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Maslanka R, Przywara M, Janeczko A, Zadrag-Tecza R. Microbial cell autofluorescence as a method for measuring the intracellular content of B2 and B6 vitamins. INT J VITAM NUTR RES 2024; 94:334-341. [PMID: 37859397 DOI: 10.1024/0300-9831/a000796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Vitamins are important organic compound required for the proper functioning of cells and organisms. Vitamins of special industrial and pharmaceutical interests include riboflavin (vitamin B2) and pyridoxine (vitamin B6). Commercial production of those biological compounds has increasingly relied on microorganisms and requires simple methods for detecting and estimating their level of synthesis during the biotechnological process. In the case of yeast, methods based on autofluorescence, i.e. natural fluorescence emitted by several cellular compounds, including vitamins, may be useful. Considering that the intensity of emitted light is proportional to the intracellular concentration of riboflavin and pyridoxine, autofluorescence may be a convenient method for their quantification. In this report, we demonstrate a simple, rapid, and sufficiently trustworthy spectrofluorimetric method for determining the content of vitamins B2 and B6 in yeast cells which consists of cells growing, harvesting, washing, and resuspending in a buffer, and then measuring the emitted visible light using specific wavelength of excitation (λex=340 nm and λem=385 nm for pyridoxine; λex=460 nm and λem=535 nm for riboflavin). The limits of detection (LOD) and quantification (LOQ) estimated through measurements of vitamin fluorescence were below 0.005 μg/ml for riboflavin and below 0.05 μg/ml for pyridoxine, respectively. In turn, the smallest credible cell density for measuring autofluorescence was set at 1×108 yeast cells/ml. The relative level of the cell's autofluorescence can be expressed in mass units by applying proper calculation formulas. A comparison of the autofluorescence-based method with the reference HPLC-UV method shows that autofluorescence measurement can be used in the screening analysis of vitamin content (especially riboflavin) in microbial cells.
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Affiliation(s)
- Roman Maslanka
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Poland
| | - Michał Przywara
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Poland
| | - Agnieszka Janeczko
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Poland
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Maslanka R, Bednarska S, Zadrag-Tecza R. Virtually identical does not mean exactly identical: Discrepancy in energy metabolism between glucose and fructose fermentation influences the reproductive potential of yeast cells. Arch Biochem Biophys 2024; 756:110021. [PMID: 38697344 DOI: 10.1016/j.abb.2024.110021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/15/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The physiological efficiency of cells largely depends on the possibility of metabolic adaptations to changing conditions, especially on the availability of nutrients. Central carbon metabolism has an essential role in cellular function. In most cells is based on glucose, which is the primary energy source, provides the carbon skeleton for the biosynthesis of important cell macromolecules, and acts as a signaling molecule. The metabolic flux between pathways of carbon metabolism such as glycolysis, pentose phosphate pathway, and mitochondrial oxidative phosphorylation is dynamically adjusted by specific cellular economics responding to extracellular conditions and intracellular demands. Using Saccharomyces cerevisiae yeast cells and potentially similar fermentable carbon sources i.e. glucose and fructose we analyzed the parameters concerning the metabolic status of the cells and connected with them alteration in cell reproductive potential. Those parameters were related to the specific metabolic network: the hexose uptake - glycolysis and activity of the cAMP/PKA pathway - pentose phosphate pathway and biosynthetic capacities - the oxidative respiration and energy generation. The results showed that yeast cells growing in a fructose medium slightly increased metabolism redirection toward respiratory activity, which decreased pentose phosphate pathway activity and cellular biosynthetic capabilities. These differences between the fermentative metabolism of glucose and fructose, lead to long-term effects, manifested by changes in the maximum reproductive potential of cells.
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Affiliation(s)
- Roman Maslanka
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland.
| | - Sabina Bednarska
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Institute of Biology, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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3
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Case N, Johnston N, Nadeau J. Fluorescence Microscopy with Deep UV, Near UV, and Visible Excitation for In Situ Detection of Microorganisms. ASTROBIOLOGY 2024; 24:300-317. [PMID: 38507693 PMCID: PMC10979697 DOI: 10.1089/ast.2023.0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 01/02/2024] [Indexed: 03/22/2024]
Abstract
We report a simple, inexpensive design of a fluorescence microscope with light-emitting diode (LED) excitation for detection of labeled and unlabeled microorganisms in mineral substrates. The use of deep UV (DUV) excitation with visible emission requires no specialized optics or slides and can be implemented easily and inexpensively using an oblique illumination geometry. DUV excitation (<280 nm) is preferable to near UV (365 nm) for avoidance of mineral autofluorescence. When excited with DUV, unpigmented bacteria show two emission peaks: one in the near UV ∼320 nm, corresponding to proteins, and another peak in the blue to green range, corresponding to flavins and/or reduced nicotinamide adenine dinucleotide (NADH). Many commonly used dyes also show secondary excitation peaks in the DUV, with identical emission spectra and quantum yields as their primary peak. However, DUV fails to excite key biosignature molecules, especially chlorophyll in cyanobacteria. Visible excitation (violet to blue) also results in less mineral autofluorescence than near UV, and most autofluorescence in the minerals seen here is green, so that red dyes and red autofluorescence of chlorophyll and porphyrins are readily distinguished. The pairing of DUV and near UV or visible excitation, with emission across the visible, represents the most thorough approach to detection of labeled and unlabeled bacteria in soil and rock.
