in return, genome-scale models are useful tools to contextualize proteomic data.
Collapse
Affiliation(s)
- Ruth Großeholz
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Ching-Chiek Koh
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Nadine Veith
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Madlen Strauss
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Brett Olivier
- Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, Amsterdam, Netherlands
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Olga T Schubert
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Frank Bergmann
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Ursula Kummer
- BioQuant, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| |
Collapse
|
18
|
Wang Y, Huang JM, Wang SL, Gao ZM, Zhang AQ, Danchin A, He LS. Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod bathynomus sp. Environ Microbiol 2016; 18:2646-59. [PMID: 27312602 DOI: 10.1111/1462-2920.13411] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 06/06/2016] [Indexed: 01/24/2023]
Abstract
Deep-sea isopod scavengers such as Bathynomus sp. are able to live in nutrient-poor environments, which is likely attributable to the presence of symbiotic microbes in their stomach. In this study we recovered two draft genomes of mycoplasmas, Bg1 and Bg2, from the metagenomes of the stomach contents and stomach sac of a Bathynomus sp. sample from the South China Sea (depth of 898 m). Phylogenetic trees revealed a considerable genetic distance to other mycoplasma species for Bg1 and Bg2. Compared with terrestrial symbiotic mycoplasmas, the Bg1 and Bg2 genomes were enriched with genes encoding phosphoenolpyruvate-dependent phosphotransferase systems (PTSs) and sodium-driven symporters responsible for the uptake of sugars, amino acids and other carbohydrates. The genome of mycoplasma Bg1 contained sialic acid lyase and transporter genes, potentially enabling the bacteria to attach to the stomach sac and obtain organic carbons from various cell walls. Both of the mycoplasma genomes contained multiple copies of genes related to proteolysis and oligosaccharide degradation, which may help the host survive in low-nutrient conditions. The discovery of the different types of mycoplasma bacteria in the stomach of this deep-sea isopod affords insights into symbiotic model of deep-sea animals and genomic plasticity of mycoplasma bacteria.
Collapse
Affiliation(s)
- Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Jiao-Mei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Shao-Lu Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Zhao-Ming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ai-Qun Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Antoine Danchin
- Hôpital de la Pitié-Salpêtrière, Institute of Cardiometabolism and Nutrition, 47 boulevard de l'Hôpital, Paris, 75013, France
| | - Li-Sheng He
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| |
Collapse
|
19
|
Willenborg J, Goethe R. Metabolic traits of pathogenic streptococci. FEBS Lett 2016; 590:3905-3919. [PMID: 27442496 DOI: 10.1002/1873-3468.12317] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/12/2016] [Accepted: 07/18/2016] [Indexed: 12/13/2022]
Abstract
Invasive and noninvasive diseases caused by facultative pathogenic streptococci depend on their equipment with virulence factors and on their ability to sense and adapt to changing nutrients in different host environments. The knowledge of the principal metabolic mechanisms which allow these bacteria to recognize and utilize nutrients in host habitats is a prerequisite for our understanding of streptococcal pathogenicity and the development of novel control strategies. This review aims to summarize and compare the central carbohydrate metabolic and amino acid biosynthetic pathways of a selected group of streptococcal species, all belonging to the naso-oropharyngeal microbiome in humans and/or animals. We also discuss the urgent need of comprehensive metabolomics approaches for a better understanding of the streptococcal metabolism during host-pathogen interaction.
