1
|
Shaiken TE, Grimm SL, Siam M, Williams A, Rezaeian AH, Kraushaar D, Ricco E, Robertson MJ, Coarfa C, Jain A, Malovannaya A, Stossi F, Opekun AR, Price AP, Dubrulle J. Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix. iScience 2023; 26:105965. [PMID: 36824274 PMCID: PMC9941065 DOI: 10.1016/j.isci.2023.105965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 11/07/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
Despite the knowledge that protein translation and various metabolic reactions that create and sustain cellular life occur in the cytoplasm, the structural organization within the cytoplasm remains unclear. Recent models indicate that cytoplasm contains viscous fluid and elastic solid phases. We separated these viscous fluid and solid elastic compartments, which we call the cytosol and cytomatrix, respectively. The distinctive composition of the cytomatrix included structural proteins, ribosomes, and metabolome enzymes. High-throughput analysis revealed unique biosynthetic pathways within the cytomatrix. Enrichment of biosynthetic pathways in the cytomatrix indicated the presence of immobilized biocatalysis. Enzymatic immobilization and segregation can surmount spatial impediments, and the local pathway segregation may form cytoplasmic organelles. Protein translation was reprogrammed within the cytomatrix under the restriction of protein synthesis by drug treatment. The cytosol and cytomatrix are an elaborately interconnected network that promotes operational flexibility in healthy cells and the survival of malignant cells.
Collapse
Affiliation(s)
- Tattym E. Shaiken
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Sandra L. Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mohamad Siam
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Amanda Williams
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
| | - Abdol-Hossein Rezaeian
- PeriNuc Labs, University of Houston Technology Bridge, Houston, TX 77023, USA
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Daniel Kraushaar
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily Ricco
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Cristian Coarfa
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antrix Jain
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Malovannaya
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fabio Stossi
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antone R. Opekun
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alyssa P. Price
- Department of Medicine-Gastroenterology and Hepatology Section, Michael E DeBakey Veteran’s Affairs Medical Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julien Dubrulle
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
2
|
Vorontsova I, Vallmitjana A, Torrado B, Schilling TF, Hall JE, Gratton E, Malacrida L. In vivo macromolecular crowding is differentially modulated by aquaporin 0 in zebrafish lens: Insights from a nanoenvironment sensor and spectral imaging. SCIENCE ADVANCES 2022; 8:eabj4833. [PMID: 35171678 PMCID: PMC8849302 DOI: 10.1126/sciadv.abj4833] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 12/23/2021] [Indexed: 05/14/2023]
Abstract
Macromolecular crowding is crucial for cellular homeostasis. In vivo studies of macromolecular crowding and water dynamics are needed to understand their roles in cellular physiology and fate determination. Macromolecular crowding in the lens is essential for normal optics, and an understanding of its regulation will help prevent cataract and presbyopia. Here, we combine the use of the nanoenvironmental sensor [6-acetyl-2-dimethylaminonaphthalene (ACDAN)] to visualize lens macromolecular crowding with in vivo studies of aquaporin 0 zebrafish mutants that disrupt its regulation. Spectral phasor analysis of ACDAN fluorescence reveals water dipolar relaxation and demonstrates that mutations in two zebrafish aquaporin 0s, Aqp0a and Aqp0b, alter water state and macromolecular crowding in living lenses. Our results provide in vivo evidence that Aqp0a promotes fluid influx in the deeper lens cortex, whereas Aqp0b facilitates fluid efflux. This evidence reveals previously unidentified spatial regulation of macromolecular crowding and spatially distinct roles for Aqp0 in the lens.
Collapse
Affiliation(s)
- Irene Vorontsova
- Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
- Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
- Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA
| | | | - Belén Torrado
- Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Thomas F. Schilling
- Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA
| | - James E. Hall
- Physiology and Biophysics, University of California, Irvine, Irvine, CA, USA
| | - Enrico Gratton
- Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Leonel Malacrida
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
- Advanced Bioimaging Unit, Institut Pasteur of Montevideo and Universidad de la República, Montevideo, Uruguay
| |
Collapse
|
3
|
Ullah M, Ng NN, Concepcion W, Thakor AS. Emerging role of stem cell-derived extracellular microRNAs in age-associated human diseases and in different therapies of longevity. Ageing Res Rev 2020; 57:100979. [PMID: 31704472 DOI: 10.1016/j.arr.2019.100979] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/17/2019] [Accepted: 10/28/2019] [Indexed: 12/15/2022]
Abstract
Organismal aging involves the progressive decline in organ function and increased susceptibility to age-associated diseases. This has been associated with the aging of stem cell populations within the body that decreases the capacity of stem cells to self-renew, differentiate, and regenerate damaged tissues and organs. This review aims to explore how aging is associated with the dysregulation of stem cell-derived extracellular vesicles (SCEVs) and their corresponding miRNA cargo (SCEV-miRNAs), which are short non-coding RNAs involved in post-transcriptional regulation of target genes. Recent evidence has suggested that in aging stem cells, SCEV-miRNAs may play a vital role regulating various processes that contribute to aging: cellular senescence, stem cell exhaustion, telomere length, and circadian rhythm. Hence, further clarifying the age-dependent molecular mechanisms through which SCEV-miRNAs exert their downstream effects may inform a greater understanding of the biology of aging, elucidate their role in stem cell function, and identify important targets for future regenerative therapies. Additionally, current studies evaluating therapeutic role of SCEVs and SCEV-miRNAs in treating several age-associated diseases are also discussed.
