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FTIR micro-spectroscopy using synchrotron-based and thermal source-based radiation for probing live bacteria. Anal Bioanal Chem 2020; 412:7049-7061. [PMID: 32839857 DOI: 10.1007/s00216-020-02835-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 11/27/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy has proven to be a non-invasive tool to analyse cells without the hurdle of employing exogenous dyes or probes. Nevertheless, the study of single live bacteria in their aqueous environment has long remained a big challenge, due to the strong infrared absorption of water and the small size of bacteria compared to the micron-range infrared wavelengths of the probing photons. To record infrared spectra of bacteria in an aqueous environment, at different spatial resolutions, two setups were developed. A custom-built attenuated total reflection inverted microscope was coupled to a synchrotron-based FTIR spectrometer, using a germanium hemisphere. With such a setup, a projected spot size of 1 × 1 μm2 was achieved, which allowed spectral acquisition at the single-cell level in the 1800-1300 cm-1 region. The second setup used a demountable liquid micro-chamber with a thermal source-powered FTIR microscope, in transmission geometry, for probing clusters of a few thousands of live cells in the mid-IR region (4000-975 cm-1). Both setups were applied for studying two strains of a model lactic acid bacterium exhibiting different cryo-resistances. The two approaches allowed the discrimination of both strains and revealed population heterogeneity among bacteria at different spatial resolutions. The multivariate analysis of spectra indicated that the cryo-sensitive cells presented the highest cell heterogeneity and the highest content of proteins with the α-helix structure. Furthermore, the results from clusters of bacterial cells evidenced phosphate and peptidoglycan vibrational bands associated with the cell envelope, as potential markers of resistance to environmental conditions. Graphical Abstract.
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Kanauchi M, Nagata A, Kondo A. Accumulation of Hydroxyl Fatty Acid inLactobacillus sakeiY-20 Cells Cultivated under Stress Conditions and Expression of Fatty Acid Hydroxylase. JOURNAL OF THE AMERICAN SOCIETY OF BREWING CHEMISTS 2018. [DOI: 10.1080/03610470.2017.1402580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Makoto Kanauchi
- Department of Food Management, Miyagi University, 2-2-1 Hatatate, Taihaku-ku, Sendai, Miyagi, Japan
| | - Ayaka Nagata
- Department of Food Management, Miyagi University, 2-2-1 Hatatate, Taihaku-ku, Sendai, Miyagi, Japan
| | - Ayaka Kondo
- Department of Food Management, Miyagi University, 2-2-1 Hatatate, Taihaku-ku, Sendai, Miyagi, Japan
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Abstract
Strains of lactic acid bacteria, yeasts, and molds have been selected over thousands of years based on the unique sensory attributes they provide to food fermentations. Over the centuries they have evolved to their domesticated roles, leading to genome decay, loss of pathways, acquisition of genomic elements, and beneficial mutations that provide an advantage in their nutrient-rich food environments. This review highlights the evolutionary traits influenced by the domestication process as these microbes adapted to nutrient-rich foods developed by humans.
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Affiliation(s)
- Grace L Douglas
- Department of Food, Bioprocessing & Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA.
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Mills S, Stanton C, Fitzgerald GF, Ross RP. Enhancing the stress responses of probiotics for a lifestyle from gut to product and back again. Microb Cell Fact 2011; 10 Suppl 1:S19. [PMID: 21995734 PMCID: PMC3231925 DOI: 10.1186/1475-2859-10-s1-s19] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Before a probiotic bacterium can even begin to fulfill its biological role, it must survive a battery of environmental stresses imposed during food processing and passage through the gastrointestinal tract (GIT). Food processing stresses include extremes in temperature, as well as osmotic, oxidative and food matrix stresses. Passage through the GIT is a hazardous journey for any bacteria with deleterious lows in pH encountered in the stomach to the detergent-like properties of bile in the duodenum. However, bacteria are equipped with an array of defense mechanisms to counteract intracellular damage or to enhance the robustness of the cell to withstand lethal external environments. Understanding these mechanisms in probiotic bacteria and indeed other bacterial groups has resulted in the development of a molecular toolbox to augment the technological and gastrointestinal performance of probiotics. This has been greatly aided by studies which examine the global cellular responses to stress highlighting distinct regulatory networks and which also identify novel mechanisms used by cells to cope with hazardous environments. This review highlights the latest studies which have exploited the bacterial stress response with a view to producing next-generation probiotic cultures and highlights the significance of studies which view the global bacterial stress response from an integrative systems biology perspective.