Collapse
Affiliation(s)
- Jörg Willenborg
- Institute for Microbiology, University of Veterinary Medicine Hannover, Germany
| | - Ralph Goethe
- Institute for Microbiology, University of Veterinary Medicine Hannover, Germany
| |
Collapse
|
20
|
Levering J, Fiedler T, Sieg A, van Grinsven KWA, Hering S, Veith N, Olivier BG, Klett L, Hugenholtz J, Teusink B, Kreikemeyer B, Kummer U. Genome-scale reconstruction of the Streptococcus pyogenes M49 metabolic network reveals growth requirements and indicates potential drug targets. J Biotechnol 2016; 232:25-37. [PMID: 26970054 DOI: 10.1016/j.jbiotec.2016.01.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 01/03/2016] [Accepted: 01/12/2016] [Indexed: 01/12/2023]
Abstract
Genome-scale metabolic models comprise stoichiometric relations between metabolites, as well as associations between genes and metabolic reactions and facilitate the analysis of metabolism. We computationally reconstructed the metabolic network of the lactic acid bacterium Streptococcus pyogenes M49. Initially, we based the reconstruction on genome annotations and already existing and curated metabolic networks of Bacillus subtilis, Escherichia coli, Lactobacillus plantarum and Lactococcus lactis. This initial draft was manually curated with the final reconstruction accounting for 480 genes associated with 576 reactions and 558 metabolites. In order to constrain the model further, we performed growth experiments of wild type and arcA deletion strains of S. pyogenes M49 in a chemically defined medium and calculated nutrient uptake and production fluxes. We additionally performed amino acid auxotrophy experiments to test the consistency of the model. The established genome-scale model can be used to understand the growth requirements of the human pathogen S. pyogenes and define optimal and suboptimal conditions, but also to describe differences and similarities between S. pyogenes and related lactic acid bacteria such as L. lactis in order to find strategies to reduce the growth of the pathogen and propose drug targets.
Collapse
Affiliation(s)
- Jennifer Levering
- Department of Modeling of Biological Processes, COS Heidelberg/BioQuant, Heidelberg University, Heidelberg, Germany.
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany.
| | - Antje Sieg
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Koen W A van Grinsven
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Amsterdam, The Netherlands
| | - Silvio Hering
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Nadine Veith
- Department of Modeling of Biological Processes, COS Heidelberg/BioQuant, Heidelberg University, Heidelberg, Germany
| | - Brett G Olivier
- Amsterdam Insitute for Molecules, Medicines and Systems, VU Amsterdam, The Netherlands
| | - Lara Klett
- Department of Modeling of Biological Processes, COS Heidelberg/BioQuant, Heidelberg University, Heidelberg, Germany
| | - Jeroen Hugenholtz
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Amsterdam, The Netherlands
| | - Bas Teusink
- Amsterdam Insitute for Molecules, Medicines and Systems, VU Amsterdam, The Netherlands
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Ursula Kummer
- Department of Modeling of Biological Processes, COS Heidelberg/BioQuant, Heidelberg University, Heidelberg, Germany
| |
Collapse
|
21
|
van Niekerk DD, Penkler GP, du Toit F, Snoep JL. Targeting glycolysis in the malaria parasite Plasmodium falciparum. FEBS J 2016; 283:634-46. [PMID: 26648082 DOI: 10.1111/febs.13615] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
UNLABELLED Glycolysis is the main pathway for ATP production in the malaria parasite Plasmodium falciparum and essential for its survival. Following a sensitivity analysis of a detailed kinetic model for glycolysis in the parasite, the glucose transport reaction was identified as the step whose activity needed to be inhibited to the least extent to result in a 50% reduction in glycolytic flux. In a subsequent inhibitor titration with cytochalasin B, we confirmed the model analysis experimentally and measured a flux control coefficient of 0.3 for the glucose transporter. In addition to the glucose transporter, the glucokinase and phosphofructokinase had high flux control coefficients, while for the ATPase a small negative flux control coefficient was predicted. In a broader comparative analysis of glycolytic models, we identified a weakness in the P. falciparum pathway design with respect to stability towards perturbations in the ATP demand. DATABASE The mathematical model described here has been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at http://jjj.bio.vu.nl/database/vanniekerk1. The SEEK-study including the experimental data set is available at DOI 10.15490/seek.1. INVESTIGATION 56 (http://dx.doi.org/10.15490/seek.1. INVESTIGATION 56).
