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Tomiyasu N, Takahashi M, Toyonaga K, Yamasaki S, Bamba T, Izumi Y. Efficient lipidomic approach for the discovery of lipid ligands for immune receptors by combining LC-HRMS/MS analysis with fractionation and reporter cell assay. Anal Bioanal Chem 2023:10.1007/s00216-023-05111-w. [PMID: 38135762 DOI: 10.1007/s00216-023-05111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
C-type lectin receptors (CLRs), which are pattern recognition receptors responsible for triggering innate immune responses, recognize damaged self-components and immunostimulatory lipids from pathogenic bacteria; however, several of their ligands remain unknown. Here, we propose a new analytical platform combining liquid chromatography-high-resolution tandem mass spectrometry with microfractionation capability (LC-FRC-HRMS/MS) and a reporter cell assay for sensitive activity measurements to develop an efficient methodology for searching for lipid ligands of CLR from microbial trace samples (crude cell extracts of approximately 5 mg dry cell/mL). We also developed an in-house lipidomic library containing accurate mass and fragmentation patterns of more than 10,000 lipid molecules predicted in silico for 90 lipid subclasses and 35 acyl side chain fatty acids. Using the developed LC-FRC-HRMS/MS system, the lipid extracts of Helicobacter pylori were separated and fractionated, and HRMS and HRMS/MS spectra were obtained simultaneously. The fractionated lipid extract samples in 96-well plates were thereafter subjected to reporter cell assays using nuclear factor of activated T cells (NFAT)-green fluorescent protein (GFP) reporter cells expressing mouse or human macrophage-inducible C-type lectin (Mincle). A total of 102 lipid molecules from all fractions were annotated using an in-house lipidomic library. Furthermore, a fraction that exhibited significant activity in the NFAT-GFP reporter cell assay contained α-cholesteryl glucoside, a type of glycolipid, which was successfully identified as a lipid ligand molecule for Mincle. Our analytical platform has the potential to be a useful tool for efficient discovery of lipid ligands for immunoreceptors.
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Affiliation(s)
- Noriyuki Tomiyasu
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Masatomo Takahashi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenji Toyonaga
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Section of Infection Biology, Department of Functional Bioscience, Fukuoka Dental College, Fukuoka, Japan
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
| | - Takeshi Bamba
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Izumi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan.
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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Park J, Lee SM, Ebrahim A, Scott-Nevros Z, Kim J, Yang L, Sastry A, Seo S, Palsson BO, Kim D. Model-driven experimental design workflow expands understanding of regulatory role of Nac in Escherichia coli. NAR Genom Bioinform 2023; 5:lqad006. [PMID: 36685725 PMCID: PMC9853098 DOI: 10.1093/nargab/lqad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/07/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
The establishment of experimental conditions for transcriptional regulator network (TRN) reconstruction in bacteria continues to be impeded by the limited knowledge of activating conditions for transcription factors (TFs). Here, we present a novel genome-scale model-driven workflow for designing experimental conditions, which optimally activate specific TFs. Our model-driven workflow was applied to elucidate transcriptional regulation under nitrogen limitation by Nac and NtrC, in Escherichia coli. We comprehensively predict alternative nitrogen sources, including cytosine and cytidine, which trigger differential activation of Nac using a model-driven workflow. In accordance with the prediction, genome-wide measurements with ChIP-exo and RNA-seq were performed. Integrative data analysis reveals that the Nac and NtrC regulons consist of 97 and 43 genes under alternative nitrogen conditions, respectively. Functional analysis of Nac at the transcriptional level showed that Nac directly down-regulates amino acid biosynthesis and restores expression of tricarboxylic acid (TCA) cycle genes to alleviate nitrogen-limiting stress. We also demonstrate that both TFs coherently modulate α-ketoglutarate accumulation stress due to nitrogen limitation by co-activating amino acid and diamine degradation pathways. A systems-biology approach provided a detailed and quantitative understanding of both TF's roles and how nitrogen and carbon metabolic networks respond complementarily to nitrogen-limiting stress.
