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Qiu X, Hu XM, Tang XX, Huang CH, Jian HH, Lin DH. Metabolic adaptations of Microbacterium sediminis YLB-01 in deep-sea high-pressure environments. Appl Microbiol Biotechnol 2024; 108:170. [PMID: 38265689 DOI: 10.1007/s00253-023-12906-5] [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: 07/10/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 01/25/2024]
Abstract
The deep-sea environment is an extremely difficult habitat for microorganisms to survive in due to its intense hydrostatic pressure. However, the mechanisms by which these organisms adapt to such extreme conditions remain poorly understood. In this study, we investigated the metabolic adaptations of Microbacterium sediminis YLB-01, a cold and stress-tolerant microorganism isolated from deep-sea sediments, in response to high-pressure conditions. YLB-01 cells were cultured at normal atmospheric pressure and 28 ℃ until they reached the stationary growth phase. Subsequently, the cells were exposed to either normal pressure or high pressure (30 MPa) at 4 ℃ for 7 days. Using NMR-based metabolomic and proteomic analyses of YLB-01 cells exposed to high-pressure conditions, we observed significant metabolic changes in several metabolic pathways, including amino acid, carbohydrate, and lipid metabolism. In particular, the high-pressure treatment stimulates cell division and triggers the accumulation of UDP-glucose, a critical factor in cell wall formation. This finding highlights the adaptive strategies used by YLB-01 cells to survive in the challenging high-pressure environments of the deep sea. Specifically, we discovered that YLB-01 cells regulate amino acid metabolism, promote carbohydrate metabolism, enhance cell wall synthesis, and improve cell membrane fluidity in response to high pressure. These adaptive mechanisms play essential roles in supporting the survival and growth of YLB-01 in high-pressure conditions. Our study offers valuable insights into the molecular mechanisms underlying the metabolic adaptation of deep-sea microorganisms to high-pressure environments. KEY POINTS: • NMR-based metabolomic and proteomic analyses were conducted on Microbacterium sediminis YLB-01 to investigate the significant alterations in several metabolic pathways in response to high-pressure treatment. • YLB-01 cells used adaptive strategies (such as regulated amino acid metabolism, promoted carbohydrate metabolism, enhanced cell wall synthesis, and improved cell membrane fluidity) to survive in the challenging high-pressure environment of the deep sea. • High-pressure treatment stimulated cell division and triggered the accumulation of UDP-glucose, a critical factor in cell wall formation, in Microbacterium sediminis YLB-01 cells.
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Affiliation(s)
- Xu Qiu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xiao-Min Hu
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Xi-Xiang Tang
- State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Fujian Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China.
| | - Cai-Hua Huang
- Research and Communication Center of Exercise and Health, Xiamen University of Technology, Xiamen, China
| | - Hua-Hua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Hai Lin
- Key Laboratory for Chemical Biology of Fujian Province, MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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diCenzo GC, Zamani M, Checcucci A, Fondi M, Griffitts JS, Finan TM, Mengoni A. Multidisciplinary approaches for studying rhizobium–legume symbioses. Can J Microbiol 2019; 65:1-33. [DOI: 10.1139/cjm-2018-0377] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The rhizobium–legume symbiosis is a major source of fixed nitrogen (ammonia) in the biosphere. The potential for this process to increase agricultural yield while reducing the reliance on nitrogen-based fertilizers has generated interest in understanding and manipulating this process. For decades, rhizobium research has benefited from the use of leading techniques from a very broad set of fields, including population genetics, molecular genetics, genomics, and systems biology. In this review, we summarize many of the research strategies that have been employed in the study of rhizobia and the unique knowledge gained from these diverse tools, with a focus on genome- and systems-level approaches. We then describe ongoing synthetic biology approaches aimed at improving existing symbioses or engineering completely new symbiotic interactions. The review concludes with our perspective of the future directions and challenges of the field, with an emphasis on how the application of a multidisciplinary approach and the development of new methods will be necessary to ensure successful biotechnological manipulation of the symbiosis.
