1
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Frizzell JK, Taylor RL, Ryno LM. Constitutive Activation of RpoH and the Addition of L-arabinose Influence Antibiotic Sensitivity of PHL628 E. coli. Antibiotics (Basel) 2024; 13:143. [PMID: 38391529 PMCID: PMC10886279 DOI: 10.3390/antibiotics13020143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Antibiotics are used to combat the ever-present threat of infectious diseases, but bacteria are continually evolving an assortment of defenses that enable their survival against even the most potent treatments. While the demand for novel antibiotic agents is high, the discovery of a new agent is exceedingly rare. We chose to focus on understanding how different signal transduction pathways in the gram-negative bacterium Escherichia coli (E. coli) influence the sensitivity of the organism to antibiotics from three different classes: tetracycline, chloramphenicol, and levofloxacin. Using the PHL628 strain of E. coli, we exogenously overexpressed two transcription factors, FliA and RpoH.I54N (a constitutively active mutant), to determine their influence on the minimum inhibitory concentration (MIC) and minimum duration of killing (MDK) concentration for each of the studied antibiotics. We hypothesized that activating these pathways, which upregulate genes that respond to specific stressors, could mitigate bacterial response to antibiotic treatment. We also compared the exogenous overexpression of the constitutively active RpoH mutant to thermal heat shock that has feedback loops maintained. While FliA overexpression had no impact on MIC or antibiotic tolerance, RpoH.I54N overexpression reduced the MIC for tetracycline and chloramphenicol but had no independent impact on antibiotic tolerance. Thermal heat shock alone also did not affect MIC or antibiotic tolerance. L-arabinose, the small molecule used to induce expression in our system, unexpectedly independently increased the MICs for tetracycline (>2-fold) and levofloxacin (3-fold). Additionally, the combination of thermal heat shock and arabinose provided a synergistic, 5-fold increase in MIC for chloramphenicol. Arabinose increased the tolerance, as assessed by MDK99, for chloramphenicol (2-fold) and levofloxacin (4-fold). These experiments highlight the potential of the RpoH pathway to modulate antibiotic sensitivity and the emerging implication of arabinose in enhanced MIC and antibiotic tolerance.
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Affiliation(s)
- Jenna K Frizzell
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA
| | - Ryan L Taylor
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA
| | - Lisa M Ryno
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, OH 44074, USA
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2
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Kumari K, Sharma PK, Singh RP. Unravelling the transcriptome response of Enterobacter sp. S-33 under varying temperature. Arch Microbiol 2024; 206:81. [PMID: 38294553 DOI: 10.1007/s00203-023-03792-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 11/22/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
Enterobacter genus includes the bacteria occupying every aspect of environment, however, their adaptability at varying temperature is not clear. In the present study, we analyzed the transcriptome response of Enterobacter sp. S-33 and their functional genes under various temperatures (30-45 ℃) that were expressed and accumulated in cells under temperature-stress. During a temperature shift from 37 to 45 ℃, 165 genes showed differential expression including 112 up-regulated and 53 down-regulated. In particular, heat-shock genes such as CspA, 16 kDa heat shock protein A/B and transcriptional regulators such as LysR, TetR, and LuxR were differentially expressed, indicating the role of complex molecular mechanism of Enterobacter adapting to temperature stress. Similarly, genes associated to signal transduction, ABC transporters, iron homeostasis, and quorum sensing were also induced. The Gene ontology enrichment analysis of differentially expressed genes (DEGs) were categorized into "transmembrane transport", "tRNA binding", "hydrogen sulfide biosynthetic process" and "sulfate assimilation" terms. In addition, Kyoto Encyclopedia of Genes and Genomes pathways showed that ABC transporter as well as quorum sensing pathways were significantly enriched. Overall, current study has contributed to explore the adaptive molecular mechanisms of Enterobacter spp. upon temperature change, which further opens new avenues for future in-depth functional studies.
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Affiliation(s)
- Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
| | - Parva Kumar Sharma
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Rajnish Prakash Singh
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India.
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3
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Zilberzwige-Tal S, Fontanarrosa P, Bychenko D, Dorfan Y, Gazit E, Myers CJ. Investigating and Modeling the Factors That Affect Genetic Circuit Performance. ACS Synth Biol 2023; 12:3189-3204. [PMID: 37916512 PMCID: PMC10661042 DOI: 10.1021/acssynbio.3c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Indexed: 11/03/2023]
Abstract
Over the past 2 decades, synthetic biology has yielded ever more complex genetic circuits that are able to perform sophisticated functions in response to specific signals. Yet, genetic circuits are not immediately transferable to an outside-the-lab setting where their performance is highly compromised. We propose introducing a broader test step to the design-build-test-learn workflow to include factors that might contribute to unexpected genetic circuit performance. As a proof of concept, we have designed and evaluated a genetic circuit in various temperatures, inducer concentrations, nonsterilized soil exposure, and bacterial growth stages. We determined that the circuit's performance is dramatically altered when these factors differ from the optimal lab conditions. We observed significant changes in the time for signal detection as well as signal intensity when the genetic circuit was tested under nonoptimal lab conditions. As a learning effort, we then proceeded to generate model predictions in untested conditions, which is currently lacking in synthetic biology application design. Furthermore, broader test and learn steps uncovered a negative correlation between the time it takes for a gate to turn ON and the bacterial growth phases. As the synthetic biology discipline transitions from proof-of-concept genetic programs to appropriate and safe application implementations, more emphasis on test and learn steps (i.e., characterizing parts and circuits for a broad range of conditions) will provide missing insights on genetic circuit behavior outside the lab.
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Affiliation(s)
- Shai Zilberzwige-Tal
- The
Shmunis School of Biomedicine and Cancer Research, Life Sciences Faculty, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel
| | - Pedro Fontanarrosa
- Department
of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Darya Bychenko
- The
Shmunis School of Biomedicine and Cancer Research, Life Sciences Faculty, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel
| | - Yuval Dorfan
- Department
of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Bio-engineering,
Electrical Engineering Faculty, Holon Institute
of Technology (HIT), Holon 5810201, Israel
- Alagene
Ltd., Innovation Center, Reichman University, Herzliya 7670608, Israel
| | - Ehud Gazit
- The
Shmunis School of Biomedicine and Cancer Research, Life Sciences Faculty, Tel Aviv University, Tel Aviv-Yafo 6997801, Israel
| | - Chris J. Myers
- Department
of Electrical, Computer, and Energy Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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4
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Son Y, Min J, Shin Y, Park W. Morphological and physiological adaptations of psychrophilic Pseudarthrobacter psychrotolerans YJ56 under temperature stress. Sci Rep 2023; 13:14970. [PMID: 37697016 PMCID: PMC10495460 DOI: 10.1038/s41598-023-42179-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
Both culture-independent and culture-dependent analyses using Nanopore-based 16S rRNA sequencing showed that short-term exposure of Antarctic soils to low temperature increased biomass with lower bacterial diversity and maintained high numbers of the phylum Proteobacteria, Firmicute, and Actinobacteria including Pseudarthrobacter species. The psychrophilic Pseudarthrobacter psychrotolerans YJ56 had superior growth at 13 °C, but could not grow at 30 °C, compared to other bacteria isolated from the same Antarctic soil. Unlike a single rod-shaped cell at 13 °C, strain YJ56 at 25 °C was morphologically shifted into a filamentous bacterium with several branches. Comparative genomics of strain YJ56 with other genera in the phylum Actinobacteria indicate remarkable copy numbers of rimJ genes that are possibly involved in dual functions, acetylation of ribosomal proteins, and stabilization of ribosomes by direct binding. Our proteomic data suggested that Actinobacteria cells experienced physiological stresses at 25 °C, showing the upregulation of chaperone proteins, GroEL and catalase, KatE. Level of proteins involved in the assembly of 50S ribosomal proteins and L29 in 50S ribosomal proteins increased at 13 °C, which suggested distinct roles of many ribosomal proteins under different conditions. Taken together, our data highlights the cellular filamentation and protein homeostasis of a psychrophilic YJ56 strain in coping with high-temperature stress.