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Affiliation(s)
- Noel Case
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Nikki Johnston
- Department of Physics, Portland State University, Portland, Oregon, USA
| | - Jay Nadeau
- Department of Physics, Portland State University, Portland, Oregon, USA
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Han Q, Erasmus SW, Bader A, Fryganas C, Elliott CT, van Ruth SM. Fluorescence lifetime imaging microscopy as a tool to characterize spice powder variations for quality and authenticity purposes: A ginger case study. Food Res Int 2024; 176:113792. [PMID: 38163706 DOI: 10.1016/j.foodres.2023.113792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/23/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
Spices are usually ground for applications and the resulting particle size of the powders is an important product attribute in view of the release of flavour. However, inhomogeneity of the original material may lead to variations in the physicochemical characteristics of the particles. This variation and its linkage to particle size may be examined by particular imaging techniques. This study aimed to explore the potential of Fluorescence Lifetime Imaging Microscopy (FLIM) to characterize spice powders according to particle size variations and correlation with their pigment contents to reveal the chemical information contained within the FLIM data. Ginger powder was used as a representative powder model. The FLIM profiles of the individual samples and populations revealed that FLIM coupled with the phasor approach has the capacity to characterize spice powder according to particle size. Meanwhile, Principal Component Analysis of pre-processed FLIM data revealed clustering of particle size groups. Further correlation analysis between the pigment compound contents and FLIM data of the ginger powders indicated that FLIM reflected chemical information of ginger powder and was able to visualize endogenous fluorophores. The current study revealed the potential of FLIM to characterize ginger powder particles. This approach may be extrapolated to other spice powder products. The new knowledge is a step further in paving the way for the application of innovative techniques, already prevalent in other domains, to food quality and authentication.
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Affiliation(s)
- Qing Han
- Food Quality and Design Group, Wageningen University & Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands; Institute for Global Food Security, Biological Sciences, 19 Chlorine Gardens, Queen's University Belfast, BT9 5DL, Belfast, Northern Ireland, United Kingdom
| | - Sara W Erasmus
- Food Quality and Design Group, Wageningen University & Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - Arjen Bader
- Department of Agrotechnology and Food Sciences, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands
| | - Christos Fryganas
- Food Quality and Design Group, Wageningen University & Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands
| | - Christopher T Elliott
- Institute for Global Food Security, Biological Sciences, 19 Chlorine Gardens, Queen's University Belfast, BT9 5DL, Belfast, Northern Ireland, United Kingdom; School of Food Science and Technology, Faculty of Science and Technology, Thammasat University, 99 Mhu 18, Phahonyothin Road, Khong Luang, Pathum Thani 12120, Thailand
| | - Saskia M van Ruth
- Food Quality and Design Group, Wageningen University & Research, P.O. Box 17, 6700 AA, Wageningen, the Netherlands; Institute for Global Food Security, Biological Sciences, 19 Chlorine Gardens, Queen's University Belfast, BT9 5DL, Belfast, Northern Ireland, United Kingdom; School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.
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Taiti C, Di Sotto A, Stefano G, Percaccio E, Iannone M, Marianelli A, Garzoli S. Identification of Volatile Molecules and Bioactivity of Gruyt Craft Beer Enriched with Citrus aurantium var. dulcis L. Essential Oil. Int J Mol Sci 2023; 25:350. [PMID: 38203520 PMCID: PMC10779301 DOI: 10.3390/ijms25010350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
In this work, for the first time, a gruyt beer and the same one after the addition of Citrus aurantium essential oil (AEO), were investigated to determine the composition of the volatile fraction. The applied analytical techniques, such as Head Space/Solid Phase Microextraction-Gas Chromatography-Mass Spectrometry (HS/SPME-GC-MS) and Proton Transfer Reaction-Time of Flight-Mass Spectrometer (PTR-ToF-MS), allowed us to identify the content of volatile organic compounds (VOCs). From the comparison between the two beer samples, it showed that the one after the addition of AEO was particularly richened in limonene and a series of minor terpene compounds. AEO was also characterized by GC/MS analysis and the results showed that limonene reached 95%. Confocal microscopy was used to look at riboflavin autofluorescence in yeast cells. It was found that beer with AEO had twice as much fluorescence intensity as the control. A spectrophotometric analysis of total polyphenols, tannins, and flavonoids, and a bioactivity screening, including 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2'-Azinobis-(3-Ethylbenzthiazolin-6-Sulfonic Acid) (ABTS) radical scavenger, chelating, reducing, antiglycative ones, were also carried out. Moreover, the tolerability of the tested samples in human H69 cholangiocytes and the cytoprotection towards the tert-butyl hydroperoxide (tBOOH)-induced oxidative damage were evaluated. Under our experimental conditions, the beers were found to be able to scavenge DPPH and ABTS radicals and chelate iron ions, despite weak antiglycative and reducing properties. The tested samples did not affect the viability of H69 cholangiocytes up to the highest concentrations; moreover, no signs of cytoprotection against the damage induced by tBOOH were highlighted. Adding AEO to beer resulted in a moderate enhancement of its DPPH scavenging and chelating abilities, without improvements in the other assays. Conversely, AEO and its major compound limonene were ineffective when assessed at the concentrations added to beer. This evidence suggests that the addition of AEO may enhance the organoleptic features of the beer and slightly potentiate some of its bioactivities.
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Affiliation(s)
- Cosimo Taiti
- Department of Agriculture, Food, Environmental and Forest, Florence University, Sesto Fiorentino, 50019 Firenze, Italy;
| | - Antonella Di Sotto
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, 00185 Rome, Italy; (A.D.S.); (E.P.)
| | - Giovanni Stefano
- Department of Biology, Florence University, 50121 Firenze, Italy;
| | - Ester Percaccio
- Department of Physiology and Pharmacology “V. Erspamer”, Sapienza University of Rome, 00185 Rome, Italy; (A.D.S.); (E.P.)
| | - Matteo Iannone
- Circolo ARCI La Staffetta, 56011 Calci, Italy; (M.I.); (A.M.)
| | | | - Stefania Garzoli
- Department of Chemistry and Technology of Drug, Sapienza University, 00185 Rome, Italy
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Lizarraga AJ, Hart L, Wright RM, Williams LR, Glavy JS. Incidents of snake fungal disease caused by the fungal pathogen Ophidiomyces ophidiicola in Texas. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1064939. [PMID: 37746129 PMCID: PMC10512329 DOI: 10.3389/ffunb.2023.1064939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 02/08/2023] [Indexed: 09/26/2023]
Abstract
The pathogen Ophidiomyces ophidiicola, widely known as the primary cause of snake fungal disease (SFD) has been detected in Texas's naïve snakes. Our team set out to characterize O. ophidiicola's spread in eastern Texas. From December 2018 until November 2021, we sampled and screened with ultraviolet (UV) light, 176 snakes across eastern Texas and detected 27. O. ophidiicola's positive snakes using qPCR and one snake in which SFD was confirmed via additional histological examination. Upon finding the ribbon snake with clear clinical display, we isolated and cultured what we believe to be the first culture from Texas. This cultured O. ophidiicola TX displays a ring halo formation when grown on a solid medium as well as cellular autofluorescence as expected. Imaging reveals individual cells within the septated hyphae branches contain a distinct nucleus separation from neighboring cells. Overall, we have found over 1/10 snakes that may be infected in East Texas, gives credence to the onset of SFD in Texas. These results add to the progress of the disease across the continental United States.
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Affiliation(s)
- Alan J. Lizarraga
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
| | - Lezley Hart
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
| | - R. Michele Wright
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
- The Department of Pharmaceutical Sciences, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, United States
| | - Lance R. Williams
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
| | - Joseph S. Glavy
- Biology Department, The University of Texas at Tyler, Tyler, TX, United States
- The Department of Pharmaceutical Sciences, Fisch College of Pharmacy, The University of Texas at Tyler, Tyler, TX, United States
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Kwolek-Mirek M, Bednarska S, Dubicka-Lisowska A, Maslanka R, Zadrag-Tecza R, Kaszycki P. Unbalance between Pyridine Nucleotide Cofactors in The SOD1 Deficient Yeast Saccharomyces cerevisiae Causes Hypersensitivity to Alcohols and Aldehydes. Int J Mol Sci 2022; 24:ijms24010659. [PMID: 36614102 PMCID: PMC9820918 DOI: 10.3390/ijms24010659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/23/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023] Open
Abstract
Alcohol and aldehyde dehydrogenases are especially relevant enzymes involved in metabolic and detoxification reactions that occur in living cells. The comparison between the gene expression, protein content, and enzymatic activities of cytosolic alcohol and aldehyde dehydrogenases of the wild-type strain and the Δsod1 mutant lacking superoxide dismutase 1, which is hypersensitive to alcohols and aldehydes, shows that the activity of these enzymes is significantly higher in the Δsod1 mutant, but this is not a mere consequence of differences in the enzymatic protein content nor in the expression levels of genes. The analysis of the NAD(H) and NADP(H) content showed that the higher activity of alcohol and aldehyde dehydrogenases in the Δsod1 mutant could be a result of the increased availability of pyridine nucleotide cofactors. The higher level of NAD+ in the Δsod1 mutant is not related to the higher level of tryptophan; in turn, a higher generation of NADPH is associated with the upregulation of the pentose phosphate pathway. It is concluded that the increased sensitivity of the Δsod1 mutant to alcohols and aldehydes is not only a result of the disorder of redox homeostasis caused by the induction of oxidative stress but also a consequence of the unbalance between pyridine nucleotide cofactors.
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Affiliation(s)
- Magdalena Kwolek-Mirek
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
- Correspondence: (M.K.-M.); (R.Z.-T.); Tel.: +48-17-785-5412 (M.K.-M.); +48-17-785-5413 (R.Z.-T.)
| | - Sabina Bednarska
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Aleksandra Dubicka-Lisowska
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31-425 Krakow, Poland
| | - Roman Maslanka
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Department of Biology, Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszow, 35-601 Rzeszow, Poland
- Correspondence: (M.K.-M.); (R.Z.-T.); Tel.: +48-17-785-5412 (M.K.-M.); +48-17-785-5413 (R.Z.-T.)
| | - Pawel Kaszycki
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, 31-425 Krakow, Poland
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Morales-Guevara R, Fuentes JA, Páez-Hernández D, Carreño A. Intramolecular Hydrogen Bond in Pyridine Schiff Bases as Ancillary Ligands of Re(I) Complexes Is a Switcher between Visible and NIR Emissions: A Relativistic Quantum Chemistry Study. J Phys Chem A 2022; 126:8997-9007. [PMID: 36413983 DOI: 10.1021/acs.jpca.2c06435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rhenium(I) tricarbonyl complexes have been described as suitable fluorophores, particularly for biological applications. fac-[Re(CO)3(N,N)L](0 or 1+) complexes, where N,N is a substituted dinitrogenated ligand (bipyridine or derivatives with relatively small substituents) and L the ancillary ligand [a pyridine Schiff base (PSB) harboring an intramolecular hydrogen bond (IHB)], have presented promissory results concerning their use as fluorophores, especially for walled cells (i.e., bacteria and fungi). In this work, we present a relativistic theoretical analysis of two series of fac-[Re(CO)3(N,N)PSB]1+ complexes to predict the role of the IHB in the ancillary ligand concerning their photophysical behavior. N,N corresponds to 2,2'-bipyridine (bpy) (series A) or 4,4'-bis(ethoxycarbonyl)-2,2'-bipyridine (deeb) (series B). We found that all the complexes present absorption in the visible light range. In addition, complexes presenting a PSB with an IHB exhibit luminescent emission suitable for biological purposes: large Stokes shift, emission in the range of 600-700 nm, and τ in the order of 10-2 to 10-3 s. By contrast, complexes with PSB lacking the IHB show a predicted emission with the lowest triplet excited-state energy entering the NIR region. These results suggest a role of the IHB as an important switcher between visible and NIR emissions in this kind of complexes. Since the PSB can be substituted to modulate the properties of the whole Re(I) complex, it will be interesting to explore whether other substitutions can also affect the photophysical properties, mainly the emission range.
