1
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Sperfeld M, Narváez-Barragán DA, Malitsky S, Frydman V, Yuda L, Rocha J, Segev E. Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria. Nat Microbiol 2024; 9:2006-2021. [PMID: 38969820 PMCID: PMC11306105 DOI: 10.1038/s41564-024-01742-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 05/22/2024] [Indexed: 07/07/2024]
Abstract
The lag phase is key in resuming bacterial growth, but it remains underexplored particularly in environmental bacteria. Here we use transcriptomics and 13C-labelled metabolomics to show that the lag phase of the model marine bacterium Phaeobacter inhibens is shortened by methylated compounds produced by the microalgal partner, Emiliania huxleyi. Methylated compounds are abundantly produced and released by microalgae, and we show that their methyl groups can be collected by bacteria and assimilated through the methionine cycle. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and highlight the adjustability of this growth phase. In addition, we show that methylated compounds, typical of photosynthetic organisms, prompt diverse reductions in lag times in bacteria associated with algae and plants, potentially favouring early growth in some bacteria. These findings suggest ways to accelerate bacterial growth and underscore the significance of studying bacteria within an environmental context.
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Affiliation(s)
- Martin Sperfeld
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Institute of Microbiology, ETH, Zurich, Switzerland
| | | | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Veronica Frydman
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Lilach Yuda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jorge Rocha
- Agricultura en Zonas Áridas, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Einat Segev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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2
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Semmler F, Regis Belisário-Ferrari M, Kulosa M, Kaysser L. The Metabolic Potential of the Human Lung Microbiome. Microorganisms 2024; 12:1448. [PMID: 39065215 PMCID: PMC11278768 DOI: 10.3390/microorganisms12071448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/05/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
The human lung microbiome remains largely underexplored, despite its potential implications in the pharmacokinetics of inhaled drugs and its involvement in lung diseases. Interactions within these bacterial communities and with the host are complex processes which often involve microbial small molecules. In this study, we employed a computational approach to describe the metabolic potential of the human lung microbiome. By utilizing antiSMASH and BiG-SCAPE software, we identified 1831 biosynthetic gene clusters for the production of specialized metabolites in a carefully compiled genome database of lung-associated bacteria and fungi. It was shown that RiPPs represent the largest class of natural products within the bacteriome, while NRPs constitute the largest class of natural products in the lung mycobiome. All predicted BGCs were further categorized into 767 gene cluster families, and a subsequent network analysis highlighted that these families are widely distributed and contain many uncharacterized members. Moreover, in-depth annotation allowed the assignment of certain gene clusters to putative lung-specific functions within the microbiome, such as osmoadaptation or surfactant synthesis. This study establishes the lung microbiome as a prolific source for secondary metabolites and lays the groundwork for detailed investigation of this unique environment.
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Affiliation(s)
| | | | | | - Leonard Kaysser
- Department of Pharmaceutical Biology, Institute for Drug Discovery, University of Leipzig, 04317 Leipzig, Germany; (F.S.); (M.R.B.-F.); (M.K.)
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3
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Foster AJ, van den Noort M, Poolman B. Bacterial cell volume regulation and the importance of cyclic di-AMP. Microbiol Mol Biol Rev 2024; 88:e0018123. [PMID: 38856222 PMCID: PMC11332354 DOI: 10.1128/mmbr.00181-23] [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] [Indexed: 06/11/2024] Open
Abstract
SUMMARYNucleotide-derived second messengers are present in all domains of life. In prokaryotes, most of their functionality is associated with general lifestyle and metabolic adaptations, often in response to environmental fluctuations of physical parameters. In the last two decades, cyclic di-AMP has emerged as an important signaling nucleotide in many prokaryotic lineages, including Firmicutes, Actinobacteria, and Cyanobacteria. Its importance is highlighted by the fact that both the lack and overproduction of cyclic di-AMP affect viability of prokaryotes that utilize cyclic di-AMP, and that it generates a strong innate immune response in eukaryotes. In bacteria that produce the second messenger, most molecular targets of cyclic di-AMP are associated with cell volume control. Besides, other evidence links the second messenger to cell wall remodeling, DNA damage repair, sporulation, central metabolism, and the regulation of glycogen turnover. In this review, we take a biochemical, quantitative approach to address the main cellular processes that are directly regulated by cyclic di-AMP and show that these processes are very connected and require regulation of a similar set of proteins to which cyclic di-AMP binds. Altogether, we argue that cyclic di-AMP is a master regulator of cell volume and that other cellular processes can be connected with cyclic di-AMP through this core function. We further highlight important directions in which the cyclic di-AMP field has to develop to gain a full understanding of the cyclic di-AMP signaling network and why some processes are regulated, while others are not.
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Affiliation(s)
- Alexander J. Foster
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Marco van den Noort
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
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4
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Wang Q, Wang Z, Guan J, Song J. Transcriptome Analysis Reveals the Important Role of Vitamin B 12 in the Response of Natronorubrum daqingense to Salt Stress. Int J Mol Sci 2024; 25:4168. [PMID: 38673755 PMCID: PMC11050368 DOI: 10.3390/ijms25084168] [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: 02/27/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Natronorubrum daqingense JX313T is an extremely halophilic archaea that can grow in a NaCl-saturated environment. The excellent salt tolerance of N. daqingense makes it a high-potential candidate for researching the salt stress mechanisms of halophilic microorganisms from Natronorubrum. In this study, transcriptome analysis revealed that three genes related to the biosynthesis of vitamin B12 were upregulated in response to salt stress. For the wild-type (WT) strain JX313T, the low-salt adaptive mutant LND5, and the vitamin B12 synthesis-deficient strain ΔcobC, the exogenous addition of 10 mg/L of vitamin B12 could maximize their cell survival and biomass in both optimal and salt stress environments. Knockout of cobC resulted in changes in the growth boundary of the strain, as well as a significant decrease in cell survival and biomass, and the inability to synthesize vitamin B12. According to the HPLC analysis, when the external NaCl concentration (w/v) increased from 17.5% (optimal) to 22.5% (5% salt stress), the intracellular accumulation of vitamin B12 in WT increased significantly from (11.54 ± 0.44) mg/L to (15.23 ± 0.20) mg/L. In summary, N. daqingense is capable of absorbing or synthesizing vitamin B12 in response to salt stress, suggesting that vitamin B12 serves as a specific compatible solute effector for N. daqingense during salt stress.
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Affiliation(s)
| | | | | | - Jinzhu Song
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China; (Q.W.); (Z.W.); (J.G.)
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5
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Sperfeld M, Narváez-Barragán DA, Malitsky S, Frydman V, Yuda L, Rocha J, Segev E. Reducing the Bacterial Lag Phase Through Methylated Compounds: Insights from Algal-Bacterial Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.06.543872. [PMID: 38645154 PMCID: PMC11030247 DOI: 10.1101/2023.06.06.543872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The bacterial lag phase is a key period for resuming growth. Despite its significance, the lag phase remains underexplored, particularly in environmental bacteria. Here, we explore the lag phase of the model marine bacterium Phaeobacter inhibens when it transitions from starvation to growth with a microalgal partner. Utilizing transcriptomics and 13 C-labeled metabolomics, our study reveals that methylated compounds, which are abundantly produced by microalgae, shorten the bacterial lag phase. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and demonstrate that methyl groups can be harvested from algal compounds and assimilated through the methionine cycle. Furthermore, we show that methylated compounds, characteristic of photosynthetic organisms, induce variable reductions in lag times among bacteria associated with algae and plants. These findings highlight the adjustability of the bacterial lag phase and emphasize the importance of studying bacteria in an environmental context. One-Sentence Summary Bacteria use algal compounds as a metabolic shortcut to transition from starvation to growth.
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6
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Valencia-Marin MF, Chávez-Avila S, Guzmán-Guzmán P, Orozco-Mosqueda MDC, de Los Santos-Villalobos S, Glick BR, Santoyo G. Survival strategies of Bacillus spp. in saline soils: Key factors to promote plant growth and health. Biotechnol Adv 2024; 70:108303. [PMID: 38128850 DOI: 10.1016/j.biotechadv.2023.108303] [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: 08/16/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023]
Abstract
Soil salinity is one of the most important abiotic factors that affects agricultural production worldwide. Because of saline stress, plants face physiological changes that have negative impacts on the various stages of their development, so the employment of plant growth-promoting bacteria (PGPB) is one effective means to reduce such toxic effects. Bacteria of the Bacillus genus are excellent PGPB and have been extensively studied, but what traits makes them so extraordinary to adapt and survive under harsh situations? In this work we review the Bacillus' innate abilities to survive in saline stressful soils, such as the production osmoprotectant compounds, antioxidant enzymes, exopolysaccharides, and the modification of their membrane lipids. Other survival abilities are also discussed, such as sporulation or a reduced growth state under the scope of a functional interaction in the rhizosphere. Thus, the most recent evidence shows that these saline adaptive activities are important in plant-associated bacteria to potentially protect, direct and indirect plant growth-stimulating activities. Additionally, recent advances on the mechanisms used by Bacillus spp. to improve the growth of plants under saline stress are addressed, including genomic and transcriptomic explorations. Finally, characterization and selection of Bacillus strains with efficient survival strategies are key factors in ameliorating saline problems in agricultural production.
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Affiliation(s)
- María F Valencia-Marin
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Salvador Chávez-Avila
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Paulina Guzmán-Guzmán
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico
| | - Ma Del Carmen Orozco-Mosqueda
- Departamento de Ingeniería Bioquímica y Ambiental, Tecnológico Nacional de México en Celaya, 38010 Celaya, Gto, Mexico
| | | | - Bernard R Glick
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Gustavo Santoyo
- Instituto de Investigaciones Químico-Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Mich. 58030, Mexico.
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7
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Butterworth SJ, Barton F, Lloyd JR. Extremophilic microbial metabolism and radioactive waste disposal. Extremophiles 2023; 27:27. [PMID: 37839067 PMCID: PMC10577106 DOI: 10.1007/s00792-023-01312-4] [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: 03/02/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.
