Molecular System Bioenergetics—New Aspects of Metabolic Research

This Special Issue is a significant step in developing a new direction of metabolic research— Molecular System Bioenergetics, which itself is a part of Systems Biology. As a new paradigm of biological sciences, Systems Biology aims at understanding of biological functions by studies and description of new, system level properties, resulting from interactions between components of biological systems at any level of organization, from molecular to population. Metabolism is the way of life of cells by exchanging mass and energy with the surrounding medium, and understanding its mechanisms requires knowledge of the complex interactions between cellular systems and components. While studies of metabolism have a long history, new concepts of Systems Biology provide useful tools for metabolic research. According to Schrödinger, living cells need to be open systems with energy and mass exchange with the surrounding medium, with the aim of maintaining their high structural and functional organization and thus their internal entropy low, achieving this by means of increasing the entropy of the medium by catabolic reactions. Thus, Schrödinger wrote: “The essential thing in metabolism is that the organism succeeds in freeing itself from all entropy it cannot help producing while alive”. Thus, free energy conversion in the cells is an important, central part of metabolism, and understanding the complex mechanisms of its regulation is the aim of Molecular System Bioenergetics. In this Special Issue, several important problems in this field were analyzed

La bioénergétique systémique moléculaire des cellules cardiaques (la relation structure-fonction dans la régulation du métabolisme énergétique compartmentalisé)

An important element of metabolic regulation of cardiac and skeletal muscle energetics is the interaction of mitochondria with cytoskeleton. Mitochondria are in charge of supplying the cells with energy, adjusting its functional activity under conditions of stress or other aspects of life. Mitochondria display a tissue-specific distribution. In adult rat cardiomyocytes, mitochondria are arranged regularly in a longitudinal lattice at the level of A band between the myofibrils and located within the limits of the sarcomeres. In interaction with cytoskeleton, sarcomeres and sarcoplasmic reticulum they form the functional complexes, the intracellular energetic units (ICEUs). The ICEUs have specialized pathways of energy transfer and metabolic feedback regulation between mitochondria and ATPases, mediated by CK and AK. The central structure of ICEUs is the mitochondrial interactosome (MI) containing ATP Synthasome, respiratory chain, mitochondrial creatine kinase and VDAC, regulated by tubulins. The main role of MI is the regulation of respiration and the intracellular energy fluxes via phosophotransfer networks. The regulation of ICEUs is associated with structural proteins. The association of mitochondria with several cytoskeletal proteins described by several groups has brought to light the importance of structure-function relationship in the metabolic regulation of adult rat cardiomyocytes. To purvey a better understanding of these findings, the present work investigated the mechanism of energy fluxes control and the role of structure-function relationship in the metabolic regulation of adult rat cardiomyocytes. To show these complex associations in adult cardiac cells several proteins were visualized by confocal microscopy: a-actinin and b-tubulin isotypes. For the first time, it was showed the existence of the specific distribution of b-tubulin isotypes in adult cardiac cells. Respiratory measurements were performed to study the role of tubulins in the regulation of oxygen consumption. These results together confirmed the crucial role of cytoskeletal proteins -i.e. tubulins, a-actinin, plectin, desmin, and others- for the normal shape of cardiac cells as well as mitochondrial arrangement and regulation. In addition, in vivo - in situ mitochondrial dynamics were studied by the transfection of GFP-a-actinin, finding that fusion phenomenon does not occur as often as it is believed in healthy adult cardiac cells.Un élément important de la régulation du métabolisme énergétique des muscles cardiaque et squelettiques est l'interaction des mitochondries avec le cytosquelette. Les mitochondries sont responsables de l'approvisionnement des cellules en énergie, elles sont capables d'ajuster leur activité fonctionnelle en fonction des conditions de stress ou d'autres aspects de la vie. Les mitochondries ont une distribution spécifique selon les tissus. Dans les cardiomyocytes de rats adultes, les mitochondries sont disposées régulièrement dans un entrelacement longitudinal au niveau des bandes A, entre les myofibrilles et dans les limites des sarcomères. En interaction avec le cytosquelette, le sarcomère et le réticulum sarcoplasmique, elles forment des complexes fonctionnels appelés unités énergétiques intracellulaires (ICEUs). Les ICEUs ont des voies spécialisées de transfert d'énergie et de régulation des feedback métaboliques entre les mitochondries et les ATPases, médiée par la CK et l'AK. La structure centrale des ICEUs est l'interactosome mitochondrial (MI) qui confient l'ATP synthasome, la chaîne respiratoire, la créatine kinase mitochondriale et VDAC, qui pourrait être régulé par les tubulines. Le rôle principal du MI est la régulation de la respiration et des flux d'énergie intracellulaires via les réseaux de phosphotransfert. La régulation des ICEUs est liée aux protéines structurales. L'association des mitochondries avec plusieurs protéines du cytosquelette, décrite par plusieurs groupes, a mis en évidence l'importance de la relation structure-fonction dans la régulation métabolique des cardiomyocytes de rats adultes. Pour fournir une meilleure compréhension de ces résultats, le présent travail étudie le mécanisme de contrôle des flux d'énergie et le rôle des relations structure-fonction dans la régulation métabolique de cardiomyocytes de rats adultes. Pour montrer ces associations complexes dans les cellules cardiaques adultes, plusieurs protéines ont été visualisées par microscopie confocale: l'a-actinine et les isoformes des b-tubulines. Pour la première fois, l'existence d'une distribution spécifique des isoformes de b-tubuline dans les cellules cardiaques adultes a été montré. Des mesures respiratoires ont été réalisées pour étudier le rôle des tubulines dans la régulation de la consommation d'oxygène. Ces résultats ont confirmé le rôle déterminant des protéines du cytosquelette -tubulines, a-actinine, plectine, desmine, et autres- pour le maintien de la forme normale des cellules cardiaques, ainsi que de l'arrangement et de la régulation mitochondrial. En outre, la dynamique mitochondriale a été étudiée in vivo et in situ par la transfection de la GFP-a-actinine, ceci permettant la mise en évidence du fait que le phénomène de fusion ne se produit pas aussi souvent qu'on ne le croit pour des cellules cardiaques adultes en bonne santé.SAVOIE-SCD - Bib.électronique (730659901) / SudocGRENOBLE1/INP-Bib.électronique (384210012) / SudocGRENOBLE2/3-Bib.électronique (384219901) / SudocSudocFranceF

