1
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Eren E, Watts NR, Montecinos F, Wingfield PT. Encapsulated Ferritin-like Proteins: A Structural Perspective. Biomolecules 2024; 14:624. [PMID: 38927029 PMCID: PMC11202242 DOI: 10.3390/biom14060624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Encapsulins are self-assembling nano-compartments that naturally occur in bacteria and archaea. These nano-compartments encapsulate cargo proteins that bind to the shell's interior through specific recognition sequences and perform various metabolic processes. Encapsulation enables organisms to perform chemical reactions without exposing the rest of the cell to potentially harmful substances while shielding cargo molecules from degradation and other adverse effects of the surrounding environment. One particular type of cargo protein, the ferritin-like protein (FLP), is the focus of this review. Encapsulated FLPs are members of the ferritin-like protein superfamily, and they play a crucial role in converting ferrous iron (Fe+2) to ferric iron (Fe+3), which is then stored inside the encapsulin in mineralized form. As such, FLPs regulate iron homeostasis and protect organisms against oxidative stress. Recent studies have demonstrated that FLPs have tremendous potential as biosensors and bioreactors because of their ability to catalyze the oxidation of ferrous iron with high specificity and efficiency. Moreover, they have been investigated as potential targets for therapeutic intervention in cancer drug development and bacterial pathogenesis. Further research will likely lead to new insights and applications for these remarkable proteins in biomedicine and biotechnology.
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Affiliation(s)
| | | | | | - Paul T. Wingfield
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Bhattacharyya S, Bhattarai N, Pfannenstiel DM, Wilkins B, Singh A, Harshey RM. A heritable iron memory enables decision-making in Escherichia coli. Proc Natl Acad Sci U S A 2023; 120:e2309082120. [PMID: 37988472 PMCID: PMC10691332 DOI: 10.1073/pnas.2309082120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 10/12/2023] [Indexed: 11/23/2023] Open
Abstract
The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when Escherichia coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This "iron" memory preexists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, which tracks with its iron memory, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We demonstrate that cellular iron levels also track with biofilm formation and antibiotic tolerance, suggesting that iron memory may impact other physiologies.
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Affiliation(s)
- Souvik Bhattacharyya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
| | - Nabin Bhattarai
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
| | - Dylan M. Pfannenstiel
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
| | - Brady Wilkins
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE19716
| | - Rasika M. Harshey
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX78712
- LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, TX78712
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3
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Rosa-Núñez E, Echavarri-Erasun C, Armas AM, Escudero V, Poza-Carrión C, Rubio LM, González-Guerrero M. Iron Homeostasis in Azotobacter vinelandii. BIOLOGY 2023; 12:1423. [PMID: 37998022 PMCID: PMC10669500 DOI: 10.3390/biology12111423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Iron is an essential nutrient for all life forms. Specialized mechanisms exist in bacteria to ensure iron uptake and its delivery to key enzymes within the cell, while preventing toxicity. Iron uptake and exchange networks must adapt to the different environmental conditions, particularly those that require the biosynthesis of multiple iron proteins, such as nitrogen fixation. In this review, we outline the mechanisms that the model diazotrophic bacterium Azotobacter vinelandii uses to ensure iron nutrition and how it adapts Fe metabolism to diazotrophic growth.
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Affiliation(s)
- Elena Rosa-Núñez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
- Escuela Técnica de Ingeniería Agraria, Alimentaria, y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, 2, 28040 Madrid, Spain
| | - Carlos Echavarri-Erasun
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
- Escuela Técnica de Ingeniería Agraria, Alimentaria, y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, 2, 28040 Madrid, Spain
| | - Alejandro M. Armas
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
| | - Viviana Escudero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
| | - César Poza-Carrión
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
| | - Luis M. Rubio
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
| | - Manuel González-Guerrero
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Campus de Montegancedo UPM, Crta. M-40 km 38, 28223 Madrid, Spain; (E.R.-N.); (C.E.-E.); (A.M.A.); (C.P.-C.); (L.M.R.)
- Escuela Técnica de Ingeniería Agraria, Alimentaria, y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro, 2, 28040 Madrid, Spain
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4
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Bhattacharyya S, Bhattarai N, Pfannenstiel DM, Wilkins B, Singh A, Harshey RM. Iron Memory in E. coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541523. [PMID: 37609133 PMCID: PMC10441380 DOI: 10.1101/2023.05.19.541523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The importance of memory in bacterial decision-making is relatively unexplored. We show here that a prior experience of swarming is remembered when E. coli encounters a new surface, improving its future swarming efficiency. We conducted >10,000 single-cell swarm assays to discover that cells store memory in the form of cellular iron levels. This memory pre-exists in planktonic cells, but the act of swarming reinforces it. A cell with low iron initiates swarming early and is a better swarmer, while the opposite is true for a cell with high iron. The swarming potential of a mother cell, whether low or high, is passed down to its fourth-generation daughter cells. This memory is naturally lost by the seventh generation, but artificially manipulating iron levels allows it to persist much longer. A mathematical model with a time-delay component faithfully recreates the observed dynamic interconversions between different swarming potentials. We also demonstrate that iron memory can integrate multiple stimuli, impacting other bacterial behaviors such as biofilm formation and antibiotic tolerance.
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Affiliation(s)
- Souvik Bhattacharyya
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
| | - Nabin Bhattarai
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
| | - Dylan M. Pfannenstiel
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
| | - Brady Wilkins
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
| | - Abhyudai Singh
- Electrical & Computer Engineering, University of Delaware, Newark, DE 19716
| | - Rasika M. Harshey
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin; Austin, TX 78712
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5
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Gorobets S, Gorobets O, Sharai I, Polyakova T, Zablotskii V. Gradient Magnetic Field Accelerates Division of E. coli Nissle 1917. Cells 2023; 12:315. [PMID: 36672251 PMCID: PMC9857180 DOI: 10.3390/cells12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/07/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
Cell-cycle progression is regulated by numerous intricate endogenous mechanisms, among which intracellular forces and protein motors are central players. Although it seems unlikely that it is possible to speed up this molecular machinery by applying tiny external forces to the cell, we show that magnetic forcing of magnetosensitive bacteria reduces the duration of the mitotic phase. In such bacteria, the coupling of the cell cycle to the splitting of chains of biogenic magnetic nanoparticles (BMNs) provides a biological realization of such forcing. Using a static gradient magnetic field of a special spatial configuration, in probiotic bacteria E. coli Nissle 1917, we shortened the duration of the mitotic phase and thereby accelerated cell division. Thus, focused magnetic gradient forces exerted on the BMN chains allowed us to intervene in the processes of division and growth of bacteria. The proposed magnetic-based cell division regulation strategy can improve the efficiency of microbial cell factories and medical applications of magnetosensitive bacteria.
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Affiliation(s)
- Svitlana Gorobets
- Faculty of Biotechnology and Biotechnics, National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”, 03056 Kyiv, Ukraine
| | - Oksana Gorobets
- Faculty of Physics and Mathematics, National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”, 03056 Kyiv, Ukraine
- Institute of Magnetism of the National Academy of Sciences of Ukraine and Ministry of Education and Science of Ukraine, 03142 Kyiv, Ukraine
| | - Iryna Sharai
- Faculty of Physics and Mathematics, National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”, 03056 Kyiv, Ukraine
- Institute of Magnetism of the National Academy of Sciences of Ukraine and Ministry of Education and Science of Ukraine, 03142 Kyiv, Ukraine
| | - Tatyana Polyakova
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague, Czech Republic
| | - Vitalii Zablotskii
- Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, 182 00 Prague, Czech Republic
- International Magnetobiology Frontier Research Center (iMFRC), Science Island, Hefei 230000, China
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6
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Sarshar M, Scribano D, Limongi D, Zagaglia C, Palamara AT, Ambrosi C. Adaptive strategies of uropathogenic Escherichia coli CFT073: from growth in lab media to virulence during host cell adhesion. Int Microbiol 2022; 25:481-494. [PMID: 35106679 DOI: 10.1007/s10123-022-00235-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 12/23/2021] [Accepted: 01/17/2022] [Indexed: 12/15/2022]
Abstract
Urinary tract infections (UTIs) are a major concern in public health. The prevalent uropathogenic bacterium in healthcare settings is Escherichia coli. The increasing rate of antibiotic-resistant strains demands studies to understand E. coli pathogenesis to drive the development of new therapeutic approaches. This study compared the gene expression profile of selected target genes in the prototype uropathogenic E. coli (UPEC) strain CFT073 grown in Luria Bertani (LB), artificial urine (AU), and during adhesion to host bladder cells by semi-quantitative real-time PCR (RT-PCR) assays. AU effectively supported the growth of strain CFT073 as well as other E. coli strains with different lifestyles, thereby confirming the appropriateness of this medium for in vitro models. Unexpectedly, gene expression of strain CFT073 in LB and AU was quite similar; conversely, during the adhesion assay, adhesins and porins were upregulated, while key global regulators were downregulated with respect to lab media. Interestingly, fimH and papGII genes were significantly expressed in all tested conditions. Taken together, these results provide for the first time insights of the metabolic and pathogenic profile of strain CFT073 during the essential phase of host cell adhesion.
