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Hertle E, Ursinus A, Martin J. Low-temperature features of the psychrophilic chaperonin from Pseudoalteromonas haloplanktis. Arch Microbiol 2024; 206:299. [PMID: 38861015 PMCID: PMC11166852 DOI: 10.1007/s00203-024-04019-y] [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: 03/28/2024] [Accepted: 05/25/2024] [Indexed: 06/12/2024]
Abstract
Chaperonins from psychrophilic bacteria have been shown to exist as single-ring complexes. This deviation from the standard double-ring structure has been thought to be a beneficial adaptation to the cold environment. Here we show that Cpn60 from the psychrophile Pseudoalteromonas haloplanktis (Ph) maintains its double-ring structure also in the cold. A strongly reduced ATPase activity keeps the chaperonin in an energy-saving dormant state, until binding of client protein activates it. Ph Cpn60 in complex with co-chaperonin Ph Cpn10 efficiently assists in protein folding up to 55 °C. Moreover, we show that recombinant expression of Ph Cpn60 can provide its host Escherichia coli with improved viability under low temperature growth conditions. These properties of the Ph chaperonin may make it a valuable tool in the folding and stabilization of psychrophilic proteins.
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Affiliation(s)
- Eva Hertle
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Astrid Ursinus
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Jörg Martin
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
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2
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Nowak JS, Otzen DE. Helping proteins come in from the cold: 5 burning questions about cold-active enzymes. BBA ADVANCES 2023; 5:100104. [PMID: 38162634 PMCID: PMC10755280 DOI: 10.1016/j.bbadva.2023.100104] [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: 07/10/2023] [Revised: 08/21/2023] [Accepted: 09/05/2023] [Indexed: 01/03/2024] Open
Abstract
Enzymes from psychrophilic (cold-loving) organisms have attracted considerable interest over the past decades for their potential in various low-temperature industrial processes. However, we still lack large-scale commercialization of their activities. Here, we review their properties, limitations and potential. Our review is structured around answers to 5 central questions: 1. How do cold-active enzymes achieve high catalytic rates at low temperatures? 2. How is protein flexibility connected to cold-activity? 3. What are the sequence-based and structural determinants for cold-activity? 4. How does the thermodynamic stability of psychrophilic enzymes reflect their cold-active capabilities? 5. How do we effectively identify novel cold-active enzymes, and can we apply them in an industrial context? We conclude that emerging screening technologies combined with big-data handling and analysis make it reasonable to expect a bright future for our understanding and exploitation of cold-active enzymes.
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Affiliation(s)
- Jan Stanislaw Nowak
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
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3
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Saroha P, Rathore AS. Production of bioactive recombinant monoclonal antibody fragment in periplasm of Escherichia coli expression system. Prep Biochem Biotechnol 2023; 53:1288-1296. [PMID: 37040146 DOI: 10.1080/10826068.2023.2195482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
The microbial expression system (Escherichia coli) is the most widely studied host for the production of biotherapeutic products, such as antibody fragments, single chain variable fragments and nanobodies. However, recombinant biotherapeutic proteins are often expressed as insoluble proteins, thereby limiting the utility of E. coli as expression system. To overcome this limitation, various strategies have been developed, such as changes at DNA level (codon optimization), fusion with soluble tags and variations in process parameters (temperature), and inducer concentration. However, there is no "one size fits all" strategy. The most commonly used approach involves induction at low temperature, as reducing the temperature during cultivation has been reported to increase bioactive protein production in E. coli. In this study, we examine the impact of various process parameters, such as temperature and inducer concentration, as well as, high plasmid copy number vector for achieving enhanced soluble expression of TNFα inhibitor Fab. An interaction amongst these parameters has been observed and their optimization has been demonstrated to result in expression of 30 ± 3 mg/L antibody fragment using E. coli. This case study illustrates how process optimization can contribute toward making biotherapeutics affordable.
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Affiliation(s)
- Preeti Saroha
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, New Delhi, India
| | - Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, New Delhi, India
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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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Pouresmaeil M, Azizi-Dargahlou S. Factors involved in heterologous expression of proteins in E. coli host. Arch Microbiol 2023; 205:212. [PMID: 37120438 PMCID: PMC10148705 DOI: 10.1007/s00203-023-03541-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/26/2023] [Accepted: 04/05/2023] [Indexed: 05/01/2023]
Abstract
The production of recombinant proteins is one of the most significant achievements of biotechnology in the last century. These proteins are produced in the eukaryotic or prokaryotic heterologous hosts. By increasing the omics data especially related to different heterologous hosts as well as the presence of new amenable genetic engineering tools, we can artificially engineer heterologous hosts to produce recombinant proteins in sufficient quantities. Numerous recombinant proteins have been produced and applied in various industries, and the global recombinant proteins market size is expected to be cast to reach USD 2.4 billion by 2027. Therefore, identifying the weakness and strengths of heterologous hosts is critical to optimize the large-scale biosynthesis of recombinant proteins. E. coli is one of the popular hosts to produce recombinant proteins. Scientists reported some bottlenecks in this host, and due to the increasing demand for the production of recombinant proteins, there is an urgent need to improve this host. In this review, we first provide general information about the E. coli host and compare it with other hosts. In the next step, we describe the factors involved in the expression of the recombinant proteins in E. coli. Successful expression of recombinant proteins in E. coli requires a complete elucidation of these factors. Here, the characteristics of each factor will be fully described, and this information can help to improve the heterologous expression of recombinant proteins in E. coli.
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Affiliation(s)
- Mahin Pouresmaeil
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Shahnam Azizi-Dargahlou
- Agricultural Biotechnology, Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran.
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6
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Danchin A, Huang JD. SynBio 2.0, a new era for synthetic life: Neglected essential functions for resilience. Environ Microbiol 2023; 25:64-78. [PMID: 36045561 DOI: 10.1111/1462-2920.16140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 07/16/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Jian Dong Huang
- School of Biomedical Sciences, Li KaShing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
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7
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Falak S, Sajed M, Rashid N. Strategies to enhance soluble production of heterologous proteins in Escherichia coli. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-021-00994-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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8
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Streamlining cell-free protein synthesis biosensors for use in human fluids: In situ RNase inhibitor production during extract preparation. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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9
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Kumari M, Padhi S, Sharma S, Phukon LC, Singh SP, Rai AK. Biotechnological potential of psychrophilic microorganisms as the source of cold-active enzymes in food processing applications. 3 Biotech 2021; 11:479. [PMID: 34790503 DOI: 10.1007/s13205-021-03008-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/29/2021] [Indexed: 12/13/2022] Open
Abstract
Microorganisms striving in extreme environments and exhibiting optimal growth and reproduction at low temperatures, otherwise known as psychrophilic microorganisms, are potential sources of cold-active enzymes. Owing to higher stability and cold activity, these enzymes are gaining enormous attention in numerous industrial bioprocesses. Applications of several cold-active enzymes have been established in the food industry, e.g., β-galactosidase, pectinase, proteases, amylases, xylanases, pullulanases, lipases, and β-mannanases. The enzyme engineering approaches and the accumulating knowledge of protein structure and function have made it possible to improve the catalytic properties of interest and express the candidate enzyme in a heterologous host for a higher level of enzyme production. This review compiles the relevant and recent information on the potential uses of different cold-active enzymes in the food industry.
