1
|
Zhang F, Yu Q, Huang Y, Luo Y, Qin J, Chen L, Li E, Wang X. Study on the osmotic response and function of myo-inositol oxygenase in euryhaline fish nile tilapia ( Oreochromis niloticus). Am J Physiol Cell Physiol 2024; 326:C1054-C1066. [PMID: 38344798 DOI: 10.1152/ajpcell.00513.2023] [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: 10/09/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 03/13/2024]
Abstract
To understand the role of myo-inositol oxygenase (miox) in the osmotic regulation of Nile tilapia, its expression was analyzed in various tissues. The results showed that the expression of miox gene was highest in the kidney, followed by the liver, and was significantly upregulated in the kidney and liver under 1 h hyperosmotic stress. The relative luminescence efficiency of the miox gene transcription starting site (-4,617 to +312 bp) under hyperosmotic stress was measured. Two fragments (-1,640/-1,619 and -620/-599) could induce the luminescence activity. Moreover, the -1,640/-1,619 and -620/-599 responded to hyperosmotic stress and high-glucose stimulation by base mutation, suggesting that osmotic and carbohydrate response elements may exist in this region. Finally, the salinity tolerance of Nile tilapia was significantly reduced after the knocking down of miox gene. The accumulation of myo-inositol was affected, and the expression of enzymes in glucose metabolism was significantly reduced after the miox gene was knocked down. Furthermore, hyperosmotic stress can cause oxidative stress, and MIOX may help maintain the cell redox balance under hyperosmotic stress. In summary, MIOX is essential in osmotic regulation to enhance the salinity tolerance of Nile tilapia by affecting myo-inositol accumulation, glucose metabolism, and antioxidant performance.NEW & NOTEWORTHY Myo-inositol oxygenase (MIOX) is the rate-limiting enzyme that catalyzes the first step of MI metabolism and determines MI content in aquatic animals. To understand the role of miox in the osmotic regulation of Nile tilapia, we analyzed its expression in different tissues and its function under hyperosmotic stress. This study showed that miox is essential in osmotic regulation to enhance the salinity tolerance of Nile tilapia by affecting myo-inositol accumulation, glucose metabolism, and antioxidant performance.
Collapse
Affiliation(s)
- Fan Zhang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Qiuran Yu
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Yuxing Huang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Yuan Luo
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Jianguang Qin
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
| | - Liqiao Chen
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Erchao Li
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| | - Xiaodan Wang
- Laboratory of Aquaculture Nutrition and Environmental Health, School of Life Sciences, East China Normal University, Shanghai, People's Republic of China
| |
Collapse
|
2
|
Huang M, Gao Q, Yang X, Jiang W, Hao L, Yu Y, Tian Y. Free amino acids in response to salinity changes in fishes: relationships to osmoregulation. FISH PHYSIOLOGY AND BIOCHEMISTRY 2023; 49:1031-1042. [PMID: 37782385 DOI: 10.1007/s10695-023-01244-y] [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: 04/13/2023] [Accepted: 09/22/2023] [Indexed: 10/03/2023]
Abstract
Free amino acids (FAAs) are believed to play important roles in osmoregulation and buffer capacity in some aquatic animals, such as fishes. However, the potential roles of FAAs have not been systematically summarized and characterized until now. In the present study, the meta-analysis was conducted to investigate the relationships between FAAs and environmental salinities. Twenty published documents were included, accounting for 106 study cases. The effect sizes of total free amino acids (TFAAs), total essential amino acids (TEAAs), and total non-essential amino acids (TNEAAs) to salinity increase were calculated and determined by the restricted maximum likelihood (REML) method. It clearly showed that the elevated salinities significantly induced the contents of TFAAs, TEAAs, and TNEAAs at the ratio of 36%, 27%, and 29%, respectively. Faced to the salinity changes, the contents of FAAs in fishes under freshwater and seawater varied significantly, while the individuals under brackish water displayed relatively constant contents of FAAs. When salinity elevated, the contents of 17 amino acids in muscles significantly increased, suggesting the important roles of FAA metabolism in osmoregulation in fishes. The results also indicated that the effect sizes of TFAAs were positively related to the rates of salinity increases, and exhibited a significant quadratic linear relationship with temperatures. Additionally, the contents of FAAs also showed positive correlation with osmotic pressure, concentrations of plasma Na+, Cl-, and urea, implying their potential roles of FAAs in osmoregulation in fishes. These findings suggested that elevated salinities greatly induced the contents of FAAs in fishes, making a great contribution to maintaining the homeostasis of fishes in response to environmental salinity changes.
Collapse
Affiliation(s)
- Ming Huang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, Shandong Province, China
| | - Qinfeng Gao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, Shandong Province, China
| | - Xiaogang Yang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, Shandong Province, China
| | - Wenxin Jiang
- Shandong Marine Group LTD., Jinan, Shandong, China
| | - Lin Hao
- Shandong Marine Group LTD., Jinan, Shandong, China
| | - Yining Yu
- Shandong Marine Group LTD., Jinan, Shandong, China
| | - Yuan Tian
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, Shandong Province, China.
| |
Collapse
|
3
|
Borkowski AK, Campbell NI, Thompson WH. Direct calculation of the temperature dependence of 2D-IR spectra: Urea in water. J Chem Phys 2023; 158:064507. [PMID: 36792517 DOI: 10.1063/5.0135627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
A method for directly calculating the temperature derivative of two-dimensional infrared (2D-IR) spectra from simulations at a single temperature is presented. The approach is demonstrated by application to the OD stretching spectrum of isotopically dilute aqueous (HOD in H2O) solutions of urea as a function of concentration. Urea is an important osmolyte because of its ability to denature proteins, which has motivated significant interest in its effect on the structure and dynamics of water. The present results show that the temperature dependence of both the linear IR and 2D-IR spectra, which report on the underlying energetic driving forces, is more sensitive to urea concentration than the spectra themselves. Additional physical insight is provided by calculation of the contributions to the temperature derivative from different interactions, e.g., water-water, water-urea, and urea-urea, present in the system. Finally, it is demonstrated how 2D-IR spectra at other temperatures can be obtained from only room temperature simulations.