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Affiliation(s)
- Meysam Sarshar
- Research Laboratories, Bambino Gesù Children's Hospital, IRCCS, 00146, Rome, Italy
| | - Daniela Scribano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185, Rome, Italy.,Dani Di Giò Foundation-Onlus, 00193, Rome, Italy
| | - Dolores Limongi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Open University, IRCCS San Raffaele Rome, 00166, Rome, Italy
| | - Carlo Zagaglia
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185, Rome, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore Di Sanità, 00161, Rome, Italy.,Department of Public Health and Infectious Diseases, Sapienza University of Rome, Laboratory affiliated to Institute Pasteur Italia- Cenci Bolognetti Foundation, 00185, Rome, Italy
| | - Cecilia Ambrosi
- Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Open University, IRCCS San Raffaele Rome, 00166, Rome, Italy.
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7
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London LY, Aubee JI, Nurse J, Thompson KM. Post-Transcriptional Regulation of RseA by Small RNAs RyhB and FnrS in Escherichia coli. Front Mol Biosci 2021; 8:668613. [PMID: 34805264 PMCID: PMC8595263 DOI: 10.3389/fmolb.2021.668613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022] Open
Abstract
RseA is the critical central regulator of the σE-dependent stress response in E. coli and other related bacteria. The synthesis of RseA is controlled at the transcriptional level by several promoters and transcriptional regulators, including σE itself at two σE-dependent promoters: rpoEP and rseAP3. The presence of these two independent polycistrons encoding rseA is potentially redundant. We hypothesized that post-transcriptional control of the rseAP3 transcript was necessary to overcome this redundancy. However, to date, nothing is known about the post-transcriptional control of the rseAP3 transcript. We executed a targeted genetic screen to identify small RNA regulators of the rseAP3 transcript and identified RyhB and FnrS as small RNA activators of the RseA P3 transcript. Through genetic analysis, we confirmed that a direct interaction occurs between RyhB and RseA. We also identified sequences within the 5′ untranslated region (UTR) of RseA that were inhibitory for RseA expression. Point mutations predicted to prevent an interaction between RyhB and RseA resulted in increased RseA expression. Taken together, this suggests that the 5’ UTR of the RseAP3 transcript prevents optimal expression of RseA, preventing redundancy due to RseA expression from the σE-dependent rpoEP, and this is overcome by the stimulatory activity of RyhB and FnrS.
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Affiliation(s)
- Laricca Y London
- Department of Biological and Environmental Sciences, Alabama A&M University, Huntsville, AL, United States
| | - Joseph I Aubee
- Department of Microbiology, College of Medicine, Howard University, Washington, DC, United States
| | - Jalisa Nurse
- Department of Microbiology, College of Medicine, Howard University, Washington, DC, United States.,Department of Biology, Howard University, Washington, DC, United States
| | - Karl M Thompson
- Department of Microbiology, College of Medicine, Howard University, Washington, DC, United States
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8
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Menghini S, Ho PS, Gwisai T, Schuerle S. Magnetospirillum magneticum as a Living Iron Chelator Induces TfR1 Upregulation and Decreases Cell Viability in Cancer Cells. Int J Mol Sci 2021; 22:ijms22020498. [PMID: 33419059 PMCID: PMC7825404 DOI: 10.3390/ijms22020498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/23/2020] [Accepted: 01/04/2021] [Indexed: 11/16/2022] Open
Abstract
Interest has grown in harnessing biological agents for cancer treatment as dynamic vectors with enhanced tumor targeting. While bacterial traits such as proliferation in tumors, modulation of an immune response, and local secretion of toxins have been well studied, less is known about bacteria as competitors for nutrients. Here, we investigated the use of a bacterial strain as a living iron chelator, competing for this nutrient vital to tumor growth and progression. We established an in vitro co-culture system consisting of the magnetotactic strain Magnetospirillum magneticum AMB-1 incubated under hypoxic conditions with human melanoma cells. Siderophore production by 108 AMB-1/mL in human transferrin (Tf)-supplemented media was quantified and found to be equivalent to a concentration of 3.78 µM ± 0.117 µM deferoxamine (DFO), a potent drug used in iron chelation therapy. Our experiments revealed an increased expression of transferrin receptor 1 (TfR1) and a significant decrease of cancer cell viability, indicating the bacteria’s ability to alter iron homeostasis in human melanoma cells. Our results show the potential of a bacterial strain acting as a self-replicating iron-chelating agent, which could serve as an additional mechanism reinforcing current bacterial cancer therapies.
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9
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Ajuzie DC, Arshad SA, Rasaputra KS, May EE. A Method for Deciphering Major Drivers of Bacterial Iron Stress Response in the Presence of Oxidative Stressors. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2020:2266-2269. [PMID: 33018459 DOI: 10.1109/embc44109.2020.9176518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This paper describes a method for deciphering major drivers of bacterial stress response using an empirically informed computational approach. We develop a working model of iron flux regulation and concomitant oxidative stress response in Escherichia coli. The integrated model is used to investigate the temporal effects of iron and hydrogen peroxide stress on bacterial growth and metabolism. We employ a sensitivity analysis platform and, using various measures, probe for major mechanistic drivers of the bacterial response to iron stress.
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10
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Krishnan J, Floros I. Adaptive information processing of network modules to dynamic and spatial stimuli. BMC SYSTEMS BIOLOGY 2019; 13:32. [PMID: 30866946 PMCID: PMC6417070 DOI: 10.1186/s12918-019-0703-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Adaptation and homeostasis are basic features of information processing in cells and seen in a broad range of contexts. Much of the current understanding of adaptation in network modules/motifs is based on their response to simple stimuli. Recently, there have also been studies of adaptation in dynamic stimuli. However a broader synthesis of how different circuits of adaptation function, and which circuits enable a broader adaptive behaviour in classes of more complex and spatial stimuli is largely missing. RESULTS We study the response of a variety of adaptive circuits to time-varying stimuli such as ramps, periodic stimuli and static and dynamic spatial stimuli. We find that a variety of responses can be seen in ramp stimuli, making this a basis for discriminating between even similar circuits. We also find that a number of circuits adapt exactly to ramp stimuli, and dissect these circuits to pinpoint what characteristics (architecture, feedback, biochemical aspects, information processing ingredients) allow for this. These circuits include incoherent feedforward motifs, inflow-outflow motifs and transcritical circuits. We find that changes in location in such circuits where a signal acts can result in non-adaptive behaviour in ramps, even though the location was associated with exact adaptation in step stimuli. We also demonstrate that certain augmentations of basic inflow-outflow motifs can alter the behaviour of the circuit from exact adaptation to non-adaptive behaviour. When subject to periodic stimuli, some circuits (inflow-outflow motifs and transcritical circuits) are able to maintain an average output independent of the characteristics of the input. We build on this to examine the response of adaptive circuits to static and dynamic spatial stimuli. We demonstrate how certain circuits can exhibit a graded response in spatial static stimuli with an exact maintenance of the spatial mean-value. Distinct features which emerge from the consideration of dynamic spatial stimuli are also discussed. Finally, we also build on these results to show how different circuits which show any combination of presence or absence of exact adaptation in ramps, exact mainenance of time average output in periodic stimuli and exact maintenance of spatial average of output in static spatial stimuli may be realized. CONCLUSIONS By studying a range of network circuits/motifs on one hand and a range of stimuli on the other, we isolate characteristics of these circuits (structural) which enable different degrees of exact adaptive and homeostatic behaviour in such stimuli, how they may be combined, and also identify cases associated with non-homeostatic behaviour. We also reveal constraints associated with locations where signals may act to enable homeostatic behaviour and constraints associated with augmentations of circuits. This consideration of multiple experimentally/naturally relevant stimuli along with circuits of adaptation of relevance in natural and engineered biology, provides a platform for deepening our understanding of adaptive and homeostatic behaviour in natural systems, bridging the gap between models of adaptation and experiments and in engineering homeostatic synthetic circuits.
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Affiliation(s)
- J Krishnan
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK.
| | - Ioannis Floros
- Department of Chemical Engineering, Centre for Process Systems Engineering, Imperial College London, South Kensington, London, SW7 2AZ, UK.,National Centre of Scientific Research "Demokritos", Athens, Greece
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11
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Bocci F, Jolly MK, Levine H, Onuchic JN. Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks. Methods Mol Biol 2019; 1912:341-366. [PMID: 30635901 DOI: 10.1007/978-1-4939-8982-9_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
RNA is mostly known for its role in protein synthesis, where it encodes information for protein sequence in its messenger RNA (mRNA) form (translation). Yet, RNA molecules regulate several cellular processes other than translation. Here, we present an overview of several mathematical models that help understanding and characterizing the role of noncoding RNA molecules (ncRNAs) in regulating gene expression and protein synthesis. First, we discuss relatively simple models where ncRNAs can modulate protein synthesis via targeting a mRNA. Then, we consider the case of feedback interactions between ncRNAs and their target proteins, and discuss several biological applications where these feedback architectures modulate a cellular phenotype and control the levels of intrinsic and extrinsic noise. Building from these simple circuit motifs, we examine feed-forward circuit motifs involving ncRNAs that generate precise spatial and temporal patterns of protein expression. Further, we investigate the competition between ncRNAs and other endogenous RNA molecules and show that the cross talk between coding and noncoding RNAs can form large genetic circuits that involve up to hundreds of chemical species. Finally, we discuss the role of ncRNAs in modulating cell-cell signaling pathways and therefore the dynamics of spatiotemporal pattern formation in a tissue.