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Affiliation(s)
- Susan Mills
- Teagasc Food Research Centre, Moorepark, Fermoy, Co, Cork, Ireland
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Metabolic impact and potential exploitation of the stress reactions in lactobacilli. Food Microbiol 2009; 26:700-11. [PMID: 19747603 DOI: 10.1016/j.fm.2009.07.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Revised: 07/09/2009] [Accepted: 07/13/2009] [Indexed: 01/03/2023]
Abstract
Lactic acid bacteria (LAB) are a functionally related group of organisms known primarily for their bioprocessing roles in food and beverages. The largest variety of metabolic properties is found in the group of lactobacilli the vast majority of which has been isolated in cereal environments, namely sourdoughs, in which their role ranges from sporadic contaminants to major fermentative flora. Growth or survival in each of these environmental niches depends on the ability of the organism to sense and respond to varying conditions such as temperature, pH, nutrients availability and cell population density. Fermentation process conditions, including temperature range, dough yield, oxygen, pH as well as the amount and composition of starter cultures, determine the cells' metabolic response. In fact, the exposure of microbial cells to stressful conditions during fermentation involves a broad transcriptional response with many induced or repressed genes. The complex network of such responses, involving several metabolic activities will reflect upon the metabolome of the fermentative flora, and thus on the composition and organoleptic properties of the final products. This review shall provide insight into stress response mechanisms and delineate the vast potential residing in the exploitation of the stress dependent metabolome of LAB focusing on bacteria of the sourdough environment as one of the richest sources of lactobacilli.
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Importance of trmE for growth of the psychrophile Pseudomonas syringae at low temperatures. Appl Environ Microbiol 2009; 75:4419-26. [PMID: 19429554 DOI: 10.1128/aem.01523-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Transposon mutagenesis of Pseudomonas syringae Lz4W, a psychrophilic bacterium capable of growing at temperatures between 2 and 30 degrees C, yielded 30 cold-sensitive mutants, and CSM1, one of these cold-sensitive mutants, was characterized. Growth of CSM1 was retarded when it was cultured at 4 degrees C but not when it was cultured at 22 degrees C and 28 degrees C compared to the growth of wild-type cells, indicating that CSM1 is a cold-sensitive mutant of P. syringae Lz4W. The mutated gene in CSM1 was identified as trmE (coding for tRNA modification GTPase), and evidence is provided that this gene is induced at low temperatures. Further, the cold-inducible nature of the trmE promoter was demonstrated. In addition, the transcription start site and the various regulatory elements of the trmE promoter, such as the -10 region, -35 region, UP element, cold box, and DEAD box, were identified, and the importance of these regulatory elements in promoter activity were confirmed. The importance of trmE in rapid adaptation to growth at low temperatures was further highlighted by plasmid-mediated complementation that alleviated the cold-sensitive phenotype of CSM1.
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Phadtare S, Severinov K. Extended -10 motif is critical for activity of the cspA promoter but does not contribute to low-temperature transcription. J Bacteriol 2005; 187:6584-9. [PMID: 16159795 PMCID: PMC1236650 DOI: 10.1128/jb.187.18.6584-6589.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial promoters belonging to the extended -10 class contain a conserved TGn motif upstream of the -10 promoter consensus element. Open promoter complexes can be formed on some extended -10 Escherichia coli promoters at temperatures as low as 6 degrees C, when complexes on most promoters are closed. The promoter of cspA, a gene that codes for the major cold shock protein CspA of E. coli, contains an extended -10 motif. CspA is dramatically induced upon temperature downshift from 37 to 15 degrees C, and its cold shock induction has been attributed to transcription, translation, and mRNA stabilization effects. Here, we show that though the extended -10 motif is critical for high-level expression of cspA, it does not contribute to low-temperature expression. In fact, transcription from the wild-type cspA promoter is cold sensitive in vitro and in vivo. Thus, transcription appears to play little or no role in low-temperature induction of cspA expression.