Collapse
Affiliation(s)
- Ashley K Borkowski
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - N Ian Campbell
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| | - Ward H Thompson
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, USA
| |
Collapse
|
4
|
Arsiccio A, Ganguly P, Shea JE. A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study. J Phys Chem B 2022; 126:4472-4482. [PMID: 35679169 DOI: 10.1021/acs.jpcb.2c00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We developed a method for implicit solvent molecular dynamics simulations of proteins in solvent mixtures (model with implicit solvation thermodynamics, MIST). The MIST method introduces experimental group transfer free energies to the generalized Born formulation for generating molecular trajectories without the need for developing rigorous explicit-solvent force fields for multicomponent solutions. As a test case, we studied the urea-induced denaturation of the Trp-cage miniprotein in water. We demonstrate that our method allows efficient exploration of the conformational space of the protein in only a few hundreds of nanoseconds of all-atom unbiased simulations. Furthermore, selective implementation of the transfer free energies of specific peptide groups, backbone, and side chains enables us to decouple their specific energetic contributions to the conformational changes of the protein. The approach herein developed can readily be extended to the investigation of complex matrices as well as to the characterization of protein aggregation. The MIST method is implemented in Plumed (ver. 2.8) as a separate module called SASA.
Collapse
Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| |
Collapse
|
5
|
Stasiulewicz M, Panuszko A, Bruździak P, Stangret J. Mechanism of Osmolyte Stabilization-Destabilization of Proteins: Experimental Evidence. J Phys Chem B 2022; 126:2990-2999. [PMID: 35441516 PMCID: PMC9059127 DOI: 10.1021/acs.jpcb.2c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this work, we
investigated the influence of stabilizing (N,N,N-trimethylglycine)
and destabilizing (urea) osmolytes on the hydration spheres of biomacromolecules
in folded forms (trpzip-1 peptide and hen egg white
lysozyme—hewl) and unfolded protein models
(glycine—GLY and N-methylglycine—NMG)
by means of infrared spectroscopy. GLY and NMG were clearly limited
as minimal models for unfolded proteins and should be treated with
caution. We isolated the spectral share of water changed simultaneously
by the biomacromolecule/model molecule and the osmolyte, which allowed
us to provide unambiguous experimental arguments for the mechanism
of stabilization/destabilization of proteins by osmolytes. In the
case of both types of osmolytes, the decisive factor determining the
equilibrium folded/unfolded state of protein was the enthalpy effect
exerted on the hydration spheres of proteins in both forms. In the
case of stabilizing osmolytes, enthalpy was also favored by entropy,
as the unfolded state of a protein was more entropically destabilized
than the folded state.
Collapse
Affiliation(s)
- Marcin Stasiulewicz
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Aneta Panuszko
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Piotr Bruździak
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Gdańsk University of Technology, Narutowicza 11/12, Gdańsk 80-233, Poland
| |
Collapse
|
6
|
Osmotic Stress Interferes with DNA Damage Response and H2AX Phosphorylation in Human Keratinocytes. Cells 2022; 11:cells11060959. [PMID: 35326410 PMCID: PMC8946833 DOI: 10.3390/cells11060959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 12/07/2022] Open
Abstract
The human skin and in particular its outermost layer, the epidermis, protects the body from potentially harmful substances, radiation as well as excessive water loss. However, the interference between the various stress responses of the epidermal keratinocytes, which often occur simultaneously, is largely unknown. The focus of this study was to investigate the interference between osmotic stress and DNA damage response. In addition to revealing the already well-described regulation of diverse gene sets, for example, cellular processes such as transcription, translation, and metabolic pathways (e.g., the KEGG citrate cycle and Reactome G2/M checkpoints), gene expression analysis of osmotically stressed keratinocytes revealed an influence on the transcription of genes also related to UV-induced DNA damage response. A gene network regulating the H2AX phosphorylation was identified to be regulated by osmotic stress. To analyze and test the interference between osmotic stress and DNA damage response, which can be triggered by UV stress on the one hand and oxidative stress on the other, in more detail, primary human keratinocytes were cultured under osmotic stress conditions and subsequently exposed to UV light and H2O2, respectively. γH2AX measurements revealed lower γH2AX levels in cells previously cultured under osmotic stress conditions.
Collapse
|
7
|
Loo RL, Chan Q, Nicholson JK, Holmes E. Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine- N-oxide. J Proteome Res 2022; 21:560-589. [PMID: 35142516 DOI: 10.1021/acs.jproteome.1c00851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Trimethylamine (TMA) and its N-oxide (TMAO) are ubiquitous in prokaryote and eukaryote organisms as well as in the environment, reflecting their fundamental importance in evolutionary biology, and their diverse biochemical functions. Both metabolites have multiple biological roles including cell-signaling. Much attention has focused on the significance of serum and urinary TMAO in cardiovascular disease risk, yet this is only one of the many facets of a deeper TMA-TMAO partnership that reflects the significance of these metabolites in multiple biological processes spanning animals, plants, bacteria, and fungi. We report on analytical methods for measuring TMA and TMAO and attempt to critically synthesize and map the global functions of TMA and TMAO in a systems biology framework.
Collapse
Affiliation(s)
- Ruey Leng Loo
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom.,MRC Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Jeremy K Nicholson
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Institute of Global Health Innovation, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, United Kingdom
| | - Elaine Holmes
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Nutrition Research, Department of Metabolism, Nutrition and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
| |
Collapse
|
8
|
Van AT, Sommer V, Glaser K. The Ecophysiological Performance and Traits of Genera within the Stichococcus-like Clade (Trebouxiophyceae) under Matric and Osmotic Stress. Microorganisms 2021; 9:1816. [PMID: 34576715 PMCID: PMC8472729 DOI: 10.3390/microorganisms9091816] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 11/30/2022] Open
Abstract
Changes in water balance are some of the most critical challenges that aeroterrestrial algae face. They have a wide variety of mechanisms to protect against osmotic stress, including, but not limited to, downregulating photosynthesis, the production of compatible solutes, spore and akinete formation, biofilms, as well as triggering structural cellular changes. In comparison, algae living in saline environments must cope with ionic stress, which has similar effects on the physiology as desiccation in addition to sodium and chloride ion toxicity. These environmental challenges define ecological niches for both specialist and generalist algae. One alga known to be aeroterrestrial and euryhaline is Stichococcus bacillaris Nägeli, possessing the ability to withstand both matric and osmotic stresses, which may contribute to wide distribution worldwide. Following taxonomic revision of Stichococcus into seven lineages, we here examined their physiological responses to osmotic and matric stress through a salt growth challenge and desiccation experiment. The results demonstrate that innate compatible solute production capacity under salt stress and desiccation tolerance are independent of one another, and that salt tolerance is more variable than desiccation tolerance in the Stichococcus-like genera. Furthermore, algae within this group likely occupy similar ecological niches, with the exception of Pseudostichococcus.
Collapse
Affiliation(s)
- Anh Tu Van
- Institute for Biological Sciences, Applied Ecology and Phycology, University of Rostock, 18059 Rostock, Germany; (V.S.); (K.G.)
| | | | | |
Collapse
|
9
|
Van Houdt R, Vandecraen J, Heylen W, Leys N, Monsieurs P, Provoost A, Aertsen A. Phenotypic and Genetic Characterization of Temperature-Induced Mutagenesis and Mortality in Cupriavidus metallidurans. Front Microbiol 2021; 12:698330. [PMID: 34305863 PMCID: PMC8299993 DOI: 10.3389/fmicb.2021.698330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/11/2021] [Indexed: 11/26/2022] Open
Abstract
Cupriavidus metallidurans strains display a decreased viability when incubated in rich medium at a temperature of 37°C compared to their normal growth temperature of 30°C, a phenomenon coined “temperature-induced mortality and mutagenesis” (TIMM). To scrutinize this aberrant phenotype further, the contributions of specific inducers and protective agents were determined. Different growth media, including lysogeny broth (LB) and Schatz, and components, including casamino acids, in particular amino acids (proline, cysteine, glycine, glutamine, leucine, histidine and phenylalanine) and ammonium, were found to induce TIMM at 37°C. Sorbitol was found to counteract TIMM. Furthermore, although TIMM is well conserved within the C. metallidurans species, multiple and strain-specific TIMM inducers exist. Twenty-nine percent of the TIMM survivors inherited resistance to TIMM. Whole-genome sequencing of two resistant derivatives revealed an important role of an uncharacterized oxidoreductase, indicating putative metabolic poisoning when grown in high-concentration nitrogen-containing media at 37°C.
Collapse
Affiliation(s)
- Rob Van Houdt
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Joachim Vandecraen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium.,Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Wietse Heylen
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Natalie Leys
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Pieter Monsieurs
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Ann Provoost
- Microbiology Unit, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| |
Collapse
|
10
|
Knoll KE, Lindeque Z, Adeniji AA, Oosthuizen CB, Lall N, Loots DT. Elucidating the Antimycobacterial Mechanism of Action of Decoquinate Derivative RMB041 Using Metabolomics. Antibiotics (Basel) 2021; 10:693. [PMID: 34200519 PMCID: PMC8228794 DOI: 10.3390/antibiotics10060693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), still remains one of the leading causes of death from a single infectious agent worldwide. The high prevalence of this disease is mostly ascribed to the rapid development of drug resistance to the current anti-TB drugs, exacerbated by lack of patient adherence due to drug toxicity. The aforementioned highlights the urgent need for new anti-TB compounds with different antimycobacterial mechanisms of action to those currently being used. An N-alkyl quinolone; decoquinate derivative RMB041, has recently shown promising antimicrobial activity against Mtb, while also exhibiting low cytotoxicity and excellent pharmacokinetic characteristics. Its exact mechanism of action, however, is still unknown. Considering this, we used GCxGC-TOFMS and well described metabolomic approaches to analyze and compare the metabolic alterations of Mtb treated with decoquinate derivative RMB041 by comparison to non-treated Mtb controls. The most significantly altered pathways in Mtb treated with this drug include fatty acid metabolism, amino acid metabolism, glycerol metabolism, and the urea cycle. These changes support previous findings suggesting this drug acts primarily on the cell wall and secondarily on the DNA metabolism of Mtb. Additionally, we identified metabolic changes suggesting inhibition of protein synthesis and a state of dormancy.
Collapse
Affiliation(s)
- Kirsten E. Knoll
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Zander Lindeque
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Adetomiwa A. Adeniji
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Carel B. Oosthuizen
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
| | - Namrita Lall
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Du Toit Loots
- Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| |
Collapse
|
11
|
Knoll KE, Lindeque Z, Adeniji AA, Oosthuizen CB, Lall N, Loots DT. Elucidating the Antimycobacterial Mechanism of Action of Ciprofloxacin Using Metabolomics. Microorganisms 2021; 9:microorganisms9061158. [PMID: 34071153 PMCID: PMC8228629 DOI: 10.3390/microorganisms9061158] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 12/21/2022] Open
Abstract
In the interest of developing more effective and safer anti-tuberculosis drugs, we used a GCxGC-TOF-MS metabolomics research approach to investigate and compare the metabolic profiles of Mtb in the presence and absence of ciprofloxacin. The metabolites that best describe the differences between the compared groups were identified as markers characterizing the changes induced by ciprofloxacin. Malic acid was ranked as the most significantly altered metabolite marker induced by ciprofloxacin, indicative of an inhibition of the tricarboxylic acid (TCA) and glyoxylate cycle of Mtb. The altered fatty acid, myo-inositol, and triacylglycerol metabolism seen in this group supports previous observations of ciprofloxacin action on the Mtb cell wall. Furthermore, the altered pentose phosphate intermediates, glycerol metabolism markers, glucose accumulation, as well as the reduction in the glucogenic amino acids specifically, indicate a flux toward DNA (as well as cell wall) repair, also supporting previous findings of DNA damage caused by ciprofloxacin. This study further provides insights useful for designing network whole-system strategies for the identification of possible modes of action of various drugs and possibly adaptations by Mtb resulting in resistance.
Collapse
Affiliation(s)
- Kirsten E. Knoll
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Zander Lindeque
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Adetomiwa A. Adeniji
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
| | - Carel B. Oosthuizen
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
| | - Namrita Lall
- Department of Plant and Soil Sciences, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0002, South Africa; (C.B.O.); (N.L.)
- School of Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Du Toit Loots
- Department of Human Metabolomics, North-West University, Private Bag x6001, Box 269, Potchefstroom 2531, South Africa; (K.E.K.); (Z.L.); (A.A.A.)