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Affiliation(s)
- Federico Bocci
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA.,Department of Chemistry, Rice University, Houston, TX, USA
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Herbert Levine
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA. .,Department of Bioengineering, Rice University, Houston, TX, USA. .,Department of Physics and Astronomy, Rice University, Houston, TX, USA.
| | - José Nelson Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA. .,Department of Chemistry, Rice University, Houston, TX, USA. .,Department of Physics and Astronomy, Rice University, Houston, TX, USA. .,Department of Biosciences, Rice University, Houston, TX, USA.
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12
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A quasi-integral controller for adaptation of genetic modules to variable ribosome demand. Nat Commun 2018; 9:5415. [PMID: 30575748 PMCID: PMC6303309 DOI: 10.1038/s41467-018-07899-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 12/03/2018] [Indexed: 01/25/2023] Open
Abstract
The behavior of genetic circuits is often poorly predictable. A gene’s expression level is not only determined by the intended regulators, but also affected by changes in ribosome availability imparted by expression of other genes. Here we design a quasi-integral biomolecular feedback controller that enables the expression level of any gene of interest (GOI) to adapt to changes in available ribosomes. The feedback is implemented through a synthetic small RNA (sRNA) that silences the GOI’s mRNA, and uses orthogonal extracytoplasmic function (ECF) sigma factor to sense the GOI’s translation and to actuate sRNA transcription. Without the controller, the expression level of the GOI is reduced by 50% when a resource competitor is activated. With the controller, by contrast, gene expression level is practically unaffected by the competitor. This feedback controller allows adaptation of genetic modules to variable ribosome demand and thus aids modular construction of complicated circuits. Competition for shared cellular resources often renders genetic circuits poorly predictable. Here the authors design a biomolecular quasi-integral controller that allows gene expression to adapt to variable demand in translation resources.
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13
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Becker F, Wienand K, Lechner M, Frey E, Jung H. Interactions mediated by a public good transiently increase cooperativity in growing Pseudomonas putida metapopulations. Sci Rep 2018; 8:4093. [PMID: 29511247 PMCID: PMC5840296 DOI: 10.1038/s41598-018-22306-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 02/21/2018] [Indexed: 01/13/2023] Open
Abstract
Bacterial communities have rich social lives. A well-established interaction involves the exchange of a public good in Pseudomonas populations, where the iron-scavenging compound pyoverdine, synthesized by some cells, is shared with the rest. Pyoverdine thus mediates interactions between producers and non-producers and can constitute a public good. This interaction is often used to test game theoretical predictions on the "social dilemma" of producers. Such an approach, however, underestimates the impact of specific properties of the public good, for example consequences of its accumulation in the environment. Here, we experimentally quantify costs and benefits of pyoverdine production in a specific environment, and build a model of population dynamics that explicitly accounts for the changing significance of accumulating pyoverdine as chemical mediator of social interactions. The model predicts that, in an ensemble of growing populations (metapopulation) with different initial producer fractions (and consequently pyoverdine contents), the global producer fraction initially increases. Because the benefit of pyoverdine declines at saturating concentrations, the increase need only be transient. Confirmed by experiments on metapopulations, our results show how a changing benefit of a public good can shape social interactions in a bacterial population.
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Affiliation(s)
- Felix Becker
- Microbiology, Department Biology 1, Ludwig-Maximilians-Universität Munich, Grosshaderner Strasse 2-4, D-82152 Martinsried, Germany
| | - Karl Wienand
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for Nanoscience, Ludwig-Maximilians-Universität, Theresienstrasse 37, D-80333, Munich, Germany
| | - Matthias Lechner
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for Nanoscience, Ludwig-Maximilians-Universität, Theresienstrasse 37, D-80333, Munich, Germany
| | - Erwin Frey
- Arnold-Sommerfeld-Center for Theoretical Physics and Center for Nanoscience, Ludwig-Maximilians-Universität, Theresienstrasse 37, D-80333, Munich, Germany.
| | - Heinrich Jung
- Microbiology, Department Biology 1, Ludwig-Maximilians-Universität Munich, Grosshaderner Strasse 2-4, D-82152 Martinsried, Germany.
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Role and regulation of ferritin-like proteins in iron homeostasis and oxidative stress survival of Caulobacter crescentus. Biometals 2016; 29:851-62. [PMID: 27484774 DOI: 10.1007/s10534-016-9956-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/26/2016] [Indexed: 10/21/2022]
Abstract
Iron is an essential nutrient that is poorly available to living organisms but can be harmful when in excess due to the production of reactive oxygen species. Bacteria and other organisms use iron storage proteins called ferritins to avoid iron toxicity and as a safe iron source in the cytosol. The alpha-proteobacterium Caulobacter crescentus has two putative ferritins, Bfr and Dps, and some other proteins belonging to the ferritin-like superfamily, among them the one encoded by CC_0557. In this work, we have analyzed the role and regulation of these three putative ferritin-like proteins. Using lacZ-transcriptional fusions, we found that bfr expression is positively regulated (2.5-fold induction) by the Fe-responsive regulator Fur in iron sufficiency, as expected for an iron storage protein. Expression of dps was induced 1.5-fold in iron limitation in a Fur-independent manner, while the expression of the product of CC_0557 was unaffected by either iron supply or Fur. With respect to growth phase, while bfr expression was constant during growth, expression of dps (1.4-fold) and CC_0557 (around seven times) increased in the transition from exponential to stationary phase. Deletion mutant strains for each gene and a double dps/bfr mutant were obtained and tested for oxidative stress resistance. The dps mutant was very sensitive to H2O2, and this phenotype was not relieved by the addition of the iron chelator 2',2-dipyridyl in the conditions tested. While bfr and CC_0557 showed no phenotype as to H2O2 resistance, the double dps/bfr mutant had a similar phenotype to the dps mutation alone. These findings indicate that in C. crescentus Bfr contributes to iron homeostasis and Dps has a role in protection against oxidative stress. The role of the protein CC_0557 containing a ferritin-like fold remains unclear.
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Effects of Four Different Regulatory Mechanisms on the Dynamics of Gene Regulatory Cascades. Sci Rep 2015; 5:12186. [PMID: 26184971 PMCID: PMC4505322 DOI: 10.1038/srep12186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 05/27/2015] [Indexed: 11/24/2022] Open
Abstract
Gene regulatory cascades (GRCs) are common motifs in cellular molecular networks. A given logical function in these cascades, such as the repression of the activity of a transcription factor, can be implemented by a number of different regulatory mechanisms. The potential consequences for the dynamic performance of the GRC of choosing one mechanism over another have not been analysed systematically. Here, we report the construction of a synthetic GRC in Escherichia coli, which allows us for the first time to directly compare and contrast the dynamics of four different regulatory mechanisms, affecting the transcription, translation, stability, or activity of a transcriptional repressor. We developed a biologically motivated mathematical model which is sufficient to reproduce the response dynamics determined by experimental measurements. Using the model, we explored the potential response dynamics that the constructed GRC can perform. We conclude that dynamic differences between regulatory mechanisms at an individual step in a GRC are often concealed in the overall performance of the GRC, and suggest that the presence of a given regulatory mechanism in a certain network environment does not necessarily mean that it represents a single optimal evolutionary solution.
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A 3′ External Transcribed Spacer in a tRNA Transcript Acts as a Sponge for Small RNAs to Prevent Transcriptional Noise. Mol Cell 2015; 58:393-405. [DOI: 10.1016/j.molcel.2015.03.013] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 02/13/2015] [Accepted: 03/09/2015] [Indexed: 10/23/2022]
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Abstract
The concept of the minimal cell has fascinated scientists for a long time, from both fundamental and applied points of view. This broad concept encompasses extreme reductions of genomes, the last universal common ancestor (LUCA), the creation of semiartificial cells, and the design of protocells and chassis cells. Here we review these different areas of research and identify common and complementary aspects of each one. We focus on systems biology, a discipline that is greatly facilitating the classical top-down and bottom-up approaches toward minimal cells. In addition, we also review the so-called middle-out approach and its contributions to the field with mathematical and computational models. Owing to the advances in genomics technologies, much of the work in this area has been centered on minimal genomes, or rather minimal gene sets, required to sustain life. Nevertheless, a fundamental expansion has been taking place in the last few years wherein the minimal gene set is viewed as a backbone of a more complex system. Complementing genomics, progress is being made in understanding the system-wide properties at the levels of the transcriptome, proteome, and metabolome. Network modeling approaches are enabling the integration of these different omics data sets toward an understanding of the complex molecular pathways connecting genotype to phenotype. We review key concepts central to the mapping and modeling of this complexity, which is at the heart of research on minimal cells. Finally, we discuss the distinction between minimizing the number of cellular components and minimizing cellular complexity, toward an improved understanding and utilization of minimal and simpler cells.
