The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

MOTIVATION: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY: The specification of SBML Level 1 is freely available from http://www.sbml.org/     

Regulation of pyruvate dehydrogenase complex activity in Ehrlich ascites carcinoma cells by Ca2+ and pyruvate

The dependence of pyruvate dehydrogenase complex (PDC) activity on [Ca2+] was determined in Ehrlich ascites carcinoma cells at different pyruvate concentrations. The resulting family of curves had the following characteristics: a) bell-shaped appearance of all curves with maximum activity at 600 nM Ca2+; b) unchanged position of maxima with changes in pyruvate concentration; c) nonmonotonous changes in PDC activity with increasing pyruvate concentration at fixed [Ca2+]. Feasible mechanisms involving Ca2+-dependent phosphatase and kinase which are consistent with the experimental findings are discussed. To determine the steps in the chain of PDC reactions which determine the observed phenomena, a mathematical model is suggested which is based on the known data on the structural--functional relationships between the complex components--pyruvate dehydrogenase (E1), dihydrolipoyl acetyl transferase (E2), dihydrolipoyl dehydrogenase (E3), protein X, kinase, and phosphatase. To adequately describe the non-trivial dependence of PDC activity on [Ca2+] at different pyruvate concentrations, it was also necessary to consider the interdependence of some steps in the general chain of PDC reactions. Phenomenon (a) is shown to be due only to the involvement of protein X in the PDC reactions, phenomenon (b) to be due to changes in the activity of kinase, and phenomenon (c) to be due to dependence of acetylation and transacetylation rates on pyruvate concentration.     

Novel Electrochemically Active Bacterium Phylogenetically Related to Arcobacter butzleri,Isolated from a Microbial Fuel Cell