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Affiliation(s)
- Yongjun Son
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Yoonjae Shin
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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5
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Moon S, Ham S, Jeong J, Ku H, Kim H, Lee C. Temperature Matters: Bacterial Response to Temperature Change. J Microbiol 2023; 61:343-357. [PMID: 37010795 DOI: 10.1007/s12275-023-00031-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 04/04/2023]
Abstract
Temperature is one of the most important factors in all living organisms for survival. Being a unicellular organism, bacterium requires sensitive sensing and defense mechanisms to tolerate changes in temperature. During a temperature shift, the structure and composition of various cellular molecules including nucleic acids, proteins, and membranes are affected. In addition, numerous genes are induced during heat or cold shocks to overcome the cellular stresses, which are known as heat- and cold-shock proteins. In this review, we describe the cellular phenomena that occur with temperature change and bacterial responses from a molecular perspective, mainly in Escherichia coli.
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Affiliation(s)
- Seongjoon Moon
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Soojeong Ham
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Juwon Jeong
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Heechan Ku
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea
| | - Hyunhee Kim
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
| | - Changhan Lee
- Department of Biological Sciences, Ajou University, Suwon, 16499, Republic of Korea.
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6
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Antibacterial Effects of ZnO Nanodisks: Shape Effect of the Nanostructure on the Lethality in Escherichia coli. Appl Biochem Biotechnol 2022; 195:3067-3095. [PMID: 36520354 DOI: 10.1007/s12010-022-04265-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/08/2022] [Indexed: 12/23/2022]
Abstract
The role of the shape of the nanostructure on the antibacterial effects of ZnO nanodisks has been investigated by detailed mass spectrometry-based proteomics along with other spectroscopic and microscopic studies on E. coli. The primary interaction study of the E. coli cells in the presence of ZnO nanodisks showed rigorous cell surface damage disrupting the cell wall/membrane components detected by microscopic and ATR-FTIR studies. Protein profiling of whole-cell extracts in the presence and absence of ZnO nanodisks identified several proteins that are upregulated and downregulated under the stress of the nanodisks. This suggests that the bacterial response to the primary stress leads to a secondary impact of ZnO nanodisk toxicity via regulation of the expression of specific proteins. Results showed that the ZnO nanodisks lead to the over-expression of peptidyl-dipeptidase Dcp, Transketolase-1, etc., which are important to maintaining the osmotic balance in the cell. The abrupt change in osmotic pressure leads to mechanical injury to the membrane, and nutritional starvation conditions, which is revealed from the expression of the key proteins involved in membrane-protein assembly, maintaining membrane integrity, cell division processes, etc. Thus, indicating a deleterious effect of ZnO nanodisk on the protective layer of E. coli. ZnO nanodisks seem to primarily affect the protective membrane layer, inducing cell death via the development of osmotic shock conditions, as one of the possible reasons for cell death. These results unravel a unique behavior of the disk-shaped ZnO nanostructure in executing lethality in E. coli, which has not been reported for other known shapes or morphologies of ZnO nanoforms.
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Kim M, Im E, Jin Ahn Y. Enhanced Acetate Tolerance and Recombinant Protein Accumulation in Escherichia coli by Transgenic Expression of a Heat Shock Protein from Carrot ( Daucus carota L.). IRANIAN JOURNAL OF BIOTECHNOLOGY 2022; 20:e3177. [PMID: 36381282 PMCID: PMC9618011 DOI: 10.30498/ijb.2022.309657.3177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND In Escherichia coli (E. coli) culture, acetate accumulates as an undesirable by-product of aerobic fermentation on glucose and inhibits cell growth and recombinant protein production. OBJECTIVES We examined whether the heterologous expression of a eukaryotic heat shock protein (Hsp) can confer tolerance to acetate in E. coli. MATERIALS AND METHODS Transgenic cell lines (TCLs) heterologously expressing a small heat shock protein (sHsp) from carrot (Daucus carota L.), DcHsp17.7, were exposed to heat, sodium acetate, and alkaline conditions. The cell growth and cell viability were examined by measuring O.D.600 and colony-forming units (CFU), respectively. The His-tagged recombinant alcohol dehydrogenase (ADH) gene cloned in a pET11a expression vector was introduced into TCL1 and expressed by isopropyl β-D-1-thiogalactopyranoside treatment. After purifying using Ni-NTA affinity chromatography, its accumulation levels were examined using SDS-PAGE in the presence of acetate. RESULTS TCLs constitutively expressing DcHsp17.7 showed improved growth, cell density, and cell viability under the stress conditions of heat, acetate, and alkaline compared to an empty vector control line. In acetate stress conditions, TCL1 accumulated more cellular proteins (approximately 130%) than the control. The recombinant ADH accumulated to a higher level in TCL1 (2.2-fold at 16 °C) than the control. The addition of acetate reduced the recombinant ADH level by 70% in the control when compared with the absence of acetate. In contrast, recombinant ADH accumulation was not affected by acetate in TCL1. In the presence of acetate, TCL1 accumulated 6.4-fold more recombinant ADH than did the control. Furthermore, recombinant ADH produced in TCL1 showed 1.5-fold higher enzyme activity than that produced in the control in the presence or absence of acetate. CONCLUSION Our study showed that heterologously expressed DcHsp17.7 from carrot can alleviate the negative effects of acetate on E. coli.
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Affiliation(s)
- Minhye Kim
- Department of Biotechnology, Sangmyung University, 20 Hongjimun 2-gil, Jongno-gu, Seoul 03016, Korea
| | - Eunju Im
- Department of Biotechnology, Sangmyung University, 20 Hongjimun 2-gil, Jongno-gu, Seoul 03016, Korea
| | - Yeh Jin Ahn
- Department of Biotechnology, Sangmyung University, 20 Hongjimun 2-gil, Jongno-gu, Seoul 03016, Korea
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8
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Dekić Rozman S, Butorac A, Bertoša R, Hrenović J, Markeš M. Loss of thermotolerance in antibiotic-resistant Acinetobacter baumannii. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1581-1593. [PMID: 33719791 DOI: 10.1080/09603123.2021.1898550] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Bacterium Acinetobacter baumannii is a leading cause of nosocomial infections. The occurrence of antibiotic-resistant A. baumannii isolates outside hospitals suggests that monitoring of this pathogen in environmental samples is needed. Survival of pandrug-resistant A. baumannii was followed on selective plates with and without carbapenems in water and soil. After a few days of starvation, A. baumannii lost the ability to be cultivated at 44°C on plates supplemented with carbapenems. Once cultivated on plates without carbapenems and/or at 36°C, A. baumannii could grow again at 44°C in the presence of carbapenems. Comparative proteomic analysis revealed that impaired membrane integrity and reduced function of efflux pumps due to elevated temperature combined with antibiotic exposure were the main reasons for this phenomenon. Loss of thermotolerance in the presence of antibiotics points to the need for temperature adjustment in long-term monitoring of A. baumannii in environmental samples, to avoid the underestimation of viable bacteria.
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Affiliation(s)
| | - Ana Butorac
- BIOCentre Ltd., Bioanalytical Laboratory II - Proteomics, Zagreb, Croatia
| | - Rea Bertoša
- BIOCentre Ltd., Bioanalytical Laboratory II - Proteomics, Zagreb, Croatia
| | - Jasna Hrenović
- Faculty of Science, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Marina Markeš
- BIOCentre Ltd., Bioanalytical Laboratory II - Proteomics, Zagreb, Croatia
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9
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García-Descalzo L, García-López E, Cid C. Comparative Proteomic Analysis of Psychrophilic vs. Mesophilic Bacterial Species Reveals Different Strategies to Achieve Temperature Adaptation. Front Microbiol 2022; 13:841359. [PMID: 35591995 PMCID: PMC9111180 DOI: 10.3389/fmicb.2022.841359] [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: 12/22/2021] [Accepted: 03/08/2022] [Indexed: 11/16/2022] Open
Abstract
The old debate of nature (genes) vs. nurture (environmental variables) is once again topical concerning the effect of climate change on environmental microorganisms. Specifically, the Polar Regions are experiencing a drastic increase in temperature caused by the rise in greenhouse gas emissions. This study, in an attempt to mimic the molecular adaptation of polar microorganisms, combines proteomic approaches with a classical microbiological analysis in three bacterial species Shewanella oneidensis, Shewanella frigidimarina, and Psychrobacter frigidicola. Both shewanellas are members of the same genus but they live in different environments. On the other hand, Shewanella frigidimarina and Psychrobacter frigidicola share the same natural environment but belong to a different genus. The comparison of the strategies employed by each bacterial species estimates the contribution of genome vs. environmental variables in the adaptation to temperature. The results show a greater versatility of acclimatization for the genus Shewanella with respect to Psychrobacter. Besides, S. frigidimarina was the best-adapted species to thermal variations in the temperature range 4–30°C and displayed several adaptation mechanisms common with the other two species. Regarding the molecular machinery used by these bacteria to face the consequences of temperature changes, chaperones have a pivoting role. They form complexes with other proteins in the response to the environment, establishing cooperation with transmembrane proteins, elongation factors, and proteins for protection against oxidative damage.