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Affiliation(s)
- Sarah Jane Butterworth
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK
| | - Franky Barton
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
| | - Jonathan Richard Lloyd
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
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8
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Boas Lichty KE, Gregory GJ, Boyd EF. NhaR, LeuO, and H-NS Are Part of an Expanded Regulatory Network for Ectoine Biosynthesis Expression. Appl Environ Microbiol 2023; 89:e0047923. [PMID: 37278653 PMCID: PMC10304999 DOI: 10.1128/aem.00479-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 05/11/2023] [Indexed: 06/07/2023] Open
Abstract
Bacteria accumulate compatible solutes to maintain cellular turgor pressure when exposed to high salinity. In the marine halophile Vibrio parahaemolyticus, the compatible solute ectoine is biosynthesized de novo, which is energetically more costly than uptake; therefore, tight regulation is required. To uncover novel regulators of the ectoine biosynthesis ectABC-asp_ect operon, a DNA affinity pulldown of proteins interacting with the ectABC-asp_ect regulatory region was performed. Mass spectrometry analysis identified, among others, 3 regulators: LeuO, NhaR, and the nucleoid associated protein H-NS. In-frame non-polar deletions were made for each gene and PectA-gfp promoter reporter assays were performed in exponential and stationary phase cells. PectA-gfp expression was significantly repressed in the ΔleuO mutant and significantly induced in the ΔnhaR mutant compared to wild type, suggesting positive and negative regulation, respectively. In the Δhns mutant, PectA-gfp showed increased expression in exponential phase cells, but no change compared to wild type in stationary phase cells. To examine whether H-NS interacts with LeuO or NhaR at the ectoine regulatory region, double deletion mutants were created. In a ΔleuO/Δhns mutant, PectA-gfp showed reduced expression, but significantly more than ΔleuO, suggesting H-NS and LeuO interact to regulate ectoine expression. However, ΔnhaR/Δhns had no additional effect compared to ΔnhaR, suggesting NhaR regulation is independent of H-NS. To examine leuO regulation further, a PleuO-gfp reporter analysis was examined that showed significantly increased expression in the ΔleuO, Δhns, and ΔleuO/Δhns mutants compared to wild type, indicating both are repressors. Growth pattern analysis of the mutants in M9G 6%NaCl showed growth defects compared to wild type, indicating that these regulators play an important physiological role in salinity stress tolerance outside of regulating ectoine biosynthesis gene expression. IMPORTANCE Ectoine is a commercially used compatible solute that acts as a biomolecule stabilizer because of its additional role as a chemical chaperone. A better understanding of how the ectoine biosynthetic pathway is regulated in natural bacterial producers can be used to increase efficient industrial production. The de novo biosynthesis of ectoine is essential for bacteria to survive osmotic stress when exogenous compatible solutes are absent. This study identified LeuO as a positive regulator and NhaR as a negative regulator of ectoine biosynthesis and showed that, similar to enteric species, LeuO is an anti-silencer of H-NS. In addition, defects in growth in high salinity among all the mutants suggest that these regulators play a broader role in the osmotic stress response beyond ectoine biosynthesis regulation.
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Affiliation(s)
| | - Gwendolyn J. Gregory
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - E. Fidelma Boyd
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
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9
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Bailoni E, Partipilo M, Coenradij J, Grundel DAJ, Slotboom DJ, Poolman B. Minimal Out-of-Equilibrium Metabolism for Synthetic Cells: A Membrane Perspective. ACS Synth Biol 2023; 12:922-946. [PMID: 37027340 PMCID: PMC10127287 DOI: 10.1021/acssynbio.3c00062] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Indexed: 04/08/2023]
Abstract
Life-like systems need to maintain a basal metabolism, which includes importing a variety of building blocks required for macromolecule synthesis, exporting dead-end products, and recycling cofactors and metabolic intermediates, while maintaining steady internal physical and chemical conditions (physicochemical homeostasis). A compartment, such as a unilamellar vesicle, functionalized with membrane-embedded transport proteins and metabolic enzymes encapsulated in the lumen meets these requirements. Here, we identify four modules designed for a minimal metabolism in a synthetic cell with a lipid bilayer boundary: energy provision and conversion, physicochemical homeostasis, metabolite transport, and membrane expansion. We review design strategies that can be used to fulfill these functions with a focus on the lipid and membrane protein composition of a cell. We compare our bottom-up design with the equivalent essential modules of JCVI-syn3a, a top-down genome-minimized living cell with a size comparable to that of large unilamellar vesicles. Finally, we discuss the bottlenecks related to the insertion of a complex mixture of membrane proteins into lipid bilayers and provide a semiquantitative estimate of the relative surface area and lipid-to-protein mass ratios (i.e., the minimal number of membrane proteins) that are required for the construction of a synthetic cell.
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Affiliation(s)
- Eleonora Bailoni
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Michele Partipilo
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Jelmer Coenradij
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Douwe A. J. Grundel
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Dirk J. Slotboom
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry and Molecular Systems Biology, Groningen Biomolecular
Sciences and Biotechnology Institute, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
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10
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Zhang K, Zhang Z, Guo X, Guo R, Zhu L, Qiu X, Yu X, Chai J, Gu C, Feng Z. Changes in nutrient consumption patterns of Lactobacillus fermentum mediated by sodium lactate. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:1775-1783. [PMID: 36305089 DOI: 10.1002/jsfa.12295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/28/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND During high-cell-density culture of Lactobacillus fermentum, the optimal pH is often maintained by adding NaOH. During cultivation at controlled pH, L. fermentum experiences osmotic stress due to the continuous accumulation of sodium lactate as a neutralizer product, affecting its survival in subsequent processing. The purpose of this study was to evaluate the nutrient consumption patterns of L. fermentum ATCC 14931 under sodium lactate stress and to screen nutrients that help it resist osmotic stress. RESULTS The consumption and consumption rates of amino acids, purines, pyrimidines, vitamins, and metal ions were analyzed in chemically defined media containing 0.13, 0.31, or 0.62 mm L-1 sodium lactate. The highest consumption rates were found for arginine, guanine, folic acid, and Mn2+ , and the most consumed nutrients were glutamate + glutamine, guanine, ascorbic acid, and Na+ . Arginine 2.58 mm L-1 , guanine 0.23 mm L-1 , and Mn2+ 0.25 mm L-1 were added to the medium at sodium lactate concentrations of 0.13 and 0.62 mm L-1 , and arginine 2.58 mm L-1 , guanine 0.26 mm L-1 , and Mn2+ 0.25 mm L-1 at a sodium lactate concentration of 0.31 mm L-1 . The viable cell counts of L. fermentum ATCC 14931 were approximately 1.02-fold (P < 0.05) of the counts observed in control medium at all three concentrations of sodium lactate. CONCLUSION The present results suggest that certain nutrients accelerate the growth of L. fermentum under sodium lactate stress and enhance its resistance to this adverse condition. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Kenan Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Zongcai Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xiaoxue Guo
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Ruijia Guo
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Lin Zhu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xinrong Qiu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Xiaohan Yu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Jun Chai
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
| | - Chunhe Gu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
| | - Zhen Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin, China
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, China
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11
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Buatong J, Mittal A, Mittraparp-arthorn P, Palamae S, Saetang J, Benjakul S. Bactericidal Action of Shrimp Shell Chitooligosaccharide Conjugated with Epigallocatechin Gallate (COS-EGCG) against Listeria monocytogenes. Foods 2023; 12:634. [PMID: 36766163 PMCID: PMC9914238 DOI: 10.3390/foods12030634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
The antibacterial effect of chitooligosaccharide conjugated with five different polyphenols, including catechin (COS-CAT), epigallocatechin gallate (COS-EGCG), gallic acid (COS-GAL), caffeic acid (COS-CAF), and ferulic acid (COS-FER), against Listeria monocytogenes was investigated. Among all the conjugates tested, COS-EGCG showed the highest inhibition toward Listeria monocytogenes, with a minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of 1024 and 1024 µg/mL, respectively. The COS-EGCG conjugate also had a bactericidal effect on the environmental and clinical strains of L. monocytogenes. The low concentration of COS-EGCG conjugate augmented the formation of biofilm and the growth of L. monocytogenes. Nevertheless, the inhibition of biofilm formation and bacterial growth was achieved when treated with the COS-EGCG conjugate at 2 × MIC for 48 h. In addition, the COS-EGCG conjugate at 2 × MIC had the potential to inactivate the pre-biofilm, and it reduced the production of the extracellular polysaccharides of L. monocytogenes. The COS-EGCG conjugate at the MIC/4 effectively impeded the motility (the swimming and swarming) of L. monocytogenes, with an 85.7-94.3% inhibition, while 100% inhibition was achieved with the MIC. Based on scanning electron microscopic (SEM) images, cell wall damage with numerous pores on the cell surface was observed. Such cell distortion resulted in protein leakage. As a result, COS-EGCG could penetrate into the cell and bind with the DNA backbone. Therefore, the COS-EGCG conjugate could be further developed as a natural antimicrobial agent for inhibiting or controlling L. monocytogenes.
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Affiliation(s)
- Jirayu Buatong
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Ajay Mittal
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Pimonsri Mittraparp-arthorn
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Suriya Palamae
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Jirakrit Saetang
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
| | - Soottawat Benjakul
- International Center of Excellence in Seafood Science and Innovation, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai 90110, Songkhla, Thailand
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12
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Deciphering the antibacterial mechanism of monocaprin against methicillin-resistant Staphylococcus aureus by integrated transcriptomic and metabolomic analyses and its application in pork preservation. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2023.114569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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13
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Vujanovic S, Vujanovic J, Vujanovic V. Microbiome-Driven Proline Biogenesis in Plants under Stress: Perspectives for Balanced Diet to Minimize Depression Disorders in Humans. Microorganisms 2022; 10:2264. [PMID: 36422335 PMCID: PMC9693749 DOI: 10.3390/microorganisms10112264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 09/10/2024] Open
Abstract
According to the World Health Organization (WHO), depression is a leading cause of disability worldwide and a major contributor to the overall global burden of mental disorders. An increasing number of studies have revealed that among 20 different amino acids, high proline consumption is a dietary factor with the strongest impact on depression in humans and animals, including insects. Recent studies acknowledged that gut microbiota play a key role in proline-related pathophysiology of depression. In addition, the multi-omics approach has alleged that a high level of metabolite proline is directly linked to depression severity, while variations in levels of circulating proline are dependent on microbiome composition. The gut-brain axis proline analysis is a gut microbiome model of studying depression, highlighting the critical importance of diet, but nothing is known about the role of the plant microbiome-food axis in determining proline concentration in the diet and thus about preventing excessive proline intake through food consumption. In this paper, we discuss the protocooperative potential of a holistic study approach combining the microbiota-gut-brain axis with the microbiota-plant-food-diet axis, as both are involved in proline biogenesis and metabolism and thus on in its effect on mood and cognitive function. In preharvest agriculture, the main scientific focus must be directed towards plant symbiotic endophytes, as scavengers of abiotic stresses in plants and modulators of high proline concentration in crops/legumes/vegetables under climate change. It is also implied that postharvest agriculture-including industrial food processing-may be critical in designing a proline-balanced diet, especially if corroborated with microbiome-based preharvest agriculture, within a circular agrifood system. The microbiome is suggested as a target for selecting beneficial plant endophytes in aiming for a balanced dietary proline content, as it is involved in the physiology and energy metabolism of eukaryotic plant/human/animal/insect hosts, i.e., in core aspects of this amino acid network, while opening new venues for an efficient treatment of depression that can be adapted to vast groups of consumers and patients. In that regard, the use of artificial intelligence (AI) and molecular biomarkers combined with rapid and non-destructive imaging technologies were also discussed in the scope of enhancing integrative science outcomes, agricultural efficiencies, and diagnostic medical precisions.
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Affiliation(s)
- Silva Vujanovic
- Hospital Pharmacy, CISSS des Laurentides, Université de Montréal, Montréal, QC J8H 4C7, Canada
| | - Josko Vujanovic
- Medical Imaging, CISSS des Laurentides, Lachute, QC J8H 4C7, Canada
| | - Vladimir Vujanovic
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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Abosamaha A, Williamson MP, Gilmour DJ. Utilization and accumulation of compatible solutes in Halomonas pacifica: a species of moderately halophilic bacteria isolated from a saline lake in South Libya. Access Microbiol 2022; 4:acmi000359. [PMID: 36003353 PMCID: PMC9394535 DOI: 10.1099/acmi.0.000359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
When grown in high salt concentrations, halophilic bacteria often accumulate compatible solutes, which have major applications in biotechnology because they stabilize cells and proteins. Four Gram-negative bacterial strains, belonging to the family Halomonadaceae, were isolated from Qaberoun and Um-Alma lakes in South Libya using high-salinity medium. The strains were identified using 16S rRNA gene sequencing as belonging to Halomonas pacifica (strain ABQ1), Halomonas venusta (ABQ2), Halomonas elongata (ABU1) and Halomonas salifodinae (ABU2). H. pacifica ABQ1 is a moderate halophile (salinity range 0.05 to 2.5 M NaCl), with a broad tolerance to pH (7 to 9) and temperature (25–37 °C). Addition of the compatible solutes glycine betaine (betaine) and ectoine (1,4,5,6-tetrahydro-2-methyl-4-pyrimidine carboxylic acid) to the medium had a positive effect on growth of H. pacifica at 2 M NaCl. In rich LB medium, betaine was the major compatible solute accumulated, with ectoine only being accumulated at salinities in excess of 1 M NaCl. In minimal M9 medium, betaine was not produced, but increasing amounts of ectoine were synthesized with increasing salinity, and hydroxyectoine [(4S,5S)−5-hydroxy-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid] was also synthesized when the cells were grown in very high salt. We have thus identified H. pacifica as a producer of ectoine and hydroxyectoine, with more being produced at higher salinities. As industrial demand for these compatible solutes continues to increase, this system has biotechnological potential.
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Affiliation(s)
- Abdolkader Abosamaha
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Mike P. Williamson
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
| | - D. James Gilmour
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK
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15
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Luo Q, Duan Y, Lu X. Biological sources, metabolism, and production of glucosylglycerols, a group of natural glucosides of biotechnological interest. Biotechnol Adv 2022; 59:107964. [PMID: 35452777 DOI: 10.1016/j.biotechadv.2022.107964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 11/02/2022]
Abstract
Glucosylglycerols (GGs) are a group of functional heterosides comprising glycerol and glucose. In nature, they are mainly produced by many moderately salt-tolerant cyanobacteria as compatible solutes in a salt-dependent manner and synthesized in a few higher plants and fermentation processes. Because of their many interesting physicochemical properties and biological activities, such as low sweetness, low hygroscopicity, high water-holding capacity, excellent biocompatibility, favorable performance in protecting macromolecules, and antitumor activity, GGs exhibit large application potential in the fields of cosmetics, health care, food service, enzyme production, and pharmaceuticals. Many in vitro systems using different members of the GH (glycoside hydrolase) family have been established for the enzymatic synthesis of GGs, and a few of them are in use for commercial production. Based on a good understanding of the genetic bases, biochemical processes, and regulatory mechanisms of GG metabolism in microorganisms (mainly cyanobacteria), in recent years GG production technologies with in vivo systems have also been developed by applying metabolic and bioprocess engineering to a few native or heterologous microbial cell factories. This successfully provides the market GG products with an alternative source. With the further elucidation of details about the biological functions of GGs and related mechanisms, the application scope of GGs will be greatly expanded. In the present review, the biological sources and physiological roles of GGs, the molecular bases and regulation of GG metabolism, and the recent progress in GG production and application are systematically summarized. A few new questions that have arisen in the basic research of GGs and perspectives on GG application are also discussed.
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Affiliation(s)
- Quan Luo
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao 266101, China.
| | - Yangkai Duan
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China.
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Rd 189, Qingdao 266101, China; Shandong Energy Institute, Songling Rd 189, Qingdao 266101, China; Qingdao New Energy Shandong Laboratory, Songling Rd 189, Qingdao 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Songling Rd 189, Qingdao 266101, China; Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Wenhai Rd 168, Qingdao 266237, China.
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16
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Three Microbial Musketeers of the Seas: Shewanella baltica, Aliivibrio fischeri and Vibrio harveyi, and Their Adaptation to Different Salinity Probed by a Proteomic Approach. Int J Mol Sci 2022; 23:ijms23020619. [PMID: 35054801 PMCID: PMC8775919 DOI: 10.3390/ijms23020619] [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: 11/27/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022] Open
Abstract
Osmotic changes are common challenges for marine microorganisms. Bacteria have developed numerous ways of dealing with this stress, including reprogramming of global cellular processes. However, specific molecular adaptation mechanisms to osmotic stress have mainly been investigated in terrestrial model bacteria. In this work, we aimed to elucidate the basis of adjustment to prolonged salinity challenges at the proteome level in marine bacteria. The objects of our studies were three representatives of bacteria inhabiting various marine environments, Shewanella baltica, Vibrio harveyi and Aliivibrio fischeri. The proteomic studies were performed with bacteria cultivated in increased and decreased salinity, followed by proteolytic digestion of samples which were then subjected to liquid chromatography with tandem mass spectrometry analysis. We show that bacteria adjust at all levels of their biological processes, from DNA topology through gene expression regulation and proteasome assembly, to transport and cellular metabolism. The finding that many similar adaptation strategies were observed for both low- and high-salinity conditions is particularly striking. The results show that adaptation to salinity challenge involves the accumulation of DNA-binding proteins and increased polyamine uptake. We hypothesize that their function is to coat and protect the nucleoid to counteract adverse changes in DNA topology due to ionic shifts.
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17
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Shao L, Liu Y, Zhao Y, Zou B, Li X, Dai R. Integrated transcriptomic and metabolomic analysis of the global response of Staphylococcus aureus to ohmic heating. INNOV FOOD SCI EMERG 2021. [DOI: 10.1016/j.ifset.2021.102870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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18
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Martin G, Sharma S, Ryan W, Srinivasan NK, Senko JM. Identification of Microbiological Activities in Wet Flue Gas Desulfurization Systems. Front Microbiol 2021; 12:675628. [PMID: 34262541 PMCID: PMC8273512 DOI: 10.3389/fmicb.2021.675628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022] Open
Abstract
Thermoelectric power generation from coal requires large amounts of water, much of which is used for wet flue gas desulfurization (wFGD) systems that minimize sulfur emissions, and consequently, acid rain. The microbial communities in wFGDs and throughout thermoelectric power plants can influence system performance, waste processing, and the long term stewardship of residual wastes. Any microorganisms that survive in wFGD slurries must tolerate high total dissolved solids concentrations (TDS) and temperatures (50–60°C), but the inocula for wFGDs are typically from fresh surface waters (e.g., lakes or rivers) of low TDS and temperatures, and whose activity might be limited under the physicochemically extreme conditions of the wFGD. To determine the extents of microbiological activities in wFGDs, we examined the microbial activities and communities associated with three wFGDs. O2 consumption rates of three wFGD slurries were optimal at 55°C, and living cells could be detected microscopically, indicating that living and active communities of organisms were present in the wFGD and could metabolize at the high temperature of the wFGD. A 16S rRNA gene-based survey revealed that the wFGD-associated microbial communities included taxa attributable to both thermophilic and mesophilic lineages. Metatranscriptomic analysis of one of the wFGDs indicated an abundance of active Burholderiaceae and several Gammaproteobacteria, and production of transcripts associated with carbohydrate metabolism, osmotic stress response, as well as phage, prophages, and transposable elements. These results illustrate that microbial activities can be sustained in physicochemically extreme wFGDs, and these activities may influence the performance and environmental impacts of thermoelectric power plants.
