1
|
Camponeschi I, Montanari A, Mazzoni C, Bianchi MM. Light Stress in Yeasts: Signaling and Responses in Creatures of the Night. Int J Mol Sci 2023; 24:ijms24086929. [PMID: 37108091 PMCID: PMC10139380 DOI: 10.3390/ijms24086929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Living organisms on the surface biosphere are periodically yet consistently exposed to light. The adaptive or protective evolution caused by this source of energy has led to the biological systems present in a large variety of organisms, including fungi. Among fungi, yeasts have developed essential protective responses against the deleterious effects of light. Stress generated by light exposure is propagated through the synthesis of hydrogen peroxide and mediated by regulatory factors that are also involved in the response to other stressors. These have included Msn2/4, Crz1, Yap1, and Mga2, thus suggesting that light stress is a common factor in the yeast environmental response.
Collapse
Affiliation(s)
- Ilaria Camponeschi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Arianna Montanari
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Cristina Mazzoni
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| | - Michele Maria Bianchi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, 00185 Rome, Italy
| |
Collapse
|
2
|
Camponeschi I, Damasco A, Uversky VN, Giuliani A, Bianchi MM. Phenotypic suppression caused by resonance with light-dark cycles indicates the presence of a 24-hours oscillator in yeast and suggests a new role of intrinsically disordered protein regions as internal mediators. J Biomol Struct Dyn 2020; 39:2490-2501. [PMID: 32223547 DOI: 10.1080/07391102.2020.1749133] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The mutual interaction between environment and life is a main topic of biological sciences. An interesting aspect of this interaction is the existence of biological rhythms spanning all the levels of organisms from bacteria to humans. On the other hand, the existence of a coupling between external oscillatory stimuli and adaptation and evolution rate of biological systems is a still unexplored issue. Here we give the demonstration of a substantial increase of heritable phenotypic changes in yeast, an organism lacking a photoreception system, when growing at 12 h light/dark cycles, with respect to both stable dark (or light) or non-12 + 12 h cycling. The model system was a yeast strain lacking a gene whose product is at the crossroad of many different physiological regulations, so ruling out any simple explanation in terms of increase in reverse gene mutations. The abundance of intrinsically disordered protein regions (IDPRs) in both deleted gene product and in its vast ensemble of interactors supports the hypothesis that resonance with the environmental cycle might be mediated by intrinsic disorder-driven interactions of protein molecules. This result opens to the speculation of the effect of environment/biological resonance phenomena in evolution and of the role of protein intrinsically disordered regions as internal mediators.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Ilaria Camponeschi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza Università di Roma, Roma, Italy
| | - Achille Damasco
- Department of Physics 'Ettore Pancini', Università di Napoli Federico II, Napoli, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Russia
| | - Alessandro Giuliani
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Michele M Bianchi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza Università di Roma, Roma, Italy
| |
Collapse
|
3
|
Polarized neural stem cells derived from adult bone marrow stromal cells develop a rosette-like structure. In Vitro Cell Dev Biol Anim 2013; 49:638-52. [DOI: 10.1007/s11626-013-9628-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/26/2013] [Indexed: 12/19/2022]
|
4
|
Plankar M, Brežan S, Jerman I. The principle of coherence in multi-level brain information processing. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 111:8-29. [PMID: 22986048 DOI: 10.1016/j.pbiomolbio.2012.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 08/02/2012] [Indexed: 02/03/2023]
Abstract
Synchronisation has become one of the major scientific tools to explain biological order at many levels of organisation. In systems neuroscience, synchronised subthreshold and suprathreshold oscillatory neuronal activity within and between distributed neuronal assemblies is acknowledged as a fundamental mode of neuronal information processing. Coherent neuronal oscillations correlate with all basic cognitive functions, mediate local and long-range neuronal communication and affect synaptic plasticity. However, it remains unclear how the very fast and complex changes of functional neuronal connectivity necessary for cognition, as mediated by dynamic patterns of neuronal synchrony, could be explained exclusively based on the well-established synaptic mechanisms. A growing body of research indicates that the intraneuronal matrix, composed of cytoskeletal elements and their binding proteins, structurally and functionally connects the synapses within a neuron, modulates neurotransmission and memory consolidation, and is hypothesised to be involved in signal integration via electric signalling due to its charged surface. Theoretical modelling, as well as emerging experimental evidence indicate that neuronal cytoskeleton supports highly cooperative energy transport and information processing based on molecular coherence. We suggest that long-range coherent dynamics within the intra- and extracellular filamentous matrices could establish dynamic ordered states, capable of rapid modulations of functional neuronal connectivity via their interactions with neuronal membranes and synapses. Coherence may thus represent a common denominator of neurophysiological and biophysical approaches to brain information processing, operating at multiple levels of neuronal organisation, from which cognition may emerge as its cardinal manifestation.