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Affiliation(s)
- Laura García-Descalzo
- Centro de Astrobiología, Department of Planetology and Habitability, CSIC-INTA, Madrid, Spain
| | - Eva García-López
- Centro de Astrobiología, Department of Molecular Ecology, CSIC-INTA, Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiología, Department of Molecular Ecology, CSIC-INTA, Madrid, Spain
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10
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RNase III Participates in the Adaptation to Temperature Shock and Oxidative Stress in Escherichia coli. Microorganisms 2022; 10:microorganisms10040699. [PMID: 35456749 PMCID: PMC9032294 DOI: 10.3390/microorganisms10040699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/05/2023] Open
Abstract
Bacteria thrive in ever-changing environments by quickly remodeling their transcriptome and proteome via complex regulatory circuits. Regulation occurs at multiple steps, from the transcription of genes to the post-translational modification of proteins, via both protein and RNA regulators. At the post-transcriptional level, the RNA fate is balanced through the binding of ribosomes, chaperones and ribonucleases. We aim to decipher the role of the double-stranded-RNA-specific endoribonuclease RNase III and to evaluate its biological importance in the adaptation to modifications of the environment. The inactivation of RNase III affects a large number of genes and leads to several phenotypical defects, such as reduced thermotolerance in Escherichia coli. In this study, we reveal that RNase III inactivation leads to an increased sensitivity to temperature shock and oxidative stress. We further show that RNase III is important for the induction of the heat shock sigma factor RpoH and for the expression of the superoxide dismutase SodA.
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11
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Amino Acid Analog Induces Stress Response in Marine Synechococcus. Appl Environ Microbiol 2021; 87:e0020021. [PMID: 33990310 DOI: 10.1128/aem.00200-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Characterizing the cell-level metabolic trade-offs that phytoplankton exhibit in response to changing environmental conditions is important for predicting the impact of these changes on marine food web dynamics and biogeochemical cycling. The time-selective proteome-labeling approach, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to provide insight into differential allocation of resources at the cellular level, especially when coupled with proteomics. However, the application of this technique in marine phytoplankton remains limited. We demonstrate that the marine cyanobacteria Synechococcus sp. and two groups of eukaryotic algae take up the modified amino acid l-homopropargylglycine (HPG), suggesting that BONCAT can be used to detect translationally active phytoplankton. However, the impact of HPG addition on growth dynamics varied between groups of phytoplankton. In addition, proteomic analysis of Synechococcus cells grown with HPG revealed a physiological shift in nitrogen metabolism, general protein stress, and energy production, indicating a potential limitation for the use of BONCAT in understanding the cell-level response of Synechococcus sp. to environmental change. Variability in HPG sensitivity between algal groups and the impact of HPG on Synechococcus physiology indicates that particular considerations should be taken when applying this technique to other marine taxa or mixed marine microbial communities. IMPORTANCE Phytoplankton form the base of the marine food web and substantially impact global energy and nutrient flow. Marine picocyanobacteria of the genus Synechococcus comprise a large portion of phytoplankton biomass in the ocean and therefore are important model organisms. The technical challenges of environmental proteomics in mixed microbial communities have limited our ability to detect the cell-level adaptations of phytoplankton communities to a changing environment. The proteome labeling technique, bioorthogonal noncanonical amino acid tagging (BONCAT), has potential to address some of these challenges by simplifying proteomic analyses. This study explores the ability of marine phytoplankton to take up the modified amino acid, l-homopropargylglycine (HPG), required for BONCAT, and investigates the proteomic response of Synechococcus to HPG. We not only demonstrate that cyanobacteria can take up HPG but also highlight the physiological impact of HPG on Synechococcus, which has implications for future applications of this technique in the marine environment.
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12
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Aabed K, Mohammed AE, Benabdelkamel H, Masood A, Alfadda AA, Alanazi IO, Alnehmi EA. Antimicrobial Mechanism and Identification of the Proteins Mediated by Extracts from Asphaltum punjabianum and Myrtus communis. ACS OMEGA 2020; 5:31019-31035. [PMID: 33324810 PMCID: PMC7726785 DOI: 10.1021/acsomega.0c04047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/06/2020] [Indexed: 06/12/2023]
Abstract
Myrtus communis ("myrtle") and Asphaltum punjabianum ("shilajeet") are a medicinal plant and a long-term-humified dead plant material, respectively. We studied their antibacterial and anticandidal activities against Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, and Candida albicans. The activities of the aqueous extracts of the studied materials were measured using agar-well diffusion methods. Furthermore, proteomic analysis of treated microbial cells was conducted to identify affected proteins. The results showed both antibacterial and anticandidal activities for the myrtle extract (ME), while the shilajeet extract (SE) showed antibacterial activity only. The highest antimicrobial activity was observed against E. coli among the microbes tested; therefore, it was taken as the model for the proteomic analysis to identify the antimicrobial mechanism of ME and SE using two-dimensional electrophoresis. Upregulation of expression of 42 proteins and downregulation of expression of 6 proteins were observed in E. coli treated with ME, whereas 12 upregulated and 104 downregulated proteins were detected in E. coli treated with SE, in comparison with the control. About 85% of identified expressed proteins were from the cytoplasm and 15% from microbial cell walls, indicating the penetration of extracts inside cells. A higher percentage of expressed proteins was recorded for enzymatic activity. Our findings suggest that the major targets of the antibacterial action were proteins involved in the outer membrane, oxidative stress, and metabolism. Our data might reveal new targets for antimicrobial agents.
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Affiliation(s)
- Kawther Aabed
- Department
of Biology, College of Science, Princess
Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Afrah E. Mohammed
- Department
of Biology, College of Science, Princess
Nourah Bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Hicham Benabdelkamel
- Proteomics
Unit, Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia
| | - Afshan Masood
- Proteomics
Unit, Obesity Research Center, College of Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia
| | - Assim A. Alfadda
- Proteomics
Unit, Obesity Research Center, Department of Medicine, College of
Medicine, King Saud University, P.O. Box 2925 (98), Riyadh 11461, Saudi Arabia
| | - Ibrahim O. Alanazi
- The
National Center for Biotechnology (NCB), Life Science and Environment
Research Institute, King Abdulaziz City
for Science and Technology (KACST), P.O.
Box 6086, Riyadh 12354, Saudi Arabia
| | - Eman A. Alnehmi
- Department
of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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13
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Kim S, Kim Y, Suh DH, Lee CH, Yoo SM, Lee SY, Yoon SH. Heat-responsive and time-resolved transcriptome and metabolome analyses of Escherichia coli uncover thermo-tolerant mechanisms. Sci Rep 2020; 10:17715. [PMID: 33077799 PMCID: PMC7572479 DOI: 10.1038/s41598-020-74606-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/05/2020] [Indexed: 11/27/2022] Open
Abstract
Current understanding of heat shock response has been complicated by the fact that heat stress is inevitably accompanied by changes in specific growth rates and growth stages. In this study, a chemostat culture was successfully performed to avoid the physico-chemical and biological changes that accompany heatshock, which provided a unique opportunity to investigate the full range of cellular responses to thermal stress, ranging from temporary adjustment to phenotypic adaptation at multi-omics levels. Heat-responsive and time-resolved changes in the transcriptome and metabolome of a widely used E. coli strain BL21(DE3) were explored in which the temperature was upshifted from 37 to 42 °C. Omics profiles were categorized into early (2 and 10 min), middle (0.5, 1, and 2 h), and late (4, 8, and 40 h) stages of heat stress, each of which reflected the initiation, adaptation, and phenotypic plasticity steps of the stress response. The continued heat stress modulated global gene expression by controlling the expression levels of sigma factors in different time frames, including unexpected downregulation of the second heatshock sigma factor gene (rpoE) upon the heat stress. Trehalose, cadaverine, and enterobactin showed increased production to deal with the heat-induced oxidative stress. Genes highly expressed at the late stage were experimentally validated to provide thermotolerance. Intriguingly, a cryptic capsular gene cluster showed considerably high expression level only at the late stage, and its expression was essential for cell growth at high temperature. Granule-forming and elongated cells were observed at the late stage, which was morphological plasticity occurred as a result of acclimation to the continued heat stress. Whole process of thermal adaptation along with the genetic and metabolic changes at fine temporal resolution will contribute to far-reaching comprehension of the heat shock response. Further, the identified thermotolerant genes will be useful to rationally engineer thermotolerant microorganisms.