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Affiliation(s)
- George C. diCenzo
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Maryam Zamani
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alice Checcucci
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Marco Fondi
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
| | - Joel S. Griffitts
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Turlough M. Finan
- Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Alessio Mengoni
- Department of Biology, University of Florence, Sesto Fiorentino, FI 50019, Italy
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Histone methyltransferase Smyd1 regulates mitochondrial energetics in the heart. Proc Natl Acad Sci U S A 2018; 115:E7871-E7880. [PMID: 30061404 DOI: 10.1073/pnas.1800680115] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Smyd1, a muscle-specific histone methyltransferase, has established roles in skeletal and cardiac muscle development, but its role in the adult heart remains poorly understood. Our prior work demonstrated that cardiac-specific deletion of Smyd1 in adult mice (Smyd1-KO) leads to hypertrophy and heart failure. Here we show that down-regulation of mitochondrial energetics is an early event in these Smyd1-KO mice preceding the onset of structural abnormalities. This early impairment of mitochondrial energetics in Smyd1-KO mice is associated with a significant reduction in gene and protein expression of PGC-1α, PPARα, and RXRα, the master regulators of cardiac energetics. The effect of Smyd1 on PGC-1α was recapitulated in primary cultured rat ventricular myocytes, in which acute siRNA-mediated silencing of Smyd1 resulted in a greater than twofold decrease in PGC-1α expression without affecting that of PPARα or RXRα. In addition, enrichment of histone H3 lysine 4 trimethylation (a mark of gene activation) at the PGC-1α locus was markedly reduced in Smyd1-KO mice, and Smyd1-induced transcriptional activation of PGC-1α was confirmed by luciferase reporter assays. Functional confirmation of Smyd1's involvement showed an increase in mitochondrial respiration capacity induced by overexpression of Smyd1, which was abolished by siRNA-mediated PGC-1α knockdown. Conversely, overexpression of PGC-1α rescued transcript expression and mitochondrial respiration caused by silencing Smyd1 in cardiomyocytes. These findings provide functional evidence for a role of Smyd1, or any member of the Smyd family, in regulating cardiac energetics in the adult heart, which is mediated, at least in part, via modulating PGC-1α.
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Gandhi A, Shah NP. Integrating omics to unravel the stress-response mechanisms in probiotic bacteria: Approaches, challenges, and prospects. Crit Rev Food Sci Nutr 2018; 57:3464-3471. [PMID: 26853094 DOI: 10.1080/10408398.2015.1136805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Identifying the stress-response mechanism of probiotic bacteria has always captivated the interest of food producers. It is crucial to identify probiotic bacteria that have increased stress tolerance to survive during production, processing, and storage of food products. However, in order to achieve high resistance to environmental factors, there is a need to better understand stress-induced responses and adaptive mechanisms. With advances in bacterial genomics, there has been an upsurge in the application of other omic platforms such as transcriptomics, proteomics, metabolomics, and some more recent ones such as interactomics, fluxomics, and phenomics. These omic technologies have revolutionized the functional genomics and their application. There have been several studies implementing various omic technologies to investigate the stress responses of probiotic bacteria. Integrated omics has the potential to provide in-depth information about the mechanisms of stress-induced responses in bacteria. However, there remain challenges in integrating information from different omic platforms. This review discusses current omic techniques and challenges faced in integrating various omic platforms with focus on their use in stress-response studies.
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Affiliation(s)
- Akanksha Gandhi
- a Food and Nutritional Science, School of Biological Sciences , The University of Hong Kong , Hong Kong
| | - Nagendra P Shah
- a Food and Nutritional Science, School of Biological Sciences , The University of Hong Kong , Hong Kong
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Koo H, Hakim JA, Morrow CD, Andersen DT, Bej AK. Microbial Community Composition and Predicted Functional Attributes of Antarctic Lithobionts Using Targeted Next-Generation Sequencing and Bioinformatics Tools. J Microbiol Methods 2018. [DOI: 10.1016/bs.mim.2018.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Abstract
Constraint-based metabolic modelling (CBMM) consists in the use of computational methods and tools to perform genome-scale simulations and predict metabolic features at the whole cellular level. This approach is rapidly expanding in microbiology, as it combines reliable predictive abilities with conceptually and technically simple frameworks. Among the possible outcomes of CBMM, the capability to i) guide a focused planning of metabolic engineering experiments and ii) provide a system-level understanding of (single or community-level) microbial metabolic circuits also represent primary aims in present-day marine microbiology. In this work we briefly introduce the theoretical formulation behind CBMM and then review the most recent and effective case studies of CBMM of marine microbes and communities. Also, the emerging challenges and possibilities in the use of such methodologies in the context of marine microbiology/biotechnology are discussed. As the potential applications of CBMM have a very broad range, the topics presented in this review span over a large plethora of fields such as ecology, biotechnology and evolution.