- Correspondence: ; Tel.: +27-(0)18-299-1818
| |
Collapse
|
12
|
Rodríguez-Pupo EC, Pérez-Llano Y, Tinoco-Valencia JR, Sánchez NS, Padilla-Garfias F, Calahorra M, Sánchez NDC, Sánchez-Reyes A, Rodríguez-Hernández MDR, Peña A, Sánchez O, Aguirre J, Batista-García RA, Folch-Mallol JL, Sánchez-Carbente MDR. Osmolyte Signatures for the Protection of Aspergillus sydowii Cells under Halophilic Conditions and Osmotic Shock. J Fungi (Basel) 2021; 7:414. [PMID: 34073303 PMCID: PMC8228332 DOI: 10.3390/jof7060414] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022] Open
Abstract
Aspergillus sydowii is a moderate halophile fungus extensively studied for its biotechnological potential and halophile responses, which has also been reported as a coral reef pathogen. In a recent publication, the transcriptomic analysis of this fungus, when growing on wheat straw, showed that genes related to cell wall modification and cation transporters were upregulated under hypersaline conditions but not under 0.5 M NaCl, the optimal salinity for growth in this strain. This led us to study osmolyte accumulation as a mechanism to withstand moderate salinity. In this work, we show that A. sydowii accumulates trehalose, arabitol, mannitol, and glycerol with different temporal dynamics, which depend on whether the fungus is exposed to hypo- or hyperosmotic stress. The transcripts coding for enzymes responsible for polyalcohol synthesis were regulated in a stress-dependent manner. Interestingly, A. sydowii contains three homologs (Hog1, Hog2 and MpkC) of the Hog1 MAPK, the master regulator of hyperosmotic stress response in S. cerevisiae and other fungi. We show a differential regulation of these MAPKs under different salinity conditions, including sustained basal Hog1/Hog2 phosphorylation levels in the absence of NaCl or in the presence of 2.0 M NaCl, in contrast to what is observed in S. cerevisiae. These findings indicate that halophilic fungi such as A. sydowii utilize different osmoadaptation mechanisms to hypersaline conditions.
Collapse
Affiliation(s)
- Eya Caridad Rodríguez-Pupo
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
- Centro de Investigación en Dinámica Celular, IICBA, UAEM, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico;
| | - Yordanis Pérez-Llano
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
- Centro de Investigación en Dinámica Celular, IICBA, UAEM, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico;
| | - José Raunel Tinoco-Valencia
- Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Campus Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62210, Morelos, Mexico;
| | - Norma Silvia Sánchez
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Francisco Padilla-Garfias
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Martha Calahorra
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Nilda del C. Sánchez
- Centro de Ciencias Genómicas, UNAM, Campus Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62210, Morelos, Mexico;
| | - Ayixón Sánchez-Reyes
- Catedras Conacyt-Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), Campus Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62210, Morelos, Mexico;
| | - María del Rocío Rodríguez-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
| | - Antonio Peña
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Olivia Sánchez
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Jesús Aguirre
- Instituto de Fisiología Celular, UNAM, Cto. Exterior s/n, Cd. Universitaria, Coyoacán, Ciudad de México C.P. 04510, Federal District, Mexico; (N.S.S.); (F.P.-G.); (M.C.); (A.P.); (O.S.); (J.A.)
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, IICBA, UAEM, Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico;
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
| | - María del Rayo Sánchez-Carbente
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos (UAEM), Av. Universidad 1001, Col. Chamilpa, Cuernavaca C.P. 62209, Morelos, Mexico; (E.C.R.-P.); (Y.P.-L.); (M.d.R.R.-H.); (J.L.F.-M.)
| |
Collapse
|
13
|
Ohsawa S, Tokushima T, Okada K. Hydration of the Zwitterionic and Protonated Forms of Glycine Betaine Probed by Soft X-ray Emission Spectroscopy Coupled with Chemometrics. J Phys Chem B 2021; 125:1881-1887. [PMID: 33570403 DOI: 10.1021/acs.jpcb.0c10712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Soft X-ray absorption and emission spectra of glycine betaine (GB) have been measured at the O K-edge in neutral and strongly acidic solutions. The absorption spectra of the neutral solutions have a resonance peak at 532.6 eV, assigned to the transition to the π* orbital, whereas in the acidic solutions, the peak is shifted by -0.3 eV. The emission spectra taken as a function of the GB concentration have been analyzed by means of a modified classical least-squares regression method to obtain the hydration number of the solute. The analysis is successful when the emission spectra have been acquired at the energy of a slightly detuned resonance, giving 28 and 24 as the minimum values for the zwitterionic and protonated GB, respectively. The number of 28 accords with the reported values for the number of water molecules in the first hydration layer of the zwitterion and is greater than that obtained by other experimental techniques. The obtained numbers are used to discuss the hydration structure of GB with the aid of ab initio molecular orbital calculations. The hydration structure of the protonated form of GB is explored for the first time.
Collapse
Affiliation(s)
- Shohei Ohsawa
- Department of Chemistry, Graduate School of Science, Hiroshima University, Hiroshima, Higashi-Hiroshima 739-8526, Japan.,RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| | | | - Kazumasa Okada
- Department of Chemistry, Graduate School of Science, Hiroshima University, Hiroshima, Higashi-Hiroshima 739-8526, Japan.,RIKEN SPring-8 Center, Sayo, Hyogo 679-5148, Japan
| |
Collapse
|
14
|
Abstract
Trimethylamine N-Oxide (TMAO) is the product of the monooxygenation reaction catalyzed by a drug-metabolizing enzyme, human flavin-containing monooxygenase 3 (hFMO3), and its animal orthologues. For several years, researchers have looked at TMAO and hFMO3 as two distinct molecules playing specific but separate roles, the former to defend saltwater animals from osmotic or hydrostatic stress and the latter to process xenobiotics in men. The presence of high levels of plasmatic TMAO in elasmobranchs and other animals was demonstrated a long time ago, whereas the actual physiological role of hFMO3 is still unknown because the enzyme has been mainly characterized for its ability to oxidize drugs. Recently TMAO was found to be related to several human health conditions such as atherosclerosis, cardiovascular, and renal diseases. This correlation poses a striking question of how other vertebrates (and invertebrates) can survive in the presence of very high TMAO concentrations (micromolar in humans, millimolar in marine mammals and several hundred millimolar in elasmobranchs). Therefore, it is important to address how TMAO, its precursors, and FMO catalytic activity are interconnected.