Exoelectrogenic bacteria are organisms that can transfer electrons to extracellular insoluble electron acceptors and have the potential to be used in devices such as microbial fuel cells (MFCs). Currently, exoelectrogens have been identified in the Alpha-, Beta-, Gamma- and Deltaproteobacteria, as well as in the Firmicutes and Acidobacteria. Here, we describe use of culture-independent methods to identify two members of the genus Arcobacter in the Epsilonproteobacteria that are selectively enriched in an acetate-fed MFC. One of these organisms, Arcobacter butzleri strain ED-1, associates with the electrode and rapidly generates a strong electronegative potential as a pure culture when it is supplied with acetate. A mixed-community MFC in which ∼90% of the population is comprised of the two Arcobacter species generates a maximal power density of 296 mW/liter. This demonstration of exoelectrogenesis by strain ED-1 is the first time that this property has been shown for members of this genus.A microbial fuel cell (MFC) is a mimic of a biological system in which microorganisms transfer electrons from organic compounds to a conductive external electron acceptor under anaerobic conditions (6). In an MFC, the electron acceptor is provided by an artificial anode, which is connected to an electric circuit. Although the basic processes involved in the generation of electricity by bacteria have been known for many years, recent interest in MFC development has been stimulated by the need to find alternative, carbon-neutral sources of energy generation. MFCs are particularly useful for breakdown of organic matter in wastewater treatment plants, in which production of electricity as a by-product can be used to power the process or can be sold to offset the cost of operation (6). At present, although the key principles of MFC design and operation are well understood (19), the technical aspects and particularly the microbiological aspects (18) are still in development. Further optimization of the design and microbial composition of these devices is desirable as current MFCs achieve power densities of no more than 1,550 mW/liter (7), which limits their real-world applications (6).The basic microbiological characteristics which influence the efficiency of an MFC are bacterial metabolism and bacterial electron transfer. Although most current MFCs perform optimally when they contain a mixed microbial community, some pure cultures that exhibit strong electrogenic activity in the MFC environment have been characterized (19). The electrogenic properties and some aspects of extracellular electron transfer have been defined for pure cultures of organisms such as Geobacter sulfurreducens (2, 3), Escherichia coli (27), Shewanella putrefaciens (15, 16), Rhodoferax ferrireducens (5), Rhodopseudomonas palustris DX-1 (40), and Ochrobactrum anthropi YZ-1 (41). The current list of confirmed exoelectrogens includes representatives of four of the five classes of Proteobacteria (only the Epsilonproteobacteria are not represented), as well as representatives of the Firmicutes and Acidobacteria (18). However, it is likely that novel electrogenic bacteria remain to be discovered.The metabolic characteristics required for an electrogenic bacterium depend upon the specific application for which an MFC is used, because not all electrogenic bacteria are able to fully oxidize several substrates. For example, Shewanella oneidensis oxidizes lactate to acetate under anaerobic conditions, while G. metallireducens oxidizes acetate but not glucose (20). R. ferrireducens can oxidize acetate, lactate, and glucose but does not degrade ethanol, another common fermentation end product (11). For this reason, MFCs which are employed in wastewater treatment when complex compounds have to be degraded are often inoculated with a diverse microbial community (for example, methanogenic sludge [30]). Degradation of acetate is a key bacterial characteristic because acetate is a primary organic intermediate in the degradation of organic matter in anoxic aquatic sediments. Moreover, the ability to use artificial electron acceptors (anodic electrodes) provides bacteria such as Geobacteraceae with a competitive advantage over other microorganisms under such conditions. Analysis of the microbial community firmly attached to anodes harvesting electricity from a variety of sediments demonstrated that microorganisms in the family Geobacteraceae were highly enriched on these anodes (2, 35). Moreover, it was shown that an MFC initially inoculated with methanogenic sludge failed to consume acetate in the absence of anodic electrodes over a 1-year period (8).Arcobacter spp. are inhabitants of human and animal hosts (14, 37) and also occur in various environments, including wastewater (24), surface water (21), seawater (9), and groundwater (32). Arcobacter spp. belong to the Epsilonproteobacteria, which includes pathogens (e.g., Campylobacter jejuni and Helicobacter pylori), opportunistic pathogens, and nonpathogenic environmental isolates (4). Typically, these bacteria have genomes with low G+C contents (27 to 30%), although some Epsilonproteobacteria, such as Wolinella spp. and Campylobacter curvus, have higher G+C contents. The environmental bacteria group into four clusters: Nautiliales, Arcobacter, Sulfurospirillum, and Thiovulgaceae. The genus Arcobacter comprises Arcobacter butzleri, Arcobacter cryaerophilus, Arcobacter skirrowii, and Arcobacter cibarius, all of which have been isolated from animals or food (particularly poultry), as well as Arcobacter halophilus, Arcobacter nitrofigilis, “Candidatus Arcobacter sulfidicus,” and a number of species characterized so far only at the 16S rRNA gene level (4). A feature of both “Ca. Arcobacter sulfidicus” and Arcobacter sp. strain FWKBO is autotrophic metabolism under microaerobic conditions, in contrast to the heterotrophic growth of A. butzleri. Both of these organisms use oxidation of sulfide to sulfur and are obligate autotrophs. Some Arcobacter spp. may be capable of Mn and Fe reduction; isolates from Black Sea sediments (36) oxidized acetate in the presence of Mn oxide. This was the first evidence of Mn or Fe reduction in nitrate-reducing Arcobacter microaerophiles and nitrate reducers; previously, the only other epsilonproteobacterium identified with this ability was Sulfurospirillum barnesii. Thus, organisms related to Arcobacter comprise an ecologically significant new group of dissimilatory Fe- and Mn-reducing bacteria.In the present study we isolated and characterized two strains phylogenetically related to Arcobacter spp. which are selectively enriched in an acetate-fed MFC. One of these strains, A. butzleri strain ED-1, which specifically associates with the MFC electrode, shows electrochemical activity when it is grown on acetate, and hence it is the first example of an exoelectrogenic epsilonproteobacterium.     