Collapse
Affiliation(s)
- David D van Niekerk
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Gerald P Penkler
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa.,Molecular Cell Physiology, Vrije Universiteit Amsterdam, The Netherlands
| | - Francois du Toit
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa
| | - Jacky L Snoep
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa.,Molecular Cell Physiology, Vrije Universiteit Amsterdam, The Netherlands.,MIB, University of Manchester, UK
| |
Collapse
|
22
|
Christensen CD, Hofmeyr JHS, Rohwer JM. Tracing regulatory routes in metabolism using generalised supply-demand analysis. BMC SYSTEMS BIOLOGY 2015; 9:89. [PMID: 26635009 PMCID: PMC4669674 DOI: 10.1186/s12918-015-0236-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/20/2015] [Indexed: 11/10/2022]
Abstract
Background Generalised supply-demand analysis is a conceptual framework that views metabolism as a molecular economy. Metabolic pathways are partitioned into so-called supply and demand blocks that produce and consume a particular intermediate metabolite. By studying the response of these reaction blocks to perturbations in the concentration of the linking metabolite, different regulatory routes of interaction between the metabolite and its supply and demand blocks can be identified and their contribution quantified. These responses are mediated not only through direct substrate/product interactions, but also through allosteric effects. Here we subject previously published kinetic models of pyruvate metabolism in Lactococcus lactis and aspartate-derived amino acid synthesis in Arabidopsis thaliana to generalised supply-demand analysis. Results Multiple routes of regulation are brought about by different mechanisms in each model, leading to behavioural and regulatory patterns that are generally difficult to predict from simple inspection of the reaction networks depicting the models. In the pyruvate model the moiety-conserved cycles of ATP/ADP and NADH/NAD + allow otherwise independent metabolic branches to communicate. This causes the flux of one ATP-producing reaction block to increase in response to an increasing ATP/ADP ratio, while an NADH-consuming block flux decreases in response to an increasing NADH/NAD + ratio for certain ratio value ranges. In the aspartate model, aspartate semialdehyde can inhibit its supply block directly or by increasing the concentration of two amino acids (Lys and Thr) that occur as intermediates in demand blocks and act as allosteric inhibitors of isoenzymes in the supply block. These different routes of interaction from aspartate semialdehyde are each seen to contribute differently to the regulation of the aspartate semialdehyde supply block. Conclusions Indirect routes of regulation between a metabolic intermediate and a reaction block that either produces or consumes this intermediate can play a much larger regulatory role than routes mediated through direct interactions. These indirect routes of regulation can also result in counter-intuitive metabolic behaviour. Performing generalised supply-demand analysis on two previously published models demonstrated the utility of this method as an entry point in the analysis of metabolic behaviour and the potential for obtaining novel results from previously analysed models by using new approaches. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0236-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Carl D Christensen
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
| | - Jan-Hendrik S Hofmeyr
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa. .,Centre for Studies in Complexity, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
| | - Johann M Rohwer
- Laboratory for Molecular Systems Biology, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa.
| |
Collapse
|
23
|
Kesten D, Kummer U, Sahle S, Hübner K. A new model for the aerobic metabolism of yeast allows the detailed analysis of the metabolic regulation during glucose pulse. Biophys Chem 2015; 206:40-57. [DOI: 10.1016/j.bpc.2015.06.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/08/2023]
|
24
|
McLauchlan CC, Peters BJ, Willsky GR, Crans DC. Vanadium–phosphatase complexes: Phosphatase inhibitors favor the trigonal bipyramidal transition state geometries. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.12.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
25
|
Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes. Curr Opin Biotechnol 2015; 36:146-53. [PMID: 26342586 DOI: 10.1016/j.copbio.2015.08.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/10/2015] [Accepted: 08/14/2015] [Indexed: 11/24/2022]
Abstract
The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico. The lack of kinetic data hampers the development of kinetic models, and most of the current models use ad hoc reduced stoichiometry or oversimplified kinetic rate expressions, which may limit their predictive strength. There is a need to introduce the community-level standards that will organize and accelerate the future developments in this area. We introduce here a set of requirements that will ensure the model quality, we examine the current kinetic models with respect to these requirements, and we propose a general workflow for constructing models that satisfy these requirements.