Collapse
|
15
|
Choi KJ, Tsoi PS, Moosa MM, Paulucci-Holthauzen A, Liao SCJ, Ferreon JC, Ferreon ACM. A Chemical Chaperone Decouples TDP-43 Disordered Domain Phase Separation from Fibrillation. Biochemistry 2018; 57:6822-6826. [PMID: 30520303 DOI: 10.1021/acs.biochem.8b01051] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Ribonucleoprotein (RNP) condensations through liquid-liquid phase separation play vital roles in the dynamic formation-dissolution of stress granules (SGs). These condensations are, however, usually assumed to be linked to pathologic fibrillation. Here, we show that physiologic condensation and pathologic fibrillation of RNPs are independent processes that can be unlinked with the chemical chaperone trimethylamine N-oxide (TMAO). Using the low-complexity disordered domain of the archetypical SG-protein TDP-43 as a model system, we show that TMAO enhances RNP liquid condensation yet inhibits protein fibrillation. Our results demonstrate effective decoupling of physiologic condensation from pathologic aggregation and suggest that selective targeting of protein fibrillation (without altering condensation) can be employed as a therapeutic strategy for RNP aggregation-associated degenerative disorders.
Collapse
Affiliation(s)
- Kyoung-Jae Choi
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza, N520.03 , Houston , Texas 77030 , United States
| | - Phoebe S Tsoi
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza, N520.03 , Houston , Texas 77030 , United States
| | - Mahdi Muhammad Moosa
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza, N520.03 , Houston , Texas 77030 , United States
| | - Adriana Paulucci-Holthauzen
- Department of Genetics , The University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Shih-Chu Jeff Liao
- ISS, Inc. , 1602 Newton Drive , Champaign , Illinois 61822 , United States
| | - Josephine C Ferreon
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza, N520.03 , Houston , Texas 77030 , United States
| | - Allan Chris M Ferreon
- Department of Pharmacology and Chemical Biology , Baylor College of Medicine , One Baylor Plaza, N520.03 , Houston , Texas 77030 , United States
| |
Collapse
|
16
|
Wang Y, Sukenik S, Davis CM, Gruebele M. Cell Volume Controls Protein Stability and Compactness of the Unfolded State. J Phys Chem B 2018; 122:11762-11770. [PMID: 30289261 DOI: 10.1021/acs.jpcb.8b08216] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Macromolecular crowding is widely accepted as one of the factors that can alter protein stability, structure, and function inside cells. Less often considered is that crowding can be dynamic: as cell volume changes, either as a result of external duress or in the course of the cell cycle, water moves in or out through membrane channels, and crowding changes in tune. Both theory and in vitro experiments predict that protein stability will be altered as a result of crowding changes. However, it is unclear how much the structural ensemble is altered as crowding changes in the cell. To test this, we look at the response of a FRET-labeled kinase to osmotically induced volume changes in live cells. We examine both the folded and unfolded states of the kinase by changing the temperature of the media surrounding the cell. Our data reveals that crowding compacts the structure of its unfolded ensemble but stabilizes the folded protein. We propose that the structure of proteins lacking a rigid, well-defined tertiary structure could be highly sensitive to both increases and decreases in cell volume. Our findings present a possible mechanism for disordered proteins to act as sensors and actuators of cell cycle or external stress events that coincide with a change in macromolecular crowding.
Collapse
Affiliation(s)
- Yuhan Wang
- Center for Biophysics and Computational Biology , University of Illinois , Urbana , Illinois 61801 , United States
| | - Shahar Sukenik
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States
| | - Caitlin M Davis
- Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States
| | - Martin Gruebele
- Center for Biophysics and Computational Biology , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Chemistry , University of Illinois , Urbana , Illinois 61801 , United States.,Department of Physics , University of Illinois , Urbana , Illinois 61801 , United States
| |
Collapse
|
17
|
Kundu A, Verma PK, Cho M. Effect of Osmolytes on the Conformational Behavior of a Macromolecule in a Cytoplasm-like Crowded Environment: A Femtosecond Mid-IR Pump-Probe Spectroscopy Study. J Phys Chem Lett 2018; 9:724-731. [PMID: 29365266 DOI: 10.1021/acs.jpclett.7b03297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Osmolytes found endogenously in almost all living beings play an important role in regulating cell volume under harsh environment. Here, to address the longstanding questions about the underlying mechanism of osmolyte effects, we use femtosecond mid-IR pump-probe spectroscopy with two different IR probes that are the OD stretching mode of HDO and the azido stretching mode of azido-derivatized poly(ethylene glycol) dimethyl ether (PEGDME). Our experimental results show that protecting osmolytes bind strongly with water molecules and dehydrate polymer surface, which results in promoting intramolecular interactions of the polymer. By contrast, urea behaves like water molecules without significantly disrupting water H-bonding network and favors extended and random-coil segments of the polymer chain by directly participating in solvation of the polymer. Our findings highlight the importance of direct interaction between urea and macromolecule, while protecting osmolytes indirectly affect the macromolecule through enhancing the water-osmolyte interaction in a crowded environment, which is the case that is often encountered in real biological systems.
Collapse
Affiliation(s)
- Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 02841, Republic of Korea
| | - Pramod Kumar Verma
- Department of Chemistry, Institute of Science, Banaras Hindu University , Varanasi-221005, India
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
| |
Collapse
|
18
|
Pandey RB, Jacobs DJ, Farmer BL. Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation. J Chem Phys 2017; 146:195101. [PMID: 28527439 PMCID: PMC5438306 DOI: 10.1063/1.4983222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 04/26/2017] [Indexed: 11/14/2022] Open
Abstract
The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (Rg) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in Rg occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.