Kinetic model of functioning and regulation of <Emphasis Type="Italic">Escherichia coli</Emphasis> isocitrate dehydrogenase

To describe published experimental data on the functioning of E. coli isocitrate dehydrogenase (IDH), a Rapid Equilibrium Random Bi Ter mechanism involving the formation of two dead-end enzyme complexes is proposed and a kinetic model of enzyme functioning is constructed. The enzyme is shown to be regulated through reversible phosphorylation by IDH kinase/phosphatase; the latter, in its turn, is controlled by IDH substrates and also by a number of central metabolites—pyruvate, 3-phosphoglycerate, and AMP—reflecting the energy demand of the cell. Using the model, it is shown that an increase in the concentration of the above effectors raises the fraction of active IDH and thus enhances the Krebs cycle flux. The ratio between the free and the phosphorylated forms of IDH is more sensitive to AMP, NADP, and isocitrate than to pyruvate and 3-phosphoglycerate. The model also predicts changes in the ratio between phosphorylated and active forms of IDH in the Krebs cycle that occur with a change in the energy and biosynthetic loads on E. coli cells.     

The reconstruction and analysis of tissue specific human metabolic networks

Human tissues have distinct biological functions. Many proteins/enzymes are known to be expressed only in specific tissues and therefore the metabolic networks in various tissues are different. Though high quality global human metabolic networks and metabolic networks for certain tissues such as liver have already been studied, a systematic study of tissue specific metabolic networks for all main tissues is still missing. In this work, we reconstruct the tissue specific metabolic networks for 15 main tissues in human based on the previously reconstructed Edinburgh Human Metabolic Network (EHMN). The tissue information is firstly obtained for enzymes from Human Protein Reference Database (HPRD) and UniprotKB databases and transfers to reactions through the enzyme-reaction relationships in EHMN. As our knowledge of tissue distribution of proteins is still very limited, we replenish the tissue information of the metabolic network based on network connectivity analysis and thorough examination of the literature. Finally, about 80% of proteins and reactions in EHMN are determined to be in at least one of the 15 tissues. To validate the quality of the tissue specific network, the brain specific metabolic network is taken as an example for functional module analysis and the results reveal that the function of the brain metabolic network is closely related with its function as the centre of the human nervous system. The tissue specific human metabolic networks are available at .     

Kinetic modeling of ace operon genetic regulation in Escherichia coli

A family of kinetic models has been developed that takes into account available experimental information on the regulation of ace operon expression in Escherichia coli. This has allowed us to study and analyze possible versions of regulation of the ace operon and to test their possibilities. Based on literature analysis, we found that there is an ambiguity of properties of IclR (main repressor of ace operon). The main aspect of this ambiguity are two different forms of IclR purified from E. coli K strain and different coeffector sets for IclR purified from E. coli K and B strains. It has been shown that the full-length form of IclR is physiologically relevant and that IclR truncation is a result of purification of the protein from E. coli K strains. We also found that the IclR protein purified from E. coli B strain carries two coeffector binding sites. Using model-developed levels of steady state aceBAK expression against physiological ranges of coeffectors, concentration has been predicted.     

基于图论的代谢网络中流通代谢物处理新方法

使用图论方法对基因组尺度代谢网络进行途径搜索是目前途径设计中最常用的方法之一.然而,由于流通代谢物(如H+、H2O、CO2和ATP等)的影响,图论搜索得到的途径在生物学上经常是不可行的.虽然前人提出了一些方法对流通代谢物进行处理,但均存在一些问题,目前还没有标准的处理方法.文中基于流通代谢物在反应中作为转移磷酸等功能基...     

Kinetic Model of Mitochondrial Krebs Cycle: Unraveling the Mechanism of Salicylate Hepatotoxic Effects

This paper studies the effect of salicylate on the energy metabolism of mitochondria using in silico simulations. A kinetic model of the mitochondrial Krebs cycle is constructed using information on the individual enzymes. Model parameters for the rate equations are estimated using in vitro experimental data from the literature. Enzyme concentrations are determined from data on respiration in mitochondrial suspensions containing glutamate and malate. It is shown that inhibition in succinate dehydrogenase and α-ketoglutarate dehydrogenase by salicