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Mukherjee P, Mazumder A. Macromolecular crowding has opposite effects on two critical sub-steps of transcription initiation. FEBS Lett 2024; 598:1022-1033. [PMID: 38479985 PMCID: PMC7615953 DOI: 10.1002/1873-3468.14851] [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: 12/23/2023] [Revised: 02/12/2024] [Accepted: 02/19/2024] [Indexed: 04/12/2024]
Abstract
Transcription initiation, the first step in gene expression, has been studied extensively in dilute buffer, a condition which fails to consider the crowded environment in live cells. Recent reports indicate the kinetics of promoter escape is altered in crowded conditions for a consensus bacterial promoter. Here, we use a real-time fluorescence enhancement assay to study the kinetics of unwound bubble formation and promoter escape for three separate promoters. We find that the effect of crowding on transcription initiation is complex, with lower rates of unwound bubble formation, higher rates of promoter escape, and large variations depending on promoter identity. Based on our results, we suggest that altered conditions of crowding inside a live cell can trigger global changes.
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Affiliation(s)
- Pratip Mukherjee
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad, India
| | - Abhishek Mazumder
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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2
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Carter EL, Constantinidou C, Alam MT. Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations. Brief Bioinform 2023; 25:bbad439. [PMID: 38048080 PMCID: PMC10694557 DOI: 10.1093/bib/bbad439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/21/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023] Open
Abstract
Environmental perturbations are encountered by microorganisms regularly and will require metabolic adaptations to ensure an organism can survive in the newly presenting conditions. In order to study the mechanisms of metabolic adaptation in such conditions, various experimental and computational approaches have been used. Genome-scale metabolic models (GEMs) are one of the most powerful approaches to study metabolism, providing a platform to study the systems level adaptations of an organism to different environments which could otherwise be infeasible experimentally. In this review, we are describing the application of GEMs in understanding how microbes reprogram their metabolic system as a result of environmental variation. In particular, we provide the details of metabolic model reconstruction approaches, various algorithms and tools for model simulation, consequences of genetic perturbations, integration of '-omics' datasets for creating context-specific models and their application in studying metabolic adaptation due to the change in environmental conditions.
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Affiliation(s)
- Elena Lucy Carter
- Warwick Medical School, University of Warwick, Coventry, CV4 7HL, UK
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3
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Kathiriya MR, Vekariya YV, Hati S. Understanding the Probiotic Bacterial Responses Against Various Stresses in Food Matrix and Gastrointestinal Tract: A Review. Probiotics Antimicrob Proteins 2023:10.1007/s12602-023-10104-3. [PMID: 37347421 DOI: 10.1007/s12602-023-10104-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/02/2023] [Indexed: 06/23/2023]
Abstract
Probiotic bacteria are known to have ability to tolerate inhospitable conditions experienced during food preparation, food storage, and gastrointestinal tract of consumer. As probiotics are living cells, they are adversely affected by the harsh environment of the carrier matrix as well as low pH, bile salts, oxidative stress, osmotic pressure, and commensal microflora of the host. To overcome the unfavorable environments, many probiotics switch on the cell-mediated protection mechanisms, which helps them to survive, acclimatize and remain operational in the harsh circumstances. In this review, we provide comprehensive understanding on the different stresses experienced by the probiotic when added in carrier food as well as during human gastrointestinal tract transit. Under such situation how these health beneficial bacteria protect themselves by activation of several defense systems and get adapted to the lethal environments.
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Affiliation(s)
- Mital R Kathiriya
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Anand-388110, Gujarat, India
| | - Yogesh V Vekariya
- Department. of Dairy Engineering, SMC College of Dairy Science, Kamdhenu University, Anand-388110, Gujarat, India
| | - Subrota Hati
- Department of Dairy Microbiology, SMC College of Dairy Science, Kamdhenu University, Anand-388110, Gujarat, India.
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4
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Tantoso E, Eisenhaber B, Sinha S, Jensen LJ, Eisenhaber F. About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature. Biol Direct 2023; 18:7. [PMID: 36855185 PMCID: PMC9976479 DOI: 10.1186/s13062-023-00362-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Although Escherichia coli (E. coli) is the most studied prokaryote organism in the history of life sciences, many molecular mechanisms and gene functions encoded in its genome remain to be discovered. This work aims at quantifying the illumination of the E. coli gene function space by the scientific literature and how close we are towards the goal of a complete list of E. coli gene functions. RESULTS The scientific literature about E. coli protein-coding genes has been mapped onto the genome via the mentioning of names for genomic regions in scientific articles both for the case of the strain K-12 MG1655 as well as for the 95%-threshold softcore genome of 1324 E. coli strains with known complete genome. The article match was quantified with the ratio of a given gene name's occurrence to the mentioning of any gene names in the paper. The various genome regions have an extremely uneven literature coverage. A group of elite genes with ≥ 100 full publication equivalents (FPEs, FPE = 1 is an idealized publication devoted to just a single gene) attracts the lion share of the papers. For K-12, ~ 65% of the literature covers just 342 elite genes; for the softcore genome, ~ 68% of the FPEs is about only 342 elite gene families (GFs). We also find that most genes/GFs have at least one mentioning in a dedicated scientific article (with the exception of at least 137 protein-coding transcripts for K-12 and 26 GFs from the softcore genome). Whereas the literature growth rates were highest for uncharacterized or understudied genes until 2005-2010 compared with other groups of genes, they became negative thereafter. At the same time, literature for anyhow well-studied genes started to grow explosively with threshold T10 (≥ 10 FPEs). Typically, a body of ~ 20 actual articles generated over ~ 15 years of research effort was necessary to reach T10. Lineage-specific co-occurrence analysis of genes belonging to the accessory genome of E. coli together with genomic co-localization and sequence-analytic exploration hints previously completely uncharacterized genes yahV and yddL being associated with osmotic stress response/motility mechanisms. CONCLUSION If the numbers of scientific articles about uncharacterized and understudied genes remain at least at present levels, full gene function lists for the strain K-12 MG1655 and the E. coli softcore genome are in reach within the next 25-30 years. Once the literature body for a gene crosses 10 FPEs, most of the critical fundamental research risk appears overcome and steady incremental research becomes possible.
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Affiliation(s)
- Erwin Tantoso
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Birgit Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore
| | - Swati Sinha
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore.,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore.,European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Lars Juhl Jensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frank Eisenhaber
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), 60 Biopolis Street, Singapore, 138672, Republic of Singapore. .,Agency for Science, Technology and Research (A*STAR), Bioinformatics Institute (BII), 30 Biopolis Street #07-01, Matrix Building, Singapore, 138671, Republic of Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Republic of Singapore.
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5
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Shift of Choline/Betaine Pathway in Recombinant Pseudomonas for Cobalamin Biosynthesis and Abiotic Stress Protection. Int J Mol Sci 2022; 23:ijms232213934. [PMID: 36430408 PMCID: PMC9699165 DOI: 10.3390/ijms232213934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
The B12-producing strains Pseudomonas nitroreducens DSM 1650 and Pseudomonas sp. CCUG 2519 (both formerly Pseudomonas denitrificans), with the most distributed pathway among bacteria for exogenous choline/betaine utilization, are promising recombinant hosts for the endogenous production of B12 precursor betaine by direct methylation of bioavailable glycine or non-proteinogenic β-alanine. Two plasmid-based de novo betaine pathways, distinguished by their enzymes, have provided an expression of the genes encoding for N-methyltransferases of the halotolerant cyanobacterium Aphanothece halophytica or plant Limonium latifolium to synthesize the internal glycine betaine or β-alanine betaine, respectively. These betaines equally allowed the recombinant pseudomonads to grow effectively and to synthesize a high level of cobalamin, as well as to increase their protective properties against abiotic stresses to a degree comparable with the supplementation of an exogenous betaine. Both de novo betaine pathways significantly enforced the protection of bacterial cells against lowering temperature to 15 °C and increasing salinity to 400 mM of NaCl. However, the expression of the single plant-derived gene for the β-alanine-specific N-methyltransferase additionally increased the effectiveness of exogenous glycine betaine almost twofold on cobalamin biosynthesis, probably due to the Pseudomonas' ability to use two independent pathways, their own choline/betaine pathway and the plant β-alanine betaine biosynthetic pathway.