Südamerakkude sünnijärgse arengu bioenergeetilised aspektid: struktuuri ja funktsiooni vaheliste seoste väljakujunemine

Taust ja eesmärk. Täiskasvanud südamerakkude bioenergeetikas on valdavaks ATP genereerimisemehhanismiks mitokondriaalne oksüdatiivne fosforüülimine, mis katab tavatingimustel üle 90% südame energeetilisest vajadusest. Mitokondrid paiknevad kardiomüotsüütides korrapäraselt müofibrillide vahel, asetudes kohakuti libisevate filamentide kontaktalaga (sarkomeeri anisotroopne (A) vööt). Aktomüosiinisüsteem, mitokondrid, sarkoplasmaatiline võrgustik ja nendega seotud tsütoskeleti valgud moodustavad rakus ühtse struktuurse ja funktsionaalse terviku, nn energeetilise üksuse (EÜ), mis reguleerib efektiivselt energia tootmist ja fosforüülrühma ülekannet. Vahetult pärast sündi on mitokondrite paigutus ebakorrapärane, täiskasvanud kardiomüotsüüdiga võrreldes on oluliselt erinev ka südamerakkude metabolism ning energiaülekande regulatsioon. Töö eesmärgiks oli uurida südame mitokondriaalse hingamise regulatsiooni mehhanismide väljakujunemist südame sünnijargses arengus ning selle seotust mitokondrite ja tubuliini isovormide rakusisese paigutusega. Töö tulemused võimaldavad selgitada südamerakkude teatud patoloogiliste seisundite etioloogiat. Metoodika. Kardiomüotsüüdid isoleeriti, perfuseerides katseloomade (Wistari liini rotid) südant kollagenaas A lahusega. Skineeritud kiudude eraldamiseks kasutati meetodit, mille käigus lihaskiud eraldatakse õrnalt pintsettidega ja töödeldakse seejärel saponiiniga. Permeabiliseeritud kardiomüotsüütide ja skineeritud kiudude hapnikutarbimine registreeriti suure lahutusvõimega oksügraafil. Preparaatide visualiseerimiseks kasutati konfokaalmikroskoope Zeiss LSM 510 ja Olympus FluoView FV10i-W. Tulemused. Katseloomade sünni järel toimuvad esimese pooleteise kuu jooksul südamerakuenergiaülekande regulatsioonis kiired muutused: mitokondrite paigutus muutub korrapäraseks, toimub tsütoskeleti funktsionaalselt oluliste komponentide paigutumine mitokondrite lähedusse ja sellega samal ajal kasvavad oluliselt difusioonitakistused adenosiindifosfaadile (Km(ADP) väärtus suureneb 75,0 ・} 4,5 μM 3 päeva vanuste rottide kardiomüotsüütides kuni 317 ・} 29,5 μM vorreldes 84päevaste katseloomadega) ning käivitub kreatiinkinaasi-fosfokreatiini ülekandevõrgustik mitokondrite ja tsütosoolsete ATPaaside vahel. Järeldused. Katseloomade sünnijargse arengu käigus toimuvad dünaamilised muutusedkardiomüotsüütide struktuuris, millega kaasnevad muutused nende funktsioonis. Funktsionaalsete vastasmõjude tekkimine mitokondrite ja tsütoskeleti komponentide vahel on eelduseks täiskasvanud südamerakule omase energiametabolismi väljakujunemiseks. Eesti Arst 2013; 92(7):372–38