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Affiliation(s)
- Sinyeon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Youngshin Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Dong Ho Suh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea
| | - Seung Min Yoo
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, KAIST, Daejeon, 34141, Republic of Korea
| | - Sung Ho Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 05029, Republic of Korea.
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14
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Fei YY, Bhat JA, Gai JY, Zhao TJ. Global Transcriptome Profiling of Enterobacter Strain NRS-1 in Response to Hydrogen Peroxide Stress Treatment. Appl Biochem Biotechnol 2020; 191:1638-1652. [PMID: 32198600 DOI: 10.1007/s12010-020-03313-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
Abstract
Microbes are often subjected to oxidative stress in nature that badly affects their growth rate and viability. Although the response of microbes against oxidative stress has been characterized at the chemical, physiological, and molecular levels, the mechanism of gene-regulation network adaptations of bacteria in response to oxidative stress remains largely unknown. In this study, transcriptomic profiling of glyphosate-tolerant Enterobacter strain NRS-1 was analyzed under 9 mM H2O2 stress using RNA-seq and qRT-PCR. The lag period in the growth of NRS-1 was very short compared with wild-type strain under H2O2 treatment. A total of 113 genes are identified as differentially expressed genes (DEGs) under H2O2 that include 38 upregulated and 75 downregulated transcripts. But not any genes regulated by major oxidative regulons, viz., oxyR, soxR, rpoS, perR, ohrR, and σв, have been reported in DEGs, hence potentially reflecting that specific changes have occurred in NRS-1 for adaptation to oxidative stress. Based on the functions of the DEGs, six elements namely formate dehydrogenase, processes associated with iron ions, repair programs, multidrug resistance, antioxidant defense, and energy generation (mqo, sdhC) might have contributed for stress tolerance in NRS-1. These elements are proposed to form a molecular network explaining gene response of NRS-1 to stress, and ensure global cell protection and growth recovery of NRS-1. These findings enrich the view of gene regulation in bacteria in response to H2O2 oxidative stress.
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Affiliation(s)
- Yun-Yan Fei
- Soybean Research Institute, Nanjing Agricultural University, Weigang 1 Hao, Xuanwu District, Nanjing, 210095, Jiangsu, People's Republic of China
- National Center for Soybean Improvement, Nanjing Agricultural University, Weigang 1 Hao, Xuanwu District, Nanjing, 210095, Jiangsu Province, People's Republic of China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing, 210095, People's Republic of China
| | - Javaid Akhter Bhat
- Soybean Research Institute, Nanjing Agricultural University, Weigang 1 Hao, Xuanwu District, Nanjing, 210095, Jiangsu, People's Republic of China
- National Center for Soybean Improvement, Nanjing Agricultural University, Weigang 1 Hao, Xuanwu District, Nanjing, 210095, Jiangsu Province, People's Republic of China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing, 210095, People's Republic of China
| | - Jun-Yi Gai
- Soybean Research Institute, Nanjing Agricultural University, Weigang 1 Hao, Xuanwu District, Nanjing, 210095, Jiangsu, People's Republic of China
- National Center for Soybean Improvement, Nanjing Agricultural University, Weigang 1 Hao, Xuanwu District, Nanjing, 210095, Jiangsu Province, People's Republic of China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, People's Republic of China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing, 210095, People's Republic of China
| | - Tuan-Jie Zhao
- Soybean Research Institute, Nanjing Agricultural University, Weigang 1 Hao, Xuanwu District, Nanjing, 210095, Jiangsu, People's Republic of China.
- National Center for Soybean Improvement, Nanjing Agricultural University, Weigang 1 Hao, Xuanwu District, Nanjing, 210095, Jiangsu Province, People's Republic of China.
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing, 210095, People's Republic of China.
- Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing, 210095, People's Republic of China.
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15
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Ng HF, Ngeow YF, Yap SF, Zin T, Tan JL. Tigecycline resistance may be associated with dysregulated response to stress in Mycobacterium abscessus. Int J Med Microbiol 2020; 310:151380. [DOI: 10.1016/j.ijmm.2019.151380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/14/2019] [Accepted: 11/17/2019] [Indexed: 01/16/2023] Open
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16
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Jevtić Ž, Stoll B, Pfeiffer F, Sharma K, Urlaub H, Marchfelder A, Lenz C. The Response of Haloferax volcanii to Salt and Temperature Stress: A Proteome Study by Label-Free Mass Spectrometry. Proteomics 2019; 19:e1800491. [PMID: 31502396 DOI: 10.1002/pmic.201800491] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 08/27/2019] [Indexed: 01/23/2023]
Abstract
In-depth proteome analysis of the haloarchaeal model organism Haloferax volcanii has been performed under standard, low/high salt, and low/high temperature conditions using label-free mass spectrometry. Qualitative analysis of protein identification data from high-pH/reversed-phase fractionated samples indicates 61.1% proteome coverage (2509 proteins), which is close to the maximum recorded values in archaea. Identified proteins match to the predicted proteome in their physicochemical properties, with only a small bias against low-molecular-weight and membrane-associated proteins. Cells grown under low and high salt stress as well as low and high temperature stress are quantitatively compared to standard cultures by sequential window acquisition of all theoretical mass spectra (SWATH-MS). A total of 2244 proteins, or 54.7% of the predicted proteome, are quantified across all conditions at high reproducibility, which allowed for global analysis of protein expression changes under these stresses. Of these, 2034 are significantly regulated under at least one stress condition. KEGG pathway enrichment analysis shows that several major cellular pathways are part of H. volcanii's universal stress response. In addition, specific pathways (purine, cobalamin, and tryptophan) are affected by temperature stress. The most strongly downregulated proteins under all stress conditions, zinc finger protein HVO_2753 and ribosomal protein S14, are found oppositely regulated to their immediate genetic neighbors from the same operon.
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Affiliation(s)
- Živojin Jevtić
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, 37077, Germany
| | | | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Kundan Sharma
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, 37077, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, 37077, Germany.,Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, 37075, Germany
| | | | - Christof Lenz
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, Göttingen, 37077, Germany.,Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, 37075, Germany
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17
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Feng X, He C, Jiao L, Liang X, Zhao R, Guo Y. Analysis of differential expression proteins reveals the key pathway in response to heat stress in Alicyclobacillus acidoterrestris DSM 3922T. Food Microbiol 2019; 80:77-84. [DOI: 10.1016/j.fm.2019.01.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 11/12/2018] [Accepted: 01/06/2019] [Indexed: 11/27/2022]
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18
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Adu KT, Wilson R, Nichols DS, Baker AL, Bowman JP, Britz ML. Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress. PLoS One 2018; 13:e0206317. [PMID: 30359441 PMCID: PMC6201924 DOI: 10.1371/journal.pone.0206317] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 10/10/2018] [Indexed: 12/14/2022] Open
Abstract
Prolonged heat stress is one of the harsh conditions Lactobacillus casei strains encounter as non-starter lactic acid bacteria in dairy product manufacture. To understand the physiological and molecular mechanisms through which Lb. casei GCRL163 adapts to persistent elevated temperature, label-free quantitative proteomics of cell-free extracts was used to characterize the global responses of the strain cultured anaerobically in bioreactors at 30 to 45°C, pH 6.5, together with GC-MS for fatty acid methyl ester analysis at different growth phases. At higher growth temperatures, repression of energy-consuming metabolic pathways, such as fatty acid, nucleotide and amino acid biosynthesis, was observed, while PTS- and ABC-type transporter systems associated with uptake of nitrogen and carbon sources were up-regulated. Alkaline shock protein Asp23_2 was only detected at 45°C, expressed at high abundance, and presumptive α-L-fucosidase only at 40 and 45°C, with highly increased abundance (log2-fold change of 7) at 45°C. We identified a novel SecB homolog as a protein export chaperone putatively involved in posttranslational translocation systems, which was down-regulated as growth temperature increased and where the modelled 3D-structure shared architectural similarities with the Escherichia coli SecB protein. Membrane lipid analyses revealed temporal changes in fatty acid composition, cyclization of oleic acid to cyclopropane and novel cyclopentenyl moieties, and reduced synthesis of vaccenic acid, at higher temperatures. An 18kDa α-crystallin domain, Hsp20 family heat shock protein was more highly up-regulated in response to heat stress compared to other molecular chaperones, suggesting this protein could be a useful biomarker of prolonged heat stress in Lb. casei GCRL163.