Collapse
Affiliation(s)
- Matej Plankar
- BION Institute, Stegne 21, 1000 Ljubljana, Slovenia.
| | | | | |
Collapse
|
5
|
Davies P, Demetrius LA, Tuszynski JA. Implications of quantum metabolism and natural selection for the origin of cancer cells and tumor progression. AIP ADVANCES 2012; 2:11101. [PMID: 22489276 PMCID: PMC3321517 DOI: 10.1063/1.3697850] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 01/09/2012] [Indexed: 05/31/2023]
Abstract
Empirical studies give increased support for the hypothesis that the sporadic form of cancer is an age-related metabolic disease characterized by: (a) metabolic dysregulation with random abnormalities in mitochondrial DNA, and (b) metabolic alteration - the compensatory upregulation of glycolysis to offset mitochondrial impairments. This paper appeals to the theory of Quantum Metabolism and the principles of natural selection to formulate a conceptual framework for a quantitative analysis of the origin and proliferation of the disease. Quantum Metabolism, an analytical theory of energy transduction in cells inspired by the methodology of the quantum theory of solids, elucidates the molecular basis for differences in metabolic rate between normal cells, utilizing predominantly oxidative phosphorylation, and cancer cells utilizing predominantly glycolysis. The principles of natural selection account for the outcome of competition between the two classes of cells. Quantum Metabolism and the principles of natural selection give an ontogenic and evolutionary rationale for cancer proliferation and furnish a framework for effective therapeutic strategies to impede the spread of the disease.
Collapse
|
6
|
Romagnoli G, Cundari E, Negri R, Crescenzi M, Farina L, Giuliani A, Bianchi MM. Synchronous protein cycling in batch cultures of the yeast Saccharomyces cerevisiae at log growth phase. Exp Cell Res 2011; 317:2958-68. [DOI: 10.1016/j.yexcr.2011.09.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 09/09/2011] [Accepted: 09/12/2011] [Indexed: 11/25/2022]
|
7
|
Davies PC, Demetrius L, Tuszynski JA. Cancer as a dynamical phase transition. Theor Biol Med Model 2011; 8:30. [PMID: 21867509 PMCID: PMC3177875 DOI: 10.1186/1742-4682-8-30] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 08/25/2011] [Indexed: 12/21/2022] Open
Abstract
This paper discusses the properties of cancer cells from a new perspective based on an analogy with phase transitions in physical systems. Similarities in terms of instabilities and attractor states are outlined and differences discussed. While physical phase transitions typically occur at or near thermodynamic equilibrium, a normal-to-cancer (NTC) transition is a dynamical non-equilibrium phenomenon, which depends on both metabolic energy supply and local physiological conditions. A number of implications for preventative and therapeutic strategies are outlined.
Collapse
Affiliation(s)
- Paul Cw Davies
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85287-1504, USA
| | | | | |
Collapse
|
8
|
Murray DB, Haynes K, Tomita M. Redox regulation in respiring Saccharomyces cerevisiae. Biochim Biophys Acta Gen Subj 2011; 1810:945-58. [PMID: 21549177 DOI: 10.1016/j.bbagen.2011.04.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 03/16/2011] [Accepted: 04/17/2011] [Indexed: 11/30/2022]
Abstract
BACKGROUND In biological systems, redox reactions are central to most cellular processes and the redox potential of the intracellular compartment dictates whether a particular reaction can or cannot occur. Indeed the widespread use of redox reactions in biological systems makes their detailed description outside the scope of one review. SCOPE OF THE REVIEW Here we will focus on how system-wide redox changes can alter the reaction and transcriptional landscape of Saccharomyces cerevisiae. To understand this we explore the major determinants of cellular redox potential, how these are sensed by the cell and the dynamic responses elicited. MAJOR CONCLUSIONS Redox regulation is a large and complex system that has the potential to rapidly and globally alter both the reaction and transcription landscapes. Although we have a basic understanding of many of the sub-systems and a partial understanding of the transcriptional control, we are far from understanding how these systems integrate to produce coherent responses. We argue that this non-linear system self-organises, and that the output in many cases is temperature-compensated oscillations that may temporally partition incompatible reactions in vivo. GENERAL SIGNIFICANCE Redox biochemistry impinges on most of cellular processes and has been shown to underpin ageing and many human diseases. Integrating the complexity of redox signalling and regulation is perhaps one of the most challenging areas of biology. This article is part of a Special Issue entitled Systems Biology of Microorganisms.
Collapse
Affiliation(s)
- Douglas B Murray
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.
| | | | | |
Collapse
|
9
|
Demetrius LA, Coy JF, Tuszynski JA. Cancer proliferation and therapy: the Warburg effect and quantum metabolism. Theor Biol Med Model 2010; 7:2. [PMID: 20085650 PMCID: PMC2819045 DOI: 10.1186/1742-4682-7-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 01/19/2010] [Indexed: 12/19/2022] Open
Abstract
Background Most cancer cells, in contrast to normal differentiated cells, rely on aerobic glycolysis instead of oxidative phosphorylation to generate metabolic energy, a phenomenon called the Warburg effect. Model Quantum metabolism is an analytic theory of metabolic regulation which exploits the methodology of quantum mechanics to derive allometric rules relating cellular metabolic rate and cell size. This theory explains differences in the metabolic rates of cells utilizing OxPhos and cells utilizing glycolysis. This article appeals to an analytic relation between metabolic rate and evolutionary entropy - a demographic measure of Darwinian fitness - to: (a) provide an evolutionary rationale for the Warburg effect, and (b) propose methods based on entropic principles of natural selection for regulating the incidence of OxPhos and glycolysis in cancer cells. Conclusion The regulatory interventions proposed on the basis of quantum metabolism have applications in therapeutic strategies to combat cancer. These procedures, based on metabolic regulation, are non-invasive, and complement the standard therapeutic methods involving radiation and chemotherapy
Collapse
Affiliation(s)
- Lloyd A Demetrius
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | | |
Collapse
|
10
|
Casey T, Patel O, Dykema K, Dover H, Furge K, Plaut K. Molecular signatures reveal circadian clocks may orchestrate the homeorhetic response to lactation. PLoS One 2009; 4:e7395. [PMID: 19816599 PMCID: PMC2754660 DOI: 10.1371/journal.pone.0007395] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 09/18/2009] [Indexed: 12/31/2022] Open
Abstract
Genes associated with lactation evolved more slowly than other genes in the mammalian genome. Higher conservation of milk and mammary genes suggest that species variation in milk composition is due in part to the environment and that we must look deeper into the genome for regulation of lactation. At the onset of lactation, metabolic changes are coordinated among multiple tissues through the endocrine system to accommodate the increased demand for nutrients and energy while allowing the animal to remain in homeostasis. This process is known as homeorhesis. Homeorhetic adaptation to lactation has been extensively described; however how these adaptations are orchestrated among multiple tissues remains elusive. To develop a clearer picture of how gene expression is coordinated across multiple tissues during the pregnancy to lactation transition, total RNA was isolated from mammary, liver and adipose tissues collected from rat dams (n = 5) on day 20 of pregnancy and day 1 of lactation, and gene expression was measured using Affymetrix GeneChips. Two types of gene expression analysis were performed. Genes that were differentially expressed between days within a tissue were identified with linear regression, and univariate regression was used to identify genes commonly up-regulated and down-regulated across all tissues. Gene set enrichment analysis showed genes commonly up regulated among the three tissues enriched gene ontologies primary metabolic processes, macromolecular complex assembly and negative regulation of apoptosis ontologies. Genes enriched in transcription regulator activity showed the common up regulation of 2 core molecular clock genes, ARNTL and CLOCK. Commonly down regulated genes enriched Rhythmic process and included: NR1D1, DBP, BHLHB2, OPN4, and HTR7, which regulate intracellular circadian rhythms. Changes in mammary, liver and adipose transcriptomes at the onset of lactation illustrate the complexity of homeorhetic adaptations and suggest that these changes are coordinated through molecular clocks.
Collapse
Affiliation(s)
- Theresa Casey
- Department of Animal Science, Michigan State University, East Lansing, Michigan, USA.
| | | | | | | | | | | |
Collapse
|
11
|
Demetrius L, Tuszynski JA. Quantum metabolism explains the allometric scaling of metabolic rates. J R Soc Interface 2009; 7:507-14. [PMID: 19734187 DOI: 10.1098/rsif.2009.0310] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A general model explaining the origin of allometric laws of physiology is proposed based on coupled energy-transducing oscillator networks embedded in a physical d-dimensional space (d = 1, 2, 3). This approach integrates Mitchell's theory of chemi-osmosis with the Debye model of the thermal properties of solids. We derive a scaling rule that relates the energy generated by redox reactions in cells, the dimensionality of the physical space and the mean cycle time. Two major regimes are found corresponding to classical and quantum behaviour. The classical behaviour leads to allometric isometry while the quantum regime leads to scaling laws relating metabolic rate and body size that cover a broad range of exponents that depend on dimensionality and specific parameter values. The regimes are consistent with a range of behaviours encountered in micelles, plants and animals and provide a conceptual framework for a theory of the metabolic function of living systems.
Collapse
Affiliation(s)
- Lloyd Demetrius
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | |
Collapse
|