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Glover G, Voliotis M, Łapińska U, Invergo BM, Soanes D, O'Neill P, Moore K, Nikolic N, Petrov PG, Milner DS, Roy S, Heesom K, Richards TA, Tsaneva-Atanasova K, Pagliara S. Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells. Commun Biol 2022; 5:385. [PMID: 35444215 PMCID: PMC9021252 DOI: 10.1038/s42003-022-03336-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
The interaction between a cell and its environment shapes fundamental intracellular processes such as cellular metabolism. In most cases growth rate is treated as a proximal metric for understanding the cellular metabolic status. However, changes in growth rate might not reflect metabolic variations in individuals responding to environmental fluctuations. Here we use single-cell microfluidics-microscopy combined with transcriptomics, proteomics and mathematical modelling to quantify the accumulation of glucose within Escherichia coli cells. In contrast to the current consensus, we reveal that environmental conditions which are comparatively unfavourable for growth, where both nutrients and salinity are depleted, increase glucose accumulation rates in individual bacteria and population subsets. We find that these changes in metabolic function are underpinned by variations at the translational and posttranslational level but not at the transcriptional level and are not dictated by changes in cell size. The metabolic response-characteristics identified greatly advance our fundamental understanding of the interactions between bacteria and their environment and have important ramifications when investigating cellular processes where salinity plays an important role.
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Affiliation(s)
- Georgina Glover
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Physics and Astronomy, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - Margaritis Voliotis
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Mathematics, University of Exeter, Stocker Road, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Brandon M Invergo
- Translational Research Exchange at Exeter, University of Exeter, Exeter, UK
| | - Darren Soanes
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Paul O'Neill
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Karen Moore
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Nela Nikolic
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - Peter G Petrov
- Department of Physics and Astronomy, University of Exeter, Stocker Road, Exeter, EX4 4QL, UK
| | - David S Milner
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Sumita Roy
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK
| | - Kate Heesom
- University of Bristol Proteomics Facility, University Walk, Bristol, BS8 1TD, UK
| | - Thomas A Richards
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Krasimira Tsaneva-Atanasova
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Department of Mathematics, University of Exeter, Stocker Road, Exeter, UK
- Department of Bioinformatics and Mathematical Modelling, Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, 105 Acad. G. Bonchev Str., 1113, Sofia, Bulgaria
| | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK.
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4Q, UK.
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7
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Agrawal A, Gopu M, Mukherjee R, Mampallil D. Microfluidic Droplet Cluster with Distributed Evaporation Rates as a Model for Bioaerosols. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:4567-4577. [PMID: 35394793 DOI: 10.1021/acs.langmuir.1c03273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Aerosols and microdroplets are known to act as carriers for pathogens or vessels for chemical reactions. The natural occurrence of evaporation of these droplets has implications for the viability of pathogens or chemical processes. For example, it is important to understand how pathogens survive extreme physiochemical conditions such as confinement and osmotic stress induced by evaporation of aerosol droplets. Previously, larger evaporating droplets were proposed as model systems as the processes in the tiny aerosol droplets are difficult to image. In this context, we propose the concept of evaporation of capillary-clustered aqueous microdroplets dispersed in a thin oil layer. The configuration produces spatially segregated evaporation rates. It allows comparing the consequences of evaporation and its rate for processes occurring in droplets. As a proof of concept, we study the consequences of evaporation and its rate using Escherichia coli (E. coli) and Bacillus subtilis as model organisms. Our experiments indicate that the rate of evaporation of microdroplets is an important parameter in deciding the viability of contained microorganisms. With slow evaporation, E. coli could mitigate the osmotic stress by K+ ion uptake. Our method may also be applicable to other evaporating droplet systems, for example, microdroplet chemistry to understand the implications of evaporation rates.
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Affiliation(s)
- Akanksha Agrawal
- Indian Institute of Science Education and Research Tirupati, Mangalam P.O. PIN 517507 Tirupati, Andhra Pradesh, India
| | - Maheshwar Gopu
- Indian Institute of Science Education and Research Tirupati, Mangalam P.O. PIN 517507 Tirupati, Andhra Pradesh, India
| | - Raju Mukherjee
- Indian Institute of Science Education and Research Tirupati, Mangalam P.O. PIN 517507 Tirupati, Andhra Pradesh, India
| | - Dileep Mampallil
- Indian Institute of Science Education and Research Tirupati, Mangalam P.O. PIN 517507 Tirupati, Andhra Pradesh, India
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8
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Nguyen K, Kumar P. Morphological Phenotypes, Cell Division, and Gene Expression of Escherichia coli under High Concentration of Sodium Sulfate. Microorganisms 2022; 10:microorganisms10020274. [PMID: 35208727 PMCID: PMC8875244 DOI: 10.3390/microorganisms10020274] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 01/10/2023] Open
Abstract
Sodium and sulfate ions are among the suggested abundant ions on Europa, a moon of Jupiter. In order to investigate the potential habitability of Europa, we study the effects of sodium sulfate (Na2SO4) on a non-halophilic bacterium by subjecting Escherichia coli (E. coli) to a wide range of Na2SO4 concentrations (0–1.0 m). We discover that, as the concentration of sodium sulfate increases, the biomass doubling time increases and the cell growth is completely inhibited at 1.0 m Na2SO4. Furthermore, we find that E. coli exhibits three distinct morphological phenotypes—(i) shortened, (ii) normal, and (iii) elongated/filamented cells at 0.6 m and 0.8 m Na2SO4. We have examined the expression of different genes involved in sodium and sulfate transport (nhaA, nhaB, cysZ, sbp), osmotically driven transport of water (aqpZ), sulfate metabolism (cysN), fatty acid production (fabA), and a global transcriptional regulator (osmZ). Our results suggest that the expression of these genes is not affected significantly at high concentrations of sodium sulfate in the exponential growth phase. Using our experimental data and the existing data in the literature, we show that the osmotic pressure difference may play a major role in determining the growth inhibition of E. coli and B. subtilis at high concentrations of salt.
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9
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Wang J, Wang X, Liang Q, Li D, Li D, Guo Q. Transcriptome analysis of L-leucine-producing Corynebacterium glutamicum under the addition of trimethylglycine. Amino Acids 2021; 54:229-240. [PMID: 34837555 DOI: 10.1007/s00726-021-03105-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/14/2021] [Indexed: 11/30/2022]
Abstract
It has been widely reported that the addition of trimethylglycine (betaine) decreases osmotic pressure inhibition for cell growth, leading to increased production of amino acids. However, the underlying mechanism is unclear. To determine the global metabolic differences that occur under the addition of trimethylglycine, transcriptome analysis was performed. Transcriptome analysis of Corynebacterium glutamicum JL1211 revealed that 272 genes exhibited significant changes under trimethylglycine addition. We performed Gene Ontology (GO) and KEGG enrichment pathway analyses on these differentially expressed genes (DEGs). Significantly upregulated genes were mainly involved in the regulation of ABC transporters, especially phosphate transporters and sulfur metabolism. The three phosphate transporter genes pstC, pstA and pstB were upregulated by 13.06-fold, 29.80-fold and 30.49-fold, respectively. Notably, the transcriptional levels of the cysD, cysN, cysH and sir genes were upregulated by 81.5-fold, 57.3-fold, 77.6-fold and 125.4-fold, respectively, consistent with assimilatory sulfate reduction under the addition of trimethylglycine. The upregulation of ilvBN and leuD genes might result in increased L-leucine formation. The data indicated changes in the transcriptome of C. glutamicum with trimethylglycine treatment, thus providing a mechanism supporting the application of trimethylglycine in the production of L-leucine and other amino acids by C. glutamicum strains.
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Affiliation(s)
- Jian Wang
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China.