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Affiliation(s)
- Rosaly Morales-Guevara
- Programa de Doctorado en Físicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago 8370146, Chile.,Laboratory of Organometallic Synthesis, Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andrés Bello, República 330, Santiago 8370186, Chile
| | - Juan A Fuentes
- Laboratorio de Genética y Patogénesis Bacteriana, Facultad de Ciencias de la Vida, Universidad Andrés Bello, República 330, Santiago 8370186, Chile
| | - Dayán Páez-Hernández
- Programa de Doctorado en Físicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago 8370146, Chile.,Laboratory of Organometallic Synthesis, Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andrés Bello, República 330, Santiago 8370186, Chile
| | - Alexander Carreño
- Programa de Doctorado en Físicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago 8370146, Chile.,Laboratory of Organometallic Synthesis, Center of Applied NanoSciences (CANS), Facultad de Ciencias Exactas, Universidad Andrés Bello, República 330, Santiago 8370186, Chile
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Sun A, Wang WX. Insights into the kinetic regulation of Zn bioaccumulation at trace levels: Lighting up Saccharomycescerevisiae. CHEMOSPHERE 2022; 308:136318. [PMID: 36075365 DOI: 10.1016/j.chemosphere.2022.136318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/24/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Zn displays a double-edged effect by acting both as a micronutrient and a toxic metal, and quantitative analysis of its kinetic flux under low environmental concentrations is critical to understand its intracellular regulation. In the present study, we employed a Zn sensitive model eukaryote, the yeast Saccharomyces cerevisiae, which responded to intracellular Zn levels by increasing its autofluorescence, to quantify Zn influx, transportation between labile and storage pools, and efflux under different Zn exposure levels (<1 μM). We demonstrated that the yeast regulated Zn uptake from the extracellular source by a gradually decreased accumulation following an initial high accumulation rate. The subsequent reduced accumulation rate resulted in a steady-state Zn accumulation at 0.061 and 0.073 μg Zn/μg P as the threshold values for the control yeast and Zn-depleted yeast, respectively, independently of the extracellular Zn concentration. Compared with the control yeast, the Zn-depleted yeast possessed a higher accumulation rate, but the difference of bioaccumulation was maintained at approximately 0.01 μg Zn/μg P under different concentrations of extracellular Zn. In contrast, transportation between labile Zn and storage Zn pools or Zn efflux to the extracellular environment was not obvious after Zn exposure, indicating that the Zn dose was below a basal requirement. Such stabilized Zn accumulation was only induced by controlling the Zn influx at the bio-interface. With the novel monitoring of the kinetic changes of autofluorescence, our study demonstrated a remarkably tight Zn regulation system in yeast, providing enlightenment for Zn homeostasis in eukaryotes under low Zn exposure in aqueous environments.
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Affiliation(s)
- Anqi Sun
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China; School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, 518057, China.
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10
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Kernbach S, Kernbach O, Kuksin I, Kernbach A, Nepomnyashchiy Y, Dochow T, Bobrov AV. The biosensor based on electrochemical dynamics of fermentation in yeast Saccharomyces cerevisiae. ENVIRONMENTAL RESEARCH 2022; 213:113535. [PMID: 35654153 DOI: 10.1016/j.envres.2022.113535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 04/10/2022] [Accepted: 05/19/2022] [Indexed: 06/15/2023]
Abstract
The zymase activity of the yeast Saccharomyces cerevisiae is sensitive to environmental parameters and is therefore used as a microbiological sensor for water quality assessment, ecotoxicological characterization or environmental monitoring. Comparing to bacterial bioluminescence approach, this method has no toxicity, excludes usage of genetically modified microorganisms, and enables low-cost express analysis. This work focuses on measuring the yeast fermentation dynamics based on multichannel pressure sensing and electrochemical impedance spectroscopy (EIS). Measurement results are compared with each other in terms of accuracy, reproducibility and ease of use in field conditions. It has been shown that EIS provides more information about ionic dynamics of metabolic processes and requires less complex measurements. The conducted experiments demonstrated the sensitivity of this approach for assessing biophotonic phenomena, non-chemical water treatments and impact of environmental stressors.
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Affiliation(s)
- Serge Kernbach
- CYBRES GmbH, Research Center of Advanced Robotics and Environmental Science, Melunerstr. 40, 70569, Stuttgart, Germany.
| | - Olga Kernbach
- CYBRES GmbH, Research Center of Advanced Robotics and Environmental Science, Melunerstr. 40, 70569, Stuttgart, Germany
| | - Igor Kuksin
- CYBRES GmbH, Research Center of Advanced Robotics and Environmental Science, Melunerstr. 40, 70569, Stuttgart, Germany
| | - Andreas Kernbach
- CYBRES GmbH, Research Center of Advanced Robotics and Environmental Science, Melunerstr. 40, 70569, Stuttgart, Germany
| | - Yury Nepomnyashchiy
- CYBRES GmbH, Research Center of Advanced Robotics and Environmental Science, Melunerstr. 40, 70569, Stuttgart, Germany
| | - Timo Dochow
- IFFP GmbH, Frieberting 12, 83137 Schonstett, Germany
| | - Andrew V Bobrov
- Orel State University, Komsomolskaya, 95, 302026, Orel, Russia
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11
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Oliphant KD, Karger M, Nakanishi Y, Mendel RR. Precise Quantification of Molybdate In Vitro by the FRET-Based Nanosensor 'MolyProbe'. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123691. [PMID: 35744816 PMCID: PMC9228995 DOI: 10.3390/molecules27123691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 06/02/2022] [Indexed: 11/27/2022]
Abstract
Molybdenum (Mo) is an essential trace element in all kingdoms of life. Mo is bioavailable as the oxyanion molybdate and gains biological activity in eukaryotes when bound to molybdopterin, forming the molybdenum cofactor. The imbalance of molybdate homeostasis results in growth deficiencies or toxic symptoms within plants, fungi and animals. Recently, fluorescence resonance energy transfer (FRET) methods have emerged, monitoring cellular and subcellular molybdate distribution dynamics using a genetically encoded molybdate-specific FRET nanosensor, named MolyProbe. Here, we show that the MolyProbe system is a fast and reliable in vitro assay for quantitative molybdate determination. We added a Strep-TagII affinity tag to the MolyProbe protein for quick and easy purification. This MolyProbe is highly stable, resistant to freezing and can be stored for several weeks at 4 °C. Furthermore, the molybdate sensitivity of the assay peaked at low nM levels. Additionally, The MolyProbe was applied in vitro for quantitative molybdate determination in cell extracts of the plant Arabidopsis thaliana, the fungus Neurospora crassa and the yeast Saccharomyces cerevisiae. Our results show the functionality of the Arabidopsis thaliana molybdate transporter MOT1.1 and indicate that FRET-based molybdate detection is an excellent tool for measuring bioavailable Mo.