Collapse
Affiliation(s)
- R B Pandey
- Department of Physics and Astronomy, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - D J Jacobs
- Department of Physics and Optical Science, University of North Carolina, Charlotte, North Carolina 28223, USA
| | - B L Farmer
- Materials and Manufacturing Directorate, Air Force Research Laboratory, Wright Patterson Air Force Base, Ohio 45433, USA and Materials Science and Engineering, North Carolina State University, Raleigh, North Carolina 27606, USA
| |
Collapse
|
19
|
Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme. Biochem J 2016; 473:3705-3724. [DOI: 10.1042/bcj20160604] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/16/2016] [Indexed: 01/08/2023]
Abstract
Osmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical denaturation of lysozyme in different solvent conditions to study the molecular mechanism by which two biologically relevant osmolytes, denaturing (urea) and stabilizing (betaine), affect the folding equilibrium. We found that urea interacts favorably with all types of residues via both hydrogen bonds and dispersion forces, and therefore accumulates in a diffuse solvation shell around the protein. This not only provides an enthalpic stabilization of the unfolded state, but also weakens the hydrophobic effect, as hydrophobic forces promote the association of urea with nonpolar residues, facilitating the unfolding. In contrast, we observed that betaine is excluded from the protein backbone and nonpolar side chains, but is accumulated near the basic residues, yielding a nonuniform distribution of betaine molecules at the protein surface. Spatially resolved solvent–protein interaction energies further suggested that betaine behaves in a ligand- rather than solvent-like manner and its exclusion from the protein surface arises mostly from the scarcity of favorable binding sites. Finally, we found that, in the presence of betaine, the reduced ability of water molecules to solvate the protein results in an additional enthalpic contribution to the betaine-induced stabilization.
Collapse
|
20
|
Usui K, Nagata Y, Hunger J, Bonn M, Sulpizi M. A new force field including charge directionality for TMAO in aqueous solution. J Chem Phys 2016. [DOI: 10.1063/1.4960207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kota Usui
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Marialore Sulpizi
- Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz, Germany
| |
Collapse
|
21
|
Rani A, Venkatesu P. A Distinct Proof on Interplay between Trehalose and Guanidinium Chloride for the Stability of Stem Bromelain. J Phys Chem B 2016; 120:8863-72. [DOI: 10.1021/acs.jpcb.6b05766] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anjeeta Rani
- Department of Chemistry, University of Delhi, Delhi 110 007, India
| | | |
Collapse
|
22
|
Koštál V, Korbelová J, Poupardin R, Moos M, Šimek P. Arginine and proline applied as food additives stimulate high freeze tolerance in larvae of Drosophila melanogaster. J Exp Biol 2016; 219:2358-67. [DOI: 10.1242/jeb.142158] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/25/2016] [Indexed: 01/18/2023]
Abstract
ABSTRACT
The fruit fly Drosophila melanogaster is an insect of tropical origin. Its larval stage is evolutionarily adapted for rapid growth and development under warm conditions and shows high sensitivity to cold. In this study, we further developed an optimal acclimation and freezing protocol that significantly improves larval freeze tolerance (an ability to survive at −5°C when most of the freezable fraction of water is converted to ice). Using the optimal protocol, freeze survival to adult stage increased from 0.7% to 12.6% in the larvae fed standard diet (agar, sugar, yeast, cornmeal). Next, we fed the larvae diets augmented with 31 different amino compounds, administered in different concentrations, and observed their effects on larval metabolomic composition, viability, rate of development and freeze tolerance. While some diet additives were toxic, others showed positive effects on freeze tolerance. Statistical correlation revealed tight association between high freeze tolerance and high levels of amino compounds involved in arginine and proline metabolism. Proline- and arginine-augmented diets showed the highest potential, improving freeze survival to 42.1% and 50.6%, respectively. Two plausible mechanisms by which high concentrations of proline and arginine might stimulate high freeze tolerance are discussed: (i) proline, probably in combination with trehalose, could reduce partial unfolding of proteins and prevent membrane fusions in the larvae exposed to thermal stress (prior to freezing) or during freeze dehydration; (ii) both arginine and proline are exceptional among amino compounds in their ability to form supramolecular aggregates which probably bind partially unfolded proteins and inhibit their aggregation under increasing freeze dehydration.
Collapse
Affiliation(s)
- Vladimír Koštál
- Biology Centre CAS, Institute of Entomology, České Budějovice 37005, Czech Republic
| | - Jaroslava Korbelová
- Biology Centre CAS, Institute of Entomology, České Budějovice 37005, Czech Republic
| | - Rodolphe Poupardin
- Biology Centre CAS, Institute of Entomology, České Budějovice 37005, Czech Republic
| | - Martin Moos
- Biology Centre CAS, Institute of Entomology, České Budějovice 37005, Czech Republic
| | - Petr Šimek
- Biology Centre CAS, Institute of Entomology, České Budějovice 37005, Czech Republic
| |
Collapse
|
23
|
Lee H, Choi JH, Verma PK, Cho M. Computational Vibrational Spectroscopy of HDO in Osmolyte–Water Solutions. J Phys Chem A 2016; 120:5874-86. [DOI: 10.1021/acs.jpca.6b06305] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Hochan Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science and ‡Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| |
Collapse
|
24
|
Sukenik S, Sapir L, Harries D. Osmolyte Induced Changes in Peptide Conformational Ensemble Correlate with Slower Amyloid Aggregation: A Coarse-Grained Simulation Study. J Chem Theory Comput 2015; 11:5918-28. [DOI: 10.1021/acs.jctc.5b00657] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Shahar Sukenik
- Institute of Chemistry and
the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Liel Sapir
- Institute of Chemistry and
the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Daniel Harries
- Institute of Chemistry and
the Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| |
Collapse
|
25
|
Lee H, Choi JH, Verma PK, Cho M. Spectral Graph Analyses of Water Hydrogen-Bonding Network and Osmolyte Aggregate Structures in Osmolyte-Water Solutions. J Phys Chem B 2015; 119:14402-12. [PMID: 26473387 DOI: 10.1021/acs.jpcb.5b08029] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, it was shown that the spectral graph theory is exceptionally useful for understanding not only morphological structural differences in ion aggregates but also similarities between an ion network and a water H-bonding network in highly concentrated salt solutions. Here, we present spectral graph analysis results on osmolyte aggregates and water H-bonding network structures in aqueous renal osmolyte solutions. The quantitative analyses of the adjacency matrices that are graph-theoretical representations of aggregates of osmolyte molecules and water H-bond structures provide the ensemble average eigenvalue spectra and degree distribution. We show that urea molecules form quite different morphological structures compared to other protecting renal osmolyte molecules in water, particularly sorbitol and trimethylglycine, which are well-known protecting osmolytes, and at high concentrations exhibit a strong propensity to form morphological structures that are graph-theoretically similar to that of the water H-bond network. Conversely, urea molecules, even at similarly high concentrations, form separated clusters instead of extended osmolyte-osmolyte networks. This difference in morphological structure of osmolyte-osmolyte aggregates between protecting and destabilizing osmolytes is considered to be an important observation that led us to propose a hypothesis on the osmolyte aggregate growth mechanism via either osmolyte network formation or segregated osmolyte cluster formation. We anticipate that the present spectral graph analyses of osmolyte aggregate structures and their interplay with the water H-bond network structure in highly concentrated renal osmolyte solutions could provide important information on the osmolyte effects of not only water structures but also protein stability in biologically relevant osmolyte solutions.