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Affiliation(s)
- Joon Young Park
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Ali Ebrahim
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zoe K Scott-Nevros
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jaehyung Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Laurence Yang
- Department of Chemical Engineering, Queen's University, Kingston, Canada
| | - Anand Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, and Interdisciplinary Program in Bioengineering, and Institute of Chemical Processes, and Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
- The Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, 6 Kogle Alle, Hørsholm, Denmark
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Republic of Korea
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Quantitative challenges and their bioinformatic solutions in mass spectrometry-based metabolomics. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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4
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Conversion of Escherichia coli into Mixotrophic CO 2 Assimilation with Malate and Hydrogen Based on Recombinant Expression of 2-Oxoglutarate:Ferredoxin Oxidoreductase Using Adaptive Laboratory Evolution. Microorganisms 2023; 11:microorganisms11020253. [PMID: 36838218 PMCID: PMC9967407 DOI: 10.3390/microorganisms11020253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023] Open
Abstract
We report the mixotrophic growth of Escherichia coli based on recombinant 2-oxoglutarate:ferredoxin oxidoreductase (OGOR) to assimilate CO2 using malate as an auxiliary carbon source and hydrogen as an energy source. We employ a long-term (~184 days) two-stage adaptive evolution to convert heterotrophic E. coli into mixotrophic E. coli. In the first stage of evolution with serine, diauxic growth emerges as a prominent feature. At the end of the second stage of evolution with malate, the strain exhibits mixotrophy with CO2 as an essential substrate for growth. We expect this work will open new possibilities in the utilization of OGOR for microbial CO2 assimilation and future hydrogen-based electro-microbial conversion.
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Chen YY, Soma Y, Ishikawa M, Takahashi M, Izumi Y, Bamba T, Hori K. Metabolic alteration of Methylococcus capsulatus str. Bath during a microbial gas-phase reaction. BIORESOURCE TECHNOLOGY 2021; 330:125002. [PMID: 33770731 DOI: 10.1016/j.biortech.2021.125002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
This study demonstrates the metabolic alteration of Methylococcus capsulatus (Bath), a representative bacterium among methanotrophs, in microbial gas-phase reactions. For comparative metabolome analysis, a bioreactor was designed to be capable of supplying gaseous substrates and liquid nutrients continuously. Methane degradation by M. capsulatus (Bath) was more efficient in a gas-phase reaction operated in the bioreactor than in an aqueous phase reaction operated in a batch reactor. Metabolome analysis revealed remarkable alterations in the metabolism of cells in the gas-phase reaction; in particular, pyruvate, 2-ketoglutarate, some amino acids, xanthine, and hypoxanthine were accumulated, whereas 2,6-diaminopimelate was decreased. Based on the results of metabolome analysis, cells in the gas-phase reaction seemed to alter their metabolism to reduce the excess ATP and NADH generated upon increased availability of methane and oxygen. Our findings will facilitate the development of efficient processes for methane-based bioproduction with low energy consumption.
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Affiliation(s)
- Yan-Yu Chen
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Yuki Soma
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masahito Ishikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
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Costa Dos Santos G, Renovato-Martins M, de Brito NM. The remodel of the "central dogma": a metabolomics interaction perspective. Metabolomics 2021; 17:48. [PMID: 33969452 PMCID: PMC8106972 DOI: 10.1007/s11306-021-01800-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/30/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND In 1957, Francis Crick drew a linear diagram on a blackboard. This diagram is often called the "central dogma." Subsequently, the relationships between different steps of the "central dogma" have been shown to be considerably complex, mostly because of the emerging world of small molecules. It is noteworthy that metabolites can be generated from the diet through gut microbiome metabolism, serve as substrates for epigenetic modifications, destabilize DNA quadruplexes, and follow Lamarckian inheritance. Small molecules were once considered the missing link in the "central dogma"; however, recently they have acquired a central role, and their general perception as downstream products has become reductionist. Metabolomics is a large-scale analysis of metabolites, and this emerging field has been shown to be the closest omics associated with the phenotype and concomitantly, the basis for all omics. AIM OF REVIEW Herein, we propose a broad updated perspective for the flux of information diagram centered in metabolomics, including the influence of other factors, such as epigenomics, diet, nutrition, and the gut- microbiome. KEY SCIENTIFIC CONCEPTS OF REVIEW Metabolites are the beginning and the end of the flux of information.