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Affiliation(s)
- Gregory Martin
- Department of Biology, The University of Akron, Akron, OH, United States
| | - Shagun Sharma
- Department of Biology, The University of Akron, Akron, OH, United States.,Integrated Bioscience Program, The University of Akron, Akron, OH, United States
| | - William Ryan
- Department of Biology, The University of Akron, Akron, OH, United States
| | | | - John M Senko
- Department of Biology, The University of Akron, Akron, OH, United States.,Integrated Bioscience Program, The University of Akron, Akron, OH, United States.,Department of Geosciences, The University of Akron, Akron, OH, United States
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19
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Van Thuoc D, Loan TT, Trung TA, Van Quyen N, Tung QN, Tien PQ, Sudesh K. Genome Mining Reveals the Biosynthetic Pathways of Polyhydroxyalkanoate and Ectoines of the Halophilic Strain Salinivibrio proteolyticus M318 Isolated from Fermented Shrimp Paste. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:651-660. [PMID: 32827070 DOI: 10.1007/s10126-020-09986-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
Salinivibrio proteolyticus M318, a halophilic bacterium isolated from fermented shrimp paste, is able to produce polyhydroxyalkanoate (PHA) from different carbon sources. In this study, we report the whole-genome sequence of strain M138, which comprises 2 separated chromosomes and 2 plasmids, and the complete genome contains 3,605,935 bp with an average GC content of 49.9%. The genome of strain M318 contains 3341 genes, 98 tRNA genes, and 28 rRNA genes. The 16S rRNA gene sequence and average nucleotide identity analysis associated with morphological and biochemical tests showed that this strain has high homology to the reference strain Salinivibrio proteolyticus DSM 8285. The genes encoding key enzymes for PHA and ectoine synthesis were identified from the bacterial genome. In addition, the TeaABC transporter responsible for ectoine uptake from the environment and the operon doeABXCD responsible for the degradation of ectoine were also detected. Strain M318 was able to produce poly(3-hydroxybutyrate) [P(3HB)] from different carbon sources such as glycerol, maltose, glucose, fructose, and starch. The ability to produce ectoines at different NaCl concentrations was investigated. High ectoine content of 26.2% of cell dry weight was obtained by this strain at 18% NaCl. This report provides genetic information regarding adaptive mechanisms of strain M318 to stress conditions, as well as new knowledge to facilitate the application of this strain as a bacterial cell factory for the production of PHA and ectoine.
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Affiliation(s)
- Doan Van Thuoc
- Faculty of Biology, Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam.
| | - Tran Thi Loan
- Faculty of Biology, Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Trieu Anh Trung
- Faculty of Biology, Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Nguyen Van Quyen
- Faculty of Biology, Hanoi National University of Education, 136 Xuan Thuy, Cau Giay, Hanoi, Vietnam
| | - Quach Ngoc Tung
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Caugiay, Hanoi, Vietnam
| | - Phi Quyet Tien
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Caugiay, Hanoi, Vietnam
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Penang, Malaysia
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20
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Nayak PK, Goode M, Chang DP, Rajagopal K. Ectoine and Hydroxyectoine Stabilize Antibodies in Spray-Dried Formulations at Elevated Temperature and during a Freeze/Thaw Process. Mol Pharm 2020; 17:3291-3297. [PMID: 32672979 DOI: 10.1021/acs.molpharmaceut.0c00395] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Maintenance of protein stability during manufacture, storage, and delivery is necessary for the successful development of a drug product. Herein, the utility of two compatible solutes-ectoine and hydroxyectoine-in stabilizing a model protein labeled Fab2 has been investigated. Specifically, the performance of ectoine and hydroxyectoine in stabilizing Fab2 in a spray-dried formulation at elevated temperature and after multiple freeze/thaw cycles has been compared with the performance of a formulation containing trehalose and a formulation containing no excipient as controls. In the solid state at 90 and 37 °C and in freeze concentrate systems, ectoine and hydroxyectoine suppress protein aggregation. Like trehalose, hydroxyectoine also limits N-terminal pyroglutamate formation in Fab2 in the solid state. The extent of protein stabilization is dependent on the excipient concentration in the formulation, but at a 1:1 excipient to protein mass ratio, hydroxyectoine is better than trehalose in stabilizing Fab2. The results presented here suggest that ectoine and hydroxyectoine are effective excipients for stabilizing therapeutic antibodies.
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Affiliation(s)
- Purnendu K Nayak
- Eurofins Lancaster Laboratories, Lancaster, Pennsylvania 17605, United States
| | - Meghan Goode
- Drug Delivery Department, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Debby P Chang
- Drug Delivery Department, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Karthikan Rajagopal
- Drug Delivery Department, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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21
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Liang R, Lau MCY, Saitta ET, Garvin ZK, Onstott TC. Genome-centric resolution of novel microbial lineages in an excavated Centrosaurus dinosaur fossil bone from the Late Cretaceous of North America. ENVIRONMENTAL MICROBIOME 2020; 15:8. [PMID: 33902738 PMCID: PMC8067395 DOI: 10.1186/s40793-020-00355-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 02/27/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Exceptional preservation of endogenous organics such as collagens and blood vessels has been frequently reported in Mesozoic dinosaur fossils. The persistence of these soft tissues in Mesozoic fossil bones has been challenged because of the susceptibility of proteins to degradation and because bone porosity allows microorganisms to colonize the inner microenvironments through geological time. Although protein lability has been studied extensively, the genomic diversity of microbiomes in dinosaur fossil bones and their potential roles in bone taphonomy remain underexplored. Genome-resolved metagenomics was performed, therefore, on the microbiomes recovered from a Late Cretaceous Centrosaurus bone and its encompassing mudstone in order to provide insight into the genomic potential for microbial alteration of fossil bone. RESULTS Co-assembly and binning of metagenomic reads resulted in a total of 46 high-quality metagenome-assembled genomes (MAGs) affiliated to six bacterial phyla (Actinobacteria, Proteobacteria, Nitrospira, Acidobacteria, Gemmatimonadetes and Chloroflexi) and 1 archaeal phylum (Thaumarchaeota). The majority of the MAGs represented uncultivated, novel microbial lineages from class to species levels based on phylogenetics, phylogenomics and average amino acid identity. Several MAGs from the classes Nitriliruptoria, Deltaproteobacteria and Betaproteobacteria were highly enriched in the bone relative to the adjacent mudstone. Annotation of the MAGs revealed that the distinct putative metabolic functions of different taxonomic groups were linked to carbon, nitrogen, sulfur and iron metabolism. Metaproteomics revealed gene expression from many of the MAGs, but no endogenous collagen peptides were identified in the bone that could have been derived from the dinosaur. Estimated in situ replication rates among the bacterial MAGs suggested that most of the microbial populations in the bone might have been actively growing but at a slow rate. CONCLUSIONS Our results indicate that excavated dinosaur bones are habitats for microorganisms including novel microbial lineages. The distinctive microhabitats and geochemistry of fossil bone interiors compared to that of the external sediment enrich a microbial biomass comprised of various novel taxa that harbor multiple gene sets related to interconnected biogeochemical processes. Therefore, the presence of these microbiomes in Mesozoic dinosaur fossils urges extra caution to be taken in the science of paleontology when hunting for endogenous biomolecules preserved from deep time.
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Affiliation(s)
- Renxing Liang
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA.
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
- Present address: Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Evan T Saitta
- Integrative Research Center, Section of Earth Sciences, Field Museum of Natural History, Chicago, USA
| | - Zachary K Garvin
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, B88, Guyot Hall, Princeton University, Princeton, NJ, 08544, USA
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22
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Mukai Y, Kamei Y, Liu X, Jiang S, Sugimoto Y, Mat Nanyan NSB, Watanabe D, Takagi H. Proline metabolism regulates replicative lifespan in the yeast Saccharomyces cerevisiae. MICROBIAL CELL 2019; 6:482-490. [PMID: 31646149 PMCID: PMC6780008 DOI: 10.15698/mic2019.10.694] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In many plants and microorganisms, intracellular proline has a protective role against various stresses, including heat-shock, oxidation and osmolarity. Environmental stresses induce cellular senescence in a variety of eukaryotes. Here we showed that intracellular proline regulates the replicative lifespan in the budding yeast Saccharomyces cerevisiae. Deletion of the proline oxidase gene PUT1 and expression of the γ-glutamate kinase mutant gene PRO1-I150T that is less sensitive to feedback inhibition accumulated proline and extended the replicative lifespan of yeast cells. Inversely, disruption of the proline biosynthetic genes PRO1, PRO2, and CAR2 decreased stationary proline level and shortened the lifespan of yeast cells. Quadruple disruption of the proline transporter genes unexpectedly did not change intracellular proline levels and replicative lifespan. Overexpression of the stress-responsive transcription activator gene MSN2 reduced intracellular proline levels by inducing the expression of PUT1, resulting in a short lifespan. Thus, the intracellular proline levels at stationary phase was positively correlated with the replicative lifespan. Furthermore, multivariate analysis of amino acids in yeast mutants deficient in proline metabolism showed characteristic metabolic profiles coincident with longevity: acidic and basic amino acids and branched-chain amino acids positively contributed to the replicative lifespan. These results allude to proline metabolism having a physiological role in maintaining the lifespan of yeast cells.
