Special Issue "Molecular System Bioenergetics"

Authors: Anna Brückner, Cécile Polge and Uwe Schlattner
Affiliation: INSERM U884, Laboratoire de la Bioénergétique et Appliquée, Université Joseph Fourier, 2280 Rue de la Piscine, BP 53, Grenoble Cedex 9, France. E-mail: brucknea@ujf-grenoble.fr; Tel. +33-476635627; Fax: +33-476514218
Type: Review
Title: Yeast-two Hybrid, a Powerful Tool for Systems Biology
Abstract: A key property of complex biological systems is the interaction network formed by its different components, primarily proteins. These interactions are crucial for all levels of cellular function, including architecture, metabolism and signalling. All these functions are regulated at some level by the availability of cellular energy. In fact, ATP generation needs a precise interplay between proteins of glycolysis, TCA cycle, mitochondrial electron transport and other cellular systems like creatine kinase, which often includes specific (micro) compartmentation of proteins. Here, protein-protein interactions play a crucial role in establishing multiprotein complexes, often linked to cellular structures like membranes or the cytoskeleton. These topologies then allow for more precise regulation and have further thermodynamic advantages like substrate channelling between active sites. A systemic approach to bioenergetics will need a full understanding of these mostly rather weak protein-protein interactions. The more recent technological development in high throughput interactomics methods is expected to dramatically increase our knowledge on protein interaction networks. The two main methods currently used are mass spectrometry and yeast-two-hybrid screening. More than 50% of the known interactions have been detected using the in vivo yeast-two-hybrid approach. However, with the massive application of this method, also some limitations became apparent. This review will focus on the strengths and weaknesses of this molecular genetic method and provides some guidelines for the verification of detected protein-protein interactions.

Regular Papers

Type of Paper: Review
Title: Learning from Huntington Disease Brain Pathology to Disclose Biomarkers in Peripheral Tissues
Authors: Orobello S, Martino T, Squitieri F and Cannella M *
Affiliations: Neurogenetics Unit, IRCCS Neuromed and Centre for Rare Diseases, Località Camerelle, 86077, Pozzilli (IS), Italy. E-mail: neurogen@neuromed.it
Abstract: Huntington disease (HD) is a progressive neurodegenerative illness caused by a dominant CAG repeat expansion mutation in the exon 1 of the gene encoding huntingtin (htt). Mutated htt is ubiquitously expressed in human tissues and, although its toxic effects are primarily in the central nervous system (CNS), many pathological changes have so far been described in periphery. An aim of the research is the identification of reliable easy-to-get biomarkers to detect abnormalities reflecting progressive neuronal degeneration and dysfunction, and which could be used to assess the effect of therapeutic drugs. Among the mechanisms of HD so far identified, transcriptional dysregulation of several genes and the abnormal growth factor activity and production, represent main features of both central and peripheral HD pathology. In this review we focused on biological changes in peripheral tissues that could mirror the CNS pathology, thus potentially representing disease biomarkers of HD.

Type of Paper: Review
Title: Mitochondrial Metabolic Signaliging: a Reverse Regulation Inherited from Endosymbiosis?
Authors: Bellance Nadège and Rossignol Rodrigue
Affiliations: INSERM U688, Bordeaux; Université Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux, France. E-mail: rossig@u-bordeaux2.fr; Tel. 33 (0) 5 57 57 47 81
Abstract: Herein we define mitochondrial metabolic signaling (MMS) as the reverse regulation of various (energy) metabolites and by-products accumulating upstream or downstream the mitochondrion, and acting on cellular gene expression. Common signaling metabolites include succinate, lactate, pyruvate, oxoglutarate or fumarate. They act as messengers to connect bioenergetic changes with the adaptation of cell physiology to environmental conditions. Deviation of MMS is also involved in pathology, as observed in tumors. According to MMS, the remodeling of mitochondrial metabolic pathways alters de facto the metabolome, which modifies in turn cellular gene expression, via the modulation of transcription factors (HIF1, HIF2) and co-activators (PGC1a) activity. More generally, this feed-back process occurs under physiological conditions, and participates to the regulation of cell homeostasy. Interestingly, under stress conditions some bacteria can extrude such metabolites, raising the question of the endosymbiotic origin of MMS.