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Affiliation(s)
- Gilson Costa Dos Santos
- Laboratory of NMR Metabolomics, IBRAG, Department of Genetics, State University of Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil.
| | - Mariana Renovato-Martins
- Department of Cellular and Molecular Biology, IB, Federal Fluminense University, Niterói, 24210-200, Brazil
| | - Natália Mesquita de Brito
- Laboratory of Cellular and Molecular Pharmacology, IBRAG, Department of Cell Biology, State University of Rio de Janeiro, Rio de Janeiro, 20551-030, Brazil.
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Rinschen MM, Ivanisevic J, Giera M, Siuzdak G. Identification of bioactive metabolites using activity metabolomics. Nat Rev Mol Cell Biol 2019; 20:353-367. [PMID: 30814649 PMCID: PMC6613555 DOI: 10.1038/s41580-019-0108-4] [Citation(s) in RCA: 530] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The metabolome, the collection of small-molecule chemical entities involved in metabolism, has traditionally been studied with the aim of identifying biomarkers in the diagnosis and prediction of disease. However, the value of metabolome analysis (metabolomics) has been redefined from a simple biomarker identification tool to a technology for the discovery of active drivers of biological processes. It is now clear that the metabolome affects cellular physiology through modulation of other 'omics' levels, including the genome, epigenome, transcriptome and proteome. In this Review, we focus on recent progress in using metabolomics to understand how the metabolome influences other omics and, by extension, to reveal the active role of metabolites in physiology and disease. This concept of utilizing metabolomics to perform activity screens to identify biologically active metabolites - which we term activity metabolomics - is already having a broad impact on biology.
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Affiliation(s)
- Markus M Rinschen
- The Scripps Research Institute, Center for Metabolomics and Mass Spectrometry, La Jolla, CA, USA
| | - Julijana Ivanisevic
- Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Martin Giera
- Leiden University Medical Center, Center for Proteomics & Metabolomics, Leiden, Netherlands.
| | - Gary Siuzdak
- The Scripps Research Institute, Center for Metabolomics and Mass Spectrometry, La Jolla, CA, USA.
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8
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Zhang CC, Zhou CZ, Burnap RL, Peng L. Carbon/Nitrogen Metabolic Balance: Lessons from Cyanobacteria. TRENDS IN PLANT SCIENCE 2018; 23:1116-1130. [PMID: 30292707 DOI: 10.1016/j.tplants.2018.09.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/07/2018] [Accepted: 09/11/2018] [Indexed: 05/20/2023]
Abstract
Carbon and nitrogen are the two most abundant nutrient elements for all living organisms, and their metabolism is tightly coupled. What are the signaling mechanisms that cells use to sense and control the carbon/nitrogen (C/N) metabolic balance following environmental changes? Based on studies in cyanobacteria, it was found that 2-phosphoglycolate derived from the oxygenase activity of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) and 2-oxoglutarate from the Krebs cycle act as the carbon- and nitrogen-starvation signals, respectively, and their concentration ratio likely reflects the status of the C/N metabolic balance. We will present and discuss the regulatory principles underlying the signaling mechanisms, which are likely to be conserved in other photosynthetic organisms. These concepts may also contribute to developments in the field of biofuel engineering or improvements in crop productivity.
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Affiliation(s)
- Cheng-Cai Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, The Chinese Academy of Sciences, Wuhan, Hubei 430072, People's Republic of China; Aix-Marseille Université, CNRS, LCB, France.
| | - Cong-Zhao Zhou
- School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, 230027, People's Republic of China
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Henry Bellmon Research Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ling Peng
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, Equipe Labellisée Ligue Contre le Cancer, CINaM UMR 7325, 13288 Marseille, France
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9
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Abstract
The metabolite 2-oxoglutarate (also known as α-ketoglutarate, 2-ketoglutaric acid, or oxoglutaric acid) lies at the intersection between the carbon and nitrogen metabolic pathways. This compound is a key intermediate of one of the most fundamental biochemical pathways in carbon metabolism, the tricarboxylic acid (TCA) cycle. In addition, 2-oxoglutarate also acts as the major carbon skeleton for nitrogen-assimilatory reactions. Experimental data support the conclusion that intracellular levels of 2-oxoglutarate fluctuate according to nitrogen and carbon availability. This review summarizes how nature has capitalized on the ability of 2-oxoglutarate to reflect cellular nutritional status through evolution of a variety of 2-oxoglutarate-sensing regulatory proteins. The number of metabolic pathways known to be regulated by 2-oxoglutarate levels has increased significantly in recent years. The signaling properties of 2-oxoglutarate are highlighted by the fact that this metabolite regulates the synthesis of the well-established master signaling molecule, cyclic AMP (cAMP), in Escherichia coli.