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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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Seo SW, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO. Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli. Nat Commun 2014; 5:4910. [PMID: 25222563 PMCID: PMC4167408 DOI: 10.1038/ncomms5910] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 08/05/2014] [Indexed: 02/07/2023] Open
Abstract
The ferric uptake regulator (Fur) plays a critical role in the transcriptional regulation of iron metabolism. However, the full regulatory potential of Fur remains undefined. Here we comprehensively reconstruct the Fur transcriptional regulatory network in Escherichia coli K-12 MG1655 in response to iron availability using genome-wide measurements (ChIP-exo and RNA-seq). Integrative data analysis reveals that a total of 81 genes in 42 transcription units are directly regulated by three different modes of Fur regulation, including apo- and holo-Fur activation and holo-Fur repression. We show that Fur connects iron transport and utilization enzymes with negative-feedback loop pairs for iron homeostasis. In addition, direct involvement of Fur in the regulation of DNA synthesis, energy metabolism, and biofilm development is found. These results show how Fur exhibits a comprehensive regulatory role affecting many fundamental cellular processes linked to iron metabolism in order to coordinate the overall response of E. coli to iron availability.
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Affiliation(s)
- Sang Woo Seo
- 1] Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA [2]
| | - Donghyuk Kim
- 1] Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA [2]
| | - Haythem Latif
- 1] Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA [2]
| | - Edward J O'Brien
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA
| | - Richard Szubin
- Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA
| | - Bernhard O Palsson
- 1] Department of Bioengineering, University of California San Diego, La Jolla, California 92093-0412, USA [2] Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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Alcanivorax borkumensis produces an extracellular siderophore in iron-limitation condition maintaining the hydrocarbon-degradation efficiency. Mar Genomics 2014; 17:43-52. [PMID: 25088485 DOI: 10.1016/j.margen.2014.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/20/2014] [Accepted: 07/21/2014] [Indexed: 11/20/2022]
Abstract
Obligate marine hydrocarbonoclastic bacteria possess genetic and physiological features to use hydrocarbons as sole source of carbon and to compete for the uptake of nutrients in usually nutrient-depleted marine habitats. In the present work we have studied the siderophore-based iron uptake systems in Alcanivorax borkumensis SK2 and their functioning during biodegradation of an aliphatic hydrocarbon, tetradecane, under iron limitation conditions. The antiSMASH analysis of SK2 genome revealed the presence of two different putative operons of siderophore synthetases. Search for the predicted core structures indicated that one siderophore is clearly affiliated to the family of complex oligopeptidic siderophores possessing an Orn-Ser-Orn carboxyl motif whereas the second one is likely to belong to the family of SA (salicylic acid)-based siderophores. Analyzing the supernatant of SK2 culture, an extracellular siderophore was identified and its structure was resolved. Thus, along with the recently described membrane-associated amphiphilic tetrapeptidic siderophore amphibactin, strain SK2 additionally produces an extracellular type of iron-chelating molecule with structural similarity to pseudomonins. Comparative Q-PCR analysis of siderophore synthetases demonstrated their significant up-regulation in iron-depleted medium. Different expression patterns were recorded for two operons during the early and late exponential phases of growth, suggesting a different function of these two siderophores under iron-depleted conditions.
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A mixed incoherent feed-forward loop allows conditional regulation of response dynamics. PLoS One 2014; 9:e91243. [PMID: 24621982 PMCID: PMC3951346 DOI: 10.1371/journal.pone.0091243] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Accepted: 02/11/2014] [Indexed: 12/21/2022] Open
Abstract
Expression of the SodA superoxide dismutase (MnSOD) in Escherichia coli is regulated by superoxide concentration through the SoxRS system and also by Fur (Ferric uptake regulator) through a mixed incoherent feed forward loop (FFL) containing the RyhB small regulatory RNA. In this work I theoretically analyze the function of this feed forward loop as part of the network controlling expression of the two cytoplasmic superoxide dismutases, SodA and SodB. I find that feed forward regulation allows faster response to superoxide stress at low intracellular iron levels compared to iron rich conditions. That is, it can conditionally modulate the response time of a superimposed transcriptional control mechanism.
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22
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Ishchukov I, Wu Y, Van Puyvelde S, Vanderleyden J, Marchal K. Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia. BMC Microbiol 2014; 14:14. [PMID: 24467879 PMCID: PMC3948049 DOI: 10.1186/1471-2180-14-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 01/09/2014] [Indexed: 12/21/2022] Open
Abstract
Background Publicly available expression compendia that measure both mRNAs and sRNAs provide a promising resource to simultaneously infer the transcriptional and the posttranscriptional network. To maximally exploit the information contained in such compendia, we propose an analysis flow that combines publicly available expression compendia and sequence-based predictions to infer novel sRNA-target interactions and to reconstruct the relation between the sRNA and the transcriptional network. Results We relied on module inference to construct modules of coexpressed genes (sRNAs). TFs and sRNAs were assigned to these modules using the state-of-the-art inference techniques LeMoNe and Context Likelihood of Relatedness (CLR). Combining these expressions with sequence-based sRNA-target interactions allowed us to predict 30 novel sRNA-target interactions comprising 14 sRNAs. Our results highlight the role of the posttranscriptional network in finetuning the transcriptional regulation, e.g. by intra-operonic regulation. Conclusion In this work we show how strategies that combine expression information with sequence-based predictions can help unveiling the intricate interaction between the transcriptional and the posttranscriptional network in prokaryotic model systems.
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Affiliation(s)
| | | | | | | | - Kathleen Marchal
- Center of Microbial and Plant Genetics, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium.
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23
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Regulation Systems of Bacteria such as Escherichia coli in Response to Nutrient Limitation and Environmental Stresses. Metabolites 2013; 4:1-35. [PMID: 24958385 PMCID: PMC4018673 DOI: 10.3390/metabo4010001] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/18/2013] [Accepted: 12/06/2013] [Indexed: 11/16/2022] Open
Abstract
An overview was made to understand the regulation system of a bacterial cell such as Escherichia coli in response to nutrient limitation such as carbon, nitrogen, phosphate, sulfur, ion sources, and environmental stresses such as oxidative stress, acid shock, heat shock, and solvent stresses. It is quite important to understand how the cell detects environmental signals, integrate such information, and how the cell system is regulated. As for catabolite regulation, F1,6B P (FDP), PEP, and PYR play important roles in enzyme level regulation together with transcriptional regulation by such transcription factors as Cra, Fis, CsrA, and cAMP-Crp. αKG plays an important role in the coordinated control between carbon (C)- and nitrogen (N)-limitations, where αKG inhibits enzyme I (EI) of phosphotransferase system (PTS), thus regulating the glucose uptake rate in accordance with N level. As such, multiple regulation systems are co-ordinated for the cell synthesis and energy generation against nutrient limitations and environmental stresses. As for oxidative stress, the TCA cycle both generates and scavenges the reactive oxygen species (ROSs), where NADPH produced at ICDH and the oxidative pentose phosphate pathways play an important role in coping with oxidative stress. Solvent resistant mechanism was also considered for the stresses caused by biofuels and biochemicals production in the cell.
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24
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Norsworthy AN, Visick KL. Gimme shelter: how Vibrio fischeri successfully navigates an animal's multiple environments. Front Microbiol 2013; 4:356. [PMID: 24348467 PMCID: PMC3843225 DOI: 10.3389/fmicb.2013.00356] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/09/2013] [Indexed: 12/19/2022] Open
Abstract
Bacteria successfully colonize distinct niches because they can sense and appropriately respond to a variety of environmental signals. Of particular interest is how a bacterium negotiates the multiple, complex environments posed during successful infection of an animal host. One tractable model system to study how a bacterium manages a host’s multiple environments is the symbiotic relationship between the marine bacterium, Vibrio fischeri, and its squid host, Euprymna scolopes. V. fischeri encounters many different host surroundings ranging from initial contact with the squid to ultimate colonization of a specialized organ known as the light organ. For example, upon recognition of the squid, V. fischeri forms a biofilm aggregate outside the light organ that is required for efficient colonization. The bacteria then disperse from this biofilm to enter the organ, where they are exposed to nitric oxide, a molecule that can act as both a signal and an antimicrobial. After successfully managing this potentially hostile environment, V. fischeri cells finally establish their niche in the deep crypts of the light organ where the bacteria bioluminesce in a pheromone-dependent fashion, a phenotype that E. scolopes utilizes for anti-predation purposes. The mechanism by which V. fischeri manages these environments to outcompete all other bacterial species for colonization of E. scolopes is an important and intriguing question that will permit valuable insights into how a bacterium successfully associates with a host. This review focuses on specific molecular pathways that allow V. fischeri to establish this exquisite bacteria–host interaction.