Type of Paper: Article
Title: Calcium Ions Regulate K⁺ Uptake into Brain Mitochondria: the Evidence for a Novel Mitochondrial Potassium Channel
Authors: Jolanta Skalska ^1,#, Piotr Bednarczyk ^1,2,#, Marta Głąb ¹, Bogusz Kulawiak ¹, Grzegorz Wilczynski ³, Krzysztof Dołowy ², Wolfram S. Kunz ^4,* and Adam Szewczyk ¹
Affiliations: ¹ Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, 3 Pasteur st., 02-093 Warsaw, Poland
² Department of Biophysics, Agricultural University SGGW, 159 Nowoursynowska St., 02-776 Warsaw, Poland
³ Laboratory of Molecular and Systemic Neuromorphology, Nencki Institute of Experimental Biology, 3 Pasteur st., 02-093 Warsaw, Poland
⁴ Division of Neurochemistry, Department of Epileptology, University Bonn Medical Center, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany
* Author to whom correspondence should be addressed;
E-mail: wolfram.kunz@ukb.uni-bonn.de
^# These authors contributed equally to this work
Abstract: Mitochondrial responses to changes of cytosolic calcium concentration have a strong impact on neuronal cell viability. We studied the Ca²⁺-induced mitochondrial depolarization and increase ofmitochondrial respiration in isolated rat brain mitochondria. These effects were found to be specific for potassium ions and depolarization and increase of respiration of mitochondria were blocked by iberiotoxin and charybdotoxin – well known inhibitors of the large conductance potassium channel (BK_Ca channel). Furthermore, NS1619 – a BK_Ca channel opener induced potassium–specific effects on mitochondria similar to that induced by Ca²⁺. The putative presence of a calcium-activated, large conductance (~265±5 pS) potassium channel (sensitive to charybdotoxin and NS1619) in rat brain mitochondria was confirmed by reconstitution of the mitochondrial inner membrane into planar lipid bilayers. We also observed immunoreactivity of anti-b4 subunit (of the BK_Ca channel) antibody with ~26 kDa proteins in brain mitochondria. Immunochemical analysis confirmed the predominant occurrence of b4 subunit in neuronal but not glial mitochondria. We hypothesize that the mitochondrial BK_Ca channel represents a new mitochondrial calcium sensor, that can contribute to neuronal signal transduction.

Type of Paper: Review
Title: Apoptotic Stimuli as Possible Effectors of Metabolic Systems: Concepts and Practical Application of Top-down Control Analysis to Attached Neurons
Author: Mika B. Jekabsons
Affiliation: Department of Biology, University of Mississippi, 110 Shoemaker Hall, University, MS 38677, USA. E-mail: jekabson@olemiss.edu
Abstract: Mitochondria are central to both energy metabolism and apoptosis. Metabolic changes have been reported during apoptosis, but it is unclear if they are important in signaling death, or merely occur as a consequence of apoptosis. One way to distinguish between these possibilities is by use of top-down control analysis, a systems biology approach that considers metabolism as an integrated unit. Top-down control analysis can be used to identify reactions whose kinetics are directly affected by apoptotic stimuli, and reactions whose rates are changed indirectly as a result of changes in the concentrations of one or more intermediates. Direct effects suggest a role in the signaling process, whereas indirect ones suggest secondary changes as a consequence of apoptosis. The concepts underlying control analysis will be reviewed. Metabolic flux measurements are an important component to this approach, but can be technically difficult, particularly when using adherent cells. A simple method will be described that renders such measurements possible in attached neurons.