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Affiliation(s)
- Kayode T. Adu
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia
| | - David S. Nichols
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania, Australia
| | - Anthony L. Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - John P. Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Margaret L. Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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19
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Molecular mechanism of the Escherichia coli AhpC in the function of a chaperone under heat-shock conditions. Sci Rep 2018; 8:14151. [PMID: 30237544 PMCID: PMC6147784 DOI: 10.1038/s41598-018-32527-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/05/2018] [Indexed: 01/24/2023] Open
Abstract
Peroxiredoxins (Prxs) are ubiquitous antioxidants utilizing a reactive cysteine for peroxide reduction and acting as a molecular chaperone under various stress conditions. Besides other stimulating factors, oxidative- and heat stress conditions trigger their ATP-independent chaperoning function. So far, many studies were intended to reveal the chaperoning mechanisms of the so-called sensitive Prxs of eukaryotes, which are susceptible to inactivation by over-oxidation of its reactive cysteine during H2O2 reduction. In contrast, the chaperone mechanisms of bacterial Prxs, which are mostly robust against inactivation by over-oxidation, are not well understood. Herein, comprehensive biochemical and biophysical studies demonstrate that the Escherichia coli alkyl hydroperoxide reductase subunit C (EcAhpC) acquires chaperone activity under heat stress. Interestingly, their chaperoning activity is independent of its redox-states but is regulated in a temperature-dependent manner. Data are presented, showing that oxidized EcAhpC, which forms dimers at 25 °C, self-assembled into high molecular weight (HMW) oligomers at higher temperatures and supressed aggregation of client proteins at heat-shock conditions. In addition, we unravelled the essential role of the C-terminal tail of EcAhpC on heat-induced HMW oligomer formation and chaperoning activity. Our findings suggest a novel molecular mechanism for bacterial Prxs to function as chaperone at heat-shock conditions.
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20
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Foshag D, Henrich E, Hiller E, Schäfer M, Kerger C, Burger-Kentischer A, Diaz-Moreno I, García-Mauriño SM, Dötsch V, Rupp S, Bernhard F. The E. coli S30 lysate proteome: A prototype for cell-free protein production. N Biotechnol 2017; 40:245-260. [PMID: 28943390 DOI: 10.1016/j.nbt.2017.09.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/28/2017] [Accepted: 09/05/2017] [Indexed: 10/18/2022]
Abstract
Protein production using processed cell lysates is a core technology in synthetic biology and these systems are excellent to produce difficult toxins or membrane proteins. However, the composition of the central lysate of cell-free systems is still a "black box". Escherichia coli lysates are most productive for cell-free expression, yielding several mgs of protein per ml of reaction. Their preparation implies proteome fractionation, resulting in strongly biased and yet unknown lysate compositions. Many metabolic pathways are expected to be truncated or completely removed. The lack of knowledge of basic cell-free lysate proteomes is a major bottleneck for directed lysate engineering approaches as well as for assay design using non-purified reaction mixtures. This study is starting to close this gap by providing a blueprint of the S30 lysate proteome derived from the commonly used E. coli strain A19. S30 lysates are frequently used for cell-free protein production and represent the basis of most commercial E. coli cell-free expression systems. A fraction of 821 proteins was identified as the core proteome in S30 lysates, representing approximately a quarter of the known E. coli proteome. Its classification into functional groups relevant for transcription/translation, folding, stability and metabolic processes will build the framework for tailored cell-free reactions. As an example, we show that SOS response induction during cultivation results in tuned S30 lysate with better folding capacity, and improved solubility and activity of synthesized proteins. The presented data and protocols can serve as a platform for the generation of customized cell-free systems and product analysis.
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Affiliation(s)
- Daniel Foshag
- Institute for Interfacial Process Engineering and Plasma Technology, University of Stuttgart, Stuttgart, Germany
| | - Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Ekkehard Hiller
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Miriam Schäfer
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | - Christian Kerger
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany
| | | | - Irene Diaz-Moreno
- Instituto de Investigaciones Químicas (IIQ) - Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ) - Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja), Universidad de Sevilla - Consejo Superior de Investigaciones Científicas (CSIC), Sevilla, Spain
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Steffen Rupp
- Fraunhofer Institute for Interfacial Engineering and Biotechnology, Stuttgart, Germany.
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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21
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Planchon M, Léger T, Spalla O, Huber G, Ferrari R. Metabolomic and proteomic investigations of impacts of titanium dioxide nanoparticles on Escherichia coli. PLoS One 2017; 12:e0178437. [PMID: 28570583 PMCID: PMC5453534 DOI: 10.1371/journal.pone.0178437] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/13/2017] [Indexed: 11/18/2022] Open
Abstract
In a previous study, it was demonstrated that the toxic impact of titanium dioxide nanoparticles on Escherichia coli starts at 10 ppm and is closely related to the presence of little aggregates. It was also assumed that only a part of the bacterial population is able to adapt to this stress and attempts to survive. Proteomic analyses, supported by results from metabolomics, reveal that exposure of E. coli to nano-TiO2 induces two main effects on bacterial metabolism: firstly, the up-regulation of proteins and the increase of metabolites related to energy and growth metabolism; secondly, the down-regulation of other proteins resulting in an increase of metabolites, particularly amino acids. Some proteins, e.g. chaperonin 1 or isocitrate dehydrogenase, and some metabolites, e.g. phenylalanine or valine, might be used as biomarkers of nanoparticles stress. Astonishingly, the ATP content gradually rises in relation with the nano-TiO2 concentration in the medium, indicating a dramatic release of ATP by the damaged cells. These apparently contradictory results accredit the thesis of a heterogeneity of the bacterial population. This heterogeneity is also confirmed by SEM images which show that while some bacteria are fully covered by nano-TiO2, the major part of the bacterial population remains free from nanoparticles, resulting in a difference of proteome and metabolome. The use of combined-omics has allowed to better understand the heterogeneous bacterial response to nano-TiO2 stress due to heterogeneous contacts between the protagonists under environmental conditions.
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Affiliation(s)
- Mariane Planchon
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
- Université Paris Diderot, Sorbonne Paris Cité, IPGP, UMR 7154, Paris Cedex 13 France
- iCEINT, International Consortium for the Environmental Implications of Nanotechnology
| | - Thibaut Léger
- Mass Spectrometry Laboratory, Institut Jacques Monod, UMR 7592, Univ Paris Diderot, CNRS, Sorbonne Paris Cité, Paris, France
| | - Olivier Spalla
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
- iCEINT, International Consortium for the Environmental Implications of Nanotechnology
| | - Gaspard Huber
- NIMBE, CEA, CNRS, Université Paris-Saclay, CEA Saclay 91191 Gif-sur-Yvette, France
- * E-mail: (GH); (RF)
| | - Roselyne Ferrari
- Université Paris Diderot, Sorbonne Paris Cité, IPGP, UMR 7154, Paris Cedex 13 France
- Université Paris Diderot, Sorbonne Paris Cité, LIED, UMR 8236, Paris, France
- * E-mail: (GH); (RF)
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22
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Baron F, Bonnassie S, Alabdeh M, Cochet MF, Nau F, Guérin-Dubiard C, Gautier M, Andrews SC, Jan S. Global Gene-expression Analysis of the Response of Salmonella Enteritidis to Egg White Exposure Reveals Multiple Egg White-imposed Stress Responses. Front Microbiol 2017; 8:829. [PMID: 28553268 PMCID: PMC5428311 DOI: 10.3389/fmicb.2017.00829] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/24/2017] [Indexed: 12/20/2022] Open
Abstract
Chicken egg white protects the embryo from bacterial invaders by presenting an assortment of antagonistic activities that combine together to both kill and inhibit growth. The key features of the egg white anti-bacterial system are iron restriction, high pH, antibacterial peptides and proteins, and viscosity. Salmonella enterica serovar Enteritidis is the major pathogen responsible for egg-borne infection in humans, which is partly explained by its exceptional capacity for survival under the harsh conditions encountered within egg white. However, at temperatures up to 42°C, egg white exerts a much stronger bactericidal effect on S. Enteritidis than at lower temperatures, although the mechanism of egg white-induced killing is only partly understood. Here, for the first time, the impact of exposure of S. Enteritidis to egg white under bactericidal conditions (45°C) is explored by global-expression analysis. A large-scale (18.7% of genome) shift in transcription is revealed suggesting major changes in specific aspects of S. Enteritidis physiology: induction of egg white related stress-responses (envelope damage, exposure to heat and alkalinity, and translation shutdown); shift in energy metabolism from respiration to fermentation; and enhanced micronutrient provision (due to iron and biotin restriction). Little evidence of DNA damage or redox stress was obtained. Instead, data are consistent with envelope damage resulting in cell death by lysis. A surprise was the high degree of induction of hexonate/hexuronate utilization genes, despite no evidence indicating the presence of these substrates in egg white.