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Affiliation(s)
- Megha Kumari
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Swati Sharma
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Loreni Chiring Phukon
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
| | - Sudhir P Singh
- Centre of Innovative and Applied Bioprocessing, Mohali, India
| | - Amit Kumar Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Sikkim, India
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10
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Ebner JN, Ritz D, von Fumetti S. Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata. Sci Rep 2020; 10:15538. [PMID: 32968134 PMCID: PMC7512004 DOI: 10.1038/s41598-020-72569-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023] Open
Abstract
Deducing impacts of environmental change on species and the populations they form in nature is an important goal in contemporary ecology. Achieving this goal is hampered by our limited understanding of the influence of naturally occurring environmental variation on the molecular systems of ecologically relevant species, as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms and under controlled laboratory conditions. Here, to test the hypothesis that proteome variation systematically relates to variation in abiotic conditions, we establish such relationships by profiling the proteomes of 24 natural populations of the spring-dwelling caddisfly Crunoecia irrorata. We identified protein networks whose abundances correlated with environmental (abiotic) gradients such as in situ pH, oxygen- and nitrate concentrations but also climatic data such as past thermal minima and temperature seasonality. Our analyses suggest that variations in abiotic conditions induce discrete proteome responses such as the differential abundance of proteins associated with cytoskeletal function, heat-shock proteins and proteins related to post-translational modification. Identifying these drivers of proteome divergence characterizes molecular "noise", and positions it as a background against which molecular signatures of species' adaptive responses to stressful conditions can be identified.
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Affiliation(s)
- Joshua Niklas Ebner
- Geoecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Danilo Ritz
- Proteomics Core Facility, University of Basel, Biozentrum Basel, Switzerland
| | - Stefanie von Fumetti
- Geoecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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11
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Gregson BH, Metodieva G, Metodiev MV, Golyshin PN, McKew BA. Protein expression in the obligate hydrocarbon-degrading psychrophile Oleispira antarctica RB-8 during alkane degradation and cold tolerance. Environ Microbiol 2020; 22:1870-1883. [PMID: 32090431 PMCID: PMC7318663 DOI: 10.1111/1462-2920.14956] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/15/2022]
Abstract
In cold marine environments, the obligate hydrocarbon‐degrading psychrophile Oleispira antarctica RB‐8, which utilizes aliphatic alkanes almost exclusively as substrates, dominates microbial communities following oil spills. In this study, LC–MS/MS shotgun proteomics was used to identify changes in the proteome induced during growth on n‐alkanes and in cold temperatures. Specifically, proteins with significantly higher relative abundance during growth on tetradecane (n‐C14) at 16°C and 4°C have been quantified. During growth on n‐C14, O. antarctica expressed a complete pathway for the terminal oxidation of n‐alkanes including two alkane monooxygenases, two alcohol dehydrogenases, two aldehyde dehydrogenases, a fatty‐acid‐CoA ligase, a fatty acid desaturase and associated oxidoreductases. Increased biosynthesis of these proteins ranged from 3‐ to 21‐fold compared with growth on a non‐hydrocarbon control. This study also highlights mechanisms O. antarctica may utilize to provide it with ecological competitiveness at low temperatures. This was evidenced by an increase in spectral counts for proteins involved in flagella structure/output to overcome higher viscosity, flagella rotation to accumulate cells and proline metabolism to counteract oxidative stress, during growth at 4°C compared with 16°C. Such species‐specific understanding of the physiology during hydrocarbon degradation can be important for parameterizing models that predict the fate of marine oil spills.
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Affiliation(s)
- Benjamin H Gregson
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Gergana Metodieva
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Metodi V Metodiev
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
| | - Peter N Golyshin
- School of Natural Sciences, College of Environmental Sciences and Engineering, Bangor University, Bangor, UK.,Centre for Environmental Biotechnology, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
| | - Boyd A McKew
- School of Life Sciences, University of Essex, Colchester, Essex, CO4 3SQ, UK
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12
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Enhancing the synthesis of latex clearing protein by different cultivation strategies. J Biotechnol 2019; 297:32-40. [DOI: 10.1016/j.jbiotec.2019.03.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/29/2019] [Accepted: 03/29/2019] [Indexed: 02/06/2023]
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13
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Kubát P, Henke P, Mosinger J. The effect of iodide and temperature on enhancing antibacterial properties of nanoparticles with an encapsulated photosensitizer. Colloids Surf B Biointerfaces 2019; 176:334-340. [PMID: 30654240 DOI: 10.1016/j.colsurfb.2019.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/12/2018] [Accepted: 01/06/2019] [Indexed: 01/25/2023]
Abstract
Aqueous dispersions of sulfonated polystyrene nanoparticles (average diameter: 30 ± 14 nm) with encapsulated 5,10,15,20-tetraphenylporphyrin (TPP) are promising candidates for antibacterial treatments due to the photogeneration of cytotoxic singlet oxygen species O2(1Δg) under physiological conditions using visible light. The antibacterial effect on gram-negative Escherichia coli was significantly enhanced after the addition of nontoxic potassium iodide (0.001-0.01 M) because photogenerated O2(1Δg) oxidized iodide to I2/I3-, which is another antibacterial species. The improved antibacterial properties were predicted using luminescence measurements of O2(1Δg), transient absorption of TPP triplets and singlet oxygen-sensitized delayed fluorescence (SODF). In contrast to a solution of free photosensitizers, the aqueous dispersion of photoactive nanoparticles did not exhibit any quenching of the excited states after the addition of iodide or any tendency toward aggregation and/or I3--induced photo-aggregation. We also observed a decrease in the lifetime of O2(1Δg) and a significant increase in SODF intensity at higher temperatures, due to the increased oxygen diffusion coefficient in nanoparticles and aqueous surroundings. This effect corresponds with the significantly stronger antibacterial effect of nanoparticles at physiological temperature (37 °C) in comparison with that at room temperature (25 °C).
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Affiliation(s)
- Pavel Kubát
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, v.v.i., Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Petr Henke
- Department of Inorganic Chemistry, Faculty of Science, Charles University, 2030 Hlavova, 128 43 Prague 2, Czech Republic
| | - Jiří Mosinger
- Department of Inorganic Chemistry, Faculty of Science, Charles University, 2030 Hlavova, 128 43 Prague 2, Czech Republic; Institute of Inorganic Chemistry of the Czech Academy of Sciences, v.v.i., Husinec-Řež 1001, 250 68 Řež, Czech Republic.
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14
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Wong CMVL, Boo SY, Voo CLY, Zainuddin N, Najimudin N. A comparative transcriptomic analysis provides insights into the cold-adaptation mechanisms of a psychrophilic yeast, Glaciozyma antarctica PI12. Polar Biol 2019. [DOI: 10.1007/s00300-018-02443-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Yokoi T, Itaya M, Mori H, Kataoka M. Optimization of RK2-based gene introduction system for Bacillus subtilis. J GEN APPL MICROBIOL 2019; 65:265-272. [DOI: 10.2323/jgam.2018.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Takahiro Yokoi
- Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | | | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology
| | - Masakazu Kataoka
- Interdisciplinary Graduate School of Science and Technology, Shinshu University
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16
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17
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Enhanced expression and purification of camelid single domain VHH antibodies from classical inclusion bodies. Protein Expr Purif 2017; 136:39-44. [DOI: 10.1016/j.pep.2017.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/10/2017] [Accepted: 02/11/2017] [Indexed: 01/05/2023]
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18
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The molecular basis of talin2's high affinity toward β1-integrin. Sci Rep 2017; 7:41989. [PMID: 28155884 PMCID: PMC5290461 DOI: 10.1038/srep41989] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/04/2017] [Indexed: 01/16/2023] Open
Abstract
Talin interacts with β-integrin tails and actin to control integrin activation, thus regulating focal adhesion dynamics and cell migration. There are two talin genes, Tln1 and Tln2, which encode talin1 and talin2, and it is generally believed that talin2 functions redundantly with talin1. However, we show here that talin2 has a higher affinity to β1-integrin tails than talin1. Mutation of talin2 S339 to leucine, which can cause Fifth Finger Camptodactyly, a human genetic disease, completely disrupted its binding to β–integrin tails. Also, substitution of talin1 C336 with Ser enhanced the affinity of talin1, whereas substitution of talin2 S339 with Cys diminished that of talin2. Further computational modeling analysis shows that talin2 S339 formed a hydrogen bond with E353, which is critical for inducing key hydrogen bonds between talin2 N326 and β1-integrin R760, and between talin2 K327 and β1-integrin D759. Mutation at any of these residues significantly diminished the interaction of talin2 with β1- integrin tails. These hydrogen bonds were not observed in talin1/β1-integrin, but did exist in talin1C336S/β1-integrin complex. These results suggest that talin2 S339 forms a hydrogen bond with E353 to mediate its high affinity to β1-integrin.
