1
|
Treviño MÁ. Counterintuitive method improves yields of isotopically labelled proteins expressed in flask-cultured Escherichia coli. JOURNAL OF BIOMOLECULAR NMR 2025; 79:129-141. [PMID: 40024995 PMCID: PMC12078410 DOI: 10.1007/s10858-025-00461-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 02/12/2025] [Indexed: 03/04/2025]
Abstract
NMR is a powerful tool for the structural and dynamic study of proteins. One of the necessary conditions for the study of these proteins is their isotopic labelling with 15N and 13C. One of the most widely used methods to obtain these labelled proteins is heterologous expression of the proteins in E. coli using 13C-D-glucose and 15NH4Cl as the sole nutrient sources. In recent years, the price of 13C-D-glucose has almost tripled, making it essential to develop labelling methods that are as cost effective as possible. In this work, different parameters were studied to achieve the most rational use of 13C-D-glucose, and an optimized method was developed to obtain labelled proteins with high labelling and low 13C-D-glucose consumption. Surprisingly, the optimized method is also simple and does not require monitoring of culture growth.
Collapse
Affiliation(s)
- Miguel Ángel Treviño
- Instituto de Química Física Blas Cabrera, Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid, Spain.
| |
Collapse
|
2
|
Zhang X, Meng Z, Beusch CM, Gharibi H, Cheng Q, Lyu H, Di Stefano L, Wang J, Saei AA, Végvári Á, Gaetani M, Zubarev RA. Ultralight Ultrafast Enzymes. Angew Chem Int Ed Engl 2024; 63:e202316488. [PMID: 38009610 DOI: 10.1002/anie.202316488] [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: 10/31/2023] [Revised: 11/24/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Inorganic materials depleted of heavy stable isotopes are known to deviate strongly in some physicochemical properties from their isotopically natural counterparts. Here we explored for the first time the effect of simultaneous depletion of the heavy carbon, hydrogen, oxygen and nitrogen isotopes on the bacterium E. coli and the enzymes expressed in it. Bacteria showed faster growth, with most proteins exhibiting higher thermal stability, while for recombinant enzymes expressed in depleted media, faster kinetics was discovered. At room temperature, luciferase, thioredoxin and dihydrofolate reductase and Pfu DNA polymerase showed up to a 250 % increase in activity compared to the native counterparts, with an additional ∼50 % increase at 10 °C. Diminished conformational and vibrational entropy is hypothesized to be the cause of the accelerated kinetics. Ultralight enzymes may find an application where extreme reaction rates are required.
Collapse
Affiliation(s)
- Xuepei Zhang
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Zhaowei Meng
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Christian M Beusch
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Hassan Gharibi
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Qing Cheng
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Hezheng Lyu
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Luciano Di Stefano
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- European Research Institute for the Biology of Aging, University Medical Center Groningen, University of Groningen, The Netherlands
| | - Jijing Wang
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Amir A Saei
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ákos Végvári
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Massimiliano Gaetani
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- Chemical Proteomics Core Facility, Department of Medical Biochemistry and Biophysics, Karolinska Institute, 17177, Stockholm, Sweden
- Chemical Proteomics, Science for Life Laboratory (SciLifeLab), 17177, Stockholm, Sweden
| | - Roman A Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
- >Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, 119146, Moscow, Russia
- The National Medical Research Center for Endocrinology, Moskva, 115478 Moscow, Russia
| |
Collapse
|
3
|
Galván I, Hassasfar A, Adams B, Petruccione F. Isotope effects on radical pair performance in cryptochrome: A new hypothesis for the evolution of animal migration: The quantum biology of migration. Bioessays 2024; 46:e2300152. [PMID: 37888800 DOI: 10.1002/bies.202300152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/28/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Abstract
Mechanisms occurring at the atomic level are now known to drive processes essential for life, as revealed by quantum effects on biochemical reactions. Some macroscopic characteristics of organisms may thus show an atomic imprint, which may be transferred across organisms and affect their evolution. This possibility is considered here for the first time, with the aim of elucidating the appearance of an animal innovation with an unclear evolutionary origin: migratory behaviour. This trait may be mediated by a radical pair (RP) mechanism in the retinal flavoprotein cryptochrome, providing essential magnetic orientation for migration. Isotopes may affect the performance of quantum processes through their nuclear spin. Here, we consider a simple model and then apply the standard open quantum system approach to the spin dynamics of cryptochrome RP. We changed the spin quantum number (I) and g-factor of hydrogen and nitrogen isotopes to investigate their effect on RP's yield and magnetic sensitivity. Strong differences arose between isotopes with I = 1 and I = 1/2 in their contribution to cryptochrome magnetic sensitivity, particularly regarding Earth's magnetic field strengths (25-65 µT). In most cases, isotopic substitution improved RP's magnetic sensitivity. Migratory behaviour may thus have been favoured in animals with certain isotopic compositions of cryptochrome.