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Affiliation(s)
- Kevin D. Oliphant
- Department of Plant Biology, Braunschweig University of Technology, 38106 Braunschweig, Germany; (K.D.O.); (M.K.)
| | - Marius Karger
- Department of Plant Biology, Braunschweig University of Technology, 38106 Braunschweig, Germany; (K.D.O.); (M.K.)
| | - Yoichi Nakanishi
- Department of Applied Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan;
| | - Ralf R. Mendel
- Department of Plant Biology, Braunschweig University of Technology, 38106 Braunschweig, Germany; (K.D.O.); (M.K.)
- Correspondence:
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12
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Cuny AP, Schlottmann FP, Ewald JC, Pelet S, Schmoller KM. Live cell microscopy: From image to insight. BIOPHYSICS REVIEWS 2022; 3:021302. [PMID: 38505412 PMCID: PMC10903399 DOI: 10.1063/5.0082799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/18/2022] [Indexed: 03/21/2024]
Abstract
Live-cell microscopy is a powerful tool that can reveal cellular behavior as well as the underlying molecular processes. A key advantage of microscopy is that by visualizing biological processes, it can provide direct insights. Nevertheless, live-cell imaging can be technically challenging and prone to artifacts. For a successful experiment, many careful decisions are required at all steps from hardware selection to downstream image analysis. Facing these questions can be particularly intimidating due to the requirement for expertise in multiple disciplines, ranging from optics, biophysics, and programming to cell biology. In this review, we aim to summarize the key points that need to be considered when setting up and analyzing a live-cell imaging experiment. While we put a particular focus on yeast, many of the concepts discussed are applicable also to other organisms. In addition, we discuss reporting and data sharing strategies that we think are critical to improve reproducibility in the field.
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Affiliation(s)
| | - Fabian P. Schlottmann
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Jennifer C. Ewald
- Interfaculty Institute of Cell Biology, University of Tuebingen, 72076 Tuebingen, Germany
| | - Serge Pelet
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
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13
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Different life strategies in genetic backgrounds of the Saccharomyces cerevisiae yeast cells. Fungal Biol 2022; 126:498-510. [DOI: 10.1016/j.funbio.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022]
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14
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Laquel P, Testet E, Tuphile K, Cullin C, Fouillen L, Bessoule JJ, Doignon F. Phosphoinositides containing stearic acid are required for interaction between Rho GTPases and the exocyst to control the late steps of polarised exocytosis. Traffic 2021; 23:120-136. [PMID: 34908215 DOI: 10.1111/tra.12829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 11/18/2021] [Accepted: 12/07/2021] [Indexed: 11/27/2022]
Abstract
Cell polarity is achieved by regulators such as small G proteins, exocyst members and phosphoinositides, with the latter playing a key role when bound to the exocyst proteins Sec3p and Exo70p, and Rho GTPases. This ensures asymmetric growth via the routing of proteins and lipids to the cell surface using actin cables. Previously, using a yeast mutant for a lysophosphatidylinositol acyl transferase encoded by the PSI1 gene, we demonstrated the role of stearic acid in the acyl chain of phosphoinositides in cytoskeletal organisation and secretion. Here, we use a genetic approach to characterise the effect on late steps of the secretory pathway. The constitutive overexpression of PSI1 in mutants affecting kinases involved in the phosphoinositide pathway demonstrated the role of molecular species containing stearic acid in bypassing a lack of phosphatidylinositol-4-phosphate PI(4)P at the plasma membrane, which is essential for the function of the Cdc42p module. Decreasing the levels of stearic acid-containing phosphoinositides modifies the environment of the actors involved in the control of late steps in the secretory pathway. This leads to decreased interactions between Exo70p and Sec3p, with Cdc42p, Rho1p and Rho3p, due to disruption of the GTP/GDP ratio of at least Rho1p and Rho3p GTPases, thereby preventing activation of the exocyst.
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Affiliation(s)
- P Laquel
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d'Ornon, France
| | - E Testet
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d'Ornon, France
| | - K Tuphile
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d'Ornon, France
| | - C Cullin
- Univ. Bordeaux, CNRS, Laboratoire de Chimie Biologie des Membranes & des Nano-objets, UMR 5248, Pessac, France
| | - L Fouillen
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d'Ornon, France.,Metabolome Facility of Bordeaux, Functional Genomics Centre, F-33883 Villenave d'Ornon, France
| | - J J Bessoule
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d'Ornon, France
| | - F Doignon
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d'Ornon, France
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15
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Seven ES, Seven YB, Zhou Y, Poudel-Sharma S, Diaz-Rucco JJ, Kirbas Cilingir E, Mitchell GS, Van Dyken JD, Leblanc RM. Crossing the blood-brain barrier with carbon dots: uptake mechanism and in vivo cargo delivery. NANOSCALE ADVANCES 2021; 3:3942-3953. [PMID: 34263140 PMCID: PMC8243484 DOI: 10.1039/d1na00145k] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/30/2021] [Indexed: 06/10/2023]
Abstract
The blood-brain barrier (BBB) is a major obstacle for drug delivery to the central nervous system (CNS) such that most therapeutics lack efficacy against brain tumors or neurological disorders due to their inability to cross the BBB. Therefore, developing new drug delivery platforms to facilitate drug transport to the CNS and understanding their mechanism of transport are crucial for the efficacy of therapeutics. Here, we report (i) carbon dots prepared from glucose and conjugated to fluorescein (GluCD-F) cross the BBB in zebrafish and rats without the need of an additional targeting ligand and (ii) uptake mechanism of GluCDs is glucose transporter-dependent in budding yeast. Glucose transporter-negative strain of yeast showed undetectable GluCD accumulation unlike the glucose transporter-positive yeast, suggesting glucose-transporter-dependent GluCD uptake. We tested GluCDs' ability to cross the BBB using both zebrafish and rat models. Following the injection to the heart, wild-type zebrafish showed GluCD-F accumulation in the central canal consistent with the transport of GluCD-F across the BBB. In rats, following intravenous administration, GluCD-F was observed in the CNS. GluCD-F was localized in the gray matter (e.g. ventral horn, dorsal horn, and middle grey) of the cervical spinal cord consistent with neuronal accumulation. Therefore, neuron targeting GluCDs hold tremendous potential as a drug delivery platform in neurodegenerative disease, traumatic injury, and malignancies of the CNS.