| | - Xuesong Wang
- College of Life Sciences, Jilin University, Changchun, China
| | - Qing Liang
- College of Life Sciences, Jilin University, Changchun, China
| | - Deheng Li
- Xinjiang Fufeng Biotechnologies Co., Urumqi, China
| | - Dawei Li
- College of Biological and Agricultural Engineering, Jilin University, Changchun, China
| | - Qunqun Guo
- Tianjin Dexiang Biotechnology Co., Ltd, Tianjin, China
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Cho ES, Cha IT, Roh SW, Seo MJ. Haloferax litoreum sp. nov., Haloferax marinisediminis sp. nov., and Haloferax marinum sp. nov., low salt-tolerant haloarchaea isolated from seawater and sediment. Antonie van Leeuwenhoek 2021; 114:2065-2082. [PMID: 34604935 DOI: 10.1007/s10482-021-01661-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 09/13/2021] [Indexed: 11/25/2022]
Abstract
Three novel halophilic archaea were isolated from seawater and sediment near Yeoungheungdo Island, Republic of Korea. The genome size and G + C content of the isolates MBLA0076T, MBLA0077T, and MBLA0078T were 3.56, 3.48, and 3.48 Mb and 61.7, 60.8, and 61.1 mol%, respectively. The three strains shared 98.5-99.5 % sequence similarity of the 16 S rRNA gene, whereas their sequence similarity to the 16 S rRNA gene of type strains was below 98.5 %. Phylogenetic analysis based on sequences of the 16 S rRNA and RNA polymerase subunit beta genes indicated that the isolates belonged to the genus Haloferax. The orthologous average nucleotide identity, average amino-acid identity, and in silico DNA-DNA hybridization values were below species delineation thresholds. Pan-genomic analysis indicated that the three novel strains and 11 reference strains had 8981 pan-orthologous groups in total. Fourteen Haloferax strains shared 1766 core pan-genome orthologous groups, which were mainly related to amino acid transport and metabolism. Cells of the three isolates were gram-negative, motile, red-pink pigmented, and pleomorphic. The strains grew optimally at 30 °C (MBLA0076T) and 40 °C (MBLA0077T, MBLA0078T) in the presence of 1.28 M (MBLA0077T) and 1.7 M (MBLA0076T, MBLA0078T) NaCl and 0.1 M (MBLA0077T), 0.2 M (MBLA0076T), and 0.3 M (MBLA0078T) MgCl2·6H2O at pH 7.0-8.0. Cells of all isolates lysed in distilled water; the minimum NaCl concentration necessary to prevent lysis was 0.43 M. The major polar lipids of the three strains were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, and sulphated diglycosyl archaeol-1. Based on their phenotypic and genotypic properties, MBLA0076T, MBLA0077T, and MBLA0078T were described as novel species of Haloferax, for which we propose the names Haloferax litoreum sp. nov., Haloferax marinisediminis sp. nov., and Haloferax marinum sp. nov., respectively. The respective type strains of these species are MBLA0076T (= KCTC 4288T = JCM 34,169T), MBLA0077T (= KCTC 4289T = JCM 34,170T), and MBLA0078T (= KCTC 4290T = JCM 34,171T).
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Affiliation(s)
- Eui-Sang Cho
- Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea
| | - In-Tae Cha
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, 22689, Republic of Korea
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea
| | - Myung-Ji Seo
- Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea.
- Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea.
- Institute for New Drug Development, Incheon National University, Incheon, 22012, Republic of Korea.
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Abstract
Bacteria have evolved to sense and respond to their environment by altering gene expression and metabolism to promote growth and survival. In this work we demonstrate that Salmonella displays an extensive (>30 hour) lag in growth when subcultured into media where dicarboxylates such as succinate are the sole carbon source. This growth lag is regulated in part by RpoS, the RssB anti-adaptor IraP, translation elongation factor P, and to a lesser degree the stringent response. We also show that small amounts of proline or citrate can trigger early growth in succinate media and that, at least for proline, this effect requires the multifunctional enzyme/regulator PutA. We demonstrate that activation of RpoS results in the repression of dctA, encoding the primary dicarboxylate importer, and that constitutive expression of dctA induced growth. This dicarboxylate growth lag phenotype is far more severe across multiple Salmonella isolates than in its close relative E. coli Replacing 200 nt of the Salmonella dctA promoter region with that of E. coli was sufficient to eliminate the observed lag in growth. We hypothesized that this cis-regulatory divergence might be an adaptation to Salmonella's virulent lifestyle where levels of phagocyte-produced succinate increase in response to bacterial LPS, however we found that impairing dctA repression had no effect on Salmonella's survival in acidified succinate or in macrophages.Importance Bacteria have evolved to sense and respond to their environment to maximize their chance of survival. By studying differences in the responses of pathogenic bacteria and closely related non-pathogens, we can gain insight into what environments they encounter inside of an infected host. Here we demonstrate that Salmonella diverges from its close relative E. coli in its response to dicarboxylates such as the metabolite succinate. We show that this is regulated by stress response proteins and ultimately can be attributed to Salmonella repressing its import of dicarboxylates. Understanding this phenomenon may reveal a novel aspect of the Salmonella virulence cycle, and our characterization of its regulation yields a number of mutant strains that can be used to further study it.
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12
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Wang S, Fang Y, Wang Z, Zhang S, Wang L, Guo Y, Wang X. Improving L-threonine production in Escherichia coli by elimination of transporters ProP and ProVWX. Microb Cell Fact 2021; 20:58. [PMID: 33653345 PMCID: PMC7927397 DOI: 10.1186/s12934-021-01546-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
Background Betaine, an osmoprotective compatible solute, has been used to improve l-threonine production in engineered Escherichia colil-threonine producer. Betaine supplementation upregulates the expression of zwf encoding glucose-6-phosphate dehydrogenase, leading to the increase of NADPH, which is beneficial for l-threonine production. In E. coli, betaine can be taken through ProP encoded by proP or ProVWX encoded by proVWX. ProP is a H+-osmolyte symporter, whereas ProVWX is an ABC transporter. ProP and ProVWX mediate osmotic stress protection by transporting zwitterionic osmolytes, including glycine betaine. Betaine can also be synthesized in E. coli by enzymes encoded by betABIT. However, the influence of ProP, ProVWX and betABIT on l-threonine production in E. coli has not been investigated. Results In this study, the influence of ProP, ProVWX and betABIT on l-threonine production in E. coli has been investigated. Addition of betaine slightly improved the growth of the l-threonine producing E. coli strain TWF001 as well as the l-threonine production. Deletion of betABIT retarded the growth of TWF001 and slightly decreased the l-threonine production. However, deletion of proP or/and proVWX significantly increased the l-threonine production. When proP was deleted, the l-threonine production increased 33.3%; when proVWX was deleted, the l-threonine production increased 40.0%. When both proP and proVWX were deleted, the resulting strain TSW003 produced 23.5 g/l l-threonine after 36 h flask cultivation. The genes betABIT, proC, fadR, crr and ptsG were individually deleted from TSW003, and it was found that further absence of either crr (TWS008) or ptsG (TWS009) improved l-threonine production. TSW008 produced 24.9 g/l l-threonine after 36 h flask cultivation with a yield of 0.62 g/g glucose and a productivity of 0.69 g/l/h. TSW009 produced 26 g/l l-threonine after 48 h flask cultivation with a yield of 0.65 g/g glucose and a productivity of 0.54 g/l/h, which is 116% increase compared to the control TWF001. Conclusions In this study, l-threonine-producing E. coli strains TSW008 and TSW009 with high l-threonine productivity were developed by regulating the intracellular osmotic pressure. This strategy could be used to improve the production of other products in microorganisms.
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Affiliation(s)
- Shuaiwen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Zhen Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Liangjia Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yong Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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13
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Mbye M, Baig MA, AbuQamar SF, El-Tarabily KA, Obaid RS, Osaili TM, Al-Nabulsi AA, Turner MS, Shah NP, Ayyash MM. Updates on understanding of probiotic lactic acid bacteria responses to environmental stresses and highlights on proteomic analyses. Compr Rev Food Sci Food Saf 2020; 19:1110-1124. [PMID: 33331686 DOI: 10.1111/1541-4337.12554] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 12/15/2022]
Abstract
Probiotics are defined as live microorganisms that improve the health of the host when administered in adequate quantities. Nonetheless, probiotics encounter extreme environmental conditions during food processing or along the gastrointestinal tract. This review discusses different environmental stresses that affect probiotics during food preparation, storage, and along the alimentary canal, including high temperature, low temperature, low and alkaline pH, oxidative stress, high hydrostatic pressure, osmotic pressure, and starvation. The understanding of how probiotics deal with environmental stress and thrive provides useful information to guide the selection of the strains with enhanced performance in specific situations, in food processing or during gastrointestinal transit. In most cases, multiple biological functions are affected upon exposure of the cell to environmental stress. Sensing of sublethal environmental stress can allow for adaptation processes to occur, which can include alterations in the expression of specific proteins.