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19
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Physical and molecular bases of protein thermal stability and cold adaptation. Curr Opin Struct Biol 2016; 42:117-128. [PMID: 28040640 DOI: 10.1016/j.sbi.2016.12.007] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/15/2016] [Accepted: 12/11/2016] [Indexed: 11/20/2022]
Abstract
The molecular bases of thermal and cold stability and adaptation, which allow proteins to remain folded and functional in the temperature ranges in which their host organisms live and grow, are still only partially elucidated. Indeed, both experimental and computational studies fail to yield a fully precise and global physical picture, essentially because all effects are context-dependent and thus quite intricate to unravel. We present a snapshot of the current state of knowledge of this highly complex and challenging issue, whose resolution would enable large-scale rational protein design.
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20
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King T, Kocharunchitt C, Gobius K, Bowman JP, Ross T. Physiological Response of Escherichia coli O157:H7 Sakai to Dynamic Changes in Temperature and Water Activity as Experienced during Carcass Chilling. Mol Cell Proteomics 2016; 15:3331-3347. [PMID: 27615263 PMCID: PMC5098033 DOI: 10.1074/mcp.m116.063065] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 09/04/2016] [Indexed: 02/03/2023] Open
Abstract
Enterohemeorrhagic Escherichia coli is a leading cause of foodborne illness, with the majority of cases linked to foods of bovine origin. Currently, no completely effective method for controlling this pathogen during carcass processing exists. Understanding how this pathogen behaves under those stress conditions experienced on the carcass during chilling in cold air could offer opportunities for development or improvement of effective decontamination processes. Therefore, we studied the growth kinetics and physiological response of exponential phase E. coli O157:H7 Sakai cultures upon an abrupt downshift in temperature and water activity (from 35 °C aw 0.993 to 14 °C aw 0.967). A parallel Biolog study was conducted to follow the phenotypic responses to 190 carbon sources. Exposure of E. coli to combined cold and water activity stresses resulted in a complex pattern of population changes. This pattern could be divided into two main phases, including adaptation and regrowth phases, based on growth kinetics and clustering analyses. The transcriptomic and proteomic studies revealed that E. coli exhibited a "window" of cell susceptibility (i.e. weaknesses) during adaptation phase. This included apparent DNA damage, the downregulation of molecular chaperones and proteins associated with responses to oxidative damage. However, E. coli also displayed a transient induction in the RpoE-controlled envelope stress response and activation of the master stress regulator RpoS and the Rcs phosphorelay system involved in colanic acid biosynthesis. Increased expression was observed for several genes and/or proteins involved in DNA repair, protein and peptide degradation, amino acid biosynthesis, and carbohydrate catabolism and energy generation. Furthermore, the Biolog study revealed reduced carbon source utilization during adaptation phase, indicating the disruption of energy-generating processes. This study provides insight into the physiological response of E. coli during exposure to combined cold and water activity stress, which could be exploited to enhance the microbiological safety of carcasses and related foods.
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Affiliation(s)
- Thea King
- From the ‡CSIRO Agriculture and Food, North Ryde, NSW 2113, Australia;
| | - Chawalit Kocharunchitt
- §Food Safety Centre, Tasmanian Institute of Agriculture, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia
| | - Kari Gobius
- ¶CSIRO Agriculture and Food, Werribee, VIC 3030, Australia
| | - John P Bowman
- §Food Safety Centre, Tasmanian Institute of Agriculture, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia
| | - Tom Ross
- §Food Safety Centre, Tasmanian Institute of Agriculture, School of Agricultural Science, University of Tasmania, Private Bag 54, Hobart TAS 7001, Australia
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21
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Hu B, Luo M, Ji X, Lin L, Wei Y, Zhang Q. Proteomic analysis of Mortierella isabellina M6-22 during cold stress. Arch Microbiol 2016; 198:869-76. [PMID: 27262947 DOI: 10.1007/s00203-016-1238-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 03/29/2016] [Accepted: 05/05/2016] [Indexed: 10/21/2022]
Abstract
We aimed to gain a better understanding of cold adaption in Mortierella isabellina M6-22 by using proteomics approaches. The temperature range and optimal temperature for M6-22 growth were investigated, and composition changes in fatty acids were analyzed. Accompanied with the 2-D gel electrophoresis, MALDI-TOF/TOF-MS analysis was conducted to characterize alterations in protein profiling in M6-22 cultured at 30 °C for 24 h and 15 °C for another 24 h when compared with those cultured at 30 °C for 48 h. Gene Ontology (GO) cluster analysis was finally conducted for successfully identified proteins. M6-22 cells could grow well at temperatures ranging from 15 to 30 °C. As temperature decreased from 30 to 15 °C, LA and GLA significantly increased from 11.63 to 17.85 % and from 9.12 to 13.19 %, respectively, while oleic acid significantly decreased from 47.25 to 36.53 %. Proteomics analyses revealed 111 differentially expressed protein spots, among which 5 unique proteins (A38, A40, A47, A49 and A58), 29 up-regulated proteins and 10 down-regulated proteins were identified by MALDI-TOF/TOF-MS. GO enrichment analysis demonstrated that these proteins mainly involved in glycolytic pathway (A34 and A50), electron transport (A28), ATP production (A35 and B39) and protein modification (A38). A total of 44 differentially expressed proteins have been successfully identified in M. isabellina M6-22 cultured at 15 °C. These proteins may play important roles in cold adaption via regulation of ATP synthesis, activation of cold-adaptive proteins, degradation of needless protein, accumulation of PUFAs, etc.
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Affiliation(s)
- Binbin Hu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Minzhou Luo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Xiuling Ji
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Lianbing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Yunlin Wei
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China
| | - Qi Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, China.
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22
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Jia J, Chen Y, Jiang Y, Li Z, Zhao L, Zhang J, Tang J, Feng L, Liang C, Xu B, Gu P, Ye X. Proteomic analysis of Vibrio metschnikovii under cold stress using a quadrupole Orbitrap mass spectrometer. Res Microbiol 2015; 166:618-25. [PMID: 26277298 DOI: 10.1016/j.resmic.2015.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 04/25/2015] [Accepted: 07/17/2015] [Indexed: 11/17/2022]
Abstract
Vibrio metschnikovii is a food-borne pathogen found in seafood worldwide. We studied the global proteome responses of V. metschnikovii under cold stress by nano-flow ultra-high-performance liquid chromatography coupled to a quadrupole Orbitrap mass spectrometer. A total of 2066 proteins were identified, among which 288 were significantly upregulated and 572 were downregulated. Functional categorization of these proteins revealed distinct differences between cold-stressed and control cells. Quantitative reverse transcription polymerase chain reaction analysis was also performed to determine the mRNA expression levels of seventeen cold stress-related genes. The results of this study should improve our understanding of the metabolic activities of cold-adapted bacteria and will facilitate a better systems-based understanding of V. metschnikovii.