Uusi suundi kasvajate energiametabolismi uuringutes

Genoomika kiire arengu käigus on selgunud, et selle valdkonna meetoditega ei ole võimalik erinevaid metabolismihäireid terviklikult kirjeldada ning täiendavalt on vaja kasutusele võtta teisi meetodeid rakuenergeetikast ning proteoomikast. Äärmiselt huvitavaks kujuneb selline süsteemsem käsitlus ulatuslike patoloogiliste muutustega maliigses koes. Eelmise sajandi alguses kirjeldas Otto Warburg efekti, kus tuumorirakkudes toimus eelistatult glükolüüs isegi normoksiatingimustes. Tema esmane arvamus, et just see asjaolu ongi raku maliigsuse allikas, lükati järgnevatel aastatel uute avastuste valguses ümber. Lisaks ulatuslikele rakuenergeetilistele ümberkorraldustele maliigse raku sees (nt kärbitud Krebsi-tsükkel, hingamisahela superkompleksid) on viimastel aastatel erinevate vähipaikmete juures korduvalt tõestatud ka kahe kompartmendi olemasolu, kus maliigne rakk allutab ümbritseva strooma enda jaoks vajalikke metaboliite tootma. Maliigsuse täpsem olemus, paremad ravimisihtmärgid ning -strateegiad võivad peituda just kasvajate süsteemsemate uuringute tulemustes. Eesti Arst 2013; 92(5):261–26

The Fungal Fast Lane: Common Mycorrhizal Networks Extend Bioactive Zones of Allelochemicals in Soils

Allelopathy, a phenomenon where compounds produced by one plant limit the growth of surrounding plants, is a controversially discussed factor in plant-plant interactions with great significance for plant community structure. Common mycorrhizal networks (CMNs) form belowground networks that interconnect multiple plant species; yet these networks are typically ignored in studies of allelopathy. We tested the hypothesis that CMNs facilitate transport of allelochemicals from supplier to target plants, thereby affecting allelopathic interactions. We analyzed accumulation of a model allelopathic substance, the herbicide imazamox, and two allelopathic thiophenes released from Tagetes tenuifolia roots, by diffusion through soil and CMNs. We also conducted bioassays to determine how the accumulated substances affected plant growth. All compounds accumulated to greater levels in target soils with CMNs as opposed to soils without CMNs. This increased accumulation was associated with reduced growth of target plants in soils with CMNs. Our results show that CMNs support transfer of allelochemicals from supplier to target plants and thus lead to allelochemical accumulation at levels that could not be reached by diffusion through soil alone. We conclude that CMNs expand the bioactive zones of allelochemicals in natural environments, with significant implications for interspecies chemical interactions in plant communities

The Metabolic Core and Catalytic Switches Are Fundamental Elements in the Self-Regulation of the Systemic Metabolic Structure of Cells

[Background] Experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a metabolic core formed by a set of enzymatic reactions which are always active under all environmental conditions, while the rest of catalytic processes are only intermittently active. The reactions of the metabolic core are essential for biomass formation and to assure optimal metabolic performance. The on-off catalytic reactions and the metabolic core are essential elements of a Systemic Metabolic Structure which seems to be a key feature common to all cellular organisms. [Methodology/Principal Findings] In order to investigate the functional importance of the metabolic core we have studied different catalytic patterns of a dissipative metabolic network under different external conditions. The emerging biochemical data have been analysed using information-based dynamic tools, such as Pearson's correlation and Transfer Entropy (which measures effective functionality). Our results show that a functional structure of effective connectivity emerges which is dynamical and characterized by significant variations of bio-molecular information flows. [Conclusions/Significance] We have quantified essential aspects of the metabolic core functionality. The always active enzymatic reactions form a hub –with a high degree of effective connectivity- exhibiting a wide range of functional information values being able to act either as a source or as a sink of bio-molecular causal interactions. Likewise, we have found that the metabolic core is an essential part of an emergent functional structure characterized by catalytic modules and metabolic switches which allow critical transitions in enzymatic activity. Both, the metabolic core and the catalytic switches in which also intermittently-active enzymes are involved seem to be fundamental elements in the self-regulation of the Systemic Metabolic Structure.Consejo Superior de Investigaciones Cientificas (CSIC),grant 201020I026. Ministerio de Ciencia e Innovacion (MICINN). Programa Ramon y Cajal. Campus de Excelencia Internacional CEI BioTIC GENIL, grant PYR-2010-14. Junta de Andalucia, grant P09-FQM-4682