Collapse
Affiliation(s)
- Ismael Galván
- Department of Evolutionary Ecology, National Museum of Natural Sciences, CSIC, Madrid, Spain
| | - Abbas Hassasfar
- Department of Physics, Stellenbosch University, Stellenbosch, South Africa
| | - Betony Adams
- Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
- The Guy Foundation, Beaminster, Dorset, UK
| | - Francesco Petruccione
- Department of Physics, Stellenbosch University, Stellenbosch, South Africa
- School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- National Institute for Theoretical and Computational Sciences (NITheCS), Stellenbosch, South Africa
| |
Collapse
|
4
|
Li Y, Collins DA, Grintzalis K. A Simple Biochemical Method for the Detection of Proteins as Biomarkers of Life on Martian Soil Simulants and the Impact of UV Radiation. Life (Basel) 2023; 13:life13051150. [PMID: 37240795 DOI: 10.3390/life13051150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 04/26/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The search for life on other planets relies on the detection of biosignatures of life. Many macromolecules have been suggested as potential targets, among which are proteins that are considered vital components of life due to their essential roles in forming cellular structures, facilitating cellular communication and signaling, and catalyzing metabolic reactions. In this context, accurate quantification of protein signatures in soil would be advantageous, and while several proposed methods exist, which are limited by their sensitivity and specificity, their applicability needs further testing and validation. To this aim, we optimized a Bradford-based assay with high sensitivity and reproducibility and a simple protocol to quantify protein extracted from a Martian soil simulant. Methods for protein spiking, extraction, and recovery were optimized, using protein standards and bacterial proteins as representative models. The proposed method achieved high sensitivity and reproducibility. Taking into account that life remains could exist on the surface of Mars, which is subjected to UV radiation, a simulation of UV exposure was performed on a spiked soil simulant. UV radiation degraded the protein spike, thus highlighting the importance of searching for the remaining signal from degraded proteins. Finally, the applicability of the method was explored in relation to the storage of the reagent which was stable even up to 12 months, thus making its application possible for future planetary exploration missions.
Collapse
Affiliation(s)
- Yongda Li
- School of Biotechnology, Dublin City University, D09 Y5NO Dublin, Ireland
| | - David A Collins
- School of Biotechnology, Dublin City University, D09 Y5NO Dublin, Ireland
| | | |
Collapse
|
5
|
Influence of Single Deuterium Replacement on Frequency of Hydrogen Bond Dissociation in IFNA17 under the Highest Critical Energy Range. Int J Mol Sci 2022; 23:ijms232415487. [PMID: 36555136 PMCID: PMC9778762 DOI: 10.3390/ijms232415487] [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: 11/03/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
The effect of single substitutions of protium for deuterium in hydrogen bonds between pairs of nitrogenous bases on the open states occurrence probability at high critical breaking energies of these bonds has been studied. The study was carried out using numerical methods based on the angular mathematical model of DNA. The IFNA17 gene was divided into three approximately equal parts. A comparison of the open states occurrence probability in these parts of the gene was done. To improve the accuracy of the results, a special data processing algorithm was developed. The developed methods have shown their suitability for taking into account the occurrence of open states in the entire range of high critical energies. It has been established that single 2H/1H substitutions in certain nitrogenous bases can be a mechanism for maintaining the vital activity of IFNA17 under critical conditions. In general, the developed method of the mathematical modeling provide unprecedented insight into the DNA behavior under the highest critical energy range, which greatly expands scientific understanding of nucleobases interaction.