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Affiliation(s)
- Juntao Jia
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Ying Chen
- Research Institute for Food Safety, Chinese Academy of Inspection and Quarantine, No. A3, Road Gaobeidian, 100123 Beijing, China.
| | - Yinghui Jiang
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Zhengyi Li
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Liqing Zhao
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Jian Zhang
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Jing Tang
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Liping Feng
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Chengzhu Liang
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Biao Xu
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
| | - Peiming Gu
- Demo Center of Thermo Fisher Scientific Inc., 201206 Shanghai, China
| | - Xiwen Ye
- Technological Center, Shandong Entry-Exit Inspection and Quarantine Bureau, 266002 Qingdao, China
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23
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Moreno R, Rojo F. Features of pseudomonads growing at low temperatures: another facet of their versatility. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:417-426. [PMID: 25646532 DOI: 10.1111/1758-2229.12150] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Pseudomonads are a diverse and ecologically successful group of γ-proteobacteria present in many environments (terrestrial, freshwater and marine), either free living or associated with plants or animals. Their success is at least partly based on their ability to grow over a wide range of temperatures, their capacity to withstand different kinds of stress and their great metabolic versatility. Although the optimal growth temperature of pseudomonads is usually close to 25–30°C, many strains can also grow between 5°C and 10°C, and some of them even close to 0°C. Such low temperatures strongly affect the physicochemical properties of macromolecules, forcing cells to evolve traits that optimize growth and help them withstand cold-induced stresses such as increased levels of reactive oxygen species, reduced membrane fluidity and enzyme activity, cold-induced protein denaturation and the greater stability of DNA and RNA secondary structures. This review gathers the information available on the strategies used by pseudomonads to adapt to low temperature growth, and briefly describes some of the biotechnological applications that might benefit from cold-adapted bacterial strains and enzymes, e.g., biotransformation or bioremediation processes to be performed at low temperatures.
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24
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García-Descalzo L, García-López E, Alcázar A, Baquero F, Cid C. Proteomic analysis of the adaptation to warming in the Antarctic bacteria Shewanella frigidimarina. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2229-40. [PMID: 25149826 DOI: 10.1016/j.bbapap.2014.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/06/2014] [Accepted: 08/11/2014] [Indexed: 12/27/2022]
Abstract
Antarctica is subjected to extremely variable conditions, but the importance of the temperature increase in cold adapted bacteria is still unknown. To study the molecular adaptation to warming of Antarctic bacteria, cultures of Shewanella frigidimarina were incubated at temperatures ranging from 0°C to 30°C, emulating the most extreme conditions that this strain could tolerate. A proteomic approach was developed to identify the soluble proteins obtained from cells growing at 4°C, 20°C and 28°C. The most drastic effect when bacteria were grown at 28°C was the accumulation of heat shock proteins as well as other proteins related to stress, redox homeostasis or protein synthesis and degradation, and the decrease of enzymes and components of the cell envelope. Furthermore, two main responses in the adaptation to warm temperature were detected: the presence of diverse isoforms in some differentially expressed proteins, and the composition of chaperone interaction networks at the limits of growth temperature. The abundance changes of proteins suggest that warming induces a stress situation in S. frigidimarina forcing cells to reorganize their molecular networks as an adaptive response to these environmental conditions.
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Affiliation(s)
| | - Eva García-López
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain
| | - Alberto Alcázar
- Department of Investigation, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Fernando Baquero
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain; Department of Microbiology, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiologia (CSIC-INTA), 28850 Torrejón de Ardoz, Spain.
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25
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King T, Kocharunchitt C, Gobius K, Bowman JP, Ross T. Global genome response of Escherichia coli O157∶H7 Sakai during dynamic changes in growth kinetics induced by an abrupt temperature downshift. PLoS One 2014; 9:e99627. [PMID: 24926786 PMCID: PMC4057180 DOI: 10.1371/journal.pone.0099627] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 05/17/2014] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli O157∶H7 is a mesophilic food-borne pathogen. We investigated the growth kinetics of E. coli O157∶H7 Sakai during an abrupt temperature downshift from 35°C to either 20°C, 17°C, 14°C or 10°C; as well as the molecular mechanisms enabling growth after cold stress upon an abrupt downshift from 35°C to 14°C in an integrated transcriptomic and proteomic analysis. All downshifts caused a lag period of growth before growth resumed at a rate typical of the post-shift temperature. Lag and generation time increased with the magnitude of the shift or with the final temperature, while relative lag time displayed little variation across the test range. Analysis of time-dependent molecular changes revealed, in keeping with a decreased growth rate at lower temperature, repression of genes and proteins involved in DNA replication, protein synthesis and carbohydrate catabolism. Consistent with cold-induced remodelling of the bacterial cell envelope, alterations occurred in the expression of genes and proteins involved in transport and binding. The RpoS regulon exhibited sustained induction confirming its importance in adaptation and growth at 14°C. The RpoE regulon was transiently induced, indicating a potential role for this extracytoplasmic stress response system in the early phase of low temperature adaptation during lag phase. Interestingly, genes previously reported to be amongst the most highly up-regulated under oxidative stress were consistently down-regulated. This comprehensive analysis provides insight into the molecular mechanisms operating during adaptation of E. coli to growth at low temperature and is relevant to its physiological state during chilling in foods, such as carcasses.
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Affiliation(s)
- Thea King
- Commonwealth Scientific and Industrial Research Organisation, Animal, Food and Health Sciences, North Ryde, New South Wales, Australia
- * E-mail:
| | - Chawalit Kocharunchitt
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Kari Gobius
- Commonwealth Scientific and Industrial Research Organisation, Animal, Food and Health Sciences, Werribee, Victoria, Australia
| | - John P. Bowman
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Tom Ross
- Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
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26
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Suchánek J, Henke P, Mosinger J, Zelinger Z, Kubát P. Effect of Temperature on Photophysical Properties of Polymeric Nanofiber Materials with Porphyrin Photosensitizers. J Phys Chem B 2014; 118:6167-74. [DOI: 10.1021/jp5029917] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jan Suchánek
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Praha 8, Czech Republic
- Faculty
of Safety Engineering, Technical University of Ostrava, Lumírova
13, Ostrava-Vyškovice, 700 30 Ostrava, Czech Republic
| | | | - Jiří Mosinger
- Faculty
of Science, Charles University in Prague, Hlavova 2030, 128 43 Praha 2, Czech Republic
- Institute
of Inorganic Chemistry, v.v.i., Academy of Sciences of the Czech Republic, 250 68 Řež, Czech Republic
| | - Zdeněk Zelinger
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Praha 8, Czech Republic
| | - Pavel Kubát
- J.
Heyrovský Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejškova 3, 18223 Praha 8, Czech Republic
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27
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Rosano GL, Ceccarelli EA. Recombinant protein expression in Escherichia coli: advances and challenges. Front Microbiol 2014; 5:172. [PMID: 24860555 PMCID: PMC4029002 DOI: 10.3389/fmicb.2014.00172] [Citation(s) in RCA: 1299] [Impact Index Per Article: 129.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 03/29/2014] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli is one of the organisms of choice for the production of recombinant proteins. Its use as a cell factory is well-established and it has become the most popular expression platform. For this reason, there are many molecular tools and protocols at hand for the high-level production of heterologous proteins, such as a vast catalog of expression plasmids, a great number of engineered strains and many cultivation strategies. We review the different approaches for the synthesis of recombinant proteins in E. coli and discuss recent progress in this ever-growing field.
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Affiliation(s)
- Germán L Rosano
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas Rosario, Argentina ; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
| | - Eduardo A Ceccarelli
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas Rosario, Argentina ; Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Rosario, Argentina
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28
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Deng LQ, Yu HQ, Liu YP, Jiao PP, Zhou SF, Zhang SZ, Li WC, Fu FL. Heterologous expression of antifreeze protein gene AnAFP from Ammopiptanthus nanus enhances cold tolerance in Escherichia coli and tobacco. Gene 2014; 539:132-40. [PMID: 24502990 DOI: 10.1016/j.gene.2014.01.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2013] [Revised: 01/02/2014] [Accepted: 01/03/2014] [Indexed: 11/23/2022]
Abstract
Antifreeze proteins are a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival under the subzero environments. Ammopiptanthus nanus is the unique evergreen broadleaf bush endemic to the Mid-Asia deserts. It survives at the west edge of the Tarim Basin from the disappearance of the ancient Mediterranean in the Tertiary Period. Its distribution region is characterized by the arid climate and extreme temperatures, where the extreme temperatures range from -30 °C to 40 °C. In the present study, the antifreeze protein gene AnAFP of A. nanus was used to transform Escherichia coli and tobacco, after bioinformatics analysis for its possible function. The transformed E. coli strain expressed the heterologous AnAFP gene under the induction of isopropyl β-D-thiogalactopyranoside, and demonstrated significant enhancement of cold tolerance. The transformed tobacco lines expressed the heterologous AnAFP gene in response to cold stress, and showed a less change of relative electrical conductivity under cold stress, and a less wilting phenotype after 16 h of -3 °C cold stress and thawing for 1h than the untransformed wild-type plants. All these results imply the potential value of the AnAFP gene to be used in genetic modification of commercially important crops for improvement of cold tolerance.