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Affiliation(s)
- Marco Fondi
- Dep. of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy.
| | - Renato Fani
- Dep. of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
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Mocali S, Chiellini C, Fabiani A, Decuzzi S, de Pascale D, Parrilli E, Tutino ML, Perrin E, Bosi E, Fondi M, Lo Giudice A, Fani R. Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic-phenomic approach. Sci Rep 2017; 7:839. [PMID: 28404986 PMCID: PMC5429795 DOI: 10.1038/s41598-017-00876-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 03/01/2017] [Indexed: 12/26/2022] Open
Abstract
Cold environments dominate Earth's biosphere, hosting complex microbial communities with the ability to thrive at low temperatures. However, the underlying molecular mechanisms and the metabolic pathways involved in bacterial cold-adaptation mechanisms are still not fully understood. Herein, we assessed the metabolic features of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125), a model organism for cold-adaptation, at both 4 °C and 15 °C, by integrating genomic and phenomic (high-throughput phenotyping) data and comparing the obtained results to the taxonomically related Antarctic bacterium Pseudoalteromonas sp. TB41 (PspTB41). Although the genome size of PspTB41 is considerably larger than PhTAC125, the higher number of genes did not reflect any higher metabolic versatility at 4 °C as compared to PhTAC125. Remarkably, protein S-thiolation regulated by glutathione and glutathionylspermidine appeared to be a new possible mechanism for cold adaptation in PhTAC125. More in general, this study represents an example of how 'multi-omic' information might potentially contribute in filling the gap between genotypic and phenotypic features related to cold-adaptation mechanisms in bacteria.
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Affiliation(s)
- Stefano Mocali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.
| | - Carolina Chiellini
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.,Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Arturo Fabiani
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy
| | - Silvia Decuzzi
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di Ricerca per l'Agrobiologia e la Pedologia (CREA-ABP), via di Lanciola 12/A, 50125, Firenze, Italy.,Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Donatella de Pascale
- Institute of Protein Biochemistry, CNR, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Ermenegilda Parrilli
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario, Monte Sant'Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Maria Luisa Tutino
- Department of Chemical Sciences, University of Naples 'Federico II', Complesso Universitario, Monte Sant'Angelo, Via Cinthia 4, 80126, Naples, Italy
| | - Elena Perrin
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Emanuele Bosi
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Marco Fondi
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
| | - Angelina Lo Giudice
- Institute for the Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98122, Messina, Italy.,Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontrès 31, 98166, Messina, Italy
| | - Renato Fani
- Department of Biology, LEMM, Laboratory of Microbial and Molecular Evolution Florence, University of Florence, I-50019, Sesto Fiorentino (FI), Italy
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Wdowiak-Wróbel S, Małek W, Palusińska-Szysz M. Low temperature adaptation and the effects of cryoprotectants on mesorhizobia strains. J Basic Microbiol 2016; 56:379-91. [PMID: 26879468 DOI: 10.1002/jobm.201500615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/05/2016] [Indexed: 11/07/2022]
Abstract
In this study, the tolerance of Mesorhizobium sp. ACMP18, Mesorhizobium sp. USDA3350, and Mesorhizobium temperatum LMG23931 strains, to cold and freezing were investigated. The ability to withstand freezing at -20 °C and -70 °C for 24 months was different among the studied strains and depended on the cryoprotectant used. The survivability of mesorhizobial strains at -20 °C and -70 °C was significantly improved by some cryoprotectans (glycerol and sucrose/peptone). It is worth noting that the greatest resistance to freezing was detected when stress treatments were performed in glycerol as a cryoprotectant. Using PCR analysis, cspA genes were identified in the studied strains. Their nucleotide sequences were most similar to the sequences of the corresponding genes of the Mesorhizobium species. The expression of the cspA gene in the studied bacteria was analyzed using the RT-PCR technique. The fatty acid composition of the mesorhizobia was determined at 5, 10, 15, and 28 °C. It was noticed that growth temperature significantly affected the fatty acid composition and the amounts of unsaturated fatty acids, especially that of cis-vaccenic acid (18:1ɷ(11)), increased markedly in bacterial cells cultivated at 5, 10, and 15 °C.