Collapse
|
6
|
Elkina AA, Tumaev EN, Basov AA, Moiseev AV, Malyshko VV, Barisheva EV, Churkina AV, Dzhimak SS. The Mechanisms of the Interaction of Stable Isotopes with Biological Objects in the Presence of an Uncompensated Neutron in Chemical Bonds. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920050048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
7
|
Volchenko NN, Samkov AA, Malyshko VV, Khudokormov AA, Moiseev AV, Elkina AA, Baryshev MG, Pershin SM. Influence of the Environmental Isotope Composition Modification on Growth and Metabolic Activity of Rhodococcus and Saccharomyces. BIOL BULL+ 2020. [DOI: 10.1134/s1062359020040135] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
8
|
Understanding the influence of heavy water stress on the physiology of Salmonella Typhimurium. Appl Radiat Isot 2020; 159:108990. [PMID: 32250754 DOI: 10.1016/j.apradiso.2019.108990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 10/31/2019] [Accepted: 11/17/2019] [Indexed: 11/21/2022]
Abstract
The heavy isotope of water is used in understanding the physiology of bacteria. Deuterium (D2O) reduces chemical reaction kinetics. In the present study, the survivability of the food-borne pathogen Salmonella Typhimurium grown in D2O supplemented medium is studied under various stress conditions. The growth of S, Typhimurium was studied in rich (Luria Broth-LB) and minimal medium (M9) prepared in D2O. The reduced growth rate of S. tTyphimurium in M9 (2.4 fold) as compared to that in LB (1.6 fold) was observed. S. tTyphimurium grown in D2O supplemented medium was significantly more tolerant to heat and gamma radiation (1.2 fold), but was sensitive to extreme pH (both alkaline and acidic) and osmotic stress (10 fold). These results suggest that the change in the biological reaction kinetics in the cell due to D2O may modify the stress tolerance of S. tTyphimurium. This is the first study carried out to understand how a bacterial system (S. Typhimurium) in D2O responds to different stresses. This study suggests that investigations on bacterial physiology in D2O supplemented medium helps in understanding the underlying mechanisms of stress tolerance.
Collapse
|
9
|
Lobysheva NV, Nesterov SV, Skorobogatova YA, Lobyshev VI. The Functional Activity of Mitochondria in Deuterium Depleted Water. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920020128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
10
|
Basov A, Fedulova L, Vasilevskaya E, Dzhimak S. Possible Mechanisms of Biological Effects Observed in Living Systems during 2H/ 1H Isotope Fractionation and Deuterium Interactions with Other Biogenic Isotopes. Molecules 2019; 24:E4101. [PMID: 31766268 PMCID: PMC6891295 DOI: 10.3390/molecules24224101] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/01/2019] [Accepted: 11/11/2019] [Indexed: 12/11/2022] Open
Abstract
This article presents the original descriptions of some recent physics mechanisms (based on the thermodynamic, kinetic, and quantum tunnel effects) providing stable 2H/1H isotope fractionation, leading to the accumulation of particular isotopic forms in intra- or intercellular space, including the molecular effects of deuterium interaction with 18O/17O/16O, 15N/14N, 13C/12C, and other stable biogenic isotopes. These effects were observed mainly at the organelle (mitochondria) and cell levels. A new hypothesis for heavy nonradioactive isotope fractionation in living systems via neutron effect realization is discussed. The comparative analysis of some experimental studies results revealed the following observation: "Isotopic shock" is highly probable and is observed mostly when chemical bonds form between atoms with a summary odd number of neutrons (i.e., bonds with a non-compensated neutron, which correspond to the following equation: Nn - Np = 2k + 1, where k ϵ Z, k is the integer, Z is the set of non-negative integers, Nn is number of neutrons, and Np is number of protons of each individual atom, or in pair of isotopes with a chemical bond). Data on the efficacy and metabolic pathways of the therapy also considered 2H-modified drinking and diet for some diseases, such as Alzheimer's disease, Friedreich's ataxia, mitochondrial disorders, diabetes, cerebral hypoxia, Parkinson's disease, and brain cancer.
Collapse
Affiliation(s)
- Alexander Basov
- Department of Fundamental and Clinical Biochemistry, Kuban State Medical University, Krasnodar 350063, Russia;
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia
| | - Liliya Fedulova
- The V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow 109316, Russia; (L.F.); (E.V.)
| | - Ekaterina Vasilevskaya
- The V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow 109316, Russia; (L.F.); (E.V.)
| | - Stepan Dzhimak
- Department of Radiophysics and Nanotechnology, Kuban State University, Krasnodar 350040, Russia
- The V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow 109316, Russia; (L.F.); (E.V.)
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, Rostov-on-Don 344006, Russia
| |
Collapse
|
11
|
Basov A, Fedulova L, Baryshev M, Dzhimak S. Deuterium-Depleted Water Influence on the Isotope 2H/ 1H Regulation in Body and Individual Adaptation. Nutrients 2019; 11:E1903. [PMID: 31443167 PMCID: PMC6723318 DOI: 10.3390/nu11081903] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/08/2019] [Accepted: 08/13/2019] [Indexed: 12/28/2022] Open
Abstract
This review article presents data about the influence of deuterium-depleted water (DDW) on biological systems. It is known that the isotope abundances of natural and bottled waters are variable worldwide. That is why different drinking rations lead to changes of stable isotopes content in body water fluxes in human and animal organisms. Also, intracellular water isotope ratios in living systems depends on metabolic activity and food consumption. We found the 2H/1H gradient in human fluids (δ2H saliva >> δ2H blood plasma > δ2Hbreast milk), which decreases significantly during DDW intake. Moreover, DDW induces several important biological effects in organism (antioxidant, metabolic detoxification, anticancer, rejuvenation, behavior, etc.). Changing the isotope 2H/1H gradient from "2H blood plasma > δ2H visceral organs" to "δ2H blood plasma << δ2H visceral organs" via DDW drinking increases individual adaptation by isotopic shock. The other possible mechanisms of long-term adaptation is DDW influence on the growth rate of cells, enzyme activity and cellular energetics (e.g., stimulation of the mitochondrion activity). In addition, DDW reduces the number of single-stranded DNA breaks and modifies the miRNA profile.
Collapse
Affiliation(s)
- Alexander Basov
- Kuban State Medical University, 350063 Krasnodar, Russia
- Kuban State University, 350040 Krasnodar, Russia
| | - Liliia Fedulova
- The V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, 109316 Moscow, Russia
| | | | - Stepan Dzhimak
- Kuban State University, 350040 Krasnodar, Russia.
- The V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, 109316 Moscow, Russia.
- Federal Research Center the Southern Scientific Center of the Russian Academy of Sciences, 344006 Rostov-on-Don, Russia.
| |
Collapse
|
12
|
Zhao J, Zhang H, Qin B, Nikolay R, He QY, Spahn CMT, Zhang G. Multifaceted Stoichiometry Control of Bacterial Operons Revealed by Deep Proteome Quantification. Front Genet 2019; 10:473. [PMID: 31178895 PMCID: PMC6544118 DOI: 10.3389/fgene.2019.00473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 05/01/2019] [Indexed: 12/03/2022] Open
Abstract
More than half of the protein-coding genes in bacteria are organized in polycistronic operons composed of two or more genes. It remains under debate whether the operon organization maintains the stoichiometric expression of the genes within an operon. In this study, we performed a label-free data-independent acquisition hyper reaction monitoring mass-spectrometry (HRM-MS) experiment to quantify the Escherichia coli proteome in exponential phase and quantified 93.6% of the cytosolic proteins, covering 67.9% and 56.0% of the translating polycistronic operons in BW25113 and MG1655 strains, respectively. We found that the translational regulation contributes largely to the proteome complexity: the shorter operons tend to be more tightly controlled for stoichiometry than longer operons; the operons which mainly code for complexes is more tightly controlled for stoichiometry than the operons which mainly code for metabolic pathways. The gene interval (distance between adjacent genes in one operon) may serve as a regulatory factor for stoichiometry. The catalytic efficiency might be a driving force for differential expression of enzymes encoded in one operon. These results illustrated the multifaceted nature of the operon regulation: the operon unified transcriptional level and gene-specific translational level. This multi-level regulation benefits the host by optimizing the efficiency of the productivity of metabolic pathways and maintenance of different types of protein complexes.
Collapse
Affiliation(s)
- Jing Zhao
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Hong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Bo Qin
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Rainer Nikolay
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| | - Christian M T Spahn
- Institut für Medizinische Physik und Biophysik, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, Jinan University, Guangzhou, China
| |
Collapse
|
13
|
Alexandrovich Basov A, Anatolyevna Elkina А, Alexandrovich Samkov A, Nikolaevich Volchenko N, Victorovich Moiseev A, Viacheslavovna Fedulova L, Gennadievich Baryshev M, Sergeevich Dzhimak S. Influence of Deuterium-Depleted Water on the Isotope D/H Composition of Liver Tissue and Morphological Development of Rats at Different Periods of Ontogenesis. IRANIAN BIOMEDICAL JOURNAL 2019; 23. [PMID: 30220191 PMCID: PMC6707107 DOI: 10.29252/.23.2.129] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Background This study aimed to evaluate the reaction of organism of laboratory animals on deuterium-depleted drinking diet. To assess the cell energy metabolism, the effect of a liquid medium with different deuterium contents on isolated liver mitochondria of random bred rats and Wistar rats was studied. Methods This experimental study on the effect of deuterium-depleted drinking water (DDW) on 16-week-old male Wistar rats lasted for four weeks. Energy metabolism of mitochondria was examined through the production of hydrogen peroxide using an Amplex® Red Hydrogen Peroxide/Peroxidase Assay Kit. Results Modification of isotope (deuterium-protium [D/H]) composition of rats’ blood and organ tissues with DDW (-705‰), introduced into rats’ diet within four weeks, led to the formation of isotope D/H gradient between blood plasma and organ tissues and affected isotope D/H exchange reactions on the adaptive processes. The isolated liver mitochondria from the random bred rats consumed DDW presented a maximum increase in H2O2 production during the incubation in DDW medium. This increased level of H2O2 production was higher in the isolated liver mitochondria of the rats consuming natural deuterium content drinking water (-24‰). Conclusion The obtained results indicate the possibility of nutritional correction of isotope D/H metabolism in blood by means of products with modified isotope composition, as well as the prospects of using isotope exchange reactions in case of imbalance in function of the body's defense systems in different generations of animals.
Collapse
Affiliation(s)
- Alexandr Alexandrovich Basov
- Kuban State Medical University, Krasnodar, Russian Federation, Russia;,Kuban State University, Krasnodar, Russian Federation, Russia
| | - Аnna Anatolyevna Elkina
- Kuban State University, Krasnodar, Russian Federation, Russia; ,Corresponding Author: Аnna Anatolyevna Elkina, Kuban State University, Krasnodar, Russian Federation, Russia; Tel.: (+7-91) 80688381; Fax: (+8-861) 2199519; E-mail:
| | | | | | | | - Liliya Viacheslavovna Fedulova
- The V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow, Russian Federation, Russia
| | | | - Stepan Sergeevich Dzhimak
- Kuban State University, Krasnodar, Russian Federation, Russia; ,The V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, Moscow, Russian Federation, Russia
| |
Collapse
|
14
|
Isotopic resonance at 370 ppm deuterium negatively affects kinetics of luciferin oxidation by luciferase. Sci Rep 2018; 8:16249. [PMID: 30390033 PMCID: PMC6215010 DOI: 10.1038/s41598-018-34704-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 10/19/2018] [Indexed: 11/09/2022] Open
Abstract
Since 1930s, it has been known that some biochemical and biological processes exhibit abnormal kinetics at a deuterium concentration in the local environment of 250–600 ppm, which is 2–4 times higher that the normal concentration of 150 ppm D. We sought to test if the kinetics of firefly luciferase oxidizing luciferin, the reaction widely used as a read-out in various biochemical assays, is also affected by an elevated deuterium content. To this end, both luciferase and luciferin substrate solutions were prepared based on water with extra deuterium added to a concentration ranging from 150 ppm and up to 10,000 ppm (1%). Upon mixing the solutions, the luminescence intensity at different times was compared with that of the corresponding control solutions with 150 ppm D. A broad negative resonance was detected (p < 10−6), with a ≈20% drop in luminescence at 370 ppm D. Given that, on average, about half of hydrogen atoms in proteins are not exchangeable in solution, this value corresponds to ≈260 ppm of deuterium in all enzyme’s hydrogens, in a very good agreement with the prediction of the Isotopic resonance hypothesis.