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Affiliation(s)
- Long-Qun Deng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Hao-Qiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Yan-Ping Liu
- Faculty of Plant Science, Tarim University, Alar, Xinjiang 843300, PR China
| | - Pei-Pei Jiao
- Faculty of Plant Science, Tarim University, Alar, Xinjiang 843300, PR China
| | - Shu-Feng Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Su-Zhi Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China
| | - Wan-Chen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
| | - Feng-Ling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, PR China.
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29
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Bakermans C, Skidmore ML, Douglas S, McKay CP. Molecular characterization of bacteria from permafrost of the Taylor Valley, Antarctica. FEMS Microbiol Ecol 2014; 89:331-46. [DOI: 10.1111/1574-6941.12310] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/18/2014] [Accepted: 02/19/2014] [Indexed: 12/01/2022] Open
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30
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Vestby LK, Johannesen KCS, Witsø IL, Habimana O, Scheie AA, Urdahl AM, Benneche T, Langsrud S, Nesse LL. Synthetic brominated furanone F202 prevents biofilm formation by potentially human pathogenic Escherichia coli O103:H2 and Salmonella ser. Agona on abiotic surfaces. J Appl Microbiol 2014; 116:258-68. [PMID: 24118802 PMCID: PMC4255294 DOI: 10.1111/jam.12355] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 09/23/2013] [Accepted: 09/24/2013] [Indexed: 02/07/2023]
Abstract
AIMS Investigate the use of a synthetic brominated furanone (F202) against the establishment of biofilm by Salmonella ser. Agona and E. coli O103:H2 under temperature conditions relevant for the food and feed industry as well as under temperature conditions optimum for growth. METHODS AND RESULTS Effect of F202 on biofilm formation by Salmonella ser. Agona and E. coli O103:H2 was evaluated using a microtiter plate assay and confocal microscopy. Effect of F202 on bacterial motility was investigated using swimming and swarming assays. Influence on flagellar synthesis by F202 was examined by flagellar staining. Results showed that F202 inhibited biofilm formation without being bactericidal. F202 was found to affect both swimming and swarming motility without, however, affecting the expression of flagella. CONCLUSIONS F202 showed its potential as a biofilm inhibitor of Salmonella ser. Agona and E. coli O103:H2 under temperature conditions relevant for the feed and food industry as well as temperatures optimum for growth. One potential mode of action of F202 was found to be by targeting flagellar function. SIGNIFICANCE AND IMPACT OF THE STUDY The present study gives valuable new knowledge to the potential use of furanones as a tool in biofilm management in the food and feed industry.
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Affiliation(s)
- L K Vestby
- Norwegian Veterinary Institute, Department of Laboratory Services, Section for Bacteriology- aquatic and terrestrial, Oslo, Norway
| | - K C S Johannesen
- Norwegian Veterinary Institute, Department of Laboratory Services, Section for Bacteriology- aquatic and terrestrial, Oslo, Norway
| | - I L Witsø
- Faculty of Dentistry, Department of Oral Biology, University of Oslo, Oslo, Norway
| | | | - A A Scheie
- Faculty of Dentistry, Department of Oral Biology, University of Oslo, Oslo, Norway
| | - A M Urdahl
- Norwegian Veterinary Institute, Department of Health Surveillance, Section for Veterinary Public Health, Oslo, Norway
| | - T Benneche
- Faculty of Mathematics and Natural Sciences, Department of Chemistry, University of Oslo, Oslo, Norway
| | | | - L L Nesse
- Norwegian Veterinary Institute, Department of Laboratory Services, Section for Bacteriology- aquatic and terrestrial, Oslo, Norway
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31
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Di Pasqua R, Mauriello G, Mamone G, Ercolini D. Expression of DnaK, HtpG, GroEL and Tf chaperones and the corresponding encoding genes during growth of Salmonella Thompson in presence of thymol alone or in combination with salt and cold stress. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.02.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Feller G. Psychrophilic enzymes: from folding to function and biotechnology. SCIENTIFICA 2013; 2013:512840. [PMID: 24278781 PMCID: PMC3820357 DOI: 10.1155/2013/512840] [Citation(s) in RCA: 162] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 11/06/2012] [Indexed: 05/10/2023]
Abstract
Psychrophiles thriving permanently at near-zero temperatures synthesize cold-active enzymes to sustain their cell cycle. Genome sequences, proteomic, and transcriptomic studies suggest various adaptive features to maintain adequate translation and proper protein folding under cold conditions. Most psychrophilic enzymes optimize a high activity at low temperature at the expense of substrate affinity, therefore reducing the free energy barrier of the transition state. Furthermore, a weak temperature dependence of activity ensures moderate reduction of the catalytic activity in the cold. In these naturally evolved enzymes, the optimization to low temperature activity is reached via destabilization of the structures bearing the active site or by destabilization of the whole molecule. This involves a reduction in the number and strength of all types of weak interactions or the disappearance of stability factors, resulting in improved dynamics of active site residues in the cold. These enzymes are already used in many biotechnological applications requiring high activity at mild temperatures or fast heat-inactivation rate. Several open questions in the field are also highlighted.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry, University of Liège, B6a, 4000 Liège, Belgium
- *Georges Feller:
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33
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Kube M, Chernikova TN, Al-Ramahi Y, Beloqui A, Lopez-Cortez N, Guazzaroni ME, Heipieper HJ, Klages S, Kotsyurbenko OR, Langer I, Nechitaylo TY, Lünsdorf H, Fernández M, Juárez S, Ciordia S, Singer A, Kagan O, Egorova O, Alain Petit P, Stogios P, Kim Y, Tchigvintsev A, Flick R, Denaro R, Genovese M, Albar JP, Reva ON, Martínez-Gomariz M, Tran H, Ferrer M, Savchenko A, Yakunin AF, Yakimov MM, Golyshina OV, Reinhardt R, Golyshin PN. Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica. Nat Commun 2013; 4:2156. [PMID: 23877221 PMCID: PMC3759055 DOI: 10.1038/ncomms3156] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 06/18/2013] [Indexed: 01/21/2023] Open
Abstract
Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis--the paradigm of mesophilic hydrocarbonoclastic bacteria--O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.