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Affiliation(s)
- Allison N Norsworthy
- Department of Microbiology and Immunology, Loyola University Medical Center Maywood, IL, USA
| | - Karen L Visick
- Department of Microbiology and Immunology, Loyola University Medical Center Maywood, IL, USA
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25
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Li F, Wang Y, Gong K, Wang Q, Liang Q, Qi Q. Constitutive expression of RyhB regulates the heme biosynthesis pathway and increases the 5-aminolevulinic acid accumulation in Escherichia coli. FEMS Microbiol Lett 2013; 350:209-15. [PMID: 24188714 DOI: 10.1111/1574-6968.12322] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 01/25/2023] Open
Abstract
In the current study, the small RNA ryhB, which regulates the metabolism of iron in Escherichia coli, was constitutively expressed in engineered E. coli DALA. The resulting strain E. coli DALRA produced 16% more 5-aminolevulinic acid (ALA) than the parent strain E. coli DALA in batch fermentation. Meanwhile, we found that addition of iron in the medium increased heme formation and reduced ALA yield, whereas the presence of iron chelator in the medium decreased heme concentration and increased the ALA production efficiency (ALA yield per OD600). The qRT-PCR analysis showed that the mRNA levels of hemB and hemH were also decreased as well as the known RyhB target genes of acnAB, sdhAB, fumA, and cydAB in E. coli DALRA. These results indicated that small RNA can be used as a tool for regulating ALA accumulation in E. coli.
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Affiliation(s)
- Fangfang Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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26
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Intracellular free iron and its potential role in ultrahigh-pressure-induced inactivation of Escherichia coli. Appl Environ Microbiol 2012; 79:722-4. [PMID: 23124235 DOI: 10.1128/aem.02202-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intracellular free iron of Escherichia coli was determined by whole-cell electron paramagnetic resonance spectrometry. Ultrahigh pressure (UHP) increased both intracellular free iron and cell lethality in a pressure-dose-dependent manner. The iron chelator 2,2'-dipyridyl protected cells against UHP treatments. A mutation that produced iron overload conditions sensitized E. coli to UHP treatment.
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27
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A self-organized model for cell-differentiation based on variations of molecular decay rates. PLoS One 2012; 7:e36679. [PMID: 22693554 PMCID: PMC3365067 DOI: 10.1371/journal.pone.0036679] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 04/11/2012] [Indexed: 11/19/2022] Open
Abstract
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation characteristic to living systems. At any point in time only small subsets of these networks are active. Any active subset of the GRN leads to the expression of particular sets of molecules (expression modes). The subsets of active networks change over time, leading to the observed complex dynamics of expression patterns. Understanding of these dynamics becomes increasingly important in systems biology and medicine. While the importance of transcription rates and catalytic interactions has been widely recognized in modeling genetic regulatory systems, the understanding of the role of degradation of biochemical agents (mRNA, protein) in regulatory dynamics remains limited. Recent experimental data suggests that there exists a functional relation between mRNA and protein decay rates and expression modes. In this paper we propose a model for the dynamics of successions of sequences of active subnetworks of the GRN. The model is able to reproduce key characteristics of molecular dynamics, including homeostasis, multi-stability, periodic dynamics, alternating activity, differentiability, and self-organized critical dynamics. Moreover the model allows to naturally understand the mechanism behind the relation between decay rates and expression modes. The model explains recent experimental observations that decay-rates (or turnovers) vary between differentiated tissue-classes at a general systemic level and highlights the role of intracellular decay rate control mechanisms in cell differentiation.
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López G, Latorre M, Reyes-Jara A, Cambiazo V, González M. Transcriptomic response of Enterococcus faecalis to iron excess. Biometals 2012; 25:737-47. [DOI: 10.1007/s10534-012-9539-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 03/07/2012] [Indexed: 11/28/2022]
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Cho BK, Federowicz S, Park YS, Zengler K, Palsson BØ. Deciphering the transcriptional regulatory logic of amino acid metabolism. Nat Chem Biol 2011; 8:65-71. [PMID: 22082910 DOI: 10.1038/nchembio.710] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 08/27/2011] [Indexed: 11/09/2022]
Abstract
Although metabolic networks have been reconstructed on a genome scale, the corresponding reconstruction and integration of governing transcriptional regulatory networks has not been fully achieved. Here we reconstruct such an integrated network for amino acid metabolism in Escherichia coli. Analysis of ChIP-chip and gene expression data for the transcription factors ArgR, Lrp and TrpR showed that 19 out of 20 amino acid biosynthetic pathways are either directly or indirectly controlled by these regulators. Classifying the regulated genes into three functional categories of transport, biosynthesis and metabolism leads to the elucidation of regulatory motifs that constitute the integrated network's basic building blocks. The regulatory logic of these motifs was determined on the basis of relationships between transcription factor binding and changes in the amount of transcript in response to exogenous amino acids. Remarkably, the resulting logic shows how amino acids are differentiated as signaling and nutrient molecules, revealing the overarching regulatory principles of the amino acid stimulon.
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Affiliation(s)
- Byung-Kwan Cho
- Department of Bioengineering, University of California at San Diego, La Jolla, California, USA.
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Mitchell RJ, Lee SK, Kim T, Ghim CM. Microbial linguistics: perspectives and applications of microbial cell-to-cell communication. BMB Rep 2011; 44:1-10. [PMID: 21266100 DOI: 10.5483/bmbrep.2011.44.1.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent "autoinducer" molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions.
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Affiliation(s)
- Robert J Mitchell
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
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Abstract
During the last decade small regulatory RNA (srRNA) emerged as central players in the regulation of gene expression in all kingdoms of life. Multiple pathways for srRNA biogenesis and diverse mechanisms of gene regulation may indicate that srRNA regulation evolved independently multiple times. However, small RNA pathways share numerous properties, including the ability of a single srRNA to regulate multiple targets. Some of the mechanisms of gene regulation by srRNAs have significant effect on the abundance of free srRNAs that are ready to interact with new targets. This results in indirect interactions among seemingly unrelated genes, as well as in a crosstalk between different srRNA pathways. Here we briefly review and compare the major srRNA pathways, and argue that the impact of srRNA is always at the system level. We demonstrate how a simple mathematical model can ease the discussion of governing principles. To demonstrate these points we review a few examples from bacteria and animals.
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Affiliation(s)
- Daniel Jost
- Department of Physics, FAS Center for Systems Biology, Harvard University, Cambridge MA 02138, USA
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Achcar F, Camadro JM, Mestivier D. A Boolean probabilistic model of metabolic adaptation to oxygen in relation to iron homeostasis and oxidative stress. BMC SYSTEMS BIOLOGY 2011; 5:51. [PMID: 21489274 PMCID: PMC3094212 DOI: 10.1186/1752-0509-5-51] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Accepted: 04/13/2011] [Indexed: 01/16/2023]
Abstract
Background In aerobically grown cells, iron homeostasis and oxidative stress are tightly linked processes implicated in a growing number of diseases. The deregulation of iron homeostasis due to gene defects or environmental stresses leads to a wide range of diseases with consequences for cellular metabolism that remain poorly understood. The modelling of iron homeostasis in relation to the main features of metabolism, energy production and oxidative stress may provide new clues to the ways in which changes in biological processes in a normal cell lead to disease. Results Using a methodology based on probabilistic Boolean modelling, we constructed the first model of yeast iron homeostasis including oxygen-related reactions in the frame of central metabolism. The resulting model of 642 elements and 1007 reactions was validated by comparing simulations with a large body of experimental results (147 phenotypes and 11 metabolic flux experiments). We removed every gene, thus generating in silico mutants. The simulations of the different mutants gave rise to a remarkably accurate qualitative description of most of the experimental phenotype (overall consistency > 91.5%). A second validation involved analysing the anaerobiosis to aerobiosis transition. Therefore, we compared the simulations of our model with different levels of oxygen to experimental metabolic flux data. The simulations reproducted accurately ten out of the eleven metabolic fluxes. We show here that our probabilistic Boolean modelling strategy provides a useful description of the dynamics of a complex biological system. A clustering analysis of the simulations of all in silico mutations led to the identification of clear phenotypic profiles, thus providing new insights into some metabolic response to stress conditions. Finally, the model was also used to explore several new hypothesis in order to better understand some unexpected phenotypes in given mutants. Conclusions All these results show that this model, and the underlying modelling strategy, are powerful tools for improving our understanding of complex biological problems.