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Affiliation(s)
- Sangita Phadtare
- Department of Biochemistry, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854, USA.
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Suokko A, Savijoki K, Malinen E, Palva A, Varmanen P. Characterization of a mobile clpL gene from Lactobacillus rhamnosus. Appl Environ Microbiol 2005; 71:2061-9. [PMID: 15812039 PMCID: PMC1082546 DOI: 10.1128/aem.71.4.2061-2069.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two genes encoding ClpL ATPase proteins were identified in a probiotic Lactobacillus rhamnosus strain, E-97800. Sequence analyses revealed that the genes, designated clpL1 and clpL2, share 80% identity. The clpL2 gene showed the highest degree of identity (98.5%) to a clpL gene from Lactobacillus plantarum WCFSI, while it was not detected in three other L. rhamnosus strains studied. According to Northern analyses, the expression of clpL1 and the clpL2 were induced during heat shock by > 20- and 3-fold, respectively. The functional promoter regions were determined by primer extension analyses, and the clpL1 promoter was found to be overlapped by an inverted repeat structure identical to the conserved CIRCE element, indicating that clpL1 belongs to the HrcA regulon in L. rhamnosus. No consensus binding sites for HrcA or CtsR could be identified in the clpL2 promoter region. Interestingly, the clpL2 gene was found to be surrounded by truncated transposase genes and flanked by inverted repeat structures nearly identical to the terminal repeats of the ISLpl1 from L. plantarum HN38. Furthermore, clpL2 was shown to be mobilized during prolonged cultivation at elevated temperature. The presence of a gene almost identical to clpL2 in L. plantarum and its absence in other L. rhamnosus strains suggest that the L. rhamnosus E-97800 has acquired the clpL2 gene via horizontal transfer. No change in the stress tolerance of the ClpL2-deficient derivative of E-97800 compared to the parental strain was observed.
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Affiliation(s)
- Aki Suokko
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, University of Helsinki, Helsinki, Finland
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Altermann E, Russell WM, Azcarate-Peril MA, Barrangou R, Buck BL, McAuliffe O, Souther N, Dobson A, Duong T, Callanan M, Lick S, Hamrick A, Cano R, Klaenhammer TR. Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci U S A 2005; 102:3906-12. [PMID: 15671160 PMCID: PMC554803 DOI: 10.1073/pnas.0409188102] [Citation(s) in RCA: 414] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Lactobacillus acidophilus NCFM is a probiotic bacterium that has been produced commercially since 1972. The complete genome is 1,993,564 nt and devoid of plasmids. The average GC content is 34.71% with 1,864 predicted ORFs, of which 72.5% were functionally classified. Nine phage-related integrases were predicted, but no complete prophages were found. However, three unique regions designated as potential autonomous units (PAUs) were identified. These units resemble a unique structure and bear characteristics of both plasmids and phages. Analysis of the three PAUs revealed the presence of two R/M systems and a prophage maintenance system killer protein. A spacers interspersed direct repeat locus containing 32 nearly perfect 29-bp repeats was discovered and may provide a unique molecular signature for this organism. In silico analyses predicted 17 transposase genes and a chromosomal locus for lactacin B, a class II bacteriocin. Several mucus- and fibronectin-binding proteins, implicated in adhesion to human intestinal cells, were also identified. Gene clusters for transport of a diverse group of carbohydrates, including fructooligosaccharides and raffinose, were present and often accompanied by transcriptional regulators of the lacI family. For protein degradation and peptide utilization, the organism encoded 20 putative peptidases, homologs for PrtP and PrtM, and two complete oligopeptide transport systems. Nine two-component regulatory systems were predicted, some associated with determinants implicated in bacteriocin production and acid tolerance. Collectively, these features within the genome sequence of L. acidophilus are likely to contribute to the organisms' gastric survival and promote interactions with the intestinal mucosa and microbiota.
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Affiliation(s)
- Eric Altermann
- Department of Food Science, Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, NC 27695, USA
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