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Affiliation(s)
- Michael Kube
- Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany
- Section Phytomedicine, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin-Dahlem D-14195, Germany
| | - Tatyana N. Chernikova
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
- School of Biological Sciences, Bangor University, Gwynedd, Wales LL57 2UW, UK
| | | | - Ana Beloqui
- Institute of Catalysis, CSIC, Madrid 28049, Spain
| | | | - María-Eugenia Guazzaroni
- Institute of Catalysis, CSIC, Madrid 28049, Spain
- Departamento de Química, Universidade de São Paulo, Ribeirao Preto 14049 901, Brazil
| | - Hermann J. Heipieper
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig D-04318, Germany
| | - Sven Klages
- Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany
| | - Oleg R. Kotsyurbenko
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Ines Langer
- Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany
| | - Taras Y. Nechitaylo
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Heinrich Lünsdorf
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
| | - Marisol Fernández
- Proteomic Facility, National Centre for Biotechnology, CSIC, Madrid 28049, Spain
| | - Silvia Juárez
- Proteomic Facility, National Centre for Biotechnology, CSIC, Madrid 28049, Spain
| | - Sergio Ciordia
- Proteomic Facility, National Centre for Biotechnology, CSIC, Madrid 28049, Spain
| | - Alexander Singer
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Olga Kagan
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Olga Egorova
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Pierre Alain Petit
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Peter Stogios
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Youngchang Kim
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Biosciences Division, Structural Biology Center, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Anatoli Tchigvintsev
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
| | - Robert Flick
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
| | - Renata Denaro
- Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
| | - Maria Genovese
- Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
| | - Juan P. Albar
- Proteomic Facility, National Centre for Biotechnology, CSIC, Madrid 28049, Spain
| | - Oleg N. Reva
- Department of Biochemistry, University of Pretoria, Pretoria 0002, South Africa
| | | | - Hai Tran
- School of Biological Sciences, Bangor University, Gwynedd, Wales LL57 2UW, UK
| | | | - Alexei Savchenko
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada M5G 2C4
- Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, Illinois 60439, USA
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Alexander F. Yakunin
- Department of Chemical Engineering and Applied Chemistry, C.H. Best Institute University of Toronto, Toronto, Canada M5G 1L6
| | - Michail M. Yakimov
- Laboratory of Marine Molecular Microbiology, Institute for Coastal Marine Environment (IAMC), CNR, Messina 98122, Italy
| | - Olga V. Golyshina
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
- School of Biological Sciences, Bangor University, Gwynedd, Wales LL57 2UW, UK
| | - Richard Reinhardt
- Max-Planck Institute for Molecular Genetics, Berlin-Dahlem D-14195, Germany
- Present address: Max-Planck Genome Centre Cologne, Max-Planck Institute for Plant Breeding Research, Cologne D-50829, Germany
| | - Peter N. Golyshin
- Environmental Microbiology Group, HZI—Helmholtz Centre for Infection Research, Braunschweig D-38124, Germany
- School of Biological Sciences, Bangor University, Gwynedd, Wales LL57 2UW, UK
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Brígido C, Robledo M, Menéndez E, Mateos PF, Oliveira S. A ClpB chaperone knockout mutant of Mesorhizobium ciceri shows a delay in the root nodulation of chickpea plants. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1594-1604. [PMID: 23134119 DOI: 10.1094/mpmi-05-12-0140-r] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Several molecular chaperones are known to be involved in bacteria stress response. To investigate the role of chaperone ClpB in rhizobia stress tolerance as well as in the rhizobia-plant symbiosis process, the clpB gene from a chickpea microsymbiont, strain Mesorhizobium ciceri LMS-1, was identified and a knockout mutant was obtained. The ClpB knockout mutant was tested to several abiotic stresses, showing that it was unable to grow after a heat shock and it was more sensitive to acid shock than the wild-type strain. A plant-growth assay performed to evaluate the symbiotic performance of the clpB mutant showed a higher proportion of ineffective root nodules obtained with the mutant than with the wild-type strain. Nodulation kinetics analysis showed a 6- to 8-day delay in nodule appearance in plants inoculated with the ΔclpB mutant. Analysis of nodC gene expression showed lower levels of transcript in the ΔclpB mutant strain. Analysis of histological sections of nodules formed by the clpB mutant showed that most of the nodules presented a low number of bacteroids. No differences in the root infection abilities of green fluorescent protein-tagged clpB mutant and wild-type strains were detected. To our knowledge, this is the first study that presents evidence of the involvement of the chaperone ClpB from rhizobia in the symbiotic nodulation process.
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Kuhn E. Toward understanding life under subzero conditions: the significance of exploring psychrophilic "cold-shock" proteins. ASTROBIOLOGY 2012; 12:1078-86. [PMID: 23082745 DOI: 10.1089/ast.2012.0858] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Understanding the behavior of proteins under freezing conditions is vital for detecting and locating extraterrestrial life in cold environments, such as those found on Mars and the icy moons of Jupiter and Saturn. This review highlights the importance of studying psychrophilic "cold-shock" proteins, a topic that has yet to be explored. A strategy for analyzing the psychrophilic RNA helicase protein CsdA (Psyc_1082) from Psychrobacter arcticus 273-4 as a key protein for life under freezing temperatures is proposed. The experimental model presented here was developed based on previous data from investigations of Escherichia coli, P. arcticus 273-4, and RNA helicases. P. arcticus 273-4 is considered a model for life in freezing environments. It is capable of growing in temperatures as cold as -10°C by using physiological strategies to survive not only in freezing temperatures but also under low-water-activity and limited-nutrient-availability conditions. The analyses of its genome, transcriptome, and proteome revealed specific adaptations that allow it to inhabit freezing environments by adopting a slow metabolic strategy rather than a cellular dormancy state. During growth at subzero temperatures, P. arcticus 273-4 genes related to energy metabolism and carbon substrate incorporation are downregulated, and genes for maintenance of membranes, cell walls, and nucleic acid motion are upregulated. At -6°C, P. arcticus 273-4 does not upregulate the expression of either RNA or protein chaperones; however, it upregulates the expression of its cold-shock induced DEAD-box RNA helicase protein A (CsdA - Psyc_1082). CsdA - Psyc_1082 was investigated as a key helper protein for sustaining life in subzero conditions. Proving CsdA - Psyc_1082 to be functional as a key protein for life under freezing temperatures may extend the known minimum growth temperature of a mesophilic cell and provide key information about the mechanisms that underlie cold-induced biological systems in icy worlds.
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Affiliation(s)
- Emanuele Kuhn
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada 89512, USA.
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Modeling growth rates as a function of temperature: Model performance evaluation with focus on the suboptimal temperature range. Int J Food Microbiol 2012; 158:73-8. [DOI: 10.1016/j.ijfoodmicro.2012.05.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 05/07/2012] [Accepted: 05/12/2012] [Indexed: 11/23/2022]
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Jagannadham MV, Chowdhury C. Differential expression of membrane proteins helps Antarctic Pseudomonas syringae to acclimatize upon temperature variations. J Proteomics 2012; 75:2488-99. [PMID: 22418587 DOI: 10.1016/j.jprot.2012.02.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Revised: 02/15/2012] [Accepted: 02/25/2012] [Indexed: 01/16/2023]
Abstract
Antarctic bacteria are adapted to the extremely low temperature. The transcriptional and translational machineries of these bacteria are adapted to the sub-zero degrees of temperature. Studies directed towards identifying the changes in the protein profiles during changes in the growth temperatures of an Antarctic bacterium Pseudomonas syringae Lz4W may help in understanding the molecular basis of cold adaptation. In this study, subcellular fractionation methods of proteins were used for the enrichment and identification of proteins including low abundance proteins. The membrane proteins of the bacterium P. syringae Lz4W were prepared employing sucrose density gradient method. The proteins were separated through 2D gel-electrophoresis with the pH ranges 3-10, 4-7 and 5-8 using the detergent, amidosulfobetaine (ASB-14). The proteins separated on the 1D SDS PAGE and 2D gels were identified with the help of LC-ESI MS/MS and MALDI TOF TOF using bioinformatic programs MASCOT and SEQUEST. Since the genome sequence of P. syringae Lz4W is not available, the proteins are identified by using the genome database of the Pseudomonas sp. available at NCBI. The present studies focus on identifying temperature dependent expression of proteins by employing LC-MS/MS method and the functional significance of these proteins is discussed.