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Affiliation(s)
- Yukio Mukai
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Yuka Kamei
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Xu Liu
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Shan Jiang
- Department of Frontier Bioscience, Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Yukiko Sugimoto
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Noreen Suliani Binti Mat Nanyan
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Daisuke Watanabe
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | - Hiroshi Takagi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
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Metabolite Cross-Feeding between Rhodococcus ruber YYL and Bacillus cereus MLY1 in the Biodegradation of Tetrahydrofuran under pH Stress. Appl Environ Microbiol 2019; 85:AEM.01196-19. [PMID: 31375492 DOI: 10.1128/aem.01196-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/23/2019] [Indexed: 11/20/2022] Open
Abstract
Bacterial consortia are among the most basic units in the biodegradation of environmental pollutants. Pollutant-degrading strains frequently encounter different types of environmental stresses and must be able to survive with other bacteria present in the polluted environments. In this study, we proposed a noncontact interaction mode between a tetrahydrofuran (THF)-degrading strain, Rhodococcus ruber YYL, and a non-THF-degrading strain, Bacillus cereus MLY1. The metabolic interaction mechanism between strains YYL and MLY1 was explored through physiological and molecular studies and was further supported by the metabolic response profile of strain YYL, both monocultured and cocultured with strain MLY1 at the optimal pH (pH 8.3) and under pH stress (pH 7.0), through a liquid chromatography-mass spectrometry-based metabolomic analysis. The results suggested that the coculture system resists pH stress in three ways: (i) strain MLY1 utilized acid metabolites and impacted the proportion of glutamine, resulting in an elevated intracellular pH of the system; (ii) strain MLY1 had the ability to degrade intermediates, thus alleviating the product inhibition of strain YYL; and (iii) strain MLY1 produced some essential micronutrients for strain YYL to aid the growth of this strain under pH stress, while strain YYL produced THF degradation intermediates for strain MLY1 as major nutrients. In addition, a metabolite cross-feeding interaction with respect to pollutant biodegradation is discussed.IMPORTANCE Rhodococcus species have been discovered in diverse environmental niches and can degrade numerous recalcitrant toxic pollutants. However, the pollutant degradation efficiency of these strains is severely reduced due to the complexity of environmental conditions and limitations in the growth of the pollutant-degrading microorganism. In our study, Bacillus cereus strain MLY1 exhibited strong stress resistance to adapt to various environments and improved the THF degradation efficiency of Rhodococcus ruber YYL by a metabolic cross-feeding interaction style to relieve the pH stress. These findings suggest that metabolite cross-feeding occurred in a complementary manner, allowing a pollutant-degrading strain to collaborate with a nondegrading strain in the biodegradation of various recalcitrant compounds. The study of metabolic exchanges is crucial to elucidate mechanisms by which degrading and symbiotic bacteria interact to survive environmental stress.
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Pan R, Bai X, Chen J, Zhang H, Wang H. Exploring Structural Diversity of Microbe Secondary Metabolites Using OSMAC Strategy: A Literature Review. Front Microbiol 2019; 10:294. [PMID: 30863377 PMCID: PMC6399155 DOI: 10.3389/fmicb.2019.00294] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022] Open
Abstract
Microbial secondary metabolites (MSMs) have played and continue to play a highly significant role in the drug discovery and development process. Genetically, MSM chemical structures are biologically synthesized by microbial gene clusters. Recently, however, the speed of new bioactive MSM discovery has been slowing down due to consistent employment of conventional cultivation and isolation procedure. In order to alleviate this challenge, a number of new approaches have been developed. The strategy of one strain many compounds (OSMAC) has been shown as a simple and powerful tool that can activate many silent biogenetic gene clusters in microorganisms to make more natural products. This review highlights important and successful examples using OSMAC approaches, which covers changing medium composition and cultivation status, co-cultivation with other strain(s), adding enzyme inhibitor(s) and MSM biosynthetic precursor(s). Available evidences had shown that variation of cultivation condition is the most effective way to produce more MSMs and facilitate the discovery of new therapeutic agents.
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Affiliation(s)
- Rui Pan
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Xuelian Bai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jianwei Chen
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Hong Wang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
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Glycine betaine transport conditions of Lactobacillus delbrueckii subsp. bulgaricus in salt induced hyperosmotic stress. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Li Y, Zhou D, Hu S, Xiao X, Yu Y, Li X. Transcriptomic analysis by RNA-seq of Escherichia coli O157:H7 response to prolonged cold stress. Lebensm Wiss Technol 2018. [DOI: 10.1016/j.lwt.2018.06.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Li J, Shi W, Jiang C, Bai L, Wang T, Yu J, Ruan W. Evaluation of potassium as promoter on anaerobic digestion of saline organic wastewater. BIORESOURCE TECHNOLOGY 2018; 266:68-74. [PMID: 29957292 DOI: 10.1016/j.biortech.2018.06.066] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 06/08/2023]
Abstract
In this work, the effect of potassium on mesophilic anaerobic digestion (AD) of saline organic wastewater, which consisted of simulated effluents obtained from heparin sodium production, was studied. The results showed that the addition of potassium chloride (KCl) to saline organic wastewater enhanced the AD efficiency. The optimal dosage was found to be 0.174% when the salt (NaCl) content was 2.0%. Under this condition, the chemical oxygen demand (COD) removal efficiency, dehydrogenase activities, and the viability of microorganisms reached 62.7%, 55.7 TF μL-1, and 78.4%, respectively, which were 115.4%, 77.2%, and 20.3% higher than those without the addition of potassium chloride. The consumption of volatile fatty acids (VFAs) was enhanced during the AD process. Moreover, less humic-like and protein-like residues appeared in the wastewater after AD. Potassium could maintain the morphology of anaerobic microorganism under high salinity and showed a long-term effect.
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Affiliation(s)
- Jing Li
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wansheng Shi
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Changwang Jiang
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Ling Bai
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Tao Wang
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jiangnan Yu
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Wenquan Ruan
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; Jiangsu Key Laboratory of Anaerobic Biotechnology, Jiangnan University, Wuxi 214122, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou 215009, China.
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Malekani F, Ryan MC, Zebarth BJ, Loo SE, Suchy M, Cey EE. A Field-Scale Approach to Estimate Nitrate Loading to Groundwater. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:795-804. [PMID: 30025041 DOI: 10.2134/jeq2017.09.0369] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The quantification of groundwater NO loading associated with a specific field or set of management practices so that groundwater quality improvements can be objectively assessed is a major challenge. The magnitude and timing of NO export from a single agricultural field under raspberry ( L.) production were investigated by combining high-resolution groundwater NO concentration profiles (sampled using passive diffusion samplers) with Darcy's flux estimation at the field's down-gradient edge (based on field-measured hydraulic gradients and laboratory-estimated hydraulic conductivity). Annual recharge estimated using Darcy's law (1002 mm) was similar to that obtained using two other approaches. The similarity in the rate of Cl applied to the field and the estimated export flux over the 1-yr monitoring period (51 vs. 56 kg Cl ha) suggested the mass flux estimation approach was robust. An estimated 80 kg NO-N ha was exported from the agricultural field over the 1-yr monitoring period. The greatest monthly groundwater mass flux exported was observed in February and March (∼11 kg NO-N ha), and was associated with NO leached from the soil zone during the onset of precipitation in the previous autumn. Provided the groundwater recharged from the field of interest can be isolated within a vertical profile, this approach is an effective method for obtaining spatially integrated estimates of the magnitude and timing of NO loading to groundwater.
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Matolygina DA, Dushutina NS, Ovchinnikova ED, Eremeev NL, Belogurova NG, Atroshenko DL, Smirnov SA, Savin SS, Tishkov VI, Levashov AV, Levashov PA. Enzymatic Lysis of Living Microbial Cells: A Universal Approach to Calculating the Rate of Cell Lysis in Turbidimetric Measurements. ACTA ACUST UNITED AC 2018. [DOI: 10.3103/s0027131418020104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Han J, Gao QX, Zhang YG, Li L, Mohamad OAA, Rao MPN, Xiao M, Hozzein WN, Alkhalifah DHM, Tao Y, Li WJ. Transcriptomic and Ectoine Analysis of Halotolerant Nocardiopsis gilva YIM 90087 T Under Salt Stress. Front Microbiol 2018; 9:618. [PMID: 29651284 PMCID: PMC5884947 DOI: 10.3389/fmicb.2018.00618] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/16/2018] [Indexed: 11/25/2022] Open
Abstract
The genus Nocardiopsis is an unique actinobacterial group that widely distributed in hypersaline environments. In this study, we investigated the growth conditions, transcriptome analysis, production and accumulation of ectoine by Nocardiopsis gilva YIM 90087T under salt stress. The colony color of N. gilva YIM 90087T changed from yellow to white under salt stress conditions. Accumulation of ectoine and hydroxyectoine in cells was an efficient way to regulate osmotic pressure. The ectoine synthesis was studied by transferring the related genes (ectA, ectB, and ectC) to Escherichia coli. Transcriptomic analysis showed that the pathways of ABC transporters (ko02010) and glycine, serine, and threonine metabolism (ko00260) played a vital role under salt stress environment. The ectABC from N. gilva YIM 90087T was activated under the salt stress. Addition of exogenous ectoine and hydroxyectoine were helpful to protect N. gilva YIM 90087T from salt stress.
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Affiliation(s)
- Jian Han
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China.,Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Quan-Xiu Gao
- Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong-Guang Zhang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
| | - Li Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China
| | - Osama A A Mohamad
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China.,Institute for Post Graduate Environmental Studies, Environmental Science Department, Arish University, North Sinai, Egypt
| | - Manik Prabhu Narsing Rao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Min Xiao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wael N Hozzein
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni Suef, Egypt.,Bioproducts Research Chair, Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Dalal H M Alkhalifah
- Biology Department, Faculty of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Yong Tao
- Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wen-Jun Li
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Ürümqi, China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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31
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Schwendner P, Bohmeier M, Rettberg P, Beblo-Vranesevic K, Gaboyer F, Moissl-Eichinger C, Perras AK, Vannier P, Marteinsson VT, Garcia-Descalzo L, Gómez F, Malki M, Amils R, Westall F, Riedo A, Monaghan EP, Ehrenfreund P, Cabezas P, Walter N, Cockell C. Beyond Chloride Brines: Variable Metabolomic Responses in the Anaerobic Organism Yersinia intermedia MASE-LG-1 to NaCl and MgSO 4 at Identical Water Activity. Front Microbiol 2018; 9:335. [PMID: 29535699 PMCID: PMC5835128 DOI: 10.3389/fmicb.2018.00335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/12/2018] [Indexed: 11/18/2022] Open
Abstract
Growth in sodium chloride (NaCl) is known to induce stress in non-halophilic microorganisms leading to effects on the microbial metabolism and cell structure. Microorganisms have evolved a number of adaptations, both structural and metabolic, to counteract osmotic stress. These strategies are well-understood for organisms in NaCl-rich brines such as the accumulation of certain organic solutes (known as either compatible solutes or osmolytes). Less well studied are responses to ionic environments such as sulfate-rich brines which are prevalent on Earth but can also be found on Mars. In this paper, we investigated the global metabolic response of the anaerobic bacterium Yersinia intermedia MASE-LG-1 to osmotic salt stress induced by either magnesium sulfate (MgSO4) or NaCl at the same water activity (0.975). Using a non-targeted mass spectrometry approach, the intensity of hundreds of metabolites was measured. The compatible solutes L-asparagine and sucrose were found to be increased in both MgSO4 and NaCl compared to the control sample, suggesting a similar osmotic response to different ionic environments. We were able to demonstrate that Yersinia intermedia MASE-LG-1 accumulated a range of other compatible solutes. However, we also found the global metabolic responses, especially with regard to amino acid metabolism and carbohydrate metabolism, to be salt-specific, thus, suggesting ion-specific regulation of specific metabolic pathways.
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Affiliation(s)
- Petra Schwendner
- School of Physics and Astronomy, UK Center for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Bohmeier
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Petra Rettberg
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Kristina Beblo-Vranesevic
- Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Cologne, Germany
| | - Frédéric Gaboyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, Orléans, France
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Alexandra K. Perras
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Department of Microbiology and Archaea, University of Regensburg, Regensburg, Germany
| | | | - Viggó T. Marteinsson
- MATIS - Prokaria, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavik, Iceland
| | | | - Felipe Gómez
- Instituto Nacional de Técnica Aeroespacial - Centro de Astrobiología, Madrid, Spain
| | - Moustafa Malki
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa (CBMSO, CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Frances Westall
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique, Orléans, France
| | - Andreas Riedo
- Leiden Observatory, Universiteit Leiden, Leiden, Netherlands
| | | | - Pascale Ehrenfreund
- Leiden Observatory, Universiteit Leiden, Leiden, Netherlands
- Space Policy Institute, George Washington University, Washington, DC, United States
| | - Patricia Cabezas
- Space Policy Institute, George Washington University, Washington, DC, United States
- European Science Foundation, Strasbourg, France
| | - Nicolas Walter
- Space Policy Institute, George Washington University, Washington, DC, United States
- European Science Foundation, Strasbourg, France
| | - Charles Cockell
- School of Physics and Astronomy, UK Center for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
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32
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Kwon HS, Park S, Lee CH, Ahn IS. CO 2 fixation stability by Sulfurovum lithotrophicum 42BKT T depending on pH and ionic strength conditions. J IND ENG CHEM 2018. [DOI: 10.1016/j.jiec.2017.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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33
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Emser K, Barbosa J, Teixeira P, Bernardo de Morais AMM. Lactobacillus plantarum survival during the osmotic dehydration and storage of probiotic cut apple. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.09.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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34
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Choi H, Lim B, Park Y, Joo W. Improvement in solvent tolerance by exogenous glycerol inPseudomonassp. BCNU 106. Lett Appl Microbiol 2017; 65:147-152. [DOI: 10.1111/lam.12754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/25/2017] [Accepted: 05/02/2017] [Indexed: 11/30/2022]
Affiliation(s)
- H.J. Choi
- Department of Biology and Chemistry; Changwon National University; Changwon Korea
| | - B.R. Lim
- Department of Biology and Chemistry; Changwon National University; Changwon Korea
| | - Y.J. Park
- Department of Biology and Chemistry; Changwon National University; Changwon Korea
| | - W.H. Joo
- Department of Biology and Chemistry; Changwon National University; Changwon Korea
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Critical role of quorum sensing-dependent glutamate metabolism in homeostatic osmolality and outer membrane vesiculation in Burkholderia glumae. Sci Rep 2017; 7:44195. [PMID: 28272446 PMCID: PMC5341150 DOI: 10.1038/srep44195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/03/2017] [Indexed: 02/08/2023] Open
Abstract
Metabolic homeostasis in cooperative bacteria is achieved by modulating primary metabolism in a quorum sensing (QS)-dependent manner. A perturbed metabolism in QS mutants causes physiological stress in the rice bacterial pathogen Burkholderia glumae. Here, we show that increased bacterial osmolality in B. glumae is caused by unusually high cellular concentrations of glutamate and betaine generated by QS deficiencies. QS negatively controls glutamate uptake and the expression of genes involved in the glutamine synthetase and glutamine oxoglutarate aminotransferase cycles. Thus, cellular glutamate levels were significantly higher in the QS mutants than in the wild type, and they caused hyperosmotic cellular conditions. Under the hypotonic conditions of the periplasm in the QS mutants, outer membrane bulging and vesiculation were observed, although these changes were rescued by knocking out the gltI gene, which encodes a glutamate transporter. Outer membrane modifications were not detected in the wild type. These results suggest that QS-dependent glutamate metabolism is critical for homeostatic osmolality. We suggest that outer membrane bulging and vesiculation might be the outcome of a physiological adaptation to relieve hypotonic osmotic stress in QS mutants. Our findings reveal how QS functions to maintain bacterial osmolality in a cooperative population.
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Salar-García MJ, Bernal V, Pastor JM, Salvador M, Argandoña M, Nieto JJ, Vargas C, Cánovas M. Understanding the interplay of carbon and nitrogen supply for ectoines production and metabolic overflow in high density cultures of Chromohalobacter salexigens. Microb Cell Fact 2017; 16:23. [PMID: 28179004 PMCID: PMC5299690 DOI: 10.1186/s12934-017-0643-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Accepted: 02/01/2017] [Indexed: 01/27/2023] Open
Abstract
Background The halophilic bacterium Chromohalobacter salexigens has been proposed as promising cell factory for the production of the compatible solutes ectoine and hydroxyectoine. This bacterium has evolved metabolic adaptations to efficiently grow under high salt concentrations by accumulating ectoines as compatible solutes. However, metabolic overflow, which is a major drawback for the efficient conversion of biological feedstocks, occurs as a result of metabolic unbalances during growth and ectoines production. Optimal production of ectoines is conditioned by the interplay of carbon and nitrogen metabolisms. In this work, we set out to determine how nitrogen supply affects the production of ectoines. Results Chromohalobacter salexigens was challenged to grow in media with unbalanced carbon/nitrogen ratio. In C. salexigens, overflow metabolism and ectoines production are a function of medium composition. At low ammonium conditions, the growth rate decreased importantly, up to 80%. Shifts in overflow metabolism were observed when changing the C/N ratio in the culture medium. 13C-NMR analysis of ectoines labelling revealed a high metabolic rigidity, with almost constant flux ratios in all conditions assayed. Unbalanced C/N ratio led to pyruvate accumulation, especially upon N-limitation. Analysis of an ect− mutant demonstrated the link between metabolic overflow and ectoine biosynthesis. Under non ectoine synthesizing conditions, glucose uptake and metabolic overflow decreased importantly. Finally, in fed-batch cultures, biomass yield was affected by the feeding scheme chosen. High growth (up to 42.4 g L−1) and volumetric ectoine yields (up to 4.21 g L−1) were obtained by minimizing metabolite overflow and nutrient accumulation in high density cultures in a low nitrogen fed-batch culture. Moreover, the yield coefficient calculated for the transformation of glucose into biomass was 30% higher in fed-batch than in the batch culture, demonstrating that the metabolic efficiency of C. salexigens can be improved by careful design of culture feeding schemes. Conclusions Metabolic shifts observed at low ammonium concentrations were explained by a shift in the energy required for nitrogen assimilation. Carbon-limited fed-batch cultures with reduced ammonium supply were the best conditions for cultivation of C. salexigens, supporting high density growth and maintaining high ectoines production. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0643-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- María J Salar-García
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain.,Departamento de Ingeniería Química y Ambiental, Universidad Politécnica de Cartagena, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", Campus Muralla del MarCalle Doctor Fleming S/N, 30202, Cartagena, Spain
| | - Vicente Bernal
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain. .,Área de Biología, Dirección de Tecnología Química y Nuevas Energías, Centro de Tecnología de Repsol S.A., Ctra. de Extremadura A-5, Km. 18, 28375, Móstoles, Spain.
| | - José M Pastor
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain
| | - Manuel Salvador
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
| | - Montserrat Argandoña
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
| | - Joaquín J Nieto
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
| | - Carmen Vargas
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
| | - Manuel Cánovas
- Departamento de Bioquímica y Biología Molecular B e Inmunología, Facultad de Química, Universidad de Murcia, Campus Regional de Excelencia Internacional "Campus Mare Nostrum", 30100, Murcia, Spain.
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Nunes-Costa D, Maranha A, Costa M, Alarico S, Empadinhas N. Glucosylglycerate metabolism, bioversatility and mycobacterial survival. Glycobiology 2016; 27:213-227. [DOI: 10.1093/glycob/cww132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022] Open
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Transcriptional analysis of degenerate strain Clostridium beijerinckii DG-8052 reveals a pleiotropic response to CaCO 3-associated recovery of solvent production. Sci Rep 2016; 6:38818. [PMID: 27966599 PMCID: PMC5155275 DOI: 10.1038/srep38818] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/14/2016] [Indexed: 12/22/2022] Open
Abstract
Degenerate Clostridium beijerinckii strain (DG-8052) can be partially recovered by supplementing CaCO3 to fermentation media. Genome resequencing of DG-8052 showed no general regulator mutated. This study focused on transcriptional analysis of DG-8052 and its response to CaCO3 treatment via microarray. The expressions of 5168 genes capturing 98.6% of C. beijerinckii NCIMB 8052 genome were examed. The results revealed that with addition of CaCO3 565 and 916 genes were significantly up-regulated, and 704 and 1044 genes significantly down-regulated at acidogenic and solventogenic phase of DG-8052, respectively. These genes are primarily responsible for glycolysis to solvent/acid production (poR, pfo), solventogensis (buk, ctf, aldh, adh, bcd) and sporulation (spo0A, sigE, sigma-70, bofA), cell motility and division (ftsA, ftsK, ftsY, ftsH, ftsE, mreB, mreC, mreD, rodA), and molecular chaperones (grpE, dnaK, dnaJ, hsp20, hsp90), etc. The functions of some altered genes in DG-8052, totalling 5.7% at acidogenisis and 8.0% at sovlentogenisis, remain unknown. The response of the degenerate strain to CaCO3 was suggested significantly pleiotropic. This study reveals the multitude of regulatory function that CaCO3 has in clostridia and provides detailed insights into degeneration mechanisms at gene regulation level. It also enables us to develop effective strategies to prevent strain degeneration in future.