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Affiliation(s)
- Fiona Achcar
- Modelling in Integrative Biology, Institut Jacques Monod - UMR7592 - CNRS - Univ. Paris-Diderot, Paris, France
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Kumar R, Shimizu K. Transcriptional regulation of main metabolic pathways of cyoA, cydB, fnr, and fur gene knockout Escherichia coli in C-limited and N-limited aerobic continuous cultures. Microb Cell Fact 2011; 10:3. [PMID: 21272324 PMCID: PMC3037301 DOI: 10.1186/1475-2859-10-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 01/27/2011] [Indexed: 01/09/2023] Open
Abstract
Background It is important to understand the cellular responses emanating from environmental perturbations to redesign the networks for practical applications. In particular, the carbon (C) metabolism, nitrogen (N) assimilation, and energy generation are by far important, where those are interconnected and integrated to maintain cellular integrity. In our previous study, we investigated the effect of C/N ratio on the metabolic regulation of gdhA, glnL, glt B,D mutants as well as wild type Escherichia coli (Kumar and Shimizu, MCF, 1-17, 9:8,2010), where it was shown that the transcript levels of cyoA and cydB which encode the terminal oxidases, fnr and fur which encode global regulators were significantly up-regulated under N-limited condition as compared to C-limited condition. In the present study, therefore, the effects of such single-gene knockout on the metabolic regulation were investigated to clarify the roles of those genes in the aerobic continuous culture at the dilution rate of 0.2 h-1. Results The specific glucose consumption rates and the specific CO2 production rates of cyoA, cydB, fnr, and fur mutants were all increased as compared to the wild type under both C-limited and N-limited conditions. The former phenomenon was consistent with the up-regulations of the transcript levels of ptsG and ptsH, which are consistent with down-regulations of crp and mlc genes. Moreover, the increase in the specific glucose consumption rate was also caused by up-regulations of the transcript levels of pfkA, pykF and possibly zwf, where those are consistent with the down regulations of cra, crp and mlc genes. Moreover, the transcript levels of rpoN together with glnK, glnB, glnE were up-regulated, and thus the transcript levels of glnA,L,G, and gltB,D as well as nac were up-regulated, while gdhA was down-regulated. This implies the interconnection between cAMP-Crp and PII-Ntr systems. Moreover, cyoA, cydB, fnr and fur gene deletions up-regulated the transcript levels of respiration (nuoA, ndh, cyoA, cydB, and atpA) and the oxidative stress related genes such as soxR, S and sodA, where this was further enhanced under N-limitation. In the cases of cyoA and cydB mutants, arcA, fnr, fur, cydB (for cyoA mutant), and cyoA (for cydB mutant) genes were up-regulated, which may be due to incomplete oxidation of quinol. It was also shown that fur gene transcript level was up-regulated in accordance with the activation of respiratory chain genes. It was shown that the deletion of fur gene activated the enterobactin pathway. Conclusion The present result demonstrated how the fermentation characteristics could be explained by the transcript levels of metabolic pathway genes as well as global regulators in relation to the knockout of such single genes as cyoA, cydB, fnr, and fur, and clarified the complex gene network regulation in relation to glycolysis, TCA cycle, respiration, and N-regulated pathways. The present result is quite important in understanding the metabolic regulation for metabolic engineering. Moreover, the present result may be useful in improving the specific glucose consumption rate and activation of the TCA cycle by modulating the respiratory chain genes and the related global regulators. The result obtained under N-limited condition may be useful for the heterologous protein production under N-limitation.
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Affiliation(s)
- Rahul Kumar
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
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Induction of a state of iron limitation in uropathogenic Escherichia coli CFT073 by cranberry-derived proanthocyanidins as revealed by microarray analysis. Appl Environ Microbiol 2010; 77:1532-5. [PMID: 21169441 DOI: 10.1128/aem.02201-10] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transcriptional profiles of uropathogenic Escherichia coli CFT073 exposed to cranberry-derived proanthocyanidins (PACs) were determined. Our results indicate that bacteria grown on media supplemented with PACs were iron deprived. To our knowledge, this is the first time that PACs have been shown to induce a state of iron limitation in this bacterium.
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35
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Hao Y, Xu L, Shi H. Theoretical analysis of catalytic-sRNA-mediated gene silencing. J Mol Biol 2010; 406:195-204. [PMID: 21145897 DOI: 10.1016/j.jmb.2010.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2010] [Revised: 11/17/2010] [Accepted: 12/01/2010] [Indexed: 11/28/2022]
Abstract
Small regulatory RNA (sRNA) that acts by an antisense mechanism is critical for gene regulation at the posttranscriptional level. Recently, an Hfq-dependent sRNA named MicM, which is related to the regulation of outer membrane protein, was verified as a novel antisense sRNA due to its catalytic mode of regulation. Here we propose a simple kinetic model for the enzyme-like regulation mode of sRNA and study in detail the noise properties of the target gene under various recycling rates of the regulator. We predict that the recycling rate of sRNA and other relative parameters have significant influence on the noise strength of target expression. In comparison with the stoichiometric regulatory mode, a lesser fluctuation of target expression was observed near the threshold at which the transcription rates of both sRNA and target mRNA equal each other. We also found that the new mode is better in terms of rapid response to external signals. However, it needs more time to achieve target recovery if the stimulating signal disappears. Additionally, the obtained time evolution results of the MicM-ybfM interaction system based on our model are consistent with previous experimental results, serving as experimental evidence to back up our theoretical analysis.
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Affiliation(s)
- Yue Hao
- Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100190, China
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36
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Abstract
In eukaryotic cells, many genes are transcribed into noncoding RNAs. Such RNAs may associate with mRNAs and inhibit their translation and facilitate degradation. To clarify what may happen in this case, we propose a kinetic model describing the effect of noncoding RNAs on a mRNA-protein network with the hierarchical three-layer architecture. For positive regulation of the layers, our model predicts either bistability with a fairly narrow hysteresis loop or a unique steady state. For negative or mixed regulation, the steady state is found to be unique.
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Affiliation(s)
- Vladimir P Zhdanov
- Department of Applied Physics, Chalmers University of Technology, S-41296 Göteborg, Sweden.
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37
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Abstract
The function of living cells is controlled by complex regulatory networks that are built of a wide diversity of interacting molecular components. The sheer size and intricacy of molecular networks of even the simplest organisms are obstacles toward understanding network functionality. This review discusses the achievements and promise of a bottom-up approach that uses well-characterized subnetworks as model systems for understanding larger networks. It highlights the interplay between the structure, logic, and function of various types of small regulatory circuits. The bottom-up approach advocates understanding regulatory networks as a collection of entangled motifs. We therefore emphasize the potential of negative and positive feedback, as well as their combinations, to generate robust homeostasis, epigenetics, and oscillations.
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Affiliation(s)
- Kim Sneppen
- Niels Bohr Institute, DK-2100, Copenhagen, Denmark.
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38
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Wang Y, Dufour YS, Carlson HK, Donohue TJ, Marletta MA, Ruby EG. H-NOX-mediated nitric oxide sensing modulates symbiotic colonization by Vibrio fischeri. Proc Natl Acad Sci U S A 2010; 107:8375-80. [PMID: 20404170 PMCID: PMC2889544 DOI: 10.1073/pnas.1003571107] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bioluminescent bacterium Vibrio fischeri initiates a specific, persistent symbiosis in the light organ of the squid Euprymna scolopes. During the early stages of colonization, V. fischeri is exposed to host-derived nitric oxide (NO). Although NO can be both an antimicrobial component of innate immunity and a key signaling molecule in eukaryotes, potential roles in beneficial host-microbe associations have not been described. V. fischeri hnoX encodes a heme NO/oxygen-binding (H-NOX) protein, a member of a family of bacterial NO- and/or O(2)-binding proteins of unknown function. We hypothesized that H-NOX acts as a NO sensor that is involved in regulating symbiosis-related genes early in colonization. Whole-genome expression studies identified 20 genes that were repressed in an NO- and H-NOX-dependent fashion. Ten of these, including hemin-utilization genes, have a promoter with a putative ferric-uptake regulator (Fur) binding site. As predicted, in the presence of NO, wild-type V. fischeri grew more slowly on hemin than a hnoX deletion mutant. Host-colonization studies showed that the hnoX mutant was also 10-fold more efficient in initially colonizing the squid host than the wild type; similarly, in mixed inoculations, it outcompeted the wild-type strain by an average of 16-fold after 24 h. However, the presence of excess hemin or iron reversed this dominance. The advantage of the mutant in colonizing the iron-limited light-organ tissues is caused, at least in part, by its greater ability to acquire host-derived hemin. Our data suggest that V. fischeri normally senses a host-generated NO signal through H-NOX(Vf) and modulates the expression of its iron uptake capacity during the early stages of the light-organ symbiosis.
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Affiliation(s)
- Yanling Wang
- Departments of Medical Microbiology and Immunology and
| | - Yann S. Dufour
- Bacteriology, University of Wisconsin, Madison, WI 53706; and
| | | | | | - Michael A. Marletta
- Departments of Chemistry and
- Molecular and Cell Biology, University of California, Berkeley, CA 94720
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Amir A, Meshner S, Beatus T, Stavans J. Damped oscillations in the adaptive response of the iron homeostasis network ofE. coli. Mol Microbiol 2010; 76:428-36. [DOI: 10.1111/j.1365-2958.2010.07111.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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40
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Dynamic features of gene expression control by small regulatory RNAs. Proc Natl Acad Sci U S A 2009; 106:10655-9. [PMID: 19541626 DOI: 10.1073/pnas.0901466106] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Small regulatory RNAs (sRNAs) in eukaryotes and bacteria play an important role in the regulation of gene expression either by binding to regulatory proteins or directly to target mRNAs. Two of the best-characterized bacterial sRNAs, Spot42 and RyhB, form a complementary pair with the ribosome binding region of their target mRNAs, thereby inhibiting translation or promoting mRNA degradation. To investigate the steady-state and dynamic potential of such sRNAs, we examine the 2 key parameters characterizing sRNA regulation: the capacity to overexpress the sRNA relative to its target mRNA and the speed at which the target mRNA is irreversibly inactivated. We demonstrate different methods to determine these 2 key parameters, for Spot42 and RyhB, which combine biochemical and genetic experiments with computational analysis. We have developed a mathematical model that describes the functional properties of sRNAs with various characteristic parameters. We observed that Spot42 and RyhB function in distinctive parameter regimes, which result in divergent mechanisms.