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Salem MA, Jüppner J, Bajdzienko K, Giavalisco P. Protocol: a fast, comprehensive and reproducible one-step extraction method for the rapid preparation of polar and semi-polar metabolites, lipids, proteins, starch and cell wall polymers from a single sample. PLANT METHODS 2016; 12:45. [PMID: 27833650 PMCID: PMC5103428 DOI: 10.1186/s13007-016-0146-2] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/26/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND The elucidation of complex biological systems requires integration of multiple molecular parameters. Accordingly, high throughput methods like transcriptomics, proteomics, metabolomics and lipidomics have emerged to provide the tools for successful system-wide investigations. Unfortunately, optimized analysis of different compounds requires specific extraction procedures in combination with specific analytical instrumentation. However, the most efficient extraction protocols often only cover a restricted number of compounds due to the different physico-chemical properties of these biological compounds. Consequently, comprehensive analysis of several molecular components like polar primary metabolites next to lipids or proteins require multiple aliquots to enable the specific extraction procedures required to cover these diverse compound classes. This multi-parallel sample handling of different sample aliquots is therefore not only more sample intensive, it also requires more time and effort to obtain the required extracts. RESULTS To circumvent large sample amounts, distributed into several aliquots for the comprehensive extraction of most relevant biological compounds, we developed a simple, robust and reproducible two-phase liquid-liquid extraction protocol. This one-step extraction protocol allows for the analysis of polar-, semi-polar and hydrophobic metabolites, next to insoluble or precipitated compounds, including proteins, starch and plant cell wall components, from a single sample. The method is scalable regarding the used sample amounts but also the employed volumes and can be performed in microcentrifuge tubes, enabling high throughput analysis. The obtained fractions are fully compatible with common analytical methods, including spectroscopic, chromatographic and mass spectrometry-based techniques. To document the utility of the described protocol, we used 25 mg of Arabidopsis thaliana rosette leaves for the generation of multi-omics data sets, covering lipidomics, metabolomics and proteomics. The obtained data allowed us to measure and annotate more than 200 lipid compounds, 100 primary metabolites, 50 secondary metabolites and 2000 proteins. CONCLUSIONS The described extraction protocol provides a simple and straightforward method for the efficient extraction of lipids, metabolites and proteins from minute amounts of a single sample, enabling the targeted but also untargeted high-throughput analyses of diverse biological tissues and samples.
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Affiliation(s)
- Mohamed A. Salem
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562 Egypt
| | - Jessica Jüppner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Krzysztof Bajdzienko
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Patrick Giavalisco
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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Zhao F, Tan X, Zhang Y, Chu H, Yang L, Zhou X. Effect of temperature on the conversion ratio of glucose to Chlorella pyrenoidosa cells: Reducing the cost of cultivation. ALGAL RES 2015. [DOI: 10.1016/j.algal.2015.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Yang N, Ding S, Chen F, Zhang X, Xia Y, Di H, Cao Q, Deng X, Wu M, Wong CCL, Tian XX, Yang CG, Zhao J, Lan L. The Crc protein participates in down-regulation of the Lon gene to promote rhamnolipid production and rhl quorum sensing in Pseudomonas aeruginosa. Mol Microbiol 2015; 96:526-47. [PMID: 25641250 DOI: 10.1111/mmi.12954] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/28/2015] [Indexed: 12/20/2022]
Abstract
Rhamnolipid acts as a virulence factor during Pseudomonas aeruginosa infection. Here, we show that deletion of the catabolite repression control (crc) gene in P. aeruginosa leads to a rhamnolipid-negative phenotype. This effect is mediated by the down-regulation of rhl quorum sensing (QS). We discover that a disruption of the gene encoding the Lon protease entirely offsets the effect of crc deletion on the production of both rhamnolipid and rhl QS signal C4-HSL. Crc is unable to bind lon mRNA in vitro in the absence of the RNA chaperon Hfq, while Crc contributes to Hfq-mediated repression of the lon gene expression at a posttranscriptional level. Deletion of crc, which results in up-regulation of lon, significantly reduces the in vivo stability and abundance of the RhlI protein that synthesizes C4-HSL, causing the attenuation of rhl QS. Lon is also capable of degrading the RhlI protein in vitro. In addition, constitutive expression of rhlI suppresses the defects of the crc deletion mutant in rhamnolipid, C4-HSL and virulence on lettuce leaves. This study therefore uncovers a novel posttranscriptional regulatory cascade, Crc-Hfq/Lon/RhlI, for the regulation of rhamnolipid production and rhl QS in P. aeruginosa.
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Affiliation(s)
- Nana Yang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong Zhangjiang Hi-Tech Park, Shanghai, 201203, China
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Matsuoka Y, Shimizu K. Current status and future perspectives of kinetic modeling for the cell metabolism with incorporation of the metabolic regulation mechanism. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-014-0031-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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14
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Gerhardt EC, Rodrigues TE, Müller-Santos M, Pedrosa FO, Souza EM, Forchhammer K, Huergo LF. The Bacterial signal transduction protein GlnB regulates the committed step in fatty acid biosynthesis by acting as a dissociable regulatory subunit of acetyl-CoA carboxylase. Mol Microbiol 2015; 95:1025-35. [DOI: 10.1111/mmi.12912] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Edileusa C.M. Gerhardt
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen; Auf der Morgenstelle 28 Tübingen 72076 Germany
| | - Thiago E. Rodrigues
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Marcelo Müller-Santos
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Fabio O. Pedrosa
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Emanuel M. Souza
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
| | - Karl Forchhammer
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin der Eberhard-Karls Universität Tübingen; Auf der Morgenstelle 28 Tübingen 72076 Germany
| | - Luciano F. Huergo
- Instituto Nacional de Ciência e Tecnologia da Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular; Universidade Federal do Paraná; CEP 81531-990 CP 19046 Curitiba PR Brazil
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Shimizu K. Metabolic Regulation and Coordination of the Metabolism in Bacteria in Response to a Variety of Growth Conditions. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 155:1-54. [PMID: 25712586 DOI: 10.1007/10_2015_320] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Living organisms have sophisticated but well-organized regulation system. It is important to understand the metabolic regulation mechanisms in relation to growth environment for the efficient design of cell factories for biofuels and biochemicals production. Here, an overview is given for carbon catabolite regulation, nitrogen regulation, ion, sulfur, and phosphate regulations, stringent response under nutrient starvation as well as oxidative stress regulation, redox state regulation, acid-shock, heat- and cold-shock regulations, solvent stress regulation, osmoregulation, and biofilm formation, and quorum sensing focusing on Escherichia coli metabolism and others. The coordinated regulation mechanisms are of particular interest in getting insight into the principle which governs the cell metabolism. The metabolism is controlled by both enzyme-level regulation and transcriptional regulation via transcription factors such as cAMP-Crp, Cra, Csr, Fis, P(II)(GlnB), NtrBC, CysB, PhoR/B, SoxR/S, Fur, MarR, ArcA/B, Fnr, NarX/L, RpoS, and (p)ppGpp for stringent response, where the timescales for enzyme-level and gene-level regulations are different. Moreover, multiple regulations are coordinated by the intracellular metabolites, where fructose 1,6-bisphosphate (FBP), phosphoenolpyruvate (PEP), and acetyl-CoA (AcCoA) play important roles for enzyme-level regulation as well as transcriptional control, while α-ketoacids such as α-ketoglutaric acid (αKG), pyruvate (PYR), and oxaloacetate (OAA) play important roles for the coordinated regulation between carbon source uptake rate and other nutrient uptake rate such as nitrogen or sulfur uptake rate by modulation of cAMP via Cya.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu Institute of Technology, Iizuka, Fukuoka, 820-8502, Japan. .,Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
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16
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Metabolic sensor governing bacterial virulence in Staphylococcus aureus. Proc Natl Acad Sci U S A 2014; 111:E4981-90. [PMID: 25368190 DOI: 10.1073/pnas.1411077111] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
An effective metabolism is essential to all living organisms, including the important human pathogen Staphylococcus aureus. To establish successful infection, S. aureus must scavenge nutrients and coordinate its metabolism for proliferation. Meanwhile, it also must produce an array of virulence factors to interfere with host defenses. However, the ways in which S. aureus ties its metabolic state to its virulence regulation remain largely unknown. Here we show that citrate, the first intermediate of the tricarboxylic acid (TCA) cycle, binds to and activates the catabolite control protein E (CcpE) of S. aureus. Using structural and site-directed mutagenesis studies, we demonstrate that two arginine residues (Arg145 and Arg256) within the putative inducer-binding cavity of CcpE are important for its allosteric activation by citrate. Microarray analysis reveals that CcpE tunes the expression of 126 genes that comprise about 4.7% of the S. aureus genome. Intriguingly, although CcpE is a major positive regulator of the TCA-cycle activity, its regulon consists predominantly of genes involved in the pathogenesis of S. aureus. Moreover, inactivation of CcpE results in increased staphyloxanthin production, improved ability to acquire iron, increased resistance to whole-blood-mediated killing, and enhanced bacterial virulence in a mouse model of systemic infection. This study reveals CcpE as an important metabolic sensor that allows S. aureus to sense and adjust its metabolic state and subsequently to coordinate the expression of virulence factors and bacterial virulence.
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17
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Wardenaar KJ, van Loo HM, Cai T, Fava M, Gruber MJ, Li J, de Jonge P, Nierenberg AA, Petukhova MV, Rose S, Sampson NA, Schoevers RA, Wilcox MA, Alonso J, Bromet EJ, Bunting B, Florescu SE, Fukao A, Gureje O, Hu C, Huang YQ, Karam AN, Levinson D, Medina Mora ME, Posada-Villa J, Scott KM, Taib NI, Viana MC, Xavier M, Zarkov Z, Kessler RC. The effects of co-morbidity in defining major depression subtypes associated with long-term course and severity. Psychol Med 2014; 44:3289-3302. [PMID: 25066141 PMCID: PMC4180779 DOI: 10.1017/s0033291714000993] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Although variation in the long-term course of major depressive disorder (MDD) is not strongly predicted by existing symptom subtype distinctions, recent research suggests that prediction can be improved by using machine learning methods. However, it is not known whether these distinctions can be refined by added information about co-morbid conditions. The current report presents results on this question. METHOD Data came from 8261 respondents with lifetime DSM-IV MDD in the World Health Organization (WHO) World Mental Health (WMH) Surveys. Outcomes included four retrospectively reported measures of persistence/severity of course (years in episode; years in chronic episodes; hospitalization for MDD; disability due to MDD). Machine learning methods (regression tree analysis; lasso, ridge and elastic net penalized regression) followed by k-means cluster analysis were used to augment previously detected subtypes with information about prior co-morbidity to predict these outcomes. RESULTS Predicted values were strongly correlated across outcomes. Cluster analysis of predicted values found three clusters with consistently high, intermediate or low values. The high-risk cluster (32.4% of cases) accounted for 56.6-72.9% of high persistence, high chronicity, hospitalization and disability. This high-risk cluster had both higher sensitivity and likelihood ratio positive (LR+; relative proportions of cases in the high-risk cluster versus other clusters having the adverse outcomes) than in a parallel analysis that excluded measures of co-morbidity as predictors. CONCLUSIONS Although the results using the retrospective data reported here suggest that useful MDD subtyping distinctions can be made with machine learning and clustering across multiple indicators of illness persistence/severity, replication with prospective data is needed to confirm this preliminary conclusion.