Collapse
|
4
|
Palmina NP, Maltseva EL, Chasovskaya TE. Effect of dilute solutions of biologically active substances on cell membranes. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914040228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
5
|
Meng L, Klinkajon W, K-hasuwan PR, Harkin S, Supaphol P, Wnek GE. Electrospun crosslinked poly(acrylic acid) fiber constructs: towards a synthetic model of the cortical layer of nerve. POLYM INT 2014. [DOI: 10.1002/pi.4793] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Linghui Meng
- Department of Macromolecular Science and Engineering; Case Western Reserve University; Cleveland OH 44106 USA
| | - Wimonwan Klinkajon
- Department of Biomedical Engineering and Master of Engineering and Management Program; Case Western Reserve University; Cleveland OH 44106 USA
| | - Prae-ravee K-hasuwan
- Department of Biomedical Engineering and Master of Engineering and Management Program; Case Western Reserve University; Cleveland OH 44106 USA
| | - Shannon Harkin
- Petroleum and Petrochemical College and Center for Petroleum, Petrochemicals, and Advanced Materials; Chulalongkorn University; Bangkok 10330 Thailand
| | - Pitt Supaphol
- Department of Biomedical Engineering and Master of Engineering and Management Program; Case Western Reserve University; Cleveland OH 44106 USA
| | - Gary E Wnek
- Department of Macromolecular Science and Engineering; Case Western Reserve University; Cleveland OH 44106 USA
| |
Collapse
|
6
|
Chasovskaya TE, Mal’tseva EL, Palmina NP. Effect of potassium phenosan on structure of plasma membranes of mice liver cells in vitro. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s0006350913010053] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
7
|
Hood JL, Wickline SA. A systematic approach to exosome-based translational nanomedicine. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2012; 4:458-67. [DOI: 10.1002/wnan.1174] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
8
|
Belov VV, Belyaeva IA, Shmatov GP, Zubareva GM, Palmina NP. IR spectroscopy of thin water layers and the mechanism of action α-tocopherol in ultra low concentrations. DOKLADY PHYSICAL CHEMISTRY 2011. [DOI: 10.1134/s0012501611070013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
9
|
Hemoglobin senses body temperature. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 38:589-600. [PMID: 19238378 DOI: 10.1007/s00249-009-0410-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 01/20/2009] [Accepted: 01/29/2009] [Indexed: 10/21/2022]
Abstract
UNLABELLED When aspirating human red blood cells (RBCs) into 1.3 mum pipettes (DeltaP = -2.3 kPa), a transition from blocking the pipette below a critical temperature T(c) = 36.3 +/- 0.3 degrees C to passing it above the T(c) occurred (micropipette passage transition). With a 1.1 mum pipette no passage was seen which enabled RBC volume measurements also above T(c). With increasing temperature RBCs lost volume significantly faster below than above a T(c) = 36.4 +/- 0.7 (volume transition). Colloid osmotic pressure (COP) measurements of RBCs in autologous plasma (25 degrees C < or = T < or = 39.5 degrees C) showed a T (c) at 37.1 +/- 0.2 degrees C above which the COP rapidly decreased (COP transition). In NMR T(1)-relaxation time measurements, the T(1) of RBCs in autologous plasma changed from a linear (r = 0.99) increment below T(c) = 37 +/- 1 degrees C at a rate of 0.023 s/K into zero slope above T(c) (RBC T(1) transition). IN CONCLUSION An amorphous hemoglobin-water gel formed in the spherical trail, the residual partial sphere of the aspirated RBC. At T(c), a sudden fluidization of the gel occurs. All changes mentioned above happen at a distinct T(c) close to body temperature. The T(c) is moved +0.8 degrees C to higher temperatures when a D(2)O buffer is used. We suggest a mechanism similar to a "glass transition" or a "colloidal phase transition". At T(c), the stabilizing Hb bound water molecules reach a threshold number enabling a partial Hb unfolding. Thus, Hb senses body temperature which must be inscribed in the primary structure of hemoglobin and possibly other proteins.