Collapse
|
26
|
Eiteman MA, Ramalingam S. Microbial production of lactic acid. Biotechnol Lett 2015; 37:955-72. [PMID: 25604523 DOI: 10.1007/s10529-015-1769-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/07/2015] [Indexed: 10/24/2022]
Abstract
Lactic acid is an important commodity chemical having a wide range of applications. Microbial production effectively competes with chemical synthesis methods because biochemical synthesis permits the generation of either one of the two enantiomers with high optical purity at high yield and titer, a result which is particularly beneficial for the production of poly(lactic acid) polymers having specific properties. The commercial viability of microbial lactic acid production relies on utilization of inexpensive carbon substrates derived from agricultural or waste resources. Therefore, optimal lactic acid formation requires an understanding and engineering of both the competing pathways involved in carbohydrate metabolism, as well as pathways leading to potential by-products which both affect product yield. Recent research leverages those biochemical pathways, while researchers also continue to seek strains with improved tolerance and ability to perform under desirable industrial conditions, for example, of pH and temperature.
Collapse
Affiliation(s)
- Mark A Eiteman
- BioChemical Engineering Program, College of Engineering, University of Georgia, Athens, GA, 30602, USA,
| | | |
Collapse
|
27
|
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
|
28
|
Streptococcus pyogenes polymyxin B-resistant mutants display enhanced ExPortal integrity. J Bacteriol 2014; 196:2563-77. [PMID: 24794568 DOI: 10.1128/jb.01596-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The ExPortal protein secretion organelle in Streptococcus pyogenes is an anionic phospholipid-containing membrane microdomain enriched in Sec translocons and postsecretion protein biogenesis factors. Polymyxin B binds to and disrupts ExPortal integrity, resulting in defective secretion of several toxins. To gain insight into factors that influence ExPortal organization, a genetic screen was conducted to select for spontaneous polymyxin B-resistant mutants displaying enhanced ExPortal integrity. Whole-genome resequencing of 25 resistant mutants revealed from one to four mutations per mutant genome clustered primarily within a core set of 10 gene groups. Construction of mutants with individual deletions or insertions demonstrated that 7 core genes confer resistance and enhanced ExPortal integrity through loss of function, while 3 were likely due to gain of function and/or combinatorial effects. Core resistance genes include a transcriptional regulator of lipid biosynthesis, several genes involved in nutrient acquisition, and a variety of genes involved in stress responses. Two members of the latter class also function as novel regulators of the secreted SpeB cysteine protease. Analysis of the most frequently isolated mutation, a single nucleotide deletion in a track of 9 consecutive adenine residues in pstS, encoding a component of a high-affinity Pi transporter, suggests that this sequence functions as a molecular switch to facilitate stress adaptation. Together, these data suggest the existence of a membrane stress response that promotes enhanced ExPortal integrity and resistance to cationic antimicrobial peptides.
Collapse
|
29
|
van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJM, Planqué R, Hulshof J, O'Toole TG, Wahl SA, Teusink B. Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science 2014; 343:1245114. [PMID: 24436182 DOI: 10.1126/science.1245114] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cells need to adapt to dynamic environments. Yeast that fail to cope with dynamic changes in the abundance of glucose can undergo growth arrest. We show that this failure is caused by imbalanced reactions in glycolysis, the essential pathway in energy metabolism in most organisms. The imbalance arises largely from the fundamental design of glycolysis, making this state of glycolysis a generic risk. Cells with unbalanced glycolysis coexisted with vital cells. Spontaneous, nongenetic metabolic variability among individual cells determines which state is reached and, consequently, which cells survive. Transient ATP (adenosine 5'-triphosphate) hydrolysis through futile cycling reduces the probability of reaching the imbalanced state. Our results reveal dynamic behavior of glycolysis and indicate that cell fate can be determined by heterogeneity purely at the metabolic level.