Collapse
|
15
|
Gangwe Nana GY, Ripoll C, Cabin-Flaman A, Gibouin D, Delaune A, Janniere L, Grancher G, Chagny G, Loutelier-Bourhis C, Lentzen E, Grysan P, Audinot JN, Norris V. Division-Based, Growth Rate Diversity in Bacteria. Front Microbiol 2018; 9:849. [PMID: 29867792 PMCID: PMC5958220 DOI: 10.3389/fmicb.2018.00849] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/12/2018] [Indexed: 01/19/2023] Open
Abstract
To investigate the nature and origins of growth rate diversity in bacteria, we grew Escherichia coli and Bacillus subtilis in liquid minimal media and, after different periods of 15N-labeling, analyzed and imaged isotope distributions in individual cells with Secondary Ion Mass Spectrometry. We find a striking inter- and intra-cellular diversity, even in steady state growth. This is consistent with the strand-dependent, hyperstructure-based hypothesis that a major function of the cell cycle is to generate coherent, growth rate diversity via the semi-conservative pattern of inheritance of strands of DNA and associated macromolecular assemblies. We also propose quantitative, general, measures of growth rate diversity for studies of cell physiology that include antibiotic resistance.
Collapse
Affiliation(s)
- Ghislain Y Gangwe Nana
- Laboratory of Microbiology Signals and Microenvironment, Department of Biology, University of Rouen, Mont Saint Aignan, France
| | - Camille Ripoll
- Department of Biology, University of Rouen, Mont Saint Aignan, France
| | - Armelle Cabin-Flaman
- Groupe de Physique des Matériaux, Centre National de la Recherche Scientifique, Département de Biologie, Université de Rouen Normandie, Saint-Etienne du Rouvray, France
| | - David Gibouin
- Groupe de Physique des Matériaux, Centre National de la Recherche Scientifique, Département de Biologie, Université de Rouen Normandie, Saint-Etienne du Rouvray, France
| | - Anthony Delaune
- Groupe de Physique des Matériaux, Centre National de la Recherche Scientifique, Département de Biologie, Université de Rouen Normandie, Saint-Etienne du Rouvray, France
| | | | - Gerard Grancher
- R. Salem Laboratory of Maths, UMR 6085 Centre National de la Recherche Scientifique-University of Rouen, Saint Etienne du Rouvray, France
| | - Gaelle Chagny
- R. Salem Laboratory of Maths, UMR 6085 Centre National de la Recherche Scientifique-University of Rouen, Saint Etienne du Rouvray, France
| | - Corinne Loutelier-Bourhis
- UMR Centre National de la Recherche Scientifique, 6014 COBRA, University of Rouen, Mont Saint Aignan, France
| | - Esther Lentzen
- Material Research & Technology Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Patrick Grysan
- Material Research & Technology Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Jean-Nicolas Audinot
- Material Research & Technology Department, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, Department of Biology, University of Rouen, Mont Saint Aignan, France
| |
Collapse
|
16
|
Mamet SD, Ma B, Ulrich A, Schryer A, Siciliano SD. Who Is the Rock Miner and Who Is the Hunter? The Use of Heavy-Oxygen Labeled Phosphate (P 18O 4) to Differentiate between C and P Fluxes in a Benzene-Degrading Consortium. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:1773-1786. [PMID: 29378402 DOI: 10.1021/acs.est.7b05773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phosphorus availability and cycling in microbial communities is a key determinant of bacterial activity. However, identifying organisms critical to P cycling in complex biodegrading consortia has proven elusive. Here we assess a new DNA stable isotope probing (SIP) technique using heavy oxygen-labeled phosphate (P18O4) and its effectiveness in pure cultures and a nitrate-reducing benzene-degrading consortium. First, we successfully labeled pure cultures of Gram-positive Micrococcus luteus and Gram-negative Bradyrhizobium elkanii and separated isotopically light and heavy DNA in pure cultures using centrifugal analyses. Second, using high-throughput amplicon sequencing of 16S rRNA genes to characterize active bacterial taxa (13C-labeled), we found taxa like Betaproteobacteria were key in denitrifying benzene degradation and that other degrading (nonhydrocarbon) inactive taxa (P18O4-labeled) like Staphylococcus and Corynebacterium may promote degradation through production of secondary metabolites (i.e., "helper" or "rock miner" bacteria). Overall, we successfully separated active and inactive taxa in contaminated soils, demonstrating the utility of P18O4-DNA SIP for identifying actively growing bacterial taxa. We also identified potential "miner" bacteria that choreograph hydrocarbon degradation by other microbes (i.e., the "hunters") without directly degrading contaminants themselves. Thus, while several taxa degrade benzene under denitrifying conditions, microbial benzene degradation may be enhanced by both direct degraders and miner bacteria.
Collapse
Affiliation(s)
- Steven D Mamet
- Department of Soil Science, University of Saskatchewan , Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Bin Ma
- Department of Civil and Environmental Engineering, University of Alberta , Edmonton, Alberta T6G 1H9, Canada
| | - Ania Ulrich
- Department of Civil and Environmental Engineering, University of Alberta , Edmonton, Alberta T6G 1H9, Canada
| | - Aimée Schryer
- Department of Soil Science, University of Saskatchewan , Saskatoon, Saskatchewan S7N 5A8, Canada
| | - Steven D Siciliano
- Department of Soil Science, University of Saskatchewan , Saskatoon, Saskatchewan S7N 5A8, Canada
| |
Collapse
|
17
|
Andriukonis E, Gorokhova E. Kinetic 15N-isotope effects on algal growth. Sci Rep 2017; 7:44181. [PMID: 28281640 PMCID: PMC5345060 DOI: 10.1038/srep44181] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/06/2017] [Indexed: 12/25/2022] Open
Abstract
Stable isotope labeling is a standard technique for tracing material transfer in molecular, ecological and biogeochemical studies. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism metabolism and growth, which is not consistent with current theoretical and empirical knowledge on kinetic isotope effects. Here, we demonstrate profound changes in growth dynamics of the green alga Raphidocelis subcapitata grown in 15N-enriched media. With increasing 15N concentration (0.37 to 50 at%), the lag phase increased, whereas maximal growth rate and total yield decreased; moreover, there was a negative relationship between the growth and the lag phase across the treatments. The latter suggests that a trade-off between growth rate and the ability to adapt to the high 15N environment may exist. Remarkably, the lag-phase response at 3.5 at% 15N was the shortest and deviated from the overall trend, thus providing partial support to the recently proposed Isotopic Resonance hypothesis, which predicts that certain isotopic composition is particularly favorable for living organisms. These findings confirm the occurrence of KIE in isotopically enriched algae and underline the importance of considering these effects when using stable isotope labeling in field and experimental studies.