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Krishna S, Semsey S, Jensen MH. Frustrated bistability as a means to engineer oscillations in biological systems. Phys Biol 2009; 6:036009. [PMID: 19461130 DOI: 10.1088/1478-3975/6/3/036009] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Oscillations play an important physiological role in a variety of biological systems. For example, respiration and carbohydrate synthesis are coupled to the circadian clock in cyanobacteria (Ishiura et al 1998 Science 281 1519) and ultradian oscillations with time periods of a few hours have been observed in immune response (NF-kappaB, Hoffmann et al 2002 Science 298 1241, Neson et al 2004 Science 306 704), apoptosis (p53, Lahav et al 2004 Nat. Genet. 36 53), development (Hes, Hirata et al 2002 Science 298 840) and growth hormone secretion (Plotsky and Vale 1985 Science 230 461, Zeitler et al 1991 Proc. Natl. Acad. Sci. USA 88 8920). Here we discuss how any bistable system can be 'frustrated' to produce oscillations of a desired nature--we use the term frustration, in analogy to frustrated spins in antiferromagnets, to refer to the addition of a negative feedback loop that destabilizes the bistable system. We show that the molecular implementation can use a wide variety of methods ranging from translation regulation, using small non-coding RNAs, to targeted protein modification to transcriptional regulation. We also introduce a simple graphical method for determining whether a particular implementation will produce oscillations. The shape of the resulting oscillations can be readily tuned to produce spiky and asymmetric oscillations--quite different from the shapes produced by synthetic oscillators (Elowitz and Leibler 2000 Nature 403 335, Fung et al 2005 Nature 435 118). The time period and amplitude can also be manipulated and these oscillators are easy to reset or switch on and off using a tunable external input. The mechanism of frustrated bistability could thus prove to be an easily implementable way to synthesize flexible, designable oscillators.
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Affiliation(s)
- S Krishna
- Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark.
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42
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Werner M, Semsey S, Sneppen K, Krishna S. Dynamics of uptake and metabolism of small molecules in cellular response systems. PLoS One 2009; 4:e4923. [PMID: 19290058 PMCID: PMC2654506 DOI: 10.1371/journal.pone.0004923] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 02/05/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Proper cellular function requires uptake of small molecules from the environment. In response to changes in extracellular conditions cells alter the import and utilization of small molecules. For a wide variety of small molecules the cellular response is regulated by a network motif that combines two feedback loops, one which regulates the transport and the other which regulates the subsequent metabolism. RESULTS We analyze the dynamic behavior of two widespread but logically distinct two-loop motifs. These motifs differ in the logic of the feedback loop regulating the uptake of the small molecule. Our aim is to examine the qualitative features of the dynamics of these two classes of feedback motifs. We find that the negative feedback to transport is accompanied by overshoot in the intracellular amount of small molecules, whereas a positive feedback to transport removes overshoot by boosting the final steady state level. On the other hand, the negative feedback allows for a rapid initial response, whereas the positive feedback is slower. We also illustrate how the dynamical deficiencies of one feedback motif can be mitigated by an additional loop, while maintaining the original steady-state properties. CONCLUSIONS Our analysis emphasizes the core of the regulation found in many motifs at the interface between the metabolic network and the environment of the cell. By simplifying the regulation into uptake and the first metabolic step, we provide a basis for elaborate studies of more realistic network structures. Particularly, this theoretical analysis predicts that FeS cluster formation plays an important role in the dynamics of iron homeostasis.
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Affiliation(s)
- Maria Werner
- Department of Computational Biology, Royal Institute of Technology, Albanova University Center, Stockholm, Sweden.
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Ghim CM, Almaas E. Genetic noise control via protein oligomerization. BMC SYSTEMS BIOLOGY 2008; 2:94. [PMID: 18980697 PMCID: PMC2584638 DOI: 10.1186/1752-0509-2-94] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2008] [Accepted: 11/03/2008] [Indexed: 11/10/2022]
Abstract
BACKGROUND Gene expression in a cell entails random reaction events occurring over disparate time scales. Thus, molecular noise that often results in phenotypic and population-dynamic consequences sets a fundamental limit to biochemical signaling. While there have been numerous studies correlating the architecture of cellular reaction networks with noise tolerance, only a limited effort has been made to understand the dynamic role of protein-protein interactions. RESULTS We have developed a fully stochastic model for the positive feedback control of a single gene, as well as a pair of genes (toggle switch), integrating quantitative results from previous in vivo and in vitro studies. In particular, we explicitly account for the fast binding-unbinding kinetics among proteins, RNA polymerases, and the promoter/operator sequences of DNA. We find that the overall noise-level is reduced and the frequency content of the noise is dramatically shifted to the physiologically irrelevant high-frequency regime in the presence of protein dimerization. This is independent of the choice of monomer or dimer as transcription factor and persists throughout the multiple model topologies considered. For the toggle switch, we additionally find that the presence of a protein dimer, either homodimer or heterodimer, may significantly reduce its random switching rate. Hence, the dimer promotes the robust function of bistable switches by preventing the uninduced (induced) state from randomly being induced (uninduced). CONCLUSION The specific binding between regulatory proteins provides a buffer that may prevent the propagation of fluctuations in genetic activity. The capacity of the buffer is a non-monotonic function of association-dissociation rates. Since the protein oligomerization per se does not require extra protein components to be expressed, it provides a basis for the rapid control of intrinsic or extrinsic noise. The stabilization of regulatory circuits and epigenetic memory in general is of direct implications to organism fitness. Our results also suggest possible avenues for the design of synthetic gene circuits with tunable robustness for a wide range of engineering purposes.
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Affiliation(s)
- Cheol-Min Ghim
- Microbial Systems Biology Group, Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Avenue Livermore, CA 94550, USA.
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44
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Mehta P, Goyal S, Wingreen NS. A quantitative comparison of sRNA-based and protein-based gene regulation. Mol Syst Biol 2008; 4:221. [PMID: 18854820 PMCID: PMC2583084 DOI: 10.1038/msb.2008.58] [Citation(s) in RCA: 160] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Accepted: 09/05/2008] [Indexed: 11/23/2022] Open
Abstract
Small non-coding RNAs (sRNAs) have important functions as genetic regulators in prokaryotes. sRNAs act post-transcriptionally through complementary pairing with target mRNAs to regulate protein expression. We use a quantitative approach to compare and contrast sRNAs with conventional transcription factors (TFs) to better understand the advantages of each form of regulation. In particular, we calculate the steady-state behavior, noise properties, frequency-dependent gain (amplification), and dynamical response to large input signals of both forms of regulation. Although the mean steady-state behavior of sRNA-regulated proteins exhibits a distinctive tunable threshold linear behavior, our analysis shows that transcriptional bursting leads to significantly higher intrinsic noise in sRNA-based regulation than in TF-based regulation in a large range of expression levels and limits the ability of sRNAs to perform quantitative signaling. Nonetheless, we find that sRNAs are better than TFs at filtering noise in input signals. Additionally, we find that sRNAs allow cells to respond rapidly to large changes in input signals. These features suggest a 'niche' for sRNAs in allowing cells to transition quickly yet reliably between distinct states. This functional niche is consistent with the widespread appearance of sRNAs in stress response and quasi-developmental networks in prokaryotes.
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Affiliation(s)
- Pankaj Mehta
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
- These authors contributed equally to this work
| | - Sidhartha Goyal
- Department of Physics, Princeton University, Princeton, NJ, USA
- These authors contributed equally to this work
| | - Ned S Wingreen
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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45
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Cui J, Kaandorp JA, Ositelu OO, Beaudry V, Knight A, Nanfack YF, Cunningham KW. Simulating calcium influx and free calcium concentrations in yeast. Cell Calcium 2008; 45:123-32. [PMID: 18783827 DOI: 10.1016/j.ceca.2008.07.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 07/01/2008] [Accepted: 07/21/2008] [Indexed: 11/26/2022]
Abstract
Yeast can proliferate in environments containing very high Ca(2+) primarily due to the activity of vacuolar Ca(2+) transporters Pmc1 and Vcx1. Yeast mutants lacking these transporters fail to grow in high Ca(2+) environments, but growth can be restored by small increases in environmental Mg(2+). Low extracellular Mg(2+) appeared to competitively inhibit novel Ca(2+) influx pathways and to diminish the concentration of free Ca(2+) in the cytoplasm, as judged from the luminescence of the photoprotein aequorin. These Mg(2+)-sensitive Ca(2+) influx pathways persisted in yvc1 cch1 double mutants. Based on mathematical models of the aequorin luminescence traces, we propose the existence in yeast of at least two Ca(2+) transporters that undergo rapid feedback inhibition in response to elevated cytosolic free Ca(2+) concentration. Finally, we show that Vcx1 helps return cytosolic Ca(2+) toward resting levels after shock with high extracellular Ca(2+) much more effectively than Pmc1 and that calcineurin, a protein phosphatase regulator of Vcx1 and Pmc1, had no detectable effects on these factors within the first few minutes of its activation. Therefore, computational modeling of Ca(2+) transport and signaling in yeast can provide important insights into the dynamics of this complex system.