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Affiliation(s)
- Mustapha Mbye
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, 15551, UAE
| | - Mohd Affan Baig
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, 15551, UAE
| | - Synan F AbuQamar
- Department of Biology, College of Science, United Arab Emirates University (UAEU), Al Ain, UAE
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University (UAEU), Al Ain, UAE.,Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University (UAEU), Al-Ain, UAE.,College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Western Australia, Australia
| | - Reyad S Obaid
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, UAE
| | - Tareq M Osaili
- Department of Clinical Nutrition and Dietetics, College of Health Sciences, University of Sharjah, Sharjah, UAE.,Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid, Jordan
| | - Anas A Al-Nabulsi
- Department of Nutrition and Food Technology, Jordan University of Science and Technology, Irbid, Jordan
| | - Mark S Turner
- School of Agriculture and Food Sciences, the University of Queensland (UQ), Brisbane, Queensland, Australia
| | - Nagendra P Shah
- Food and Nutritional Science, School of Biological Sciences, the University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Mutamed M Ayyash
- Department of Food, Nutrition and Health, College of Food and Agriculture, United Arab Emirates University (UAEU), Al Ain, 15551, UAE
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14
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Stirling F, Naydich A, Bramante J, Barocio R, Certo M, Wellington H, Redfield E, O’Keefe S, Gao S, Cusolito A, Way J, Silver P. Synthetic Cassettes for pH-Mediated Sensing, Counting, and Containment. Cell Rep 2020; 30:3139-3148.e4. [DOI: 10.1016/j.celrep.2020.02.033] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/15/2019] [Accepted: 02/07/2020] [Indexed: 12/18/2022] Open
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15
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A novel Xanthomonas citri subsp. citri NADPH quinone reductase involved in salt stress response and virulence. Biochim Biophys Acta Gen Subj 2020; 1864:129514. [PMID: 31911239 DOI: 10.1016/j.bbagen.2020.129514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 12/20/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND Xanthomonas citri subsp. citri (Xcc), the causal agent of citrus canker is maintained as an epiphyte on citrus leaves until entering the plant tissue. During epiphytic survival, bacteria may encounter low water availability that challenges the infection process. Proteomics analyses of Xcc under saline stress, mimicking the conditions found during epiphytic survival, showed increased abundance of a putative NAD(P)H dehydrogenase encoded by XAC2229. METHODS Expression levels of XAC2229 and a Xcc mutant in XAC2229 were analyzed in salt and oxidative stress and during plant-pathogen interaction. An Escherichia coli expressing XAC2229 was obtained, and the role of this protein in oxidative stress resistance and in reactive oxygen species production was studied. Finally, Xac2229 protein was purified, spectrophotometric and cofactor analyses were done and enzymatic activities determined. RESULTS XAC2229 was expressed under salt stress and during plant-pathogen interaction. ΔXAC2229 mutant showed less number of cankers and impaired epiphytic survival than the wild type strain. ΔXAC2229 survived less in the presence of H2O2 and produced more reactive oxygen species and thiobarbituric acid-reactive substances than the wild type strain. Similar results were observed for E. coli expressing XAC2229. Xac2229 is a FAD containing flavoprotein, displays diaphorase activity with an optimum at pH 6.0 and has quinone reductase activity using NADPH as an electron donor. CONCLUSIONS A FAD containing flavoprotein from Xcc is a new NADPH quinone reductase required for bacterial virulence, particularly in Xcc epiphytic survival on citrus leaves. GENERAL SIGNIFICANCE A novel protein involved in the worldwide disease citrus canker was characterized.
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16
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Mukherjee R, Verma T, Nandi D, Umapathy S. Understanding the effects of culture conditions in bacterial growth: A biochemical perspective using Raman microscopy. JOURNAL OF BIOPHOTONICS 2020; 13:e201900233. [PMID: 31444944 DOI: 10.1002/jbio.201900233] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/16/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
Rapid, sensitive and label-free methods to probe bacterial growth irrespective of the culture conditions can shed light on the mechanisms by which bacteria adapt to different environmental stimuli. Raman spectroscopy can rapidly and continuously monitor the growth of bacteria under varied conditions. In this study, the growth of Escherichia coli in Luria broth (nutrient rich conditions) and minimal media with either glucose or glycerol as carbon source (nutrient limiting conditions) is profiled using Raman spectroscopy. Moreover, the study also gives insights into the altered bacterial biochemistry upon exposure to low- (25°C) and high-temperature (45°C) stress. Raman spectral measurement was performed on bulk bacteria cultured under laboratory conditions. A detailed analysis of the spectra as a function of bacterial growth reveals changes in Raman band intensities/area of biomolecules such as DNA, proteins and lipids. We also report five novel ratiometric markers (I830 /I810 , I1126 /I1100 , I1340 /I1440 , I1207 /I1240 and I1580 /I1440 ) that can identify the phase of growth, independent of the culture condition. Unsupervised multivariate methods like Principal Component Analysis also corroborate the aforementioned markers of growth. Altogether, our findings highlight the potential of Raman spectroscopy in yielding universal biochemical signatures that may be indicative of stress and aging in a growth milieu.
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Affiliation(s)
- Ria Mukherjee
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Taru Verma
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, India
| | - Dipankar Nandi
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, India
- Department of Biochemistry, Indian Institute of Science Bangalore, Bangalore, Karnataka, India
| | - Siva Umapathy
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka, India
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka, India
- Department of Instrumentation and Applied Physics, Indian Institute of Science Bangalore, Bangalore, Karnataka, India
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17
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Yu Z, Li W, Tan S. Real-time monitoring of the membrane biofouling based on spectroscopic analysis in a marine MBBR-MBR (moving bed biofilm reactor-membrane bioreactor) for saline wastewater treatment. CHEMOSPHERE 2019; 235:1154-1161. [PMID: 31561306 DOI: 10.1016/j.chemosphere.2019.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 06/06/2019] [Accepted: 07/01/2019] [Indexed: 06/10/2023]
Abstract
A MBBR-MBR system has been developed with marine microorganisms enriched for saline wastewater treatment in this work, showing high COD and NH3-N removals. The behaviour of fouling-related components (EPS and SMP) has been studied as functions of operating time (40-90 days), salinity (0-30 g/L NaCl) and backflow ratio (0-300%, from MBR to MBBR). High biodegradability of the MBBR-MBR at optimal conditions can induce more biodegradation of humic acid-like (λex/λem: 350nm/430 nm) and fulvic acid-like (260nm/445 nm) molecules to soluble microbial by-product-like molecules (275nm/325 nm), reducing the membrane biofouling rate. The biodegradation process is suggested by the excitation-emission matrix (EEM) images. In the study of sudden salinity shock, results show that real-time monitoring the concentration of biofoulants is more effective (operative time extended by 60%) than monitoring the transmembrane pressure (operative time extended by 33%) to prevent membrane fouling. Due to an early warning from the real-time monitoring, the coming membrane-fouling is predictable and the operating conditions, such as backflow ratio, can be changed to minimize the biofouling rate.
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Affiliation(s)
- Zhengyu Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China; Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW, 2007, Australia
| | - Weiguo Li
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai, Shandong, 264209, China
| | - Songwen Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China; Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai, Shandong, 264209, China.
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18
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Barcarolo MV, Garavaglia BS, Thomas L, Marondedze C, Gehring C, Gottig N, Ottado J. Proteome changes and physiological adaptations of the phytopathogen Xanthomonas citri subsp. citri under salt stress and their implications for virulence. FEMS Microbiol Ecol 2019; 95:5509571. [DOI: 10.1093/femsec/fiz081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/30/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- María Victoria Barcarolo
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR). Ocampo y Esmeralda, Rosario, 2000, Argentina
| | - Betiana S Garavaglia
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR). Ocampo y Esmeralda, Rosario, 2000, Argentina
| | - Ludivine Thomas
- HM.Clause, rue Louis Saillant, 26801 Portes-lès-Valence, France
| | - Claudius Marondedze
- Laboratoire de Physiologie Cellulaire et Végétale, Université Grenoble Alpes, CEA/DRF/BIG, INRA UMR1417, CNRS UMR5168, 38054 Grenoble Cedex 9, France
| | - Chris Gehring
- Department of Chemistry, Biology & Biotechnology, University of Perugia,
06121 Perugia, Italy
| | - Natalia Gottig
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR). Ocampo y Esmeralda, Rosario, 2000, Argentina
| | - Jorgelina Ottado
- Instituto de Biología Molecular y Celular de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas (IBR-CONICET) and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario (UNR). Ocampo y Esmeralda, Rosario, 2000, Argentina
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19
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Padilla-Vaca F, Vargas-Maya NI, Elizarrarás-Vargas NU, Rangel-Serrano Á, Cardoso-Reyes LR, Razo-Soria T, Membrillo-Hernández J, Franco B. Flotillin homologue is involved in the swimming behavior of Escherichia coli. Arch Microbiol 2019; 201:999-1008. [PMID: 31062059 DOI: 10.1007/s00203-019-01670-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 04/22/2019] [Accepted: 04/24/2019] [Indexed: 01/22/2023]
Abstract
Cellular membrane is a key component for maintaining cell shape and integrity. The classical membrane structure and function by Singer and Nicolson groundbreaking model has depicted the membrane as a homogeneous fluid structure. This view has changed by the discovery of discrete domains containing different lipid compositions, called lipid rafts, which play a key role in signal transduction in eukaryotic cells. In the past few years, lipid raft-like structures have been found in bacteria also, constituted by cardiolipin and other modified lipids, perhaps involved in generating a specific site for protein clustering. Here, we report the analysis of a protein termed YqiK from Escherichia coli, a prohibitin homolog that has been implicated in stress sensing by the formation of membrane-associated microdomains. The E. coli yqiK-deficient mutant strain showed an enhanced swimming behavior and was resistant to ampicillin but its response to other stressing conditions was similar to that of the wild-type strain. The abnormal swimming behavior is reversed when the protein is expressed in trans from a plasmid. Also, we demonstrate that YqiK is not redundant with QmcA, another flotillin homolog found in E. coli. Our results, along with the data available in the literature, suggest that YqiK may be involved in the formation of discrete membrane-associated signaling complexes that regulate and agglomerate signaling proteins to generate cell response to chemotaxis.