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Affiliation(s)
- Elif S Seven
- Department of Chemistry, University of Miami 1301 Memorial Dr. Coral Gables FL 33146 USA
| | - Yasin B Seven
- Department of Physical Therapy, University of Florida 101 Newell Dr. Gainesville FL 32603 USA
- McKnight Brain Institute, University of Florida 1149 Newell Dr. Gainesville FL 32610 USA
| | - Yiqun Zhou
- Department of Chemistry, University of Miami 1301 Memorial Dr. Coral Gables FL 33146 USA
| | - Sijan Poudel-Sharma
- Department of Biology, University of Miami 1301 Memorial Dr. Coral Gables FL 33146 USA
| | - Juan J Diaz-Rucco
- Department of Chemistry, University of Miami 1301 Memorial Dr. Coral Gables FL 33146 USA
| | - Emel Kirbas Cilingir
- Department of Chemistry, University of Miami 1301 Memorial Dr. Coral Gables FL 33146 USA
| | - Gordon S Mitchell
- Department of Physical Therapy, University of Florida 101 Newell Dr. Gainesville FL 32603 USA
- McKnight Brain Institute, University of Florida 1149 Newell Dr. Gainesville FL 32610 USA
| | - J David Van Dyken
- Department of Biology, University of Miami 1301 Memorial Dr. Coral Gables FL 33146 USA
| | - Roger M Leblanc
- Department of Chemistry, University of Miami 1301 Memorial Dr. Coral Gables FL 33146 USA
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16
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Sun A, Wang WX. Adenine deficient yeast: A fluorescent biosensor for the detection of Labile Zn(II) in aqueous solution. Biosens Bioelectron 2021; 179:113075. [DOI: 10.1016/j.bios.2021.113075] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/28/2022]
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Reproductive Potential of Yeast Cells Depends on Overall Action of Interconnected Changes in Central Carbon Metabolism, Cellular Biosynthetic Capacity, and Proteostasis. Int J Mol Sci 2020; 21:ijms21197313. [PMID: 33022992 PMCID: PMC7582853 DOI: 10.3390/ijms21197313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
Carbon metabolism is a crucial aspect of cell life. Glucose, as the primary source of energy and carbon skeleton, determines the type of cell metabolism and biosynthetic capabilities, which, through the regulation of cell size, may affect the reproductive capacity of the yeast cell. Calorie restriction is considered as the most effective way to improve cellular physiological capacity, and its molecular mechanisms are complex and include several nutrient signaling pathways. It is widely assumed that the metabolic shift from fermentation to respiration is treated as a substantial driving force for the mechanism of calorie restriction and its influence on reproductive capabilities of cells. In this paper, we propose another approach to this issue based on analysis the connection between energy-producing and biomass formation pathways which are closed in the metabolic triangle, i.e., the respiration-glycolysis-pentose phosphate pathway. The analyses were based on the use of cells lacking hexokinase 2 (∆hxk2) and conditions of different glucose concentration corresponding to the calorie restriction and the calorie excess. Hexokinase 2 is the key enzyme involved in central carbon metabolism and is also treated as a calorie restriction mimetic. The experimental model used allows us to explain both the role of increased respiration as an effect of calorie restriction but also other aspects of carbon metabolism and the related metabolic flux in regulation of reproductive potential of the cells. The obtained results reveal that increased respiration is not a prerequisite for reproductive potential extension but rather an accompanying effect of the positive role of calorie restriction. More important seems to be the changes connected with fluxes in central carbon metabolic pathways resulting in low biosynthetic capabilities and improved proteostasis.
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18
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Štefl M, Herbst K, Rübsam M, Benda A, Knop M. Single-Color Fluorescence Lifetime Cross-Correlation Spectroscopy In Vivo. Biophys J 2020; 119:1359-1370. [PMID: 32919495 DOI: 10.1016/j.bpj.2020.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 05/29/2020] [Accepted: 06/16/2020] [Indexed: 01/18/2023] Open
Abstract
The ability to quantify protein concentrations and to measure protein interactions in vivo is key information needed for the understanding of complex processes inside cells, but the acquisition of such information from living cells is still demanding. Fluorescence-based methods like two-color fluorescence cross-correlation spectroscopy can provide this information, but measurement precision is hampered by various sources of errors caused by instrumental or optical limitations such as imperfect overlap of detection volumes or detector cross talk. Furthermore, the nature and properties of used fluorescent proteins or fluorescent dyes, such as labeling efficiency, fluorescent protein maturation, photostability, bleaching, and fluorescence brightness can have an impact. Here, we take advantage of previously published fluorescence lifetime correlation spectroscopy which relies on lifetime differences as a mean to discriminate fluorescent proteins with similar spectral properties and to use them for single-color fluorescence lifetime cross-correlation spectroscopy (sc-FLCCS). By using only one excitation and one detection wavelength, this setup avoids all sources of errors resulting from chromatic aberrations and detector cross talk. To establish sc-FLCCS, we first engineered and tested multiple green fluorescent protein (GFP)-like fluorescent proteins for their suitability. This identified a novel, to our knowledge, GFP variant termed short-lifetime monomeric GFP with the so-far shortest lifetime. Monte-Carlo simulations were employed to explore the suitability of different combinations of GFP variants. Two GFPs, Envy and short-lifetime monomeric GFP, were predicted to constitute the best performing couple for sc-FLCCS measurements. We demonstrated application of this GFP pair for measuring protein interactions between the proteasome and interacting proteins and for measuring protein interactions between three partners when combined with a red florescent protein. Together, our findings establish sc-FLCCS as a valid alternative for conventional dual-color fluorescence cross-correlation spectroscopy measurements.
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Affiliation(s)
- Martin Štefl
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Prague, Czech Republic.
| | - Konrad Herbst
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Marc Rübsam
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Aleš Benda
- IMCF at BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), University of Heidelberg, Heidelberg, Germany; Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany.