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Affiliation(s)
- Sylwia Wdowiak-Wróbel
- Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
| | - Wanda Małek
- Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
| | - Marta Palusińska-Szysz
- Department of Genetics and Microbiology, Maria Curie Sklodowska University, Lublin, Poland
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Hagel JM, Mandal R, Han B, Han J, Dinsmore DR, Borchers CH, Wishart DS, Facchini PJ. Metabolome analysis of 20 taxonomically related benzylisoquinoline alkaloid-producing plants. BMC PLANT BIOLOGY 2015; 15:220. [PMID: 26369413 PMCID: PMC4570626 DOI: 10.1186/s12870-015-0594-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 08/14/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND Recent progress toward the elucidation of benzylisoquinoline alkaloid (BIA) metabolism has focused on a small number of model plant species. Current understanding of BIA metabolism in plants such as opium poppy, which accumulates important pharmacological agents such as codeine and morphine, has relied on a combination of genomics and metabolomics to facilitate gene discovery. Metabolomics studies provide important insight into the primary biochemical networks underpinning specialized metabolism, and serve as a key resource for metabolic engineering, gene discovery, and elucidation of governing regulatory mechanisms. Beyond model plants, few broad-scope metabolomics reports are available for the vast number of plant species known to produce an estimated 2500 structurally diverse BIAs, many of which exhibit promising medicinal properties. RESULTS We applied a multi-platform approach incorporating four different analytical methods to examine 20 non-model, BIA-accumulating plant species. Plants representing four families in the Ranunculales were chosen based on reported BIA content, taxonomic distribution and importance in modern/traditional medicine. One-dimensional (1)H NMR-based profiling quantified 91 metabolites and revealed significant species- and tissue-specific variation in sugar, amino acid and organic acid content. Mono- and disaccharide sugars were generally lower in roots and rhizomes compared with stems, and a variety of metabolites distinguished callus tissue from intact plant organs. Direct flow infusion tandem mass spectrometry provided a broad survey of 110 lipid derivatives including phosphatidylcholines and acylcarnitines, and high-performance liquid chromatography coupled with UV detection quantified 15 phenolic compounds including flavonoids, benzoic acid derivatives and hydroxycinnamic acids. Ultra-performance liquid chromatography coupled with high-resolution Fourier transform mass spectrometry generated extensive mass lists for all species, which were mined for metabolites putatively corresponding to BIAs. Different alkaloids profiles, including both ubiquitous and potentially rare compounds, were observed. CONCLUSIONS Extensive metabolite profiling combining multiple analytical platforms enabled a more complete picture of overall metabolism occurring in selected plant species. This study represents the first time a metabolomics approach has been applied to most of these species, despite their importance in modern and traditional medicine. Coupled with genomics data, these metabolomics resources serve as a key resource for the investigation of BIA biosynthesis in non-model plant species.
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Affiliation(s)
- Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1 N4, Canada.
| | - Rupasri Mandal
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - Beomsoo Han
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - Jun Han
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada.
| | - Donald R Dinsmore
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1 N4, Canada.
| | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada.
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1 N4, Canada.
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Ghobakhlou AF, Johnston A, Harris L, Antoun H, Laberge S. Microarray transcriptional profiling of Arctic Mesorhizobium strain N33 at low temperature provides insights into cold adaption strategies. BMC Genomics 2015; 16:383. [PMID: 25975821 PMCID: PMC4432818 DOI: 10.1186/s12864-015-1611-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 05/01/2015] [Indexed: 11/29/2022] Open
Abstract
Background Arctic Mesorhizobium strain N33 was isolated from nodules of the legume Oxytropis arctobia in Canada’s eastern Arctic. This symbiotic bacterium can grow at temperatures ranging from 0 to 30 °C, fix nitrogen at 10 °C, and is one of the best known cold-adapted rhizobia. Despite the economic potential of this bacterium for northern regions, the key molecular mechanisms of its cold adaptation remain poorly understood. Results Using a microarray printed with 5760 Arctic Mesorhizobium genomic clones, we performed a partial transcriptome analysis of strain N33 grown under eight different temperature conditions, including both sustained and transient cold treatments, compared with cells grown at room temperature. Cells treated under constant (4 and 10 °C) low temperatures expressed a prominent number of induced genes distinct from cells treated to short-term cold-exposure (<60 min), but exhibited an intermediate expression profile when exposed to a prolonged cold exposure (240 min). The most prominent up-regulated genes encode proteins involved in metabolite transport, transcription regulation, protein turnover, oxidoreductase activity, cryoprotection (mannitol, polyamines), fatty acid metabolism, and membrane fluidity. The main categories of genes affected in N33 during cold treatment are sugar transport and protein translocation, lipid biosynthesis, and NADH oxidoreductase (quinone) activity. Some genes were significantly down-regulated and classified in secretion, energy production and conversion, amino acid transport, cell motility, cell envelope and outer membrane biogenesis functions. This might suggest growth cessation or reduction, which is an important strategy to adjust cellular function and save energy under cold stress conditions. Conclusion Our analysis revealed a complex series of changes associated with cold exposure adaptation and constant growth at low temperatures. Moreover, it highlighted some of the strategies and different physiological states that Mesorhizobium strain N33 has developed to adapt to the cold environment of the Canadian high Arctic and has revealed candidate genes potentially involved in cold adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1611-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abdollah-Fardin Ghobakhlou
- Graduate Programs in Agri-Food Microbiology, Faculty of Agriculture and Food Sciences, Laval University, Quebec City, Quebec, G1V 0A6, Canada.