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Affiliation(s)
- Felipe Padilla-Vaca
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto, 36050, Mexico
| | - Naurú Idalia Vargas-Maya
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto, 36050, Mexico
| | - Narciso Ulises Elizarrarás-Vargas
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto, 36050, Mexico
| | - Ángeles Rangel-Serrano
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto, 36050, Mexico
| | - Luis Rafael Cardoso-Reyes
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto, 36050, Mexico
| | - Tannia Razo-Soria
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto, 36050, Mexico
| | - Jorge Membrillo-Hernández
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Mexico
| | - Bernardo Franco
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato, Noria Alta s/n, Guanajuato, Gto, 36050, Mexico.
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20
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Decreased Effective Macromolecular Crowding in Escherichia coli Adapted to Hyperosmotic Stress. J Bacteriol 2019; 201:JB.00708-18. [PMID: 30833357 PMCID: PMC6482933 DOI: 10.1128/jb.00708-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/21/2019] [Indexed: 11/20/2022] Open
Abstract
Bacteria adapt to ever-changing environmental conditions such as osmotic stress and energy limitation. It is not well understood how biomolecules reorganize themselves inside Escherichia coli under these conditions. An altered biochemical organization would affect macromolecular crowding, which could influence reaction rates and diffusion of macromolecules. In cells adapted to osmotic upshift, protein diffusion is indeed faster than expected on the basis of the biopolymer volume fraction. We now probe the effects of macromolecular crowding in cells adapted to osmotic stress or depleted in metabolic energy with a genetically encoded fluorescence-based probe. We find that the effective macromolecular crowding in adapted and energy-depleted cells is lower than in unstressed cells, indicating major alterations in the biochemical organization of the cytoplasm. Escherichia coli adapts to changing environmental osmolality to survive and maintain growth. It has been shown that the diffusion of green fluorescent protein (GFP) in cells adapted to osmotic upshifts is higher than expected from the increase in biopolymer volume fraction. To better understand the physicochemical state of the cytoplasm in adapted cells, we now follow the macromolecular crowding during adaptation with fluorescence resonance energy transfer (FRET)-based sensors. We apply an osmotic upshift and find that after an initial increase, the apparent crowding decreases over the course of hours to arrive at a value lower than that before the osmotic upshift. Crowding relates to cell volume until cell division ensues, after which a transition in the biochemical organization occurs. Analysis of single cells by microfluidics shows that changes in cell volume, elongation, and division are most likely not the cause for the transition in organization. We further show that the decrease in apparent crowding upon adaptation is similar to the apparent crowding in energy-depleted cells. Based on our findings in combination with literature data, we suggest that adapted cells have indeed an altered biochemical organization of the cytoplasm, possibly due to different effective particle size distributions and concomitant nanoscale heterogeneity. This could potentially be a general response to accommodate higher biopolymer fractions yet retaining crowding homeostasis, and it could apply to other species or conditions as well. IMPORTANCE Bacteria adapt to ever-changing environmental conditions such as osmotic stress and energy limitation. It is not well understood how biomolecules reorganize themselves inside Escherichia coli under these conditions. An altered biochemical organization would affect macromolecular crowding, which could influence reaction rates and diffusion of macromolecules. In cells adapted to osmotic upshift, protein diffusion is indeed faster than expected on the basis of the biopolymer volume fraction. We now probe the effects of macromolecular crowding in cells adapted to osmotic stress or depleted in metabolic energy with a genetically encoded fluorescence-based probe. We find that the effective macromolecular crowding in adapted and energy-depleted cells is lower than in unstressed cells, indicating major alterations in the biochemical organization of the cytoplasm.
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21
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Tan X, Acquah I, Liu H, Li W, Tan S. A critical review on saline wastewater treatment by membrane bioreactor (MBR) from a microbial perspective. CHEMOSPHERE 2019; 220:1150-1162. [PMID: 33395802 DOI: 10.1016/j.chemosphere.2019.01.027] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/01/2019] [Accepted: 01/03/2019] [Indexed: 05/12/2023]
Abstract
This work has reviewed from a microbial perspective and listed the typical studies on MBR techniques for saline wastewater treatments. When the salinity of influent is lower than 10 g/L NaCl, conventional MBR can be easily applied with adjusted operating conditions. For better biodegradation and anti-fouling ability at higher salinities (10-100 g/L), modified and hybrid MBR systems may need to be wisely designed according to the change in the microbial community and contents of EPS/SMP. To treat hypersaline wastewaters with salinities of up to 100 g/L NaCl, inoculation of halophilic bacteria has been applied in MBR works. Microbial community structures in some typical works have been discussed from a microbial perspective to benefit the identification and isolation of halophilic bacteria for future works. The following aspects are also suggested in future MBR research for saline wastewater treatment: (1) The structure design of MBR and the manufacture of advanced membranes; (2) The maintenance of the microbial biodiversity for anti-membrane fouling; (3) The metabolic mechanism for halophilic (or salt-tolerant) microorganisms against salinity shocks; (4) The revolution stage and process of microorganisms during saline wastewater treatment in MBR; (5) The effects of characteristics (cell structure, shape and metabolic pathways) of microorganisms on the salt tolerance; (6) Applying halophilic microorganisms for salinities over 150 g/L NaCl.
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Affiliation(s)
- Xu Tan
- School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China; Department of Civil and Environmental Engineering, University of Technology Sydney, Sydney 2007, Australia
| | - Isaac Acquah
- Programme of Biomedical Engineering, Kwame Nkrumah University of Science and Technology, PMB, University Post, Kumasi, Ghana
| | - Hanzhe Liu
- Department of Chemistry, Yanbian University, Yanji, 133002, China
| | - Weiguo Li
- Department of Environmental Engineering, Harbin Institute of Technology (Weihai), Weihai 264209, China
| | - Songwen Tan
- School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China.
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22
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Lensmire JM, Pratt ZL, Wong ACL, Kaspar CW. Phosphate and carbohydrate facilitate the formation of filamentous Salmonella enterica during osmotic stress. MICROBIOLOGY-SGM 2018; 164:1503-1513. [PMID: 30325297 DOI: 10.1099/mic.0.000731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Salmonella enterica is a human pathogen that can produce filamentous cells in response to environmental stress. The molecular mediators and biosynthetic pathways that contribute to the formation of filamentous cells (>10 µm in length) during osmotic stress are mostly unknown. The comparison of filamentous and non-filamentous cells in this study was aided by the use of a filtration step to separate cell types. Osmotic stress caused an efflux of phosphate from cells, and the addition of phosphate and a carbohydrate to Luria broth with 7 % NaCl (LB-7NaCl) significantly increased the proportion of filamentous cells in the population (58 %). In addition to direct measurements of intracellular and extracellular phosphate concentrations, the relative abundance of the iraP transcript that is induced by phosphate limitation was monitored. Non-filamentous cells had a greater relative abundance of iraP transcript than filamentous cells. IraP also affects the stability of RpoS, which regulates the general stress regulon, and was detected in non-filamentous cells but not filamentous cells. Markers of metabolic pathways for the production of acetyl-CoA (pflB, encoding for pyruvate formate lyase) and fatty acids (fabH) that are essential to membrane biosynthesis were found in greater abundance in filamentous cells than non-filamentous cells. There were no differences in the DNA, protein and biomass levels in filamentous and non-filamentous cells after 48 h of incubation, although the filamentous cells produced significantly (P<0.05) more acetate. This study found that phosphate and carbohydrate enhanced the formation of filamentous cells during osmotic stress, and there were differences in key regulatory elements and markers of metabolic pathways in filamentous and non-filamentous S. enterica.