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Affiliation(s)
- Florence Baron
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Sylvie Bonnassie
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- Science de la Vie et de la Terre, Université de Rennes IRennes, France
| | - Mariah Alabdeh
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Marie-Françoise Cochet
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Françoise Nau
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Catherine Guérin-Dubiard
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | - Michel Gautier
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
| | | | - Sophie Jan
- Agrocampus Ouest, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
- INRA, UMR1253 Science et Technologie du Lait et de l'OeufRennes, France
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23
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Zhong J, Xiao C, Gu W, Du G, Sun X, He QY, Zhang G. Transfer RNAs Mediate the Rapid Adaptation of Escherichia coli to Oxidative Stress. PLoS Genet 2015; 11:e1005302. [PMID: 26090660 PMCID: PMC4474833 DOI: 10.1371/journal.pgen.1005302] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/27/2015] [Indexed: 11/18/2022] Open
Abstract
Translational systems can respond promptly to sudden environmental changes to provide rapid adaptations to environmental stress. Unlike the well-studied translational responses to oxidative stress in eukaryotic systems, little is known regarding how prokaryotes respond rapidly to oxidative stress in terms of translation. In this study, we measured protein synthesis from the entire Escherichia coli proteome and found that protein synthesis was severely slowed down under oxidative stress. With unchanged translation initiation, this slowdown was caused by decreased translation elongation speed. We further confirmed by tRNA sequencing and qRT-PCR that this deceleration was caused by a global, enzymatic downregulation of almost all tRNA species shortly after exposure to oxidative agents. Elevation in tRNA levels accelerated translation and protected E. coli against oxidative stress caused by hydrogen peroxide and the antibiotic ciprofloxacin. Our results showed that the global regulation of tRNAs mediates the rapid adjustment of the E. coli translation system for prompt adaptation to oxidative stress. All organisms need to respond quickly to sudden environmental changes. Translational regulation can occur in response to environmental stresses within minutes, which is much faster than transcriptional regulation, and thus normally provides immediate adaptation. Eukaryotic cells can manipulate their tRNA molecules, mainly in a reversible manner, to suppress translation. Here, we showed for the first time that bacteria respond to oxidative stress by adjusting the translational system in a manner that differs from that of eukaryotes. The bacteria nonspecifically, irreversibly, and enzymatically degrade tRNAs to block protein synthesis. Interestingly, we showed that elevated tRNA concentrations lead to opposing effects by causing increased protein aggregation, which impairs fitness under normal conditions but facilitates adaptation under oxidative stress, including that caused by antibiotics. Our results provide a new understanding of the role of global adjustments to the entire translation system during stress adaptation in bacteria. This mechanism may also be involved in the development of antibiotic resistance in bacteria.
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Affiliation(s)
- Jiayong Zhong
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Chuanle Xiao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Wei Gu
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Gaofei Du
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Xuesong Sun
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (QYH); (GZ)
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, China
- * E-mail: (QYH); (GZ)
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24
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Oide S, Gunji W, Moteki Y, Yamamoto S, Suda M, Jojima T, Yukawa H, Inui M. Thermal and solvent stress cross-tolerance conferred to Corynebacterium glutamicum by adaptive laboratory evolution. Appl Environ Microbiol 2015; 81:2284-98. [PMID: 25595768 PMCID: PMC4357955 DOI: 10.1128/aem.03973-14] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 01/12/2015] [Indexed: 11/20/2022] Open
Abstract
Reinforcing microbial thermotolerance is a strategy to enable fermentation with flexible temperature settings and thereby to save cooling costs. Here, we report on adaptive laboratory evolution (ALE) of the amino acid-producing bacterium Corynebacterium glutamicum under thermal stress. After 65 days of serial passage of the transgenic strain GLY3, in which the glycolytic pathway is optimized for alanine production under oxygen deprivation, three strains adapted to supraoptimal temperatures were isolated, and all the mutations they acquired were identified by whole-genome resequencing. Of the 21 mutations common to the three strains, one large deletion and two missense mutations were found to promote growth of the parental strain under thermal stress. Additive effects on thermotolerance were observed among these mutations, and the combination of the deletion with the missense mutation on otsA, encoding a trehalose-6-phosphate synthase, allowed the parental strain to overcome the upper limit of growth temperature. Surprisingly, the three evolved strains acquired cross-tolerance for isobutanol, which turned out to be partly attributable to the genomic deletion associated with the enhanced thermotolerance. The deletion involved loss of two transgenes, pfk and pyk, encoding the glycolytic enzymes, in addition to six native genes, and elimination of the transgenes, but not the native genes, was shown to account for the positive effects on thermal and solvent stress tolerance, implying a link between energy-producing metabolism and bacterial stress tolerance. Overall, the present study provides evidence that ALE can be a powerful tool to refine the phenotype of C. glutamicum and to investigate the molecular bases of stress tolerance.
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Affiliation(s)
- Shinichi Oide
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Wataru Gunji
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Yasuhiro Moteki
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Shogo Yamamoto
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Masako Suda
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Toru Jojima
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Hideaki Yukawa
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kizugawa, Kyoto, Japan Graduate School of Biological Sciences, Nara Institute of Science and Technology, Takayama, Ikoma, Nara, Japan
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Xiong H, Yang Y, Hu XP, He YM, Ma BG. Sequence determinants of prokaryotic gene expression level under heat stress. Gene 2014; 551:92-102. [PMID: 25168890 DOI: 10.1016/j.gene.2014.08.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
Abstract
Prokaryotic gene expression is environment-dependent and temperature plays an important role in shaping the gene expression profile. Revealing the regulation mechanisms of gene expression pertaining to temperature has attracted tremendous efforts in recent years particularly owning to the yielding of transcriptome and proteome data by high-throughput techniques. However, most of the previous works concentrated on the characterization of the gene expression profile of individual organism and little effort has been made to disclose the commonality among organisms, especially for the gene sequence features. In this report, we collected the transcriptome and proteome data measured under heat stress condition from recently published literature and studied the sequence determinants for the expression level of heat-responsive genes on multiple layers. Our results showed that there indeed exist commonness and consistent patterns of the sequence features among organisms for the differentially expressed genes under heat stress condition. Some features are attributed to the requirement of thermostability while some are dominated by gene function. The revealed sequence determinants of bacterial gene expression level under heat stress complement the knowledge about the regulation factors of prokaryotic gene expression responding to the change of environmental conditions. Furthermore, comparisons to thermophilic adaption have been performed to reveal the similarity and dissimilarity of the sequence determinants for the response to heat stress and for the adaption to high habitat temperature, which elucidates the complex landscape of gene expression related to the same physical factor of temperature.
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Affiliation(s)
- Heng Xiong
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Yang
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao-Pan Hu
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Ming He
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin-Guang Ma
- Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Sowa SW, Baldea M, Contreras LM. Optimizing metabolite production using periodic oscillations. PLoS Comput Biol 2014; 10:e1003658. [PMID: 24901332 PMCID: PMC4046915 DOI: 10.1371/journal.pcbi.1003658] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 04/17/2014] [Indexed: 12/20/2022] Open
Abstract
Methods for improving microbial strains for metabolite production remain the subject of constant research. Traditionally, metabolic tuning has been mostly limited to knockouts or overexpression of pathway genes and regulators. In this paper, we establish a new method to control metabolism by inducing optimally tuned time-oscillations in the levels of selected clusters of enzymes, as an alternative strategy to increase the production of a desired metabolite. Using an established kinetic model of the central carbon metabolism of Escherichia coli, we formulate this concept as a dynamic optimization problem over an extended, but finite time horizon. Total production of a metabolite of interest (in this case, phosphoenolpyruvate, PEP) is established as the objective function and time-varying concentrations of the cellular enzymes are used as decision variables. We observe that by varying, in an optimal fashion, levels of key enzymes in time, PEP production increases significantly compared to the unoptimized system. We demonstrate that oscillations can improve metabolic output in experimentally feasible synthetic circuits.