Collapse
Affiliation(s)
- Hochan Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 136-701, Republic of Korea.,Department of Chemistry, Korea University , Seoul 136-713, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Korea University , Seoul 136-713, Republic of Korea
| | - Pramod Kumar Verma
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 136-701, Republic of Korea.,Department of Chemistry, Korea University , Seoul 136-713, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 136-701, Republic of Korea.,Department of Chemistry, Korea University , Seoul 136-713, Republic of Korea
| |
Collapse
|
26
|
Usui K, Hunger J, Sulpizi M, Ohto T, Bonn M, Nagata Y. Ab Initio Liquid Water Dynamics in Aqueous TMAO Solution. J Phys Chem B 2015; 119:10597-606. [DOI: 10.1021/acs.jpcb.5b02579] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kota Usui
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Johannes Hunger
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Marialore Sulpizi
- Johannes Gutenberg University Mainz, Staudingerweg 7, 55099 Mainz, Germany
| | - Tatsuhiko Ohto
- Graduate
School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Mischa Bonn
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| | - Yuki Nagata
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany
| |
Collapse
|
27
|
Sukenik S, Sapir L, Gilman-Politi R, Harries D. Diversity in the mechanisms of cosolute action on biomolecular processes. Faraday Discuss 2013; 160:225-37; discussion 311-27. [PMID: 23795502 DOI: 10.1039/c2fd20101a] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Numerous cellular cosolutes significantly impact the way that proteins and other biomacromolecules act and interact. We have followed the thermodynamic effect of several cosolute classes, including polymers, cellular osmolytes, and inorganic salts, on the stability of biomolecular folding and complexation. By comparing changes in free energy, enthalpy, and entropy upon cosolutes addition for these processes, we identify several thermodynamically distinct mechanisms. Surprisingly, even while many cosolutes display similar scaling of the change in stabilizing free energy with their concentration, a breakdown of this free energy into enthalpic and entropic contributions distinguishes different families of cosolutes. We discuss how these "thermodynamic fingerprints" can direct towards possible underlying mechanisms that govern the cosolute effect.
Collapse
Affiliation(s)
- Shahar Sukenik
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem, Israel
| | | | | | | |
Collapse
|
28
|
Elnitsky MA, Benoit JB, Lopez-Martinez G, Denlinger DL, Lee RE. Osmoregulation and salinity tolerance in the Antarctic midge, Belgica antarctica: seawater exposure confers enhanced tolerance to freezing and dehydration. ACTA ACUST UNITED AC 2009; 212:2864-71. [PMID: 19684222 DOI: 10.1242/jeb.034173] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Summer storms along the Antarctic Peninsula can cause microhabitats of the terrestrial midge Belgica antarctica to become periodically inundated with seawater from tidal spray. As microhabitats dry, larvae may be exposed to increasing concentrations of seawater. Alternatively, as a result of melting snow or following rain, larvae may be immersed in freshwater for extended periods. The present study assessed the tolerance and physiological response of B. antarctica larvae to salinity exposure, and examined the effect of seawater acclimation on their subsequent tolerance of freezing, dehydration and heat shock. Midge larvae tolerated extended exposure to hyperosmotic seawater; nearly 50% of larvae survived a 10-day exposure to 1000 mOsm kg(-1) seawater and approximately 25% of larvae survived 6 days in 2000 mOsm kg(-1) seawater. Exposure to seawater drastically reduced larval body water content and increased hemolymph osmolality. By contrast, immersion in freshwater did not affect water content or hemolymph osmolality. Hyperosmotic seawater exposure, and the accompanying osmotic dehydration, resulted in a significant correlation between the rate of oxygen consumption and larval water content and induced the de novo synthesis and accumulation of several organic osmolytes. A 3-day exposure of larvae to hyperosmotic seawater increased freezing tolerance relative to freshwater-acclimated larvae. Even after rehydration, the freezing survival of larvae acclimated to seawater was greater than freshwater-acclimated larvae. Additionally, seawater exposure increased the subsequent tolerance of larvae to dehydration. Our results further illustrate the similarities between these related, yet distinct, forms of osmotic stress and add to the suite of physiological responses used by larvae to enhance survival in the harsh and unpredictable Antarctic environment.
Collapse
|
29
|
Abstract
SUMMARYThe role of urea as a balancing osmolyte in osmotic adaptation is well known, but this `waste product' also has myriad other functions in diverse taxa. We report that urea plays an important, previously undocumented role in freezing tolerance of the wood frog (Rana sylvatica), a northern woodland species that hibernates terrestrially in sites where dehydration and freezing may occur. Wood frogs inhabiting an outdoor enclosure accumulated urea to 65 mmol l-1 in autumn and early winter, when soil moisture was scarce, but subsequently urea levels fell to ∼2 mmol l-1 as the availability of environmental water increased. Laboratory experiments showed that hibernating R. sylvatica can accumulate at least 90 mmol l-1 urea under relatively dry, warm conditions. During experimental freezing, frogs synthesized glucose but did not accumulate additional urea. Nevertheless, the concentrations of urea and glucose in some tissues were similar. We tested urea's efficacy as a cryoprotectant by measuring lysis and lactate dehydrogenase (LDH) leakage in samples of R. sylvaticaerythrocytes frozen/thawed in the presence of physiological levels of urea or other osmolytes. In conferring protection against freeze/thaw damage, urea was comparable to glycerol and as good as or better than glucose, cryoprotectants found in freeze-tolerant frogs and other animals. Urea treatment also improved the viability of intact tissues frozen in vitro, as demonstrated by post-thaw measures of metabolic activity and LDH leakage. Collectively, our findings suggest that urea functions both as an osmoprotectant and a cryoprotectant in terrestrially hibernating amphibians.