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Affiliation(s)
- Joshua M Lensmire
- 1Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA
| | | | - Amy C L Wong
- 1Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA.,3Food Research Institute, University of Wisconsin - Madison, Madison, WI, USA
| | - Charles W Kaspar
- 3Food Research Institute, University of Wisconsin - Madison, Madison, WI, USA.,1Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA
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In Vivo Titration of Folate Pathway Enzymes. Appl Environ Microbiol 2018; 84:AEM.01139-18. [PMID: 30030232 DOI: 10.1128/aem.01139-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 07/18/2018] [Indexed: 12/12/2022] Open
Abstract
How enzymes behave in cells is likely different from how they behave in the test tube. Previous in vitro studies find that osmolytes interact weakly with folate. Removal of the osmolyte from the solvation shell of folate is more difficult than removal of water, which weakens binding of folate to its enzyme partners. To examine if this phenomenon occurs in vivo, osmotic stress titrations were performed with Escherichia coli Two strategies were employed: resistance to an antibacterial drug and complementation of a knockout strain by the appropriate gene cloned into a plasmid that allows tight control of expression levels as well as labeling by a degradation tag. The abilities of the knockout and complemented strains to grow under osmotic stress were compared. Typically, the knockout strain could grow to high osmolalities on supplemented medium, while the complemented strain stopped growing at lower osmolalities on minimal medium. This pattern was observed for an R67 dihydrofolate reductase clone rescuing a ΔfolA strain, for a methylenetetrahydrofolate reductase clone rescuing a ΔmetF strain, and for a serine hydroxymethyltransferase clone rescuing a ΔglyA strain. Additionally, an R67 dihydrofolate reductase clone allowed E. coli DH5α to grow in the presence of trimethoprim until an osmolality of ∼0.81 is reached, while cells in a control titration lacking antibiotic could grow to 1.90 osmol.IMPORTANCEE. coli can survive in drought and flooding conditions and can tolerate large changes in osmolality. However, the cell processes that limit bacterial growth under high osmotic stress conditions are not known. In this study, the dose of four different enzymes in E. coli was decreased by using deletion strains complemented by the gene carried in a tunable plasmid. Under conditions of limiting enzyme concentration (lower than that achieved by chromosomal gene expression), cell growth can be blocked by osmotic stress conditions that are normally tolerated. These observations indicate that E. coli has evolved to deal with variations in its osmotic environment and that normal protein levels are sufficient to buffer the cell from environmental changes. Additional factors involved in the osmotic pressure response may include altered protein concentration/activity levels, weak solute interactions with ligands which can make it more difficult for proteins to bind their substrates/inhibitors/cofactors in vivo, and/or viscosity effects.
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24
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Zhang W, Zhu J, Zhu X, Song M, Zhang T, Xin F, Dong W, Ma J, Jiang M. Expression of global regulator IrrE for improved succinate production under high salt stress by Escherichia coli. BIORESOURCE TECHNOLOGY 2018; 254:151-156. [PMID: 29413916 DOI: 10.1016/j.biortech.2018.01.091] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/16/2018] [Accepted: 01/19/2018] [Indexed: 06/08/2023]
Abstract
Poor high salt stress resistance remained as a main hurdle limiting the efficient bio-based succinic acid production. In this study, the metabolically engineered E. coli not only showed improvement of high salt stress tolerance through expression of a global regulator IrrE, but also could use seawater for succinic acid fermentation. The recombinant strain showed an increased 1.20-fold of cell growth rate and 1.24-fold of succinic acid production. Expression levels of genes related glucose uptake and succinic acid synthesis were up-regulated, and more glycerol and trehalose were accumulated. Moreover, no significant differences were observed in cell growth even when tap water was replaced by 60% artificial seawater. In the fermentation using Yellow Sea seawater, 24.5 g/L succinic acid was achieved with a yield of 0.88 g/g. This strategy set up a platform for improving abiotic stress tolerances and provide a possible approach for fermentation processes with low cost.
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Affiliation(s)
- Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China
| | - Junru Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Xinggui Zhu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Meng Song
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Ting Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing 211800, PR China.
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25
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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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26
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Pumirat P, Vanaporn M, Boonyuen U, Indrawattana N, Rungruengkitkun A, Chantratita N. Effects of sodium chloride on heat resistance, oxidative susceptibility, motility, biofilm and plaque formation of Burkholderia pseudomallei. Microbiologyopen 2017. [PMID: 28643413 PMCID: PMC5552950 DOI: 10.1002/mbo3.493] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Burkholderia pseudomallei is an environmental saprophyte and the causative agent of melioidosis, a severe infectious disease prevalent in tropical areas, including southeast Asia and northern Australia. In Thailand, the highest incidence of melioidosis is in the northeast region, where saline soil and water are abundant. We hypothesized that B. pseudomallei develops an ability to thrive in saline conditions and gains a selective ecological advantage over other soil-dwelling microorganisms. However, little is known about how an elevated NaCl concentration affects survival and adaptive changes in this pathogen. In this study, we examined the adaptive changes in six isolates of B. pseudomallei after growth in Luria-Bertani medium containing different concentrations of NaCl at 37°C for 6 hr. The bacteria were then investigated for resistance to heat at 50°C and killing by hydrogen peroxide (H2 O2 ). In addition, flagellar production, biofilm formation, and the plaque formation efficiency of B. pseudomallei after culture in saline conditions were observed. In response to exposure to 150 and 300 mmol L-1 NaCl, all B. pseudomallei isolates showed significantly increased thermal tolerance, oxidative resistance, and plaque-forming efficiency. However, NaCl exposure notably decreased the number of B. pseudomallei flagella. Taken together, these results provide insight into the adaptations of B. pseudomallei that might be crucial for survival and persistence in the host and/or endemic environments with high salinity.
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Affiliation(s)
- Pornpan Pumirat
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Muthita Vanaporn
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Usa Boonyuen
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nitaya Indrawattana
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Amporn Rungruengkitkun
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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27
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Liu Q, Wu J, Lim ZY, Aggarwal A, Yang H, Wang S. Evaluation of the metabolic response of Escherichia coli to electrolysed water by 1 H NMR spectroscopy. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.01.066] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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28
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Guan N, Li J, Shin HD, Du G, Chen J, Liu L. Microbial response to environmental stresses: from fundamental mechanisms to practical applications. Appl Microbiol Biotechnol 2017; 101:3991-4008. [PMID: 28409384 DOI: 10.1007/s00253-017-8264-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 10/19/2022]
Abstract
Environmental stresses are usually active during the process of microbial fermentation and have significant influence on microbial physiology. Microorganisms have developed a series of strategies to resist environmental stresses. For instance, they maintain the integrity and fluidity of cell membranes by modulating their structure and composition, and the permeability and activities of transporters are adjusted to control nutrient transport and ion exchange. Certain transcription factors are activated to enhance gene expression, and specific signal transduction pathways are induced to adapt to environmental changes. Besides, microbial cells also have well-established repair mechanisms that protect their macromolecules against damages inflicted by environmental stresses. Oxidative, hyperosmotic, thermal, acid, and organic solvent stresses are significant in microbial fermentation. In this review, we summarize the modus operandi by which these stresses act on cellular components, as well as the corresponding resistance mechanisms developed by microorganisms. Then, we discuss the applications of these stress resistance mechanisms on the production of industrially important chemicals. Finally, we prospect the application of systems biology and synthetic biology in the identification of resistant mechanisms and improvement of metabolic robustness of microorganisms in environmental stresses.
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Affiliation(s)
- Ningzi Guan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Hyun-Dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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29
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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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30
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He G, Deng J, Wu C, Huang J. A partial proteome reference map of Tetragenococcus halophilus and comparative proteomic and physiological analysis under salt stress. RSC Adv 2017. [DOI: 10.1039/c6ra22521g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Tetragenococcus halophilus, a moderately halophilic Gram-positive lactic acid bacteria, was widely existed in many food fermentation systems, where salt stress is an environmental condition commonly encountered.
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Affiliation(s)
- Guiqiang He
- College of Light Industry, Textile & Food Engineering
- Sichuan University
- Chengdu 610065
- China
- Key Laboratory of Leather Chemistry and Engineering
| | - Jingcheng Deng
- College of Light Industry, Textile & Food Engineering
- Sichuan University
- Chengdu 610065
- China
- Key Laboratory of Leather Chemistry and Engineering
| | - Chongde Wu
- College of Light Industry, Textile & Food Engineering
- Sichuan University
- Chengdu 610065
- China
- Key Laboratory of Leather Chemistry and Engineering
| | - Jun Huang
- College of Light Industry, Textile & Food Engineering
- Sichuan University
- Chengdu 610065
- China
- Key Laboratory of Leather Chemistry and Engineering
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31
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Ma Y, Wang Q, Gao X, Zhang Y. Biosynthesis and uptake of glycine betaine as cold-stress response to low temperature in fish pathogen Vibrio anguillarum. J Microbiol 2016; 55:44-55. [PMID: 28035596 DOI: 10.1007/s12275-017-6370-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 12/28/2022]
Abstract
Fish pathogen Vibrio anguillarum, a mesophile bacterium, is usually found in estuarine and marine coastal ecosystems worldwide that pose a constant stress to local organism by its fluctuation in salinity as well as notable temperature change. Though V. anguillarum is able to proliferate while maintain its pathogenicity under low temperature (5-18°C), so far, coldadaption molecular mechanism of the bacteria is unknown. In this study, V. anguillarum was found possessing a putative glycine betaine synthesis system, which is encoded by betABI and synthesizes glycine betaine from its precursor choline. Furthermore, significant up-regulation of the bet gene at the transcriptional level was noted in log phase in response to cold-stress. Moreover, the accumulation of betaine glycine was only found appearing at low growth temperatures, suggesting that response regulation of both synthesis system and transporter system are cold-dependent. Furthermore, in-frame deletion mutation in the two putative ABC transporters and three putative BCCT family transporters associated with glycine betaine uptake could not block cellular accumulation of betaine glycine in V. anguillarum under coldstress, suggesting the redundant feature in V. anguillarum betaine transporter system. These findings confirmed that glycine betaine serves as an effective cold stress protectant and highlighted an underappreciated facet of the acclimatization of V. anguillarum to cold environments.
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Affiliation(s)
- Yue Ma
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, P. R. China
| | - Xiating Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, P. R. China.
- Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai, 200237, P. R. China.
- Shanghai Collaborative Innovation Center for Biomanufacturing, Shanghai, 200237, P. R. China.
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32
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Kurt-Kızıldoğan A, Abanoz B, Okay S. Global transcriptome analysis of Halolamina sp. to decipher the salt tolerance in extremely halophilic archaea. Gene 2016; 601:56-64. [PMID: 27919704 DOI: 10.1016/j.gene.2016.11.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/17/2016] [Accepted: 11/30/2016] [Indexed: 12/21/2022]
Abstract
Extremely halophilic archaea survive in the hypersaline environments such as salt lakes or salt mines. Therefore, these microorganisms are good sources to investigate the molecular mechanisms underlying the tolerance to high salt concentrations. In this study, a global transcriptome analysis was conducted in an extremely halophilic archaeon, Halolamina sp. YKT1, isolated from a salt mine in Turkey. A comparative RNA-seq analysis was performed using YKT1 isolate grown either at 2.7M NaCl or 5.5M NaCl concentrations. A total of 2149 genes were predicted to be up-regulated and 1638 genes were down-regulated in the presence of 5.5M NaCl. The salt tolerance of Halolamina sp. YKT1 involves the up-regulation of genes related with membrane transporters, CRISPR-Cas systems, osmoprotectant solutes, oxidative stress proteins, and iron metabolism. On the other hand, the genes encoding the proteins involved in DNA replication, transcription, translation, mismatch and nucleotide excision repair were down-regulated. The RNA-seq data were verified for seven up-regulated genes as well as six down-regulated genes via qRT-PCR analysis. This comprehensive transcriptome analysis showed that the halophilic archaeon canalizes its energy towards keeping the intracellular osmotic balance minimizing the production of nucleic acids and peptides.
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Affiliation(s)
- Aslıhan Kurt-Kızıldoğan
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55139 Samsun, Turkey
| | - Büşra Abanoz
- Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, 55139 Samsun, Turkey
| | - Sezer Okay
- Department of Biology, Faculty of Science, Çankırı Karatekin University, 18100 Çankırı, Turkey.
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33
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Hall LW, Dunshea FR, Allen JD, Rungruang S, Collier JL, Long NM, Collier RJ. Evaluation of dietary betaine in lactating Holstein cows subjected to heat stress. J Dairy Sci 2016; 99:9745-9753. [PMID: 27720159 DOI: 10.3168/jds.2015-10514] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Accepted: 08/09/2016] [Indexed: 02/01/2023]
Abstract
Betaine (BET), a natural, organic osmolyte, improves cellular efficiency by acting as a chaperone, refolding denatured proteins. To test if dietary BET reduced the effect of heat stress (HS) in lactating dairy cows, multiparous, lactating Holstein cows (n=24) were blocked by days in milk (101.4±8.6 d) and randomly assigned to 1 of 3 daily intakes of dietary BET: the control (CON) group received no BET, mid intake (MID) received 57mg of BET/kg of body weight, and high dose (HI) received 114mg of BET/kg of body weight. Cows were fed twice daily and BET was top-dressed at each feeding. Cows were milked 2 times/d and milk samples were taken daily for analysis. Milk components, yield, feed intake, and water intake records were taken daily. Rectal temperature and respiration rate were taken 3 times/d at 0600, 1400, and 1800h. Cows were housed in environmentally controlled rooms and were allowed acclimation for 7d at thermoneutral (TN) conditions with a mean temperature-humidity index of 56.6. Cows were then exposed to 7d of TN followed by 7d of HS represented by a temperature-humidity index of 71.5 for 14d. This was followed by a recovery period of 3d at TN. Dietary BET increased milk yield during the TN period. No differences were found between BET and CON in total milk production or milk composition during HS. The increase in water intake during HS was not as great for cows fed BET compared with controls. The cows on CON diets had higher p.m. respiration rate than both MID and HI BET during HS, but lower rectal temperature compared with BET. No difference was found in serum glucose during TN, but cows given HI had elevated glucose levels during HS compared with CON. No differences were found in serum insulin levels between CON and BET but an intake by environment interaction was present with insulin increasing in HI-treated lactating dairy cows during HS. The heat shock response [heat shock protein (HSP) 27 and HSP70] was upregulated in bovine mammary epithelial cells in vitro. Blood leukocyte HSP27 was downregulated at the HI dose under TN conditions and HSP70 was upregulated at the HI dose and this effect was increased by HS. No effect was seen with the MID dose with HSP27 or HSP70. The lack of effect of BET at MID may be associated with uptake across the gut. We conclude that BET increased milk production under TN conditions and was associated with reduced feed and water intake and slightly increased body temperatures during HS of cows fed BET. The effect of BET on milk production was lost during HS with HI BET, whereas serum glucose levels increased during HS.
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Affiliation(s)
- L W Hall
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson 85719
| | - F R Dunshea
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - J D Allen
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson 85719
| | - S Rungruang
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson 85719
| | - J L Collier
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson 85719
| | - N M Long
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson 85719
| | - R J Collier
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson 85719.
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Mahmoud RY, Li W, Eldomany RA, Emara M, Yu J. The Shigella ProU system is required for osmotic tolerance and virulence. Virulence 2016; 8:362-374. [PMID: 27558288 DOI: 10.1080/21505594.2016.1227906] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
To cope with hyperosmotic stress encountered in the environments and in the host, the pathogenic as well as non-pathogenic microbes use diverse transport systems to obtain osmoprotectants. To study the role of Shigella sonnei ProU system in response to hyperosmotic stress and virulence, we constructed deletion and complementation strains of proV and used an RNAi approach to silence the whole ProU operon. We compared the response between wild type and the mutants to the hyperosmotic pressure in vitro, and assessed virulence properties of the mutants using gentamicin protection assay as well as Galleria mellonella moth larvae model. In response to osmotic stress by either NaCl or KCl, S. sonnei highly up-regulates transcription of proVWX genes. Supplementation of betaine greatly elevates the growth of the wild type S. sonnei but not the proV mutants in M9 medium containing 0.2 M NaCl or 0.2 M KCl. The proV mutants are also defective in intracellular growth compared with the wild type. The moth larvae model of G. mellonella shows that either deletion of proV gene or knockdown of proVWX transcripts by RNAi significantly attenuates virulence. ProU system in S. sonnei is required to cope with osmotic stress for survival and multiplication in vitro, and for infection.