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Affiliation(s)
- Steven W. Sowa
- Microbiology Graduate Program, University of Texas at Austin, Austin, Texas, United States of America
| | - Michael Baldea
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (MB); (LMC)
| | - Lydia M. Contreras
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, United States of America
- * E-mail: (MB); (LMC)
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Erm S, Adamberg K, Vilu R. Multiplying steady-state culture in multi-reactor system. Bioprocess Biosyst Eng 2014; 37:2361-70. [DOI: 10.1007/s00449-014-1214-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 05/06/2014] [Indexed: 11/24/2022]
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Physiological and proteomic analysis of Escherichia coli iron-limited chemostat growth. J Bacteriol 2014; 196:2748-61. [PMID: 24837288 DOI: 10.1128/jb.01606-14] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Iron bioavailability is a major limiter of bacterial growth in mammalian host tissue and thus represents an important area of study. Escherichia coli K-12 metabolism was studied at four levels of iron limitation in chemostats using physiological and proteomic analyses. The data documented an E. coli acclimation gradient where progressively more severe iron scarcity resulted in a larger percentage of substrate carbon being directed into an overflow metabolism accompanied by a decrease in biomass yield on glucose. Acetate was the primary secreted organic by-product for moderate levels of iron limitation, but as stress increased, the metabolism shifted to secrete primarily lactate (∼70% of catabolized glucose carbon). Proteomic analysis reinforced the physiological data and quantified relative increases in glycolysis enzyme abundance and decreases in tricarboxylic acid (TCA) cycle enzyme abundance with increasing iron limitation stress. The combined data indicated that E. coli responds to limiting iron by investing the scarce resource in essential enzymes, at the cost of catabolic efficiency (i.e., downregulating high-ATP-yielding pathways containing enzymes with large iron requirements, like the TCA cycle). Acclimation to iron-limited growth was contrasted experimentally with acclimation to glucose-limited growth to identify both general and nutrient-specific acclimation strategies. While the iron-limited cultures maximized biomass yields on iron and increased expression of iron acquisition strategies, the glucose-limited cultures maximized biomass yields on glucose and increased expression of carbon acquisition strategies. This study quantified ecologically competitive acclimations to nutrient limitations, yielding knowledge essential for understanding medically relevant bacterial responses to host and to developing intervention strategies.
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Alam M, Ghosh W. Optimization of a phenol extraction-based protein preparation method amenable to downstream 2DE and MALDI-MS based analysis of bacterial proteomes. Proteomics 2014; 14:216-21. [DOI: 10.1002/pmic.201300146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 10/25/2013] [Accepted: 11/25/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Masrure Alam
- Department of Microbiology; Bose Institute; Kolkata India
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Harikrishnan H, Ismail A, Banga Singh KK. Temperature-regulated expression of outer membrane proteins in Shigella flexneri. Gut Pathog 2013; 5:38. [PMID: 24330657 PMCID: PMC4029548 DOI: 10.1186/1757-4749-5-38] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 11/18/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteria exist widely in a diversity of natural environments. In order to survive adverse conditions such as nutrient depletion, biochemical and biological disturbances, and high temperature, bacteria have developed a wide variety of coping mechanisms. Temperature is one of the most important factors that can enhance the expression of microbial proteins. This study was conducted to investigate how outer membrane proteins (OMPs) of the bacterium Shigella flexneri respond to stress, especially during fever when the host's body temperature is elevated. METHODS OMPs of S. flexneri ATCC 12022 and clinical isolate SH057 were extracted from an overnight culture grown at 37, 38.5, and 40°C. Comparisons of the expressed proteins under the different growth conditions were based on equal numbers of bacterial cells loaded in the SDS-PAGE gels. Separated proteins were stained with Coomassie brilliant blue. Selected proteins showing increased expression at 38.5 and 40°C were characterized by performing MALDI-ToF-ToF. RESULTS Different degrees of expression were demonstrated for different proteins expressed at 37°C compared to 38.5 and 40°C. The proteins with molecular sizes of 18.4, 25.6, and 57.0 kDa showed increased expression level at increasing temperature and were identified as Dps, WrbA, and PepA, respectively. CONCLUSION This study revealed that strains of S. flexneri respond at the proteomic level during stress caused by elevated temperature by decreasing the expression of proteins, maintaining the level of important proteins, or enhancing the levels of proteins presumably involved in survival and virulence.
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Affiliation(s)
| | | | - Kirnpal-Kaur Banga Singh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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Wilson CM, Yang S, Rodriguez M, Ma Q, Johnson CM, Dice L, Xu Y, Brown SD. Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:131. [PMID: 24028713 PMCID: PMC3848806 DOI: 10.1186/1754-6834-6-131] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 09/04/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. A previous C. thermocellum ethanol stress study showed that the largest transcriptomic response was in genes and proteins related to nitrogen uptake and metabolism. RESULTS In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68°C respectively to investigate general and specific physiological and regulatory stress responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and fermentation product determinations and compared to a published dataset from an ethanol stress study. Urea uptake genes were induced following furfural stress, but not to the same extent as ethanol stress and transcription from these genes was largely unaffected by heat stress. The largest transcriptomic response to furfural stress was genes for sulfate transporter subunits and enzymes in the sulfate assimilatory pathway, although these genes were also affected late in the heat and ethanol stress responses. Lactate production was higher in furfural treated culture, although the lactate dehydrogenase gene was not differentially expressed under this condition. Other redox related genes such as a copy of the rex gene, a bifunctional acetaldehyde-CoA/alcohol dehydrogenase and adjacent genes did show lower expression after furfural stress compared to the control, heat and ethanol fermentation profiles. Heat stress induced expression from chaperone related genes and overlap was observed with the responses to the other stresses. This study suggests the involvement of C. thermocellum genes with functions in oxidative stress protection, electron transfer, detoxification, sulfur and nitrogen acquisition, and DNA repair mechanisms in its stress responses and the use of different regulatory networks to coordinate and control adaptation. CONCLUSIONS This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism's physiology and regulation.
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Affiliation(s)
- Charlotte M Wilson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Present address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Qin Ma
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
| | - Courtney M Johnson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Lezlee Dice
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Ying Xu
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Rangeshwaran R, Ashwitha K, Sivakumar G, Jalali SK. Analysis of Proteins Expressed by an Abiotic Stress Tolerant Pseudomonas putida (NBAII-RPF9) Isolate Under Saline and High Temperature Conditions. Curr Microbiol 2013; 67:659-67. [DOI: 10.1007/s00284-013-0416-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 06/05/2013] [Indexed: 11/24/2022]
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Michta E, Schad K, Blin K, Ort-Winklbauer R, Röttig M, Kohlbacher O, Wohlleben W, Schinko E, Mast Y. The bifunctional role of aconitase in Streptomyces viridochromogenes Tü494. Environ Microbiol 2012; 14:3203-19. [PMID: 23116164 DOI: 10.1111/1462-2920.12006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/24/2012] [Indexed: 12/01/2022]
Abstract
In many organisms, aconitases have dual functions; they serve as enzymes in the tricarboxylic acid cycle and as regulators of iron metabolism. In this study we defined the role of the aconitase AcnA in Streptomyces viridochromogenes Tü494, the producer of the herbicide phosphinothricyl-alanyl-alanine, also known as phosphinothricin tripeptide or bialaphos. A mutant in which the aconitase gene acnA was disrupted showed severe defects in morphology and physiology, as it was unable to form any aerial mycelium, spores nor phosphinothricin tripeptide. AcnA belongs to the iron regulatory proteins (IRPs). In addition to its catalytic function, AcnA plays a regulatory role by binding to iron responsive elements (IREs) located on the untranslated region of certain mRNAs. A mutation preventing the formation of the [4Fe-4S] cluster of AcnA eliminated its catalytic activity, but did not inhibit RNA-binding ability. In silico analysis of the S. viridochromogenes genome revealed several IRE-like structures. One structure is located upstream of recA, which is involved in the bacterial SOS response, and another one was identified upstream of ftsZ, which is required for the onset of sporulation in streptomycetes. The functionality of different IRE structures was proven with gel shift assays and specific IRE consensus sequences were defined. Furthermore, RecA was shown to be upregulated on post-transcriptional level under oxidative stress conditions in the wild-type strain but not in the acnA mutant, suggesting a regulatory role of AcnA in oxidative stress response.