Südamelihase rakkude struktuuri olulisus rakuhingamise regulatsioonis

Viimastel aastatel on järjest selgemaks saanud seos raku energeetilise ainevahetuse ja südamehaiguste vahel, mistõttu on oluline uurida seda mõjutavaid tegureid. Töös uuriti südamelihase rakkude mitokondriaalse hingamise regulatsiooni väga erineva rakustruktuuriga preparaatides: 1) permeabiliseeritud kardiomüotsüütides, kus mitokondrid on regulaarselt organiseeritud; 2) südamelihase fenotüübiga sarnastes kontraheeruvates HL-1 (B HL-1) rakkudes ja 3) HL-1 mittekontraheeruvates (NB HL-1) rakkudes. Nende preparaatide vahel esines suur erinevus mitokondriaalse hingamise regulatsioonis. Selline tulemus näitab raku struktuuri ja funktsiooni vaheliste seoste tähtsust südamelihase rakkudes ning võimaldab paremini mõista protsesse nii terves kui ka patoloogilises südamelihases. Eesti Arst 2008; 87(1):19−2

Phosphocreatine interacts with phospholipids, affects membrane properties and exerts membrane-protective effects

A broad spectrum of beneficial effects has been ascribed to creatine (Cr), phosphocreatine (PCr) and their cyclic analogues cyclo-(cCr) and phospho-cyclocreatine (PcCr). Cr is widely used as nutritional supplement in sports and increasingly also as adjuvant treatment for pathologies such as myopathies and a plethora of neurodegenerative diseases. Additionally, Cr and its cyclic analogues have been proposed for anti-cancer treatment. The mechanisms involved in these pleiotropic effects are still controversial and far from being understood. The reversible conversion of Cr and ATP into PCr and ADP by creatine kinase, generating highly diffusible PCr energy reserves, is certainly an important element. However, some protective effects of Cr and analogues cannot be satisfactorily explained solely by effects on the cellular energy state. Here we used mainly liposome model systems to provide evidence for interaction of PCr and PcCr with different zwitterionic phospholipids by applying four independent, complementary biochemical and biophysical assays: (i) chemical binding assay, (ii) surface plasmon resonance spectroscopy (SPR), (iii) solid-state (31)P-NMR, and (iv) differential scanning calorimetry (DSC). SPR revealed low affinity PCr/phospholipid interaction that additionally induced changes in liposome shape as indicated by NMR and SPR. Additionally, DSC revealed evidence for membrane packing effects by PCr, as seen by altered lipid phase transition. Finally, PCr efficiently protected against membrane permeabilization in two different model systems: liposome-permeabilization by the membrane-active peptide melittin, and erythrocyte hemolysis by the oxidative drug doxorubicin, hypoosmotic stress or the mild detergent saponin. These findings suggest a new molecular basis for non-energy related functions of PCr and its cyclic analogue. PCr/phospholipid interaction and alteration of membrane structure may not only protect cellular membranes against various insults, but could have more general implications for many physiological membrane-related functions that are relevant for health and disease

Molecular System Bioenergics of the Heart: Experimental Studies of Metabolic Compartmentation and Energy Fluxes versus Computer Modeling †

In this review we analyze the recent important and remarkable advancements in studies of compartmentation of adenine nucleotides in muscle cells due to their binding to macromolecular complexes and cellular structures, which results in non-equilibrium steady state of the creatine kinase reaction. We discuss the problems of measuring the energy fluxes between different cellular compartments and their simulation by using different computer models. Energy flux determinations by 18O transfer method have shown that in heart about 80% of energy is carried out of mitochondrial intermembrane space into cytoplasm by phosphocreatine fluxes generated by mitochondrial creatine kinase from adenosine triphosphate (ATP), produced by ATP Synthasome. We have applied the mathematical model of compartmentalized energy transfer for analysis of experimental data on the dependence of oxygen consumption rate on heart workload in isolated working heart reported by Williamson et al. The analysis of these data show that even at the maximal workloads and respiration rates, equal to 174 μmol O2 per min per g dry weight, phosphocreatine flux, and not ATP, carries about 80–85% percent of energy needed out of mitochondria into the cytosol. We analyze also the reasons of failures of several computer models published in the literature to correctly describe the experimental data