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Affiliation(s)
- K J Wardenaar
- Department of Psychiatry,University of Groningen, University Medical Center Groningen,The Netherlands
| | - H M van Loo
- Department of Psychiatry,University of Groningen, University Medical Center Groningen,The Netherlands
| | - T Cai
- Department of Biostatistics,Harvard School of Public Health,Boston, MA,USA
| | - M Fava
- Department of Psychiatry,MGH Clinical Trials Network and Institute,Depression Clinical and Research Program, Massachusetts General Hospital, Boston, MA,USA
| | - M J Gruber
- Department of Health Care Policy,Harvard Medical School,Boston, MA,USA
| | - J Li
- Department of Biostatistics,Harvard School of Public Health,Boston, MA,USA
| | - P de Jonge
- Department of Psychiatry,University of Groningen, University Medical Center Groningen,The Netherlands
| | - A A Nierenberg
- Depression Clinical and Research Program and the Bipolar Clinic and Research Program,Massachusetts General Hospital and Harvard Medical School,Boston, MA,USA
| | - M V Petukhova
- Department of Health Care Policy,Harvard Medical School,Boston, MA,USA
| | - S Rose
- Department of Health Care Policy,Harvard Medical School,Boston, MA,USA
| | - N A Sampson
- Department of Health Care Policy,Harvard Medical School,Boston, MA,USA
| | - R A Schoevers
- Department of Psychiatry,University of Groningen, University Medical Center Groningen,The Netherlands
| | - M A Wilcox
- Johnson & Johnson Pharmaceutical Research and Development,Titusville, NJ,USA
| | - J Alonso
- IMIM-Hospital del Mar Research Institute, Parc de Salut Mar,Pompeu Fabra University (UPF), andCIBER en Epidemiología y Salud Pública (CIBERESP), Barcelona,Spain
| | - E J Bromet
- Department of Psychiatry and Behavioral Science, Stony Brook School of Medicine,State University of New York at Stony Brook,Stony Brook, NY,USA
| | - B Bunting
- Psychology Research Institute,University of Ulster,Londonderry,UK
| | - S E Florescu
- National School of Public Health,Management and Professional Development, Bucharest,Romania
| | - A Fukao
- Department of Public Health,Yamagata University School of Medicine,Japan
| | - O Gureje
- University College Hospital,Ibadan,Nigeria
| | - C Hu
- Shenzhen Institute of Mental Health and Shenzhen Kangning Hospital,Guangdong Province,People's Republic of China
| | - Y Q Huang
- Institute of Mental Health, Peking University,Beijing,People's Republic of China
| | - A N Karam
- Department of Psychiatry and Clinical Psychology,St George Hospital University Medical Center,Department of Psychiatry and Clinical Psychology, Faculty of Medicine, Balamand University Medical School, andInstitute for Development Research Advocacy and Applied Care (IDRAAC), Beirut,Lebanon
| | - D Levinson
- Research and Planning,Mental Health Services,Ministry of Health, Jerusalem,Israel
| | - M E Medina Mora
- National Institute of Psychiatry,Calzada Mexico Xochimilco, Mexico City,Mexico
| | - J Posada-Villa
- Universidad Colegio Mayor de Cundinamarca,Bogota,Colombia
| | - K M Scott
- Department of Psychological Medicine,University of Otago,Dunedin,New Zealand
| | - N I Taib
- Mental Health Center-Duhok,Kurdistan Region,Iraq
| | - M C Viana
- Department of Social Medicine,Federal University of Espirito Santo,Vitoria,Brazil
| | - M Xavier
- Department of Mental Health,Universidade Nova de Lisboa,Lisbon,Portugal
| | - Z Zarkov
- National Center of Public Health and Analyses,Department of Mental Health, Sofia,Bulgaria
| | - R C Kessler
- Department of Health Care Policy,Harvard Medical School,Boston, MA,USA
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18
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van Loo HM, Cai T, Gruber MJ, Li J, de Jonge P, Petukhova M, Rose S, Sampson NA, Schoevers RA, Wardenaar KJ, Wilcox MA, Al-Hamzawi AO, Andrade LH, Bromet EJ, Bunting B, Fayyad J, Florescu SE, Gureje O, Hu C, Huang Y, Levinson D, Medina-Mora ME, Nakane Y, Posada-Villa J, Scott KM, Xavier M, Zarkov Z, Kessler RC. Major depressive disorder subtypes to predict long-term course. Depress Anxiety 2014; 31:765-77. [PMID: 24425049 PMCID: PMC5125445 DOI: 10.1002/da.22233] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/05/2013] [Accepted: 12/07/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Variation in the course of major depressive disorder (MDD) is not strongly predicted by existing subtype distinctions. A new subtyping approach is considered here. METHODS Two data mining techniques, ensemble recursive partitioning and Lasso generalized linear models (GLMs), followed by k-means cluster analysis are used to search for subtypes based on index episode symptoms predicting subsequent MDD course in the World Mental Health (WMH) surveys. The WMH surveys are community surveys in 16 countries. Lifetime DSM-IV MDD was reported by 8,261 respondents. Retrospectively reported outcomes included measures of persistence (number of years with an episode, number of years with an episode lasting most of the year) and severity (hospitalization for MDD, disability due to MDD). RESULTS Recursive partitioning found significant clusters defined by the conjunctions of early onset, suicidality, and anxiety (irritability, panic, nervousness-worry-anxiety) during the index episode. GLMs found additional associations involving a number of individual symptoms. Predicted values of the four outcomes were strongly correlated. Cluster analysis of these predicted values found three clusters having consistently high, intermediate, or low predicted scores across all outcomes. The high-risk cluster (30.0% of respondents) accounted for 52.9-69.7% of high persistence and severity, and it was most strongly predicted by index episode severe dysphoria, suicidality, anxiety, and early onset. A total symptom count, in comparison, was not a significant predictor. CONCLUSIONS Despite being based on retrospective reports, results suggest that useful MDD subtyping distinctions can be made using data mining methods. Further studies are needed to test and expand these results with prospective data.