Collapse
Affiliation(s)
- Johan H van Heerden
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
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
|
31
|
Marín-Hernández A, López-Ramírez SY, Gallardo-Pérez JC, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E. Systems Biology Approaches to Cancer Energy Metabolism. SYSTEMS BIOLOGY OF METABOLIC AND SIGNALING NETWORKS 2014. [DOI: 10.1007/978-3-642-38505-6_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
32
|
Mora D, Arioli S, Compagno C. Food environments select microorganisms based on selfish energetic behavior. Front Microbiol 2013; 4:348. [PMID: 24319442 PMCID: PMC3837229 DOI: 10.3389/fmicb.2013.00348] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/03/2013] [Indexed: 11/13/2022] Open
Abstract
Nutrient richness, and specifically the abundance of mono- and disaccharides that characterize several food matrixes, such as milk and grape juice, has allowed the speciation of lactic acid bacteria and yeasts with a high fermentation capacity instead of energetically favorable respiratory metabolism. In these environmental contexts, rapid sugar consumption and lactic acid or ethanol production, accumulation, and tolerance, together with the ability to propagate in the absence of oxygen, are several of the "winning" traits that have apparently evolved and become specialized to perfection in these fermenting microorganisms. Here, we summarize and discuss the evolutionary context that has driven energetic metabolism in food-associated microorganisms, using the dairy species Lactococcus lactis and Streptococcus thermophilus among prokaryotes and the bakers' yeast Saccharomyces cerevisiae among eukaryotes as model organisms.
Collapse
Affiliation(s)
- Diego Mora
- Department of Food, Environmental, and Nutritional Sciences, University of Milan Milan, Italy
| | | | | |
Collapse
|
33
|
From physiology to systems metabolic engineering for the production of biochemicals by lactic acid bacteria. Biotechnol Adv 2013; 31:764-88. [DOI: 10.1016/j.biotechadv.2013.03.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 03/28/2013] [Accepted: 03/31/2013] [Indexed: 11/21/2022]
|
34
|
Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation. Appl Microbiol Biotechnol 2013; 97:8729-39. [DOI: 10.1007/s00253-013-5140-2] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Revised: 07/15/2013] [Accepted: 07/17/2013] [Indexed: 10/26/2022]
|
35
|
Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC. Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PLoS Comput Biol 2013; 9:e1003159. [PMID: 23946717 PMCID: PMC3738050 DOI: 10.1371/journal.pcbi.1003159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 06/11/2013] [Indexed: 11/19/2022] Open
Abstract
Pyruvate kinase (PYK) is a critical allosterically regulated enzyme that links glycolysis, the primary energy metabolism, to cellular metabolism. Lactic acid bacteria rely almost exclusively on glycolysis for their energy production under anaerobic conditions, which reinforces the key role of PYK in their metabolism. These organisms are closely related, but have adapted to a huge variety of native environments. They include food-fermenting organisms, important symbionts in the human gut, and antibiotic-resistant pathogens. In contrast to the rather conserved inhibition of PYK by inorganic phosphate, the activation of PYK shows high variability in the type of activating compound between different lactic acid bacteria. System-wide comparative studies of the metabolism of lactic acid bacteria are required to understand the reasons for the diversity of these closely related microorganisms. These require knowledge of the identities of the enzyme modifiers. Here, we predict potential allosteric activators of PYKs from three lactic acid bacteria which are adapted to different native environments. We used protein structure-based molecular modeling and enzyme kinetic modeling to predict and validate potential activators of PYK. Specifically, we compared the electrostatic potential and the binding of phosphate moieties at the allosteric binding sites, and predicted potential allosteric activators by docking. We then made a kinetic model of Lactococcus lactis PYK to relate the activator predictions to the intracellular sugar-phosphate conditions in lactic acid bacteria. This strategy enabled us to predict fructose 1,6-bisphosphate as the sole activator of the Enterococcus faecalis PYK, and to predict that the PYKs from Streptococcus pyogenes and Lactobacillus plantarum show weaker specificity for their allosteric activators, while still having fructose 1,6-bisphosphate play the main activator role in vivo. These differences in the specificity of allosteric activation may reflect adaptation to different environments with different concentrations of activating compounds. The combined computational approach employed can readily be applied to other enzymes.