| | - Anne Johnston
- Eastern Cereal & Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada.
| | - Linda Harris
- Eastern Cereal & Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, K1A 0C6, Canada.
| | - Hani Antoun
- Department of Soils and Agri-Food Engineering, Laval University, Quebec City, Quebec, G1V 0A6, Canada.
| | - Serge Laberge
- Soils and Crops Research Development Center, Agriculture and Agri-Food Canada, Quebec City, Quebec, G1V 2 J3, Canada.
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Alreshidi MM, Dunstan RH, Macdonald MM, Smith ND, Gottfries J, Roberts TK. Metabolomic and proteomic responses of Staphylococcus aureus to prolonged cold stress. J Proteomics 2015; 121:44-55. [PMID: 25782752 DOI: 10.1016/j.jprot.2015.03.010] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 02/18/2015] [Accepted: 03/09/2015] [Indexed: 02/06/2023]
Abstract
UNLABELLED The high pathogenicity of Staphylococcus aureus is thought to be due to its extraordinary capacity to rapidly adapt to changes in environmental conditions. This study was carried out to investigate whether the cytoplasmic profiles of metabolites and proteins of S. aureus were altered in response to prolonged exposure to cold stress. Metabolic profiling and proteomics were used to characterise alterations in cytoplasmic proteins and metabolites in cells from the mid-exponential phase of growth under ideal conditions at 37°C and compared with equivalent cells exposed to prolonged cold stress for 2 weeks at 4°C. Principle component analysis (PCA) of the metabolomic and proteomic data indicated that, at the mid-exponential phase of growth, prolonged cold stress conditions generated cells with different metabolite and protein profiles compared with those grown at 37°C. Nine ribosomal proteins and citric acid were substantially elevated in the cytoplasmic fractions from the cells adapted to cold-stress but most amino acids showed a reduction in their concentration in cold-stressed samples. The data provided strong evidence supporting the hypothesis that specific changes in metabolic homeostasis and protein composition were critical to the adaptive processes required for survival under cold stress. BIOLOGICAL SIGNIFICANCE Work in our laboratory has shown that prolonged exposure of S. aureus to cold stress can result in the formation of small colony variants (SCVs) associated with significant alterations in the cell wall composition. Further studies revealed that S. aureus altered cell size and cell wall thickness in response to exposure to cold temperatures, alterations in pH and exposure to antibiotics. The current study has utilised the prolonged exposure to cold stress as a model system to explore changes in the proteome and associated metabolic homeostasis following environmental challenges. The study provides an improved understanding of how S. aureus adapts to the changing environment whilst in transition between human hosts. The results indicated an unexpected production of 9 ribosomal proteins and citric acid in response to cold stress suggesting specific survival roles for these proteins and citric acid as an adaptation mechanism for empowering survival under these conditions.
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Affiliation(s)
- Mousa M Alreshidi
- Pathogenic Microbiology Laboratory, Faculty of Science and Information Technology, School of Environmental and Life Sciences, Department of Biology, University Drive, Callaghan, 2308 NSW, Australia
| | - R Hugh Dunstan
- Pathogenic Microbiology Laboratory, Faculty of Science and Information Technology, School of Environmental and Life Sciences, Department of Biology, University Drive, Callaghan, 2308 NSW, Australia.
| | - Margaret M Macdonald
- Pathogenic Microbiology Laboratory, Faculty of Science and Information Technology, School of Environmental and Life Sciences, Department of Biology, University Drive, Callaghan, 2308 NSW, Australia
| | - Nathan D Smith
- Analytical and Biomolecular Research Facility (ABRF), University of Newcastle, Callaghan, NSW 2308, Australia
| | | | - Tim K Roberts
- Pathogenic Microbiology Laboratory, Faculty of Science and Information Technology, School of Environmental and Life Sciences, Department of Biology, University Drive, Callaghan, 2308 NSW, Australia
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