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Affiliation(s)
- Jiangjun Cui
- Section Computational Science, Faculty of Science, University of Amsterdam, Kruislaan 403, 1098 SJ Amsterdam, The Netherlands.
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Krishna S, Semsey S, Sneppen K. Combinatorics of feedback in cellular uptake and metabolism of small molecules. Proc Natl Acad Sci U S A 2007; 104:20815-9. [PMID: 18093927 PMCID: PMC2409224 DOI: 10.1073/pnas.0706231105] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Indexed: 11/18/2022] Open
Abstract
We analyze the connection between structure and function for regulatory motifs associated with cellular uptake and usage of small molecules. Based on the boolean logic of the feedback we suggest four classes: the socialist, consumer, fashion, and collector motifs. We find that the socialist motif is good for homeostasis of a useful but potentially poisonous molecule, whereas the consumer motif is optimal for nutrition molecules. Accordingly, examples of these motifs are found in, respectively, the iron homeostasis system in various organisms and in the uptake of sugar molecules in bacteria. The remaining two motifs have no obvious analogs in small molecule regulation, but we illustrate their behavior using analogies to fashion and obesity. These extreme motifs could inspire construction of synthetic systems that exhibit bistable, history-dependent states, and homeostasis of flux (rather than concentration).
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Affiliation(s)
- Sandeep Krishna
- Department of Genetics, Eotvos Lorand University, Budapest H-1117, Hungary.
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47
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Benjamin E, Reznik A, Benjamin E, Williams AL. Mathematical models of cobalt and iron ions catalyzed microwave bacterial deactivation. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2007; 4:203-10. [PMID: 17911658 PMCID: PMC3731635 DOI: 10.3390/ijerph2007030002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Time differences for Enterococcus faecalis, Staphylococcus aureus, and Escherichia coli survival during microwave irradiation (power 130 W) in the presence of aqueous cobalt and iron ions were investigated. Measured dependencies had “bell” shape forms with maximum bacterial viability between 1 – 2 min becoming insignificant at 3 minutes. The deactivation time for E. faecalis, S. aureus and E.coli in the presence of metal ions were smaller compared to a water control (4–5 min). Although various sensitivities to the metal ions were observed, S. aureus and E. coli and were the most sensitive for cobalt and iron, respectively. The rapid reduction of viable bacteria during microwave treatment in the presence of metal ions could be explained by increased metal ion penetration into bacteria. Additionally, microwave irradiation may have increased the kinetic energy of the metal ions resulting in lower survival rates. The proposed mathematical model for microwave heating took into account the “growth” and “death” factors of the bacteria, forming second degree polynomial functions. Good relationships were found between the proposed mathematical models and the experimental data for bacterial deactivation (coefficient of correlation 0.91 – 0.99).
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Affiliation(s)
- Earl Benjamin
- Arkansas State University, College of Sciences and Mathematics, Department of Chemistry and Physics, PO Box 419, State University, AR 72467,
USA
| | - Aron Reznik
- Morgan State University, School of Computer, Mathematical, and Natural Sciences, Mathematics Department, 1700 East Cold Spring Lane, Baltimore MD 21251,
USA
| | - Ellis Benjamin
- Arkansas State University, College of Sciences and Mathematics, Department of Chemistry and Physics, PO Box 419, State University, AR 72467,
USA
| | - Arthur L. Williams
- Morgan State University, School of Computer, Mathematical, and Natural Sciences, Biology Department, 1700 East Cold Spring Lane, Baltimore MD 21251,
USA
- Correspondence to Dr. Arthur L. Williams; E-mail:
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Mitarai N, Andersson AMC, Krishna S, Semsey S, Sneppen K. Efficient degradation and expression prioritization with small RNAs. Phys Biol 2007; 4:164-71. [PMID: 17928655 DOI: 10.1088/1478-3975/4/3/003] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We build a simple model for feedback systems involving small RNA (sRNA) molecules based on the iron metabolism system in the bacterium E. coli, and compare it with the corresponding system in H. pylori which uses purely transcriptional regulation. This reveals several unique features of sRNA-based regulation that could be exploited by cells. Firstly, we show that sRNA regulation can maintain a smaller turnover of target mRNAs than transcriptional regulation, without sacrificing the speed of response to external shocks. Secondly, we propose that a single sRNA can prioritize the usage of different target mRNAs. This suggests that sRNA regulation would be more common in more complex systems which need to co-regulate many mRNAs efficiently.
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Affiliation(s)
- Namiko Mitarai
- Niels Bohr Institute, Blegdamsvej 17, DK-2100, Copenhagen, Denmark.
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Campos E, Montella C, Garces F, Baldoma L, Aguilar J, Badia J. Aerobic l-ascorbate metabolism and associated oxidative stress in Escherichia coli. Microbiology (Reading) 2007; 153:3399-3408. [PMID: 17906139 DOI: 10.1099/mic.0.2007/009613-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The anaerobic utilization of L-ascorbate by gene products of the ula regulon in Escherichia coli has been widely documented. Under aerobic conditions, we have shown that this metabolism is only functional in the presence of casein acid hydrolysate. Transcriptional fusions and proteomic analysis indicated that both the ula regulon and the yiaK-S operon are required for the aerobic utilization of this compound. The aerobic dissimilation of l-ascorbate shares the function of three paralogous proteins, UlaD/YiaQ, UlaE/YiaR and UlaF/YiaS, which encode a decarboxylase, a 3-epimerase and a 4-epimerase, respectively. In contrast, l-ascorbate enters the cells through the ula-encoded phosphotransferase transport system, but it is not carried by the yiaMNO-encoded ABC transporter. Proteomic analysis also indicated enhanced expression of the alkyl hydroperoxide reductase encoded by the ahpC gene, suggesting a response to oxidative stress generated during the aerobic metabolism of l-ascorbate. Control of ahpC expression by the OxyR global regulator in response to l-ascorbate concentration is consistent with the formation of hydrogen peroxide under our experimental conditions. The presence of certain amino acids such as proline, threonine or glutamine in the culture medium allowed aerobic l-ascorbate utilization by Escherichia coli cells. This effect could be explained by the ability of these amino acids to allow yiaK-S operon induction by l-ascorbate, thus increasing the metabolic flux of l-ascorbate dissimilation. Alternatively, these amino acids may slow the rate of L-ascorbate oxidation.
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Affiliation(s)
- Evangelina Campos
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Avda Diagonal 643, E-08028 Barcelona, Spain
| | - Cristina Montella
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Avda Diagonal 643, E-08028 Barcelona, Spain
| | - Fernando Garces
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Avda Diagonal 643, E-08028 Barcelona, Spain
| | - Laura Baldoma
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Avda Diagonal 643, E-08028 Barcelona, Spain
| | - Juan Aguilar
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Avda Diagonal 643, E-08028 Barcelona, Spain
| | - Josefa Badia
- Department of Biochemistry, School of Pharmacy, University of Barcelona, Avda Diagonal 643, E-08028 Barcelona, Spain
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Matte A, Jia Z, Sunita S, Sivaraman J, Cygler M. Insights into the biology of Escherichia coli through structural proteomics. ACTA ACUST UNITED AC 2007; 8:45-55. [PMID: 17668295 DOI: 10.1007/s10969-007-9019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 06/28/2007] [Indexed: 10/23/2022]
Abstract
Escherichia coli has historically been an important organism for understanding a multitude of biological processes, and represents a model system as we attempt to simulate the workings of living cells. Many E. coli strains are also important human and animal pathogens for which new therapeutic strategies are required. For both reasons, a more complete and comprehensive understanding of the protein structure complement of E. coli is needed at the genome level. Here, we provide examples of insights into the mechanism and function of bacterial proteins that we have gained through the Bacterial Structural Genomics Initiative (BSGI), focused on medium-throughput structure determination of proteins from E. coli. We describe the structural characterization of several enzymes from the histidine biosynthetic pathway, the structures of three pseudouridine synthases, enzymes that synthesize one of the most abundant modified bases in RNA, as well as the combined use of protein structure and focused functional analysis to decipher functions for hypothetical proteins. Together, these results illustrate the power of structural genomics to contribute to a deeper biological understanding of bacterial processes.
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Affiliation(s)
- Allan Matte
- Biotechnology Research Institute, National Research Council Canada, Montreal, QC, Canada.
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