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19
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Ferro DM, Müller CMO, Ferreira SRS. Photostability and characterization of spray-dried maltodextrin powders loaded with Sida rhombifolia extract. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Goh JPZ, Ianiri G, Heitman J, Dawson TL. Expression of a Malassezia Codon Optimized mCherry Fluorescent Protein in a Bicistronic Vector. Front Cell Infect Microbiol 2020; 10:367. [PMID: 32793513 PMCID: PMC7387403 DOI: 10.3389/fcimb.2020.00367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/15/2020] [Indexed: 12/29/2022] Open
Abstract
The use of fluorescent proteins allows a multitude of approaches from live imaging and fixed cells to labeling of whole organisms, making it a foundation of diverse experiments. Tagging a protein of interest or specific cell type allows visualization and studies of cell localization, cellular dynamics, physiology, and structural characteristics. In specific instances fluorescent fusion proteins may not be properly functional as a result of structural changes that hinder protein function, or when overexpressed may be cytotoxic and disrupt normal biological processes. In our study, we describe application of a bicistronic vector incorporating a Picornavirus 2A peptide sequence between a NAT antibiotic selection marker and mCherry. This allows expression of multiple genes from a single open reading frame and production of discrete protein products through a cleavage event within the 2A peptide. We demonstrate integration of this bicistronic vector into a model Malassezia species, the haploid strain M. furfur CBS 14141, with both active selection, high fluorescence, and proven proteolytic cleavage. Potential applications of this technology can include protein functional studies, Malassezia cellular localization, and co-expression of genes required for targeted mutagenesis.
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Affiliation(s)
- Joleen P. Z. Goh
- Skin Research Institute of Singapore, Agency of Science, Technology and Research, Singapore, Singapore
| | - Giuseppe Ianiri
- Department of Agricultural, Environmental and Food Sciences, University of Molise, Campobasso, Italy
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, United States
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Centre, Durham, NC, United States
| | - Thomas L. Dawson
- Skin Research Institute of Singapore, Agency of Science, Technology and Research, Singapore, Singapore
- Department of Drug Discovery, School of Pharmacy, Medical University of South Carolina, Charleston, SC, United States
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21
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Linkage between Carbon Metabolism, Redox Status and Cellular Physiology in the Yeast Saccharomyces cerevisiae Devoid of SOD1 or SOD2 Gene. Genes (Basel) 2020; 11:genes11070780. [PMID: 32664606 PMCID: PMC7397328 DOI: 10.3390/genes11070780] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/30/2020] [Accepted: 07/09/2020] [Indexed: 12/17/2022] Open
Abstract
Saccharomyces cerevisiae yeast cells may generate energy both by fermentation and aerobic respiration, which are dependent on the type and availability of carbon sources. Cells adapt to changes in nutrient availability, which entails the specific costs and benefits of different types of metabolism but also may cause alteration in redox homeostasis, both by changes in reactive oxygen species (ROS) and in cellular reductant molecules contents. In this study, yeast cells devoid of the SOD1 or SOD2 gene and fermentative or respiratory conditions were used to unravel the connection between the type of metabolism and redox status of cells and also how this affects selected parameters of cellular physiology. The performed analysis provides an argument that the source of ROS depends on the type of metabolism and non-mitochondrial sources are an important pool of ROS in yeast cells, especially under fermentative metabolism. There is a strict interconnection between carbon metabolism and redox status, which in turn has an influence on the physiological efficiency of the cells. Furthermore, pyridine nucleotide cofactors play an important role in these relationships.
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22
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Bourges AC, Lazarev A, Declerck N, Rogers KL, Royer CA. Quantitative High-Resolution Imaging of Live Microbial Cells at High Hydrostatic Pressure. Biophys J 2020; 118:2670-2679. [PMID: 32402241 DOI: 10.1016/j.bpj.2020.04.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 03/19/2020] [Accepted: 04/16/2020] [Indexed: 10/24/2022] Open
Abstract
The majority of the Earth's microbial biomass exists in the deep biosphere, in the deep ocean, and within the Earth's crust. Although other physical parameters in these environments, such as temperature or pH, can differ substantially, they are all under high pressures. Beyond emerging genomic information, little is known about the molecular mechanisms underlying the ability of these organisms to survive and grow at pressures that can reach over 1000-fold the pressure on the Earth's surface. The mechanisms of pressure adaptation are also important in food safety, with the increasing use of high-pressure food processing. Advanced imaging represents an important tool for exploring microbial adaptation and response to environmental changes. Here, we describe implementation of a high-pressure sample chamber with a two-photon scanning microscope system, allowing for the first time, to our knowledge, quantitative high-resolution two-photon imaging at 100 MPa of living microbes from all three kingdoms of life. We adapted this setup for fluorescence lifetime imaging microscopy with phasor analysis (FLIM/Phasor) and investigated metabolic responses to pressure of live cells from mesophilic yeast and bacterial strains, as well as the piezophilic archaeon Archaeoglobus fulgidus. We also monitored by fluorescence intensity fluctuation-based methods (scanning number and brightness and raster scanning imaging correlation spectroscopy) the effect of pressure on the chromosome-associated protein HU and on the ParB partition protein in Escherichia coli, revealing partially reversible dissociation of ParB foci and concomitant nucleoid condensation. These results provide a proof of principle that quantitative, high-resolution imaging of live microbial cells can be carried out at pressures equivalent to those in the deepest ocean trenches.
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Affiliation(s)
- Anais C Bourges
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York; Centre de Biochimie Structrurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France; INRAE, MICA Department, Jouy-en-Josas, France
| | | | - Nathalie Declerck
- Centre de Biochimie Structrurale (CBS), INSERM, CNRS, Université de Montpellier, Montpellier, France; INRAE, MICA Department, Jouy-en-Josas, France
| | - Karyn L Rogers
- Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York.