Collapse
Affiliation(s)
- Nadine Veith
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
| | - Anna Feldman-Salit
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
- Center for Modelling and Simulation in the Biosciences (BIOMS), Heidelberg, Germany
| | - Vlad Cojocaru
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Stefan Henrich
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Ursula Kummer
- Department of Modelling Biological Processes, Centre for Organismal Studies (COS)/BIOQUANT, Heidelberg University, Heidelberg, Germany
| | - Rebecca C. Wade
- Molecular and Cellular Modelling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
- Center for Molecular Biology (ZMBH), Heidelberg University, Heidelberg, Germany
| |
Collapse
|
36
|
Hering S, Sieg A, Kreikemeyer B, Fiedler T. Kinetic characterization of arginine deiminase and carbamate kinase from Streptococcus pyogenes M49. Protein Expr Purif 2013; 91:61-8. [PMID: 23867361 DOI: 10.1016/j.pep.2013.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 06/27/2013] [Accepted: 07/08/2013] [Indexed: 11/28/2022]
Abstract
Streptococcus pyogenes (group A Streptococcus, GAS) is an important human pathogen causing mild superficial infections of skin and mucous membranes, but also life-threatening systemic diseases. S. pyogenes and other prokaryotic organisms use the arginine deiminase system (ADS) for survival in acidic environments. In this study, the arginine deiminase (AD), and carbamate kinase (CK) from S. pyogenes M49 strain 591 were heterologously expressed in Escherichia coli DH5α, purified, and kinetically characterized. AD and CK from S. pyogenes M49 share high amino acid sequence similarity with the respective enzymes from Lactococcus lactis subsp. lactis IL1403 (45.6% and 53.5% identical amino acids) and Enterococcus faecalis V583 (66.8% and 66.8% identical amino acids). We found that the arginine deiminase of S. pyogenes is not allosterically regulated by the intermediates and products of the arginine degradation (e.g., ATP, citrulline, carbamoyl phosphate). The Km and Vmax values for arginine were 1.13±0.12mM (mean±SD) and 1.51±0.07μmol/min/mg protein. The carbamate kinase is inhibited by ATP but unaffected by arginine and citrulline. The Km and Vmax values for ADP were 0.72±0.08mM and 1.10±0.10μmol/min/mg protein and the Km for carbamoyl phosphate was 0.65±0.07mM. The optimum pH and temperature for both enzymes were 6.5 and 37°C, respectively.
Collapse
Affiliation(s)
- Silvio Hering
- Rostock University Medical Centre, Institute of Medical Microbiology, Virology, and Hygiene, Schillingallee 70, 18057 Rostock, Germany
| | | | | | | |
Collapse
|
37
|
Mn2+/Mg2+-dependent pyruvate kinase from a d-lactic acid-producing bacterium Sporolactobacillus inulinus: characterization of a novel Mn2+-mediated allosterically regulated enzyme. Appl Microbiol Biotechnol 2013; 98:1583-93. [DOI: 10.1007/s00253-013-4907-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/21/2013] [Accepted: 04/06/2013] [Indexed: 10/26/2022]
|
38
|
Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T. Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria. J Biol Chem 2013; 288:21295-21306. [PMID: 23720742 DOI: 10.1074/jbc.m113.458265] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Despite high similarity in sequence and catalytic properties, the l-lactate dehydrogenases (LDHs) in lactic acid bacteria (LAB) display differences in their regulation that may arise from their adaptation to different habitats. We combined experimental and computational approaches to investigate the effects of fructose 1,6-bisphosphate (FBP), phosphate (Pi), and ionic strength (NaCl concentration) on six LDHs from four LABs studied at pH 6 and pH 7. We found that 1) the extent of activation by FBP (Kact) differs. Lactobacillus plantarum LDH is not regulated by FBP, but the other LDHs are activated with increasing sensitivity in the following order: Enterococcus faecalis LDH2 ≤ Lactococcus lactis LDH2 < E. faecalis LDH1 < L. lactis LDH1 ≤ Streptococcus pyogenes LDH. This trend reflects the electrostatic properties in the allosteric binding site of the LDH enzymes. 2) For L. plantarum, S. pyogenes, and E. faecalis, the effects of Pi are distinguishable from the effect of changing ionic strength by adding NaCl. 3) Addition of Pi inhibits E. faecalis LDH2, whereas in the absence of FBP, Pi is an activator of S. pyogenes LDH, E. faecalis LDH1, and L. lactis LDH1 and LDH2 at pH 6. These effects can be interpreted by considering the computed binding affinities of Pi to the catalytic and allosteric binding sites of the enzymes modeled in protonation states corresponding to pH 6 and pH 7. Overall, the results show a subtle interplay among the effects of Pi, FBP, and pH that results in different regulatory effects on the LDHs of different LABs.