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Affiliation(s)
- Hanna M. van Loo
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen The Netherlands
| | - Tianxi Cai
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Michael J. Gruber
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Junlong Li
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Peter de Jonge
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen The Netherlands
| | - Maria Petukhova
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Sherri Rose
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Nancy A. Sampson
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Robert A. Schoevers
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen The Netherlands
| | - Klaas J. Wardenaar
- Department of Psychiatry, University of Groningen, University Medical Center Groningen, Groningen The Netherlands
| | - Marsha A. Wilcox
- Johnson and Johnson Pharmaceutical Research and Development, Titusville, NJ, USA
| | | | - Laura Helena Andrade
- Section of Psychiatric Epidemiology-LIM 23 Department and Institute of Psychiatry, University of São Paulo Medical School, São Paulo, Brazil
| | - Evelyn J. Bromet
- State University of New York at Stony Brook, Stony Brook, New York, USA
| | - Brendan Bunting
- Psychology Research Institute, University of Ulster, Londonderry, UK
| | - John Fayyad
- Institute for Development Research, Advocacy, and Applied Care and St.George Hospital University Medical Center, Beirut, Lebanon
| | - Silvia E. Florescu
- National School of Public Health, Management and Professional Development, Bucharest, Romania
| | - Oye Gureje
- University College Hospital, Ibadan, Nigeria
| | - Chiyi Hu
- Shenzhen Institute of Mental Health and Shenzhen Kangning Hospital, Guangdong Province, People's Republic of China
| | - Yueqin Huang
- Institute of Mental Health, Peking University, Beijing, People's Republic of China
| | - Daphna Levinson
- Research and Planning, Mental Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Yoshibumi Nakane
- Department of Social Work, The Faculty of Human Sociology, Nagasaki International University, Nagasaki, Japan
| | | | - Kate M. Scott
- Department of Psychological Medicine, Otago University, Dunedin, New Zealand
| | - Miguel Xavier
- Department of Mental Health, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Zahari Zarkov
- National Center of Public Health and Analyses Department Mental Health, Sofia, Bulgaria
| | - Ronald C. Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA,Address correspondence to Ronald C. Kessler, Ph.D., Department of Health Care Policy, Harvard Medical School, 180 Longwood Avenue, Boston, MA 02115. Tel. (617) 432-3587, Fax (617) 432-3588,
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Klumpp S, Hwa T. Bacterial growth: global effects on gene expression, growth feedback and proteome partition. Curr Opin Biotechnol 2014; 28:96-102. [PMID: 24495512 DOI: 10.1016/j.copbio.2014.01.001] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/21/2013] [Accepted: 01/03/2014] [Indexed: 02/01/2023]
Abstract
The function of endogenous as well as synthetic genetic circuits is generically coupled to the physiological state of the cell. For exponentially growing bacteria, a key characteristic of the state of the cell is the growth rate and thus gene expression is often growth-rate dependent. Here we review recent results on growth-rate dependent gene expression. We distinguish different types of growth-rate dependencies by the mechanisms of regulation involved and the presence or absence of an effect of the gene product on growth. The latter can lead to growth feedback, feedback mediated by changes of the global state of the cell. Moreover, we discuss how growth rate dependence can be used as a guide to study the molecular implementation of physiological regulation.
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Affiliation(s)
- Stefan Klumpp
- Max Planck Institute of Colloids and Interfaces, 14424 Potsdam, Germany.
| | - Terence Hwa
- Department of Physics, University of California at San Diego, La Jolla, CA 92093-0374, United States; Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0374, United States; Section of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0374, United States
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