Collapse
Affiliation(s)
- Eivydas Andriukonis
- Faculty of Chemistry and Geosciences, Department of Physical Chemistry, Vilnius University, Vilnius, Lithuania
- Laboratory of Bio-Nanotechnology, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| |
Collapse
|
18
|
Gorokhova E. Shifts in rotifer life history in response to stable isotope enrichment: testing theories of isotope effects on organismal growth. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160810. [PMID: 28405367 PMCID: PMC5383824 DOI: 10.1098/rsos.160810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/01/2017] [Indexed: 06/07/2023]
Abstract
In ecology, stable isotope labelling is commonly used for tracing material transfer in trophic interactions, nutrient budgets and biogeochemical processes. The main assumption in this approach is that the enrichment with a heavy isotope has no effect on the organism growth and metabolism. This assumption is, however, challenged by theoretical considerations and experimental studies on kinetic isotope effects in vivo. Here, I demonstrate profound changes in life histories of the rotifer Brachionus plicatilis fed 15N-enriched algae (0.4-5.0 at%); i.e. at the enrichment levels commonly used in ecological studies. These findings support theoretically predicted effects of heavy isotope enrichment on growth, metabolism and ageing in biological systems and underline the importance of accounting for such effects when using stable isotope labelling in experimental studies.
Collapse
Affiliation(s)
- Elena Gorokhova
- Department of Environmental Science and Analytical Chemistry , Stockholm University , Svante Arrhenius väg 8, 10691 Stockholm , Sweden
| |
Collapse
|
19
|
Xie X, Zubarev RA. On the Effect of Planetary Stable Isotope Compositions on Growth and Survival of Terrestrial Organisms. PLoS One 2017; 12:e0169296. [PMID: 28052100 PMCID: PMC5215764 DOI: 10.1371/journal.pone.0169296] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/14/2016] [Indexed: 11/19/2022] Open
Abstract
Isotopic compositions of reactants affect the rates of chemical and biochemical reactions. Usually it is assumed that heavy stable isotope enrichment leads to progressively slower reactions. Yet the effect of stable isotopes may be nonlinear, as exemplified by the "isotopic resonance" phenomenon. Since the isotopic compositions of other planets of Solar system, including Mars and Venus, are markedly different from terrestrial (e.g., deuterium content is ≈5 and ≈100 times higher, respectively), it is far from certain that terrestrial life will thrive in these isotopic conditions. Here we found that Martian deuterium content negatively affected survival of shrimp in semi-closed biosphere on a year-long time scale. Moreover, the bacterium Escherichia coli grows slower at Martian isotopic compositions and even slower at Venus's compositions. Thus, the biological impact of varying stable isotope compositions needs to be taken into account when planning interplanetary missions.
Collapse
Affiliation(s)
- Xueshu Xie
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Roman A. Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
20
|
Xie X, Backman D, Lebedev AT, Artaev VB, Jiang L, Ilag LL, Zubarev RA. Primordial soup was edible: abiotically produced Miller-Urey mixture supports bacterial growth. Sci Rep 2015; 5:14338. [PMID: 26412575 PMCID: PMC4585927 DOI: 10.1038/srep14338] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/25/2015] [Indexed: 11/09/2022] Open
Abstract
Sixty years after the seminal Miller-Urey experiment that abiotically produced a mixture of racemized amino acids, we provide a definite proof that this primordial soup, when properly cooked, was edible for primitive organisms. Direct admixture of even small amounts of Miller-Urey mixture strongly inhibits E. coli bacteria growth due to the toxicity of abundant components, such as cyanides. However, these toxic compounds are both volatile and extremely reactive, while bacteria are highly capable of adaptation. Consequently, after bacterial adaptation to a mixture of the two most abundant abiotic amino acids, glycine and racemized alanine, dried and reconstituted MU soup was found to support bacterial growth and even accelerate it compared to a simple mixture of the two amino acids. Therefore, primordial Miller-Urey soup was perfectly suitable as a growth media for early life forms.
Collapse
Affiliation(s)
- Xueshu Xie
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelesväg 2, SE-17 177 Stockholm, Sweden
| | - Daniel Backman
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelesväg 2, SE-17 177 Stockholm, Sweden
| | - Albert T Lebedev
- Department of Organic Chemistry, Moscow State M. V. Lomonosov University, 119991, Moscow, Russia
| | | | - Liying Jiang
- Department of Environmental Science and Analytical Chemistry, University of Stockholm, Stockholm, Sweden
| | - Leopold L Ilag
- Department of Environmental Science and Analytical Chemistry, University of Stockholm, Stockholm, Sweden
| | - Roman A Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelesväg 2, SE-17 177 Stockholm, Sweden
| |
Collapse
|