Collapse
Affiliation(s)
- Anna Feldman-Salit
- From the Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany,; BioQuant and
| | - Silvio Hering
- Institute of Medical Microbiology, Virology, and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Hanan L Messiha
- Manchester Centre for Integrative Systems Biology, MIB, The University of Manchester, Manchester M1 7DN, United Kingdom, and
| | - Nadine Veith
- From the Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany,; BioQuant and
| | - Vlad Cojocaru
- From the Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany
| | - Antje Sieg
- Institute of Medical Microbiology, Virology, and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Hans V Westerhoff
- Manchester Centre for Integrative Systems Biology, MIB, The University of Manchester, Manchester M1 7DN, United Kingdom, and; Synthetic Systems Biology, SILS, the University of Amsterdam, and Molecular Cell Physiology, FALW, Netherlands Institute for Systems Biology, VU University Amsterdam, NL-1018 HV Amsterdam, The Netherlands
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology, and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Rebecca C Wade
- From the Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany,; Center for Molecular Biology, Heidelberg University, 69120 Heidelberg, Germany,.
| | - Tomas Fiedler
- Institute of Medical Microbiology, Virology, and Hygiene, University Medicine Rostock, 18057 Rostock, Germany,.
| |
Collapse
|
39
|
Pinna F, Sahle S, Beuke K, Bissinger M, Tuncay S, D'Alessandro LA, Gauges R, Raue A, Timmer J, Klingmüller U, Schirmacher P, Kummer U, Breuhahn K. A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes. Front Physiol 2012; 3:466. [PMID: 23293603 PMCID: PMC3533138 DOI: 10.3389/fphys.2012.00466] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Accepted: 11/26/2012] [Indexed: 12/14/2022] Open
Abstract
The cytokine tumor necrosis factor-alpha (TNFα) is one of the key factors during the priming phase of liver regeneration as well as in hepatocarcinogenesis. TNFα activates the nuclear factor κ-light-chain-enhancer of activated B cells (NFκB) signaling pathway and contributes to the conversion of quiescent hepatocytes to activated hepatocytes that are able to proliferate in response to growth factor stimulation. Different mathematical models have been previously established for TNFα/NFκB signaling in the context of tumor cells. Combining these mathematical models with time-resolved measurements of expression and phosphorylation of TNFα/NFκB pathway constituents in primary mouse hepatocytes revealed that an additional phosphorylation step of the NFκB isoform p65 has to be considered in the mathematical model in order to sufficiently describe the dynamics of pathway activation in the primary cells. Also, we addressed the role of basal protein turnover by experimentally measuring the degradation rate of pivotal players in the absence of TNFα and including this information in the model. To elucidate the impact of variations in the protein degradation rates on TNFα/NFκB signaling on the overall dynamic behavior we used global sensitivity analysis that accounts for parameter uncertainties and showed that degradation and translation of p65 had a major impact on the amplitude and the integral of p65 phosphorylation. Finally, our mathematical model of TNFα/NFκB signaling was able to predict the time-course of the complex formation of p65 and of the inhibitor of NFκB (IκB) in primary mouse hepatocytes, which was experimentally verified. Hence, we here present a mathematical model for TNFα/NFκB signaling in primary mouse hepatocytes that provides an important basis to quantitatively disentangle the complex interplay of multiple factors in liver regeneration and tumorigenesis.