Collapse
|
10
|
Abstract
Functional neuroimaging has emerged as an important approach to study the brain and the mind. Surprisingly, although they are based on radically different physical approaches both positron emission tomography (PET) and magnetic resonance imaging (MRI) make brain activation imaging possible through measurements involving water molecules. So far, PET and MRI functional imaging have relied on the principle that neuronal activation and blood flow are coupled through metabolism. However, a new paradigm has emerged to look at brain activity through the observation with MRI of the molecular diffusion of water. In contrast with the former approaches diffusion MRI has the potential to reveal changes in the intrinsic water physical properties during brain activation, which could be more intimately linked to the neuronal activation mechanisms and lead to an improved spatial and temporal resolution. However, this link has yet to be fully confirmed and understood. To shed light on the possible relationship between water and brain activation, this introductory paper reviews the most recent data on the physical properties of water and on the status of water in biological tissues, and evaluates their relevance to brain diffusion MRI. The biophysical mechanisms of brain activation are then reassessed to reveal their intimacy with the physical properties of water, which may come to be regarded as the 'molecule of the mind'.
Collapse
Affiliation(s)
- Denis Le Bihan
- NeuroSpin, Bâtiment 145, CEA Saclay, 91191 Gif-sur-Yvette, France.
| |
Collapse
|
11
|
Dadarlat VM, Post CB. Decomposition of protein experimental compressibility into intrinsic and hydration shell contributions. Biophys J 2006; 91:4544-54. [PMID: 16997864 PMCID: PMC1779936 DOI: 10.1529/biophysj.106.087726] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The experimental determination of protein compressibility reflects both the protein intrinsic compressibility and the difference between the compressibility of water in the protein hydration shell and bulk water. We use molecular dynamics simulations to explore the dependence of the isothermal compressibility of the hydration shell surrounding globular proteins on differential contributions from charged, polar, and apolar protein-water interfaces. The compressibility of water in the protein hydration shell is accounted for by a linear combination of contributions from charged, polar, and apolar solvent-accessible surfaces. The results provide a formula for the deconvolution of experimental data into intrinsic and hydration contributions when a protein of known structure is investigated. The physical basis for the model is the variation in water density shown by the surface-specific radial distribution functions of water molecules around globular proteins. The compressibility of water hydrating charged atoms is lower than bulk water compressibility, the compressibility of water hydrating apolar atoms is somewhat larger than bulk water compressibility, and the compressibility of water around polar atoms is about the same as the compressibility of bulk water. We also assess whether hydration water compressibility determined from small compound data can be used to estimate the compressibility of hydration water surrounding proteins. The results, based on an analysis from four dipeptide solutions, indicate that small compound data cannot be used directly to estimate the compressibility of hydration water surrounding proteins.
Collapse
Affiliation(s)
- Voichita M Dadarlat
- Department of Medicinal Chemistry and Molecular Pharmacology, Markey Center for Structural Biology, Purdue Cancer Center, Purdue University, West Lafayette, IN, USA
| | | |
Collapse
|
12
|
Hood JL, Brooks WH, Roszman TL. Subcellular mobility of the calpain/calpastatin network: an organelle transient. Bioessays 2006; 28:850-9. [PMID: 16927317 DOI: 10.1002/bies.20440] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Calpain (Cp) is a calcium (Ca(2+))-dependent cysteine protease. Activation of the major isoforms of Cp, CpI and CpII, are required for a number of important cellular processes including adherence, shape change and migration. The current concept that cytoplasmic Cp locates and associates with its regulatory subunit (Rs) and substrates as well as translocates throughout the cell via random diffusion is not compatible with the spatial and temporal constraints of cellular metabolism. The novel finding that Cp and Rs function relies upon tenacious hydrophobic interactions with organelle membranes offers a unifying explanation for the paradoxical and puzzling features of Cp activation and regulation such as how nM concentrations of intracellular Ca(2+) can activate Cp molecules requiring muM to mM concentrations of Ca(2+) for in vitro activation, and how this protease can spatially and temporally locate specific substrates and translocate throughout the cell. We hypothesize that Cp and its regulatory moieties associate with organelles to facilitate the activation of this protease resulting in the cleavage of substrates and aid in its translocation throughout the cell.
Collapse
Affiliation(s)
- Joshua L Hood
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky Medical Center, Lexington, Kentucky, USA
| | | | | |
Collapse
|
13
|
Mahalingam R, Fedoroff N. Stress response, cell death and signalling: the many faces of reactive oxygen species. PHYSIOLOGIA PLANTARUM 2003; 119:56-68. [PMID: 0 DOI: 10.1034/j.1399-3054.2003.00156.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
|