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Affiliation(s)
- Rasha Y Mahmoud
- a Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS) , University of Strathclyde , Glasgow , Scotland , UK.,b Department of Microbiology and Immunology, Faculty of Pharmacy , Helwan University , Cairo , Egypt
| | - Wenqin Li
- a Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS) , University of Strathclyde , Glasgow , Scotland , UK
| | - Ramadan A Eldomany
- c Department of Microbiology and Immunology, Faculty of Pharmacy , Kafr Elsheikh University , Kafr Elsheikh , Egypt
| | - Mohamed Emara
- b Department of Microbiology and Immunology, Faculty of Pharmacy , Helwan University , Cairo , Egypt
| | - Jun Yu
- a Strathclyde Institute of Pharmacy and Biomedical Sciences (SIPBS) , University of Strathclyde , Glasgow , Scotland , UK
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Métris A, George SM, Ropers D. Piecewise linear approximations to model the dynamics of adaptation to osmotic stress by food-borne pathogens. Int J Food Microbiol 2016; 240:63-74. [PMID: 27377009 DOI: 10.1016/j.ijfoodmicro.2016.06.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 06/09/2016] [Accepted: 06/19/2016] [Indexed: 01/08/2023]
Abstract
Addition of salt to food is one of the most ancient and most common methods of food preservation. However, little is known of how bacterial cells adapt to such conditions. We propose to use piecewise linear approximations to model the regulatory adaptation of Escherichiacoli to osmotic stress. We apply the method to eight selected genes representing the functions known to be at play during osmotic adaptation. The network is centred on the general stress response factor, sigma S, and also includes a module representing the catabolic repressor CRP-cAMP. Glutamate, potassium and supercoiling are combined to represent the intracellular regulatory signal during osmotic stress induced by salt. The output is a module where growth is represented by the concentration of stable RNAs and the transcription of the osmotic gene osmY. The time course of gene expression of transport of osmoprotectant represented by the symporter proP and of the osmY is successfully reproduced by the network. The behaviour of the rpoS mutant predicted by the model is in agreement with experimental data. We discuss the application of the model to food-borne pathogens such as Salmonella; although the genes considered have orthologs, it seems that supercoiling is not regulated in the same way. The model is limited to a few selected genes, but the regulatory interactions are numerous and span different time scales. In addition, they seem to be condition specific: the links that are important during the transition from exponential to stationary phase are not all needed during osmotic stress. This model is one of the first steps towards modelling adaptation to stress in food safety and has scope to be extended to other genes and pathways, other stresses relevant to the food industry, and food-borne pathogens. The method offers a good compromise between systems of ordinary differential equations, which would be unmanageable because of the size of the system and for which insufficient data are available, and the more abstract Boolean methods.
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Affiliation(s)
- Aline Métris
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.
| | - Susie M George
- Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.
| | - Delphine Ropers
- Inria Grenoble - Rhône-Alpes Research Center, Saint Ismier, France.
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36
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The response of foodborne pathogens to osmotic and desiccation stresses in the food chain. Int J Food Microbiol 2016; 221:37-53. [PMID: 26803272 DOI: 10.1016/j.ijfoodmicro.2015.12.014] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 12/22/2015] [Accepted: 12/30/2015] [Indexed: 12/24/2022]
Abstract
In combination with other strategies, hyperosmolarity and desiccation are frequently used by the food processing industry as a means to prevent bacterial proliferation, and particularly that of foodborne pathogens, in food products. However, it is increasingly observed that bacteria, including human pathogens, encode mechanisms to survive and withstand these stresses. This review provides an overview of the mechanisms employed by Salmonella spp., Shiga toxin producing E. coli, Cronobacter spp., Listeria monocytogenes and Campylobacter spp. to tolerate osmotic and desiccation stresses and identifies gaps in knowledge which need to be addressed to ensure the safety of low water activity and desiccated food products.
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37
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To Modulate Survival under Secondary Stress Conditions, Listeria monocytogenes 10403S Employs RsbX To Downregulate σB Activity in the Poststress Recovery Stage or Stationary Phase. Appl Environ Microbiol 2015; 82:1126-1135. [PMID: 26637594 DOI: 10.1128/aem.03218-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 11/27/2015] [Indexed: 01/12/2023] Open
Abstract
Listeria monocytogenes is a saprophytic bacterium that thrives in diverse environments and causes listeriosis via ingestion of contaminated food. RsbX, a putative sigma B (σ(B)) regulator, is thought to maintain the ready state in the absence of stress and reset the bacterium to the initial state in the poststress stage in Bacillus subtilis. We wondered whether RsbX is functional in L. monocytogenes under different stress scenarios. Genetic deletion and complementation of the rsbX gene were combined with survival tests and transcriptional and translational analyses of σ(B) expression in response to stresses. We found that deletion of rsbX increased survival under secondary stress following recovery of growth after primary stress or following stationary-phase culturing. The ΔrsbX mutant had higher expression of σ(B) than its parent strain in the recovery stage following primary sodium stress and in stationary-phase cultures. Apparently, increased σ(B) expression had contributed to improved survival in the absence of RsbX. There were no significant differences in survival rates or σ(B) expression levels in response to primary stresses between the rsbX mutant and its parent strain during the exponential phase. Therefore, we provide clear evidence that RsbX is a negative regulator of L. monocytogenes σ(B) during the recovery period after a primary stress or in the stationary phase, thus affecting its survival under secondary stress.
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Finn S, Rogers L, Händler K, McClure P, Amézquita A, Hinton JCD, Fanning S. Exposure of Salmonella enterica Serovar Typhimurium to Three Humectants Used in the Food Industry Induces Different Osmoadaptation Systems. Appl Environ Microbiol 2015; 81:6800-11. [PMID: 26209672 PMCID: PMC4561688 DOI: 10.1128/aem.01379-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/15/2015] [Indexed: 11/22/2022] Open
Abstract
Common salt (NaCl) is frequently used by the food industry to add flavor and to act as a humectant in order to reduce the water content of a food product. The improved health awareness of consumers is leading to a demand for food products with reduced salt content; thus, manufacturers require alternative water activity-reducing agents which elicit the same general effects as NaCl. Two examples include KCl and glycerol. These agents lower the water activity of a food matrix and also contribute to limit the growth of the microbiota, including foodborne pathogens. Little is currently known about how foodborne pathogens respond to these water activity-lowering agents. Here we examined the response of Salmonella enterica serovar Typhimurium 4/74 to NaCl, KCl, and glycerol at three time points, using a constant water activity level, compared with the response of a control inoculum. All conditions induced the upregulation of gluconate metabolic genes after 6 h of exposure. Bacteria exposed to NaCl and KCl demonstrated the upregulation of the osmoprotective transporter mechanisms encoded by the proP, proU, and osmU (STM1491 to STM1494) genes. Glycerol exposure elicited the downregulation of these osmoadaptive mechanisms but stimulated an increase in lipopolysaccharide and membrane protein-associated genes after 1 h. The most extensive changes in gene expression occurred following exposure to KCl. Because many of these genes were of unknown function, further characterization may identify KCl-specific adaptive processes that are not stimulated by NaCl. This study shows that the response of S. Typhimurium to different humectants does not simply reflect reduced water activity and likely involves systems that are linked to specific humectants.
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Affiliation(s)
- Sarah Finn
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland
| | - Lisa Rogers
- Conway Institute, UCD School of Biomolecular & Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kristian Händler
- Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Peter McClure
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, United Kingdom
| | - Alejandro Amézquita
- Unilever, Safety and Environmental Assurance Centre, Sharnbrook, Bedfordshire, United Kingdom
| | - Jay C D Hinton
- Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Séamus Fanning
- UCD Centre for Food Safety, School of Public Health, Physiotherapy & Population Science, University College Dublin, Belfield, Dublin, Ireland Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast, Northern Ireland
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Integrated kinetic and probabilistic modeling of the growth potential of bacterial populations. Appl Environ Microbiol 2015; 81:3228-34. [PMID: 25747002 PMCID: PMC4393428 DOI: 10.1128/aem.04018-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/23/2015] [Indexed: 11/20/2022] Open
Abstract
When bacteria are exposed to osmotic stress, some cells recover and grow, while others die or are unculturable. This leads to a viable count growth curve where the cell number decreases before the onset of the exponential growth phase. From such curves, it is impossible to estimate what proportion of the initial cells generates the growth because it leads to an ill-conditioned numerical problem. Here, we applied a combination of experimental and statistical methods, based on optical density measurements, to infer both the probability of growth and the maximum specific growth rate of the culture. We quantified the growth potential of a bacterial population as a quantity composed from the probability of growth and the “suitability” of the growing subpopulation to the new environment. We found that, for all three laboratory media studied, the probability of growth decreased while the “work to be done” by the growing subpopulation (defined as the negative logarithm of their suitability parameter) increased with NaCl concentration. The results suggest that the effect of medium on the probability of growth could be described by a simple shift parameter, a differential NaCl concentration that can be accounted for by the change in the medium composition. Finally, we highlighted the need for further understanding of the effect of the osmoprotectant glycine betaine on metabolism.
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Baranyi J, Metris A, George SM. Bacterial economics: adaptation to stress conditions via stage-wise changes in the response mechanism. Food Microbiol 2014; 45:162-6. [PMID: 25500381 DOI: 10.1016/j.fm.2014.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 05/26/2014] [Accepted: 05/30/2014] [Indexed: 11/28/2022]
Abstract
Common features of microbial adaptation are analysed with mathematical models and extended to stress conditions when the bacterial population declines before growing again. A parallel is drawn between bacterial and human communities in terms of non-mutation-based adaptation (acclimation) to stress. For a case study, the behaviour of Escherichia coli under osmotic stress, is detailed. It is suggested that stress modelling adaptation should be the focus of further developments in predictive food microbiology.
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Affiliation(s)
- J Baranyi
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom.
| | - A Metris
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom
| | - S M George
- Gut Health and Food Safety Research Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom
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