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Budiman C, Koga Y, Takano K, Kanaya S. FK506-Binding protein 22 from a psychrophilic bacterium, a cold shock-inducible peptidyl prolyl isomerase with the ability to assist in protein folding. Int J Mol Sci 2011; 12:5261-84. [PMID: 21954357 PMCID: PMC3179164 DOI: 10.3390/ijms12085261] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/28/2011] [Accepted: 08/09/2011] [Indexed: 11/23/2022] Open
Abstract
Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization at low temperatures is much slower than that at higher temperatures and may cause problems in protein folding. However, the mechanisms by which PPIases are involved in cold adaptation remain unclear. Here we used FK506-binding protein 22, a cold shock protein from the psychrophilic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) as a model protein to decipher the involvement of PPIases in cold adaptation. SIB1 FKBP22 is homodimer that assumes a V-shaped structure based on a tertiary model. Each monomer consists of an N-domain responsible for dimerization and a C-catalytic domain. SIB1 FKBP22 is a typical cold-adapted enzyme as indicated by the increase of catalytic efficiency at low temperatures, the downward shift in optimal temperature of activity and the reduction in the conformational stability. SIB1 FKBP22 is considered as foldase and chaperone based on its ability to catalyze refolding of a cis-proline containing protein and bind to a folding intermediate protein, respectively. The foldase and chaperone activites of SIB1 FKBP22 are thought to be important for cold adaptation of Shewanella sp. SIB1. These activities are also employed by other PPIases for being involved in cold adaptation of various microorganisms. Despite other biological roles of PPIases, we proposed that foldase and chaperone activities of PPIases are the main requirement for overcoming the cold-stress problem in microorganisms due to folding of proteins.
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Affiliation(s)
- Cahyo Budiman
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mails: (C.B.); (Y.K.); (S.K.)
| | - Yuichi Koga
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mails: (C.B.); (Y.K.); (S.K.)
| | - Kazufumi Takano
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mails: (C.B.); (Y.K.); (S.K.)
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-Cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Shigenori Kanaya
- Department of Material and Life Science, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; E-Mails: (C.B.); (Y.K.); (S.K.)
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Sung MS, Im HN, Lee KH. Molecular Cloning and Chaperone Activity of DnaK from Cold-adapted Bacteria, KOPRI22215. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.6.1925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Poly(3-hydroxybutyrate) influences biofilm formation and motility in the novel Antarctic species Pseudomonas extremaustralis under cold conditions. Extremophiles 2011; 15:541-7. [DOI: 10.1007/s00792-011-0384-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
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Fonseca P, Moreno R, Rojo F. Growth of Pseudomonas putida at low temperature: global transcriptomic and proteomic analyses. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:329-339. [PMID: 23761279 DOI: 10.1111/j.1758-2229.2010.00229.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In its natural habitats (soil, water and rhizosphere), Pseudomonas putida can suffer frequent and long-term changes in temperature that affect its growth and survival. Pseudomonas putida KT2440, a well-characterized model strain, grows optimally at 30°C but can proliferate at temperatures as low as 4°C. However, little information is available on the physiological changes that occur when P. putida grows at low temperatures. To investigate this area, the transcriptome and proteome profiles of cells exponentially growing in a complex medium at 10°C were compared with those of cells exponentially growing at 30°C. Low temperature modified the expression of at least 266 genes (some 5% of the genome). Many of the genes showing differential expression were involved in energy metabolism or in the transport and binding of substrates, although genes implicated in other cellular functions were also affected. Several changes seemed directed towards neutralizing problems created by low temperature, such as increased protein misfolding, the increased stability of DNA/RNA secondary structures, reduced membrane fluidity and a reduced growth rate. The present results improve our understanding of the P. putida lifestyle at low temperature, which may be relevant for its applications in bioremediation and in promotion of plant growth.
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Affiliation(s)
- Pilar Fonseca
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Campus UAM, Cantoblanco, 28049 Madrid, Spain
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Jagannadham M, Saranya S. Analysis of the Membrane proteins of an Antarctic Bacterium Pseudomonas Syringae. PROTEOMICS INSIGHTS 2011. [DOI: 10.4137/pri.s5383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The proteins of an Antarctic bacterium Pseudomonas syringae Lz4W, identified earlier by different membrane protein preparation methods, were combined together and the redundant identities removed. In total, 1479 proteins including 148 outer membrane proteins from this bacterium were predicted by the algorithm PSORTb3.0. A detailed analysis on their subcellular localization was undertaken which was determined using TMHMM, TMB-hunt and BOMP. A comparison of PSORTb predicted outer membrane proteins with BOMP, revealed that most of the proteins predicted by the former, contained β–barrels in the outer membranes. A comparative analysis of PSORTb, TMHMM and TMB-hunt reveals that most of the outer membranes proteins of this bacterium could be identified using this approach. Thus, by using a combination of biochemical and different bioinformatics algorithms, the membrane proteins of P. syringae are analyzed. In particular, PSORTb results are compared and supported by other algorithms, to improve the strength of OM proteins prediction. Several proteins, having an important role in cold adaptation of the organism, could also be identified.
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Affiliation(s)
- M.V. Jagannadham
- Scientist, Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Tarnaka, Hyderabad, India
| | - S. Saranya
- Depatment of Life Sciences, Bharathidasan University, Tiruchirapalli, Tamil Nadu, India
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Jagannadham MV, Abou-Eladab EF, Kulkarni HM. Identification of outer membrane proteins from an Antarctic bacterium Pseudomonas syringae Lz4W. Mol Cell Proteomics 2011; 10:M110.004549. [PMID: 21447709 DOI: 10.1074/mcp.m110.004549] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Subcellular fractionation of proteins is a preferred method of choice for detection and identification of proteins from complex mixtures such as bacterial cells. To characterize the membrane proteins of the Antarctic bacterium Pseudomonas syringae Lz4W, the membrane fractions were prepared using three different methods, namely Triton X-100 solubilization, sucrose density gradient, and carbonate extraction methods. The proteins were separated on one-dimensional polyacrylamide gels and analyzed using a combination of liquid chromatography-coupled electrospray ionization-MS. The membrane proteins that were prepared by carbonate extraction were separated on two-dimensional PAGE in different pI ranges using the detergent 2% amidosulfobetaine (ASB). The proteins were then subjected to matrix-assisted laser desorption ionization-time-of-flight/time-of-flight for analysis and identification. Because the genome sequence of P. syringae Lz4W is not known, the proteins were identified by using the relevant sequence databases of the Pseudomonas sp available at National Centre for Biotechnology Information (NCBI). The sequence identification of some tryptic peptides were validated by de novo sequencing and others by chemical modification and mass spectrometry. The peptide sequences of P. syringae Lz4W were then matched with the sequences of the peptides from different Pseudomonas sp. by similarity search of the proteins from different species using clustal W2 program. Thus by using a combination of the methods, we have been able to identify large number of proteins of this bacterial strain, which include most of the outer membrane proteins.
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Affiliation(s)
- M V Jagannadham
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Hyderabad, India.
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García-Descalzo L, Alcazar A, Baquero F, Cid C. Identification of in vivo HSP90-interacting proteins reveals modularity of HSP90 complexes is dependent on the environment in psychrophilic bacteria. Cell Stress Chaperones 2011; 16:203-18. [PMID: 20890740 PMCID: PMC3059794 DOI: 10.1007/s12192-010-0233-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 09/15/2010] [Accepted: 09/16/2010] [Indexed: 12/29/2022] Open
Abstract
Heat shock protein 90 (HSP90) is a conserved molecular chaperone that functions as part of complexes in which different client proteins target it to diverse sets of substrates. In this paper, HSP90 complexes were investigated in γ-proteobacteria from mild (Shewanella oneidensis) and cold environments (Shewanella frigidimarina and Psychrobacter frigidicola), to determine changes in HSP90 interactions with client proteins in response to the adaptation to cold environments. HSP90 participation in cold adaptation was determined using the specific inhibitor 17-allylamino-geldanamycin. Then, HSP90 was immunoprecipitated from bacterial cultures, and the proteins in HSP90 complexes were analyzed by two-dimensional gel electrophoresis and identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. According to HSP90-associated protein analysis, only 15 common proteins were found in both species from the same genus, S. oneidensis and S. frigidimarina, whereas a significant higher number of common proteins were found in both psychrophilic species S. frigidimarina and P. frigidicola 21 (p < 0.001). Only two HSP90-interacting proteins, the chaperone proteins DnaK and GroEL, were common to the three species. Interestingly, some proteins related to energy metabolism (isocitrate lyase, succinyl-CoA synthetase, alcohol dehydrogenase, NAD(+) synthase, and malate dehydrogenase) and some translation factors only interacted with HSP90 in psychrophilic bacteria. We can conclude that HSP90 and HSP90-associated proteins might take part in the mechanism of adaptation to cold environments, and interestingly, organisms living in similar environments conserve similar potential HSP90 interactors in opposition to phylogenetically closely related organisms of the same genus but from different environments.