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Trimethylated homoserine functions as the major compatible solute in the globally significant oceanic cyanobacterium Trichodesmium. Proc Natl Acad Sci U S A 2016; 113:13191-13196. [PMID: 27799527 DOI: 10.1073/pnas.1611666113] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The oceanic N2-fixing cyanobacterium Trichodesmium spp. form extensive surface blooms and contribute significantly to marine carbon and nitrogen cycles in the oligotrophic subtropical and tropical oceans. Trichodesmium grows in salinities from 27 to 43 parts per thousand (ppt), yet its salt acclimation strategy remains enigmatic because the genome of Trichodesmium erythraeum strain IMS101 lacks all genes for the biosynthesis of any known compatible solute. Using NMR and liquid chromatography coupled to mass spectroscopy, we identified the main compatible solute in T. erythraeum strain IMS101 as the quaternary ammonium compound N,N,N-trimethyl homoserine (or homoserine betaine) and elucidated its biosynthetic pathway. The identification of this compatible solute explains how Trichodesmium spp. can thrive in the marine system at varying salinities and provides further insight into the diversity of microbial salt acclimation.
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Huynh TN, Choi PH, Sureka K, Ledvina HE, Campillo J, Tong L, Woodward JJ. Cyclic di-AMP targets the cystathionine beta-synthase domain of the osmolyte transporter OpuC. Mol Microbiol 2016; 102:233-243. [PMID: 27378384 DOI: 10.1111/mmi.13456] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2016] [Indexed: 12/26/2022]
Abstract
Cellular turgor is of fundamental importance to bacterial growth and survival. Changes in external osmolarity as a consequence of fluctuating environmental conditions and colonization of diverse environments can significantly impact cytoplasmic water content, resulting in cellular lysis or plasmolysis. To ensure maintenance of appropriate cellular turgor, bacteria import ions and small organic osmolytes, deemed compatible solutes, to equilibrate cytoplasmic osmolarity with the extracellular environment. Here, we show that elevated levels of c-di-AMP, a ubiquitous second messenger among bacteria, result in significant susceptibility to elevated osmotic stress in the bacterial pathogen Listeria monocytogenes. We found that levels of import of the compatible solute carnitine show an inverse correlation with intracellular c-di-AMP content and that c-di-AMP directly binds to the CBS domain of the ATPase subunit of the carnitine importer OpuC. Biochemical and structural studies identify conserved residues required for this interaction and transport activity in bacterial cells. Overall, these studies reveal a role for c-di-AMP mediated regulation of compatible solute import and provide new insight into the molecular mechanisms by which this essential second messenger impacts bacterial physiology and adaptation to changing environmental conditions.
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Affiliation(s)
- TuAnh Ngoc Huynh
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Philip H Choi
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Kamakshi Sureka
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Hannah E Ledvina
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Julian Campillo
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA.
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA.
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Moreno-Forero SK, Rojas E, Beggah S, van der Meer JR. Comparison of differential gene expression to water stress among bacteria with relevant pollutant-degradation properties. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:91-102. [PMID: 26616826 DOI: 10.1111/1758-2229.12356] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 11/15/2015] [Accepted: 11/15/2015] [Indexed: 06/05/2023]
Abstract
Resistance to semi-dry environments has been considered a crucial trait for superior growth and survival of strains used for bioaugmentation in contaminated soils. In order to compare water stress programmes, we analyse differential gene expression among three phylogenetically different strains capable of aromatic compound degradation: Arthrobacter chlorophenolicus A6, Sphingomonas wittichii RW1 and Pseudomonas veronii 1YdBTEX2. Standardized laboratory-induced water stress was imposed by shock exposure of liquid cultures to water potential decrease, induced either by addition of solutes (NaCl, solute stress) or by addition of polyethylene glycol (matric stress), both at absolute similar stress magnitudes and at those causing approximately similar decrease of growth rates. Genome-wide differential gene expression was recorded by micro-array hybridizations. Growth of P. veronii 1YdBTEX2 was the most sensitive to water potential decrease, followed by S. wittichii RW1 and A. chlorophenolicus A6. The number of genes differentially expressed under decreasing water potential was lowest for A. chlorophenolicus A6, increasing with increasing magnitude of the stress, followed by S. wittichii RW1 and P. veronii 1YdBTEX2. Gene inspection and gene ontology analysis under stress conditions causing similar growth rate reduction indicated that common reactions among the three strains included diminished expression of flagellar motility and increased expression of compatible solutes (which were strain-specific). Furthermore, a set of common genes with ill-defined function was found between all strains, including ABC transporters and aldehyde dehydrogenases, which may constitute a core conserved response to water stress. The data further suggest that stronger reduction of growth rate of P. veronii 1YdBTEX2 under water stress may be an indirect result of the response demanding heavy NADPH investment, rather than the presence or absence of a suitable stress defence mechanism per se.
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Affiliation(s)
- Silvia K Moreno-Forero
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Edward Rojas
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Siham Beggah
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
| | - Jan R van der Meer
- Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL-Sorge, Lausanne, 1015, Switzerland
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Pepe-Ranney C, Koechli C, Potrafka R, Andam C, Eggleston E, Garcia-Pichel F, Buckley DH. Non-cyanobacterial diazotrophs mediate dinitrogen fixation in biological soil crusts during early crust formation. THE ISME JOURNAL 2016; 10:287-98. [PMID: 26114889 PMCID: PMC4737922 DOI: 10.1038/ismej.2015.106] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 05/19/2015] [Accepted: 05/25/2015] [Indexed: 11/08/2022]
Abstract
Biological soil crusts (BSCs) are key components of ecosystem productivity in arid lands and they cover a substantial fraction of the terrestrial surface. In particular, BSC N2-fixation contributes significantly to the nitrogen (N) budget of arid land ecosystems. In mature crusts, N2-fixation is largely attributed to heterocystous cyanobacteria; however, early successional crusts possess few N2-fixing cyanobacteria and this suggests that microorganisms other than cyanobacteria mediate N2-fixation during the critical early stages of BSC development. DNA stable isotope probing with (15)N2 revealed that Clostridiaceae and Proteobacteria are the most common microorganisms that assimilate (15)N2 in early successional crusts. The Clostridiaceae identified are divergent from previously characterized isolates, though N2-fixation has previously been observed in this family. The Proteobacteria identified share >98.5% small subunit rRNA gene sequence identity with isolates from genera known to possess diazotrophs (for example, Pseudomonas, Klebsiella, Shigella and Ideonella). The low abundance of these heterotrophic diazotrophs in BSCs may explain why they have not been characterized previously. Diazotrophs have a critical role in BSC formation and characterization of these organisms represents a crucial step towards understanding how anthropogenic change will affect the formation and ecological function of BSCs in arid ecosystems.
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Affiliation(s)
- Charles Pepe-Ranney
- Department of Crop and Soil Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
| | - Chantal Koechli
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Ruth Potrafka
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Cheryl Andam
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Erin Eggleston
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | - Daniel H Buckley
- Department of Crop and Soil Sciences, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, USA
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Illeghems K, De Vuyst L, Weckx S. Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes. BMC Genomics 2015; 16:766. [PMID: 26459565 PMCID: PMC4604094 DOI: 10.1186/s12864-015-1927-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 09/12/2015] [Indexed: 12/22/2022] Open
Abstract
Background Lactobacillus fermentum 222 and Lactobacillus plantarum 80, isolates from a spontaneous Ghanaian cocoa bean fermentation process, proved to be interesting functional starter culture strains for cocoa bean fermentations. Lactobacillus fermentum 222 is a thermotolerant strain, able to dominate the fermentation process, thereby converting citrate and producing mannitol. Lactobacillus plantarum 80 is an acid-tolerant and facultative heterofermentative strain that is competitive during cocoa bean fermentation processes. In this study, whole-genome sequencing and comparative genome analysis was used to investigate the mechanisms of these strains to dominate the cocoa bean fermentation process. Results Through functional annotation and analysis of the high-coverage contigs obtained through 454 pyrosequencing, plantaricin production was predicted for L. plantarum 80. For L. fermentum 222, genes encoding a complete arginine deiminase pathway were attributed. Further, in-depth functional analysis revealed the capacities of these strains associated with carbohydrate and amino acid metabolism, such as the ability to use alternative external electron acceptors, the presence of an extended pyruvate metabolism, and the occurrence of several amino acid conversion pathways. A comparative genome sequence analysis using publicly available genome sequences of strains of the species L. plantarum and L. fermentum revealed unique features of both strains studied. Indeed, L. fermentum 222 possessed genes encoding additional citrate transporters and enzymes involved in amino acid conversions, whereas L. plantarum 80 is the only member of this species that harboured a gene cluster involved in uptake and consumption of fructose and/or sorbose. Conclusions In-depth genome sequence analysis of the candidate functional starter culture strains L. fermentum 222 and L. plantarum 80 revealed their metabolic capacities, niche adaptations and functionalities that enable them to dominate the cocoa bean fermentation process. Further, these results offered insights into the cocoa bean fermentation ecosystem as a whole and will facilitate the selection of appropriate starter culture strains for controlled cocoa bean fermentation processes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1927-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Koen Illeghems
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium.
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium.
| | - Stefan Weckx
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050, Brussels, Belgium.