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Affiliation(s)
- Ewelina Michta
- Interfakultäres Institut für Mikrobiologie und Infektionsmedizin (IMIT), Mikrobiologie/Biotechnologie, Fakultät für Biologie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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Differential proteome analysis of a selected bacterial strain isolated from a high background radiation area in response to radium stress. J Proteomics 2012; 75:4820-32. [DOI: 10.1016/j.jprot.2012.05.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 04/24/2012] [Accepted: 05/13/2012] [Indexed: 10/28/2022]
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35
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Bower DM, Lee KS, Ram RJ, Prather KL. Fed-batch microbioreactor platform for scale down and analysis of a plasmid DNA production process. Biotechnol Bioeng 2012; 109:1976-86. [DOI: 10.1002/bit.24498] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/07/2012] [Accepted: 03/08/2012] [Indexed: 02/03/2023]
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36
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Lara-Ortíz T, Castro-Dorantes J, Ramírez-Santos J, Gómez-Eichelmann MC. Role of the DnaK-ClpB bichaperone system in DNA gyrase reactivation during a severe heat-shock response in Escherichia coli. Can J Microbiol 2012; 58:195-9. [PMID: 22263929 DOI: 10.1139/w11-118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In Escherichia coli cells, an increase in temperature induces immediate DNA relaxation, followed by the fast recovery of DNA supercoiling. DNA gyrase, proteins synthesized during heat stress, and chaperone DnaK have been proposed to participate in this recovery. However, the mechanism of DNA supercoiling recovery has not been completely elucidated. The results presented here suggest that in cells exposed to severe heat-shock stress, DNA supercoiling levels are recovered by the reactivation of DNA gyrase. This reactivation involves solubilization of a fraction of protein GyrA present in protein aggregates, by the bichaperone DnaK-ClpB system.
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Affiliation(s)
- Teresa Lara-Ortíz
- Departamento de Bioquímica, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México D.F, México
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Gonçalves GAL, Bower DM, Prazeres DMF, Monteiro GA, Prather KLJ. Rational engineering of Escherichia coli strains for plasmid biopharmaceutical manufacturing. Biotechnol J 2011; 7:251-61. [PMID: 21913330 DOI: 10.1002/biot.201100062] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2011] [Revised: 06/10/2011] [Accepted: 07/08/2011] [Indexed: 01/08/2023]
Abstract
Plasmid DNA (pDNA) has become very attractive as a biopharmaceutical, especially for gene therapy and DNA vaccination. Currently, there are a few products licensed for veterinary applications and numerous plasmids in clinical trials for use in humans. Recent work in both academia and industry demonstrates a need for technological and economical improvement in pDNA manufacturing. Significant progress has been achieved in plasmid design and downstream processing, but there is still a demand for improved production strains. This review focuses on engineering of Escherichia coli strains for plasmid DNA production, understanding the differences between the traditional use of pDNA for recombinant protein production and its role as a biopharmaceutical. We will present recent developments in engineering of E. coli strains, highlight essential genes for improvement of pDNA yield and quality, and analyze the impact of various process strategies on gene expression in pDNA production strains.
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Affiliation(s)
- Geisa A L Gonçalves
- Department of Bioengineering, Instituto Superior Técnico (IST), Lisbon, Portugal
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Korneli C, David F, Godard T, Franco-Lara E. Influence of fructose and oxygen gradients on fed-batch recombinant protein production using Bacillus megaterium. Eng Life Sci 2011. [DOI: 10.1002/elsc.201000161] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Jia M, Souchelnytskyi S. Proteome profiling of heat shock of human primary breast epithelial cells, a dataset report. Cell Stress Chaperones 2011; 16:459-67. [PMID: 21221872 PMCID: PMC3118829 DOI: 10.1007/s12192-010-0253-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 12/13/2010] [Accepted: 12/17/2010] [Indexed: 01/24/2023] Open
Abstract
Exposure to elevated temperatures has a strong effect on cell functions, and is used in clinical practice. Hyperthermia may affect multiple regulatory mechanisms in cells. To understand better the response to hyperthermia of immortalized primary human breast epithelial cells, we performed a proteomics study of these cells cultured at 34°C or 39°C. Twenty-four proteins were shown to be differentially expressed due to hyperthermia. Analysis of these proteins showed the potential involvement of various biological processes in response to hyperthermia, e.g., cell adhesion, cell communication, and cell cycle. Transforming growth factor-β2 (TGF-β2) and heat shock protein 27 (HSP27) were found to be upregulated at 39°C. TGF-β2 was found to affect expression of HSP27, and to have a protective role in hyperthermia-induced cell death. Thus, the dataset described here of hyperthermia-related proteins in human primary breast epithelial cells predicts a number of cellular activities affected by exposure to high temperatures and provides a set of proteins for further studies.
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Affiliation(s)
- Min Jia
- Department of Oncology-Pathology, Karolinska Biomics Center, Karolinska Institutet, Stockholm, Sweden.
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40
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Wu D, He J, Gong Y, Chen D, Zhu X, Qiu N, Sun M, Li M, Yu Z. Proteomic analysis reveals the strategies of Bacillus thuringiensis
YBT-1520 for survival under long-term heat stress. Proteomics 2011; 11:2580-91. [DOI: 10.1002/pmic.201000392] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 03/04/2011] [Accepted: 03/14/2011] [Indexed: 11/05/2022]
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Buranajitpakorn S, Piwkam A, Charoenlap N, Vattanaviboon P, Mongkolsuk S. Genes for hydrogen peroxide detoxification and adaptation contribute to protection against heat shock in Xanthomonas campestris pv. campestris. FEMS Microbiol Lett 2011; 317:60-6. [PMID: 21219417 DOI: 10.1111/j.1574-6968.2011.02211.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Xanthomonas campestris pv. campestris, a soil-borne plant-pathogenic bacterium, is exposed to multiple stresses in the environment and during interaction with a host plant. The roles of hydrogen peroxide (H(2) O(2) )-protective genes (katA, katG, and ahpC) and a peroxide sensor/transcription regulator (oxyR) in the viability of X. campestris pv. campestris at an elevated temperature were evaluated. The single katA and katG mutants showed moderate decreased survival after the heat treatment, while the double katA-katG and oxyR mutants were the most vulnerable to the heat treatment compared with a wild-type strain. However, ahpC provided no protective function against the heat treatment. Flow cytometric analysis revealed an increased accumulation of peroxide in cells treated with heat. Altogether, the data revealed a crucial role of genes in the H(2) O(2) detoxification system for protection against lethal heat shock in X. campestris pv. campestris.
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Bull AT. The renaissance of continuous culture in the post-genomics age. J Ind Microbiol Biotechnol 2010; 37:993-1021. [PMID: 20835748 DOI: 10.1007/s10295-010-0816-4] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 08/11/2010] [Indexed: 01/08/2023]
Abstract
The development of continuous culture techniques 60 years ago and the subsequent formulation of theory and the diversification of experimental systems revolutionised microbiology and heralded a unique period of innovative research. Then, progressively, molecular biology and thence genomics and related high-information-density omics technologies took centre stage and microbial growth physiology in general faded from educational programmes and research funding priorities alike. However, there has been a gathering appreciation over the past decade that if the claims of systems biology are going to be realised, they will have to be based on rigorously controlled and reproducible microbial and cell growth platforms. This revival of continuous culture will be long lasting because its recognition as the growth system of choice is firmly established. The purpose of this review, therefore, is to remind microbiologists, particularly those new to continuous culture approaches, of the legacy of what I call the first age of continuous culture, and to explore a selection of researches that are using these techniques in this post-genomics age. The review looks at the impact of continuous culture across a comprehensive range of microbiological research and development. The ability to establish (quasi-) steady state conditions is a frequently stated advantage of continuous cultures thereby allowing environmental parameters to be manipulated without causing concomitant changes in the specific growth rate. However, the use of continuous cultures also enables the critical study of specified transition states and chemical, physical or biological perturbations. Such dynamic analyses enhance our understanding of microbial ecology and microbial pathology for example, and offer a wider scope for innovative drug discovery; they also can inform the optimization of batch and fed-batch operations that are characterized by sequential transitions states.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury, Kent CT27NJ, UK.
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