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Affiliation(s)
- Laura García-Descalzo
- Centro de Astrobiologia (CSIC-INTA), Ctra. Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - Alberto Alcazar
- Department of Investigation, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Fernando Baquero
- Centro de Astrobiologia (CSIC-INTA), Ctra. Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
- Department of Microbiology, Hospital Ramon y Cajal, 28034 Madrid, Spain
| | - Cristina Cid
- Centro de Astrobiologia (CSIC-INTA), Ctra. Ajalvir, km 4, Torrejón de Ardoz, 28850 Madrid, Spain
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Protection of Bacillus subtilis against cold stress via compatible-solute acquisition. J Bacteriol 2011; 193:1552-62. [PMID: 21296969 DOI: 10.1128/jb.01319-10] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Accumulation of compatible solutes is a strategy widely employed by bacteria to achieve cellular protection against high osmolarity. These compounds are also used in some microorganisms as thermostress protectants. We found that Bacillus subtilis uses the compatible solute glycine betaine as an effective cold stress protectant. Glycine betaine strongly stimulated growth at 15°C and permitted cell proliferation at the growth-inhibiting temperature of 13°C. Initial uptake of glycine betaine at 15°C was low but led eventually to the buildup of an intracellular pool whose size was double that found in cells grown at 35°C. Each of the three glycine betaine transporters (OpuA, OpuC, and OpuD) contributed to glycine betaine accumulation in the cold. Protection against cold stress was also accomplished when glycine betaine was synthesized from its precursor choline. Growth of a mutant defective in the osmoadaptive biosynthesis for the compatible solute proline was not impaired at low temperature (15°C). In addition to glycine betaine, the compatible solutes and osmoprotectants l-carnitine, crotonobetaine, butyrobetaine, homobetaine, dimethylsulfonioactetate, and proline betaine all served as cold stress protectants as well and were accumulated via known Opu transport systems. In contrast, the compatible solutes and osmoprotectants choline-O-sulfate, ectoine, proline, and glutamate were not cold protective. Our data highlight an underappreciated facet of the acclimatization of B. subtilis to cold environments and allow a comparison of the characteristics of compatible solutes with respect to their osmotic, heat, and cold stress-protective properties for B. subtilis cells.
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Ting L, Williams TJ, Cowley MJ, Lauro FM, Guilhaus M, Raftery MJ, Cavicchioli R. Cold adaptation in the marine bacterium, Sphingopyxis alaskensis, assessed using quantitative proteomics. Environ Microbiol 2011; 12:2658-76. [PMID: 20482592 DOI: 10.1111/j.1462-2920.2010.02235.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The cold marine environment constitutes a large proportion of the Earth's biosphere. Sphingopyxis alaskensis was isolated as a numerically abundant bacterium from several cold marine locations, and has been extensively studied as a model marine bacterium. Recently, a metabolic labelling platform was developed to comprehensively identify and quantify proteins from S. alaskensis. The approach incorporated data normalization and statistical validation for the purpose of generating highly confident quantitative proteomics data. Using this approach, we determined quantitative differences between cells grown at 10°C (low temperature) and 30°C (high temperature). Cold adaptation was linked to specific aspects of gene expression: a dedicated protein-folding system using GroESL, DnaK, DnaJ, GrpE, SecB, ClpB and PPIase; polyhydroxyalkanoate-associated storage materials; a link between enzymes in fatty acid metabolism and energy generation; de novo synthesis of polyunsaturated fatty acids in the membrane and cell wall; inorganic phosphate ion transport by a phosphate import PstB homologue; TonB-dependent receptor and bacterioferritin in iron homeostasis; histidine, tryptophan and proline amino acid metabolism; and a large number of proteins without annotated functions. This study provides a new level of understanding on how important marine bacteria can adapt to compete effectively in cold marine environments. This study is also a benchmark for comparative proteomic analyses with other important marine bacteria and other cold-adapted organisms.
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Affiliation(s)
- Lily Ting
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
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47
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Abstract
Low temperature environments are numerous on Earth and have been successfully colonized by cold-loving organisms termed psychrophiles. Cold-adapted microorganisms can be used as cell factories for the production of unstable compounds as well as for bioremediation of polluted cold soils and wastewaters. Furthermore, their biomolecules, mainly proteins and enzymes characterized by a high catalytic activity and pronounced heat-lability, have already found useful applications in various domains such as molecular biology, medical research, industrial food or feed technologies, detergents or cosmetics.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, Innsbruck, Austria
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48
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Choi AR, Na JM, Sung MS, Im HN, Lee KH. Identification and Cloning of the ClpB Gene in Psychromonas arctica by Inverse PCR and Cassette PCR Technology. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.04.887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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49
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Piette F, D'Amico S, Struvay C, Mazzucchelli G, Renaut J, Tutino ML, Danchin A, Leprince P, Feller G. Proteomics of life at low temperatures: trigger factor is the primary chaperone in the Antarctic bacteriumPseudoalteromonas haloplanktisTAC125. Mol Microbiol 2010; 76:120-32. [DOI: 10.1111/j.1365-2958.2010.07084.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Prakash JSS, Krishna PS, Sirisha K, Kanesaki Y, Suzuki I, Shivaji S, Murata N. An RNA helicase, CrhR, regulates the low-temperature-inducible expression of heat-shock genes groES, groEL1 and groEL2 in Synechocystis sp. PCC 6803. MICROBIOLOGY-SGM 2009; 156:442-451. [PMID: 19926653 DOI: 10.1099/mic.0.031823-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The crhR gene for RNA helicase, CrhR, was one of the most highly induced genes when the cyanobacterium Synechocystis sp. PCC 6803 was exposed to a downward shift in ambient temperature. Although CrhR may be involved in the acclimatization of cyanobacterial cells to low-temperature environments, its functional role during the acclimatization is not known. In the present study, we mutated the crhR gene by replacement with a spectinomycin-resistance gene cassette. The resultant DeltacrhR mutant exhibited a phenotype of slow growth at low temperatures. DNA microarray analysis of the genome-wide expression of genes, and Northern and Western blotting analyses indicated that mutation of the crhR gene repressed the low-temperature-inducible expression of heat-shock genes groEL1 and groEL2, at the transcript and protein levels. The kinetics of the groESL co-transcript and the groEL2 transcript after addition of rifampicin suggested that CrhR stabilized these transcripts at an early phase, namely 5-60 min, during acclimatization to low temperatures, and enhanced the transcription of these genes at a later time, namely 3-5 h. Our results suggest that CrhR regulates the low-temperature-inducible expression of these heat-shock proteins, which, in turn, may be essential for acclimatization of Synechocystis cells to low temperatures.
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Affiliation(s)
- Jogadhenu S S Prakash
- National Institute for Basic Biology (NIBB), Okazaki 444-8585, Japan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Pilla Sankara Krishna
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Kodru Sirisha
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500 046, India
| | - Yu Kanesaki
- National Institute for Basic Biology (NIBB), Okazaki 444-8585, Japan
| | - Iwane Suzuki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Sisinthy Shivaji
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
| | - Norio Murata
- National Institute for Basic Biology (NIBB), Okazaki 444-8585, Japan
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