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Bräuer S, Cadillo-Quiroz H, Kyrpides N, Woyke T, Goodwin L, Detter C, Podell S, Yavitt JB, Zinder SH. Genome of Methanoregula boonei 6A8 reveals adaptations to oligotrophic peatland environments. MICROBIOLOGY-SGM 2015; 161:1572-1581. [PMID: 25998264 DOI: 10.1099/mic.0.000117] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analysis of the genome sequence of Methanoregula boonei strain 6A8, an acidophilic methanogen isolated from an ombrotrophic (rain-fed) peat bog, has revealed unique features that likely allow it to survive in acidic, nutrient-poor conditions. First, M. boonei is predicted to generate ATP using protons that are abundant in peat, rather than sodium ions that are scarce, and the sequence of a membrane-bound methyltransferase, believed to pump Na+ in all methanogens, shows differences in key amino acid residues. Further, perhaps reflecting the hypokalemic status of many peat bogs, M. boonei demonstrates redundancy in the predicted potassium uptake genes trk, kdp and kup, some of which may have been horizontally transferred to methanogens from bacteria, possibly Geobacter spp. Overall, the putative functions of the potassium uptake, ATPase and methyltransferase genes may, at least in part, explain the cosmopolitan success of group E1/E2 and related methanogenic archaea in acidic peat bogs.
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Affiliation(s)
- Suzanna Bräuer
- Department of Biology, Appalachian State University, Boone, NC 28608, USA
| | - Hinsby Cadillo-Quiroz
- Swette Center for Environmental Biotechnology at the Biodesign Institute, Arizona State University, Tempe, AZ 85287-4501, USA
| | - Nikos Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Lynne Goodwin
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Chris Detter
- Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Sheila Podell
- Scripps Institution of Oceanography, La Jolla, CA 92093, USA
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY 14853, USA
| | - Stephen H Zinder
- Department of Microbiology, Cornell University, Ithaca, NY 14853, USA
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Lee S, Lee JH, Mitchell RJ. Analysis of Clostridium beijerinckii NCIMB 8052's transcriptional response to ferulic acid and its application to enhance the strain tolerance. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:68. [PMID: 25904983 PMCID: PMC4406174 DOI: 10.1186/s13068-015-0252-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 04/07/2015] [Indexed: 05/26/2023]
Abstract
BACKGROUND Plant-based cellulose presents the best source of renewable sugars for biofuel production. However, the lignin associated with plant cellulose presents a hurdle as hydrolysis of this component leads to the production of inhibitory compounds, such as ferulic acid. RESULTS The impacts of ferulic acid, a phenolic compound commonly found in lignin hydrolysates, on the growth, solvent production, and transcriptional responses of Clostridium beijerinckii NCIMB 8052 were determined. Addition of ferulic acid to growing cultures resulted in a decrease in the growth and solvent production by 30% and 25%, respectively, when compared to the control cultures. To better understand the toxicity of this compound, microarray analyses were performed using samples taken from these cultures at three different growth states. Several gene ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified showing significant change at each status, including ATP-binding cassette (ABC) transporters, two component system, and oxidoreductase activity. Moreover, genes related with efflux systems and heat shock proteins were also strongly up-regulated. Among these, expression of the groESL operon was induced by more than fourfold and was consequently selected to improve C. beijerinckii tolerance to ferulic acid. Real-time quantitative PCR (RT-qPCR) analysis confirmed that C. beijerinckii harboring the plasmid, pSAAT-ptb_Gro, had a two- to fivefold increased groESL operon expression during growth of these cultures. Moreover, this strain was more tolerant to ferulic acid as the growth of this recombinant strain and its bioconversion of glucose into solvents were both improved. CONCLUSIONS Using transcriptomics, we identified numerous genes that are differentially expressed when C. beijerinckii cultures were exposed to ferulic acid for varying amounts of time. The operon expressing groESL was consistently up-regulated, suggesting that this gene cluster may contribute to strain tolerance. This was confirmed as recombinant cultures showed both an enhanced growth and solvent yield in the presence of 0.5 g/L ferulic acid.
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Affiliation(s)
- Siseon Lee
- />School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulsan, 689-798 South Korea
| | - Jin Hyung Lee
- />Korea Institute for Ceramic Engineering and Technology, 101, Soho-ro, Jinju-si, Gyeongsangnam-do 660-031 South Korea
| | - Robert J Mitchell
- />School of Life Sciences, Ulsan National Institute of Science and Technology, 50 UNIST-gil, Eonyang-eup, Ulsan, 689-798 South Korea
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Salt acclimation of cyanobacteria and their application in biotechnology. Life (Basel) 2014; 5:25-49. [PMID: 25551682 PMCID: PMC4390839 DOI: 10.3390/life5010025] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/19/2014] [Indexed: 12/25/2022] Open
Abstract
The long evolutionary history and photo-autotrophic lifestyle of cyanobacteria has allowed them to colonize almost all photic habitats on Earth, including environments with high or fluctuating salinity. Their basal salt acclimation strategy includes two principal reactions, the active export of ions and the accumulation of compatible solutes. Cyanobacterial salt acclimation has been characterized in much detail using selected model cyanobacteria, but their salt sensing and regulatory mechanisms are less well understood. Here, we briefly review recent advances in the identification of salt acclimation processes and the essential genes/proteins involved in acclimation to high salt. This knowledge is of increasing importance because the necessary mass cultivation of cyanobacteria for future use in biotechnology will be performed in sea water. In addition, cyanobacterial salt resistance genes also can be applied to improve the salt tolerance of salt sensitive organisms, such as crop plants.
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Chen CW, Hsu CY, Lai SM, Syu WJ, Wang TY, Lai PS. Metal nanobullets for multidrug resistant bacteria and biofilms. Adv Drug Deliv Rev 2014; 78:88-104. [PMID: 25138828 DOI: 10.1016/j.addr.2014.08.004] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Revised: 06/27/2014] [Accepted: 08/11/2014] [Indexed: 12/19/2022]
Abstract
Infectious diseases were one of the major causes of mortality until now because drug-resistant bacteria have arisen under broad use and abuse of antibacterial drugs. These multidrug-resistant bacteria pose a major challenge to the effective control of bacterial infections and this threat has prompted the development of alternative strategies to treat bacterial diseases. Recently, use of metallic nanoparticles (NPs) as antibacterial agents is one of the promising strategies against bacterial drug resistance. This review first describes mechanisms of bacterial drug resistance and then focuses on the properties and applications of metallic NPs as antibiotic agents to deal with antibiotic-sensitive and -resistant bacteria. We also provide an overview of metallic NPs as bactericidal agents combating antibiotic-resistant bacteria and their potential in vivo toxicology for further drug development.
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Affiliation(s)
- Ching-Wen Chen
- Department of Chemistry, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Chia-Yen Hsu
- Department of Chemistry, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Syu-Ming Lai
- Department of Chemistry, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Wei-Jhe Syu
- Department of Chemistry, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Ting-Yi Wang
- Department of Chemistry, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung 402, Taiwan
| | - Ping-Shan Lai
- Department of Chemistry, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung 402, Taiwan; Research Center for Sustainable Energy and Nanotechnology, National Chung Hsing University, 250, Kuo Kuang Rd., Taichung 402, Taiwan.
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Zhao S, Zhang Q, Hao G, Liu X, Zhao J, Chen Y, Zhang H, Chen W. The protective role of glycine betaine in Lactobacillus plantarum ST-III against salt stress. Food Control 2014. [DOI: 10.1016/j.foodcont.2014.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Dynamic metabolic and transcriptional profiling of Rhodococcus sp. strain YYL during the degradation of tetrahydrofuran. Appl Environ Microbiol 2014; 80:2656-64. [PMID: 24532074 DOI: 10.1128/aem.04131-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Although tetrahydrofuran-degrading Rhodococcus sp. strain YYL possesses tetrahydrofuran (THF) degradation genes similar to those of other tetrahydrofuran-degrading bacteria, a much higher degradation efficiency has been observed in strain YYL. In this study, nuclear magnetic resonance (NMR)-based metabolomics analyses were performed to explore the metabolic profiling response of strain YYL to exposure to THF. Exposure to THF slightly influenced the metabolome of strain YYL when yeast extract was present in the medium. The metabolic profile of strain YYL over time was also investigated using THF as the sole carbon source to identify the metabolites associated with high-efficiency THF degradation. Lactate, alanine, glutarate, glutamate, glutamine, succinate, lysine, trehalose, trimethylamine-N-oxide (TMAO), NAD(+), and CTP were significantly altered over time in strain YYL grown in 20 mM THF. Real-time quantitative PCR (RT-qPCR) revealed changes in the transcriptional expression levels of 15 genes involved in THF degradation, suggesting that strain YYL could accumulate several disturbances in osmoregulation (trehalose, glutamate, glutamine, etc.), with reduced glycolysis levels, an accelerated tricarboxylic acid cycle, and enhanced protein synthesis. The findings obtained through (1)H NMR metabolomics analyses and the transcriptional expression of the corresponding genes are complementary for exploring the dynamic metabolic profile in organisms.
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Abstract
The proteome responses to heat stress have not been well understood. In this study, alfalfa (Medicago sativa L. cv. Huaiyin) seedlings were exposed to 25°C (control) and 40°C (heat stress) in growth chambers, and leaves were collected at 24, 48 and 72 h after treatment, respectively. The morphological, physiological and proteomic processes were negatively affected under heat stress. Proteins were extracted and separated by two-dimensional polyacrylamide gel electrophoresis (2-DE), and differentially expressed protein spots were identified by mass spectrometry (MS). Totally, 81 differentially expressed proteins were identified successfully by MALDI-TOF/TOF. These proteins were categorized into nine classes: including metabolism, energy, protein synthesis, protein destination/storage, transporters, intracellular traffic, cell structure, signal transduction and disease/defence. Five proteins were further analyzed for mRNA levels. The results of the proteomics analyses provide a better understanding of the molecular basis of heat-stress responses in alfalfa.
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