Collapse
Affiliation(s)
- Federico Pinna
- Institute of Pathology, University Hospital of Heidelberg Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Martinussen J, Solem C, Holm AK, Jensen PR. Engineering strategies aimed at control of acidification rate of lactic acid bacteria. Curr Opin Biotechnol 2012; 24:124-9. [PMID: 23266099 DOI: 10.1016/j.copbio.2012.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/21/2012] [Accepted: 11/22/2012] [Indexed: 10/27/2022]
Abstract
The ability of lactic acid bacteria to produce lactic acid from various sugars plays an important role in food fermentations. Lactic acid is derived from pyruvate, the end product of glycolysis and thus a fast lactic acid production rate requires a high glycolytic flux. In addition to lactic acid, alternative end products--ethanol, acetic acid and formic acid--are formed by many species. The central role of glycolysis in lactic acid bacteria has provoked numerous studies aiming at identifying potential bottleneck(s) since knowledge about flux control could be important not only for optimizing food fermentation processes, but also for novel applications of lactic acid bacteria, such as cell factories for the production of green fuels and chemicals. With respect to the control and regulation of the fermentation mode, some progress has been made, but the question of which component(s) control the main glycolytic flux remains unanswered.
Collapse
Affiliation(s)
- Jan Martinussen
- Center for Systems Microbiology, Department of Systems Biology, Technical University of Denmark, Matematiktorvet, Building 301, 2800 Kgs. Lyngby, Denmark
| | | | | | | |
Collapse
|
41
|
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
|
42
|
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
|
43
|
Goel A, Wortel MT, Molenaar D, Teusink B. Metabolic shifts: a fitness perspective for microbial cell factories. Biotechnol Lett 2012; 34:2147-60. [PMID: 22936303 PMCID: PMC3487007 DOI: 10.1007/s10529-012-1038-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 08/16/2012] [Indexed: 04/28/2023]
Abstract
Performance of industrial microorganisms as cell factories is limited by the capacity to channel nutrients to desired products, of which optimal production usually requires careful manipulation of process conditions, or strain improvement. The focus in process improvement is often on understanding and manipulating the regulation of metabolism. Nonetheless, one encounters situations where organisms are remarkably resilient to further optimization or their properties become unstable. Therefore it is important to understand the origin of these apparent limitations to find whether and how they can be improved. We argue that by considering fitness effects of regulation, a more generic explanation for certain behaviour can be obtained. In this view, apparent process limitations arise from trade-offs that cells faced as they evolved to improve fitness. A deeper understanding of such trade-offs using a systems biology approach can ultimately enhance performance of cell factories.
Collapse
Affiliation(s)
- Anisha Goel
- Systems Bioinformatics IBIVU, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | | | | | | |
Collapse
|
44
|
Effects of the ERES pathogenicity region regulator Ralp3 on Streptococcus pyogenes serotype M49 virulence factor expression. J Bacteriol 2012; 194:3618-26. [PMID: 22544273 DOI: 10.1128/jb.00227-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Streptococcus pyogenes (group A streptococcus [GAS]) is a highly virulent Gram-positive bacterium. For successful infection, GAS expresses many virulence factors, which are clustered together with transcriptional regulators in distinct genomic regions. Ralp3 is a central regulator of the ERES region. In this study, we investigated the role of Ralp3 in GAS M49 pathogenesis. The inactivation of Ralp3 resulted in reduced attachment to and internalization into human keratinocytes. The Δralp3 mutant failed to survive in human blood and serum, and the hyaluronic acid capsule was slightly decreased. In addition, the mutant showed a lower binding capacity to human plasminogen, and the SpeB activity was significantly decreased. Complementation of the Δralp3 mutant restored the wild-type phenotype. The transcriptome and quantitative reverse transcription-PCR analysis of the serotype M49 GAS strain and its isogenic Δralp3 mutant identified 16 genes as upregulated, and 43 genes were found to be downregulated. Among the downregulated genes, there were open reading frames encoding proteins involved in metabolism (e.g., both lac operons and the fru operon), genes encoding lantibiotics (e.g., the putative salivaricin operon), and ORFs encoding virulence factors (such as the whole Mga core regulon and further genes under Mga control). In summary, the ERES region regulator Ralp3 is an important serotype-specific transcriptional regulator for virulence and metabolic control.
Collapse
|
45
|
Abstract
Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications.
Collapse
Affiliation(s)
- Willem M de Vos
- Laboratory of Microbiology, Wageningen University, The Netherlands.
| |
Collapse
|