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23
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A quest for coordination among activities at the replisome. Biochem Soc Trans 2019; 47:1067-1075. [PMID: 31395754 DOI: 10.1042/bst20180402] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/17/2022]
Abstract
Faithful DNA replication is required for transmission of the genetic material across generations. The basic mechanisms underlying this process are shared among all organisms: progressive unwinding of the long double-stranded DNA; synthesis of RNA primers; and synthesis of a new DNA chain. These activities are invariably performed by a multi-component machine called the replisome. A detailed description of this molecular machine has been achieved in prokaryotes and phages, with the replication processes in eukaryotes being comparatively less known. However, recent breakthroughs in the in vitro reconstitution of eukaryotic replisomes have resulted in valuable insight into their functions and mechanisms. In conjunction with the developments in eukaryotic replication, an emerging overall view of replisomes as dynamic protein ensembles is coming into fruition. The purpose of this review is to provide an overview of the recent insights into the dynamic nature of the bacterial replisome, revealed through single-molecule techniques, and to describe some aspects of the eukaryotic replisome under this framework. We primarily focus on Escherichia coli and Saccharomyces cerevisiae (budding yeast), since a significant amount of literature is available for these two model organisms. We end with a description of the methods of live-cell fluorescence microscopy for the characterization of replisome dynamics.
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Kwolek-Mirek M, Maslanka R, Molon M. Disorders in NADPH generation via pentose phosphate pathway influence the reproductive potential of the Saccharomyces cerevisiae yeast due to changes in redox status. J Cell Biochem 2019; 120:8521-8533. [PMID: 30474881 DOI: 10.1002/jcb.28140] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/31/2018] [Indexed: 01/24/2023]
Abstract
Intermediary metabolites have a crucial impact on basic cell functions. There is a relationship between cellular metabolism and redox balance. To maintain redox homoeostasis, the cooperation of both glutathione and nicotine adenine dinucleotides is necessary. Availability of nicotinamide adenine dinucleotide phosphate (NADPH) as a major electron donor is critical for many intracellular redox reactions. The activity of glucose-6-phosphate dehydrogenase (Zwf1p) and 6-phosphogluconate dehydrogenase (Gnd1p and Gnd2p) is responsible for NADPH formation in a pentose phosphate (PP) pathway. In this study, we examine the impact of redox homoeostasis on cellular physiology and proliferation. We have noted that the Δzwf1 mutant lacking the rate-limiting enzyme of the PP pathway shows changes in the cellular redox status caused by disorders in NADPH generation. This leads to a decrease in reproductive potential but without affecting the total lifespan of the cell. The results presented in this paper show that nicotine adenine dinucleotides play a central role in cellular physiology.
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Affiliation(s)
- Magdalena Kwolek-Mirek
- Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszow, Rzeszow, Poland
| | - Roman Maslanka
- Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszow, Rzeszow, Poland
| | - Mateusz Molon
- Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszow, Rzeszow, Poland
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25
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Reines D. A fluorescent assay for the genetic dissection of the RNA polymerase II termination machinery. Methods 2019; 159-160:124-128. [PMID: 30616008 DOI: 10.1016/j.ymeth.2018.12.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 01/25/2023] Open
Abstract
RNA polymerase II is a highly processive enzyme that synthesizes mRNAs and some non-protein coding RNAs. Termination of transcription, which entails release of the transcript and disengagement of the polymerase, requires an active process. In yeast, there are at least two multi-protein complexes needed for termination of transcription, depending upon which class of RNAs are being acted upon. In general, the two classes are relatively short non-coding RNAs (e.g. snoRNAs) and relatively long mRNAs, although there are exceptions. Here, a procedure is described in which defective termination can be detected in living cells, resulting in a method that allows strains with mutations in termination factors or cis-acting sequences, to be identified and recovered. The strategy employs a reporter plasmid with a galactose inducible promoter driving transcription of green fluorescent protein which yields highly fluorescent cells. When a test terminator is inserted between the promoter and the fluorescent protein reading frame, cells fail to fluoresce. Mutant strains that have lost termination capability, so called terminator-override mutants, gain expression of the fluorescent protein and can be collected by fluorescence activated cell sorting. The strategy is robust since acquisition of fluorescence is a positive trait that has a low probability of happening adventitiously. Live mutant cells can easily be cloned from the population of positive candidates. Flow sorting is a sensitive, high-throughput detection step capable of discovering spontaneous mutations in yeast with high fidelity.
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Affiliation(s)
- Daniel Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States.
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26
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Maslanka R, Zadrag-Tecza R. Less is more or more is less: Implications of glucose metabolism in the regulation of the reproductive potential and total lifespan of the Saccharomyces cerevisiae yeast. J Cell Physiol 2019; 234:17622-17638. [PMID: 30805924 DOI: 10.1002/jcp.28386] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 01/10/2023]
Abstract
Carbohydrates are dietary nutrients that have an influence on cells physiology, cell reproductive capacity and, consequently, the lifespan of organisms. They are used in cellular processes after conversion to glucose, which is the primary source of energy and carbon skeleton for biosynthetic processes. Studies of the influence of glucose on cellular parameters and lifespan of organisms are primarily concerned with the effect of low glucose concentration defined as calorie restriction conditions. However, the effect of high glucose concentration on cell physiology is also very important. Thus, a comparative analysis of the effects of low and high glucose concentration conditions on cell efficiency was proposed with regard to reproductive capacity and total lifespan of the cell. Glucose concentration determines the type of metabolism and biosynthetic capabilities, which in turn, through the regulation on the cell size, may affect the reproductive capacity of cells. This study was conducted on yeast cells of wild-type and mutant strains Δgpa2 and Δgpr1 with glucose signalling pathway impairment. Such an experimental model enabled testing both the role of glucose concentration in the regulation of metabolic changes and the extent to which these changes depend on the extracellular or intracellular glucose concentrations. It has been shown here that calorie/glucose excess connected with changes in cell metabolic fluxes increases biosynthetic capabilities of yeast cells. This leads to an increase in cell dry weight accompanied by the increase in cell size and a simultaneous decrease in the reproductive potential and the overall length of cell life.
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Affiliation(s)
- Roman Maslanka
- Department of Biochemistry and Cell Biology, Faculty of Biotechnology, University of Rzeszow, Rzeszow, Poland
| | - Renata Zadrag-Tecza
- Department of Biochemistry and Cell Biology, Faculty of Biotechnology, University of Rzeszow, Rzeszow, Poland
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