Collapse
Affiliation(s)
- Jon P Costanzo
- Department of Zoology, Miami University, Oxford, OH 45056, USA.
| | | |
Collapse
|
30
|
Yancey PH. Organic osmolytes as compatible, metabolic and counteracting cytoprotectants in high osmolarity and other stresses. J Exp Biol 2005; 208:2819-30. [PMID: 16043587 DOI: 10.1242/jeb.01730] [Citation(s) in RCA: 1104] [Impact Index Per Article: 58.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
SUMMARYOrganic osmolytes are small solutes used by cells of numerous water-stressed organisms and tissues to maintain cell volume. Similar compounds are accumulated by some organisms in anhydrobiotic, thermal and possibly pressure stresses. These solutes are amino acids and derivatives,polyols and sugars, methylamines, methylsulfonium compounds and urea. Except for urea, they are often called `compatible solutes', a term indicating lack of perturbing effects on cellular macromolecules and implying interchangeability. However, these features may not always exist, for three reasons. First, some of these solutes may have unique protective metabolic roles, such as acting as antioxidants (e.g. polyols, taurine, hypotaurine),providing redox balance (e.g. glycerol) and detoxifying sulfide (hypotaurine in animals at hydrothermal vents and seeps). Second, some of these solutes stabilize macromolecules and counteract perturbants in non-interchangeable ways. Methylamines [e.g. trimethylamine N-oxide (TMAO)] can enhance protein folding and ligand binding and counteract perturbations by urea (e.g. in elasmobranchs and mammalian kidney), inorganic ions, and hydrostatic pressure in deep-sea animals. Trehalose and proline in overwintering insects stabilize membranes at subzero temperatures. Trehalose in insects and yeast,and anionic polyols in microorganisms around hydrothermal vents, can protect proteins from denaturation by high temperatures. Third, stabilizing solutes appear to be used in nature only to counteract perturbants of macromolecules,perhaps because stabilization is detrimental in the absence of perturbation. Some of these solutes have applications in biotechnology, agriculture and medicine, including in vitro rescue of the misfolded protein of cystic fibrosis. However, caution is warranted if high levels cause overstabilization of proteins.
Collapse
Affiliation(s)
- Paul H Yancey
- Biology Department, Whitman College, Walla Walla, WA 99362, USA.
| |
Collapse
|
31
|
Steele SL, Yancey PH, Wright PA. Dogmas and controversies in the handling of nitrogenous wastes: osmoregulation during early embryonic development in the marine little skate Raja erinacea; response to changes in external salinity. ACTA ACUST UNITED AC 2004; 207:2021-31. [PMID: 15143136 DOI: 10.1242/jeb.00959] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Marine elasmobranchs retain relatively high levels of urea to counterbalance the osmotic strength of seawater. Oviparous species, such as the little skate Raja erinacea, release encapsulated embryos that hatch after about 9 months on the seafloor. To study the ureosmotic capability of skate embryos, we measured a variety of possible osmolytes and ornithine-urea cycle (OUC) enzyme activities in little skate embryos, and determined their physiological response to dilute seawater (75% SW) exposure relative to controls (100% SW). The urea:trimethylamine oxide (TMAO) + other osmolytes ratio was 2.3-2.7:1. At the earliest stage of development investigated (4 months), there were significant levels of the key OUC enzyme, carbamoyl phosphate synthetase III, as well as ornithine transcarbamoylase, arginase and glutamine synthetase, providing evidence for a functional OUC. Embryos (4 and 8 months) survived and recovered from exposure to 5 days of 75% SW. There was a significant increase in the rate of urea excretion (five- to tenfold), no change in OUC enzyme activities, and significant decreases in the tissue content of urea, TMAO and other osmolytes in embryos exposed to 75% SW compared to 100% SW. Taken together, the data indicate that little skate embryos synthesize and retain urea, as well as a suite of other osmolytes, in order to regulate osmotic balance with the external environment. Interestingly, these ureosmotic mechanisms are in place as early as 4 months, around the time at which the egg capsule opens and the embryo is in more direct contact with the external environment.
Collapse
Affiliation(s)
- S L Steele
- Department of Zoology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | | | | |
Collapse
|
32
|
Holt SM, Kinsey ST. Osmotic effects on arginine kinase function in living muscle of the blue crab Callinectes sapidus. J Exp Biol 2002; 205:1775-85. [PMID: 12042336 DOI: 10.1242/jeb.205.12.1775] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
Flux was examined through the reaction catalyzed by arginine kinase in intact blue crab (Callinectes sapidus) muscle during simulated changes in salinity. Isolated dark levator muscles from the swimming leg were superfused with a saline solution that had an osmolarity equivalent to that of the hemolymph under different salinity regimes. Animals were acclimated for 7 days to a salinity of 5, 17 or 35‰, which corresponds to a hemolymph osmolarity of 640, 720 or 960 mosmoll-1, respectively. Experiments were conducted under control conditions, in which the osmolarity of the superfusion medium matched that of the acclimated hemolymph, as well as under hypo- and hyperosmotic conditions. These latter treatments were meant to simulate a rapid change in environmental salinity. Pseudo-first-order unidirectional rate constants and flux rates were measured for arginine kinase in the forward and reverse directions using a 31P-nuclear magnetic resonance saturation transfer method. There were no differences in the rate constants or flux rates among the controls, indicating that arginine kinase function is not modulated by salinity if the animal has had sufficient acclimation time. However, the rate constants and flux rates of arginine kinase varied over a modest 1.7-fold range across the three types of osmotic treatments, although the range for the flux data was reduced when cell volume changes were taken into account. The hyperosmotic treatments led to a reduction in arginine kinase flux, while the hypo-osmotic treatments led to an enhanced arginine kinase flux. We propose that this effect is mediated by an increase in the concentration of perturbing inorganic ions under hyperosmotic conditions and a decrease in the concentration of such ions during the hypo-osmotic treatments.
Collapse
Affiliation(s)
- Stewart M Holt
- Department of Biological Sciences, University of North Carolina at Wilmington, 601 South College Road, Wilmington, NC 28403-3297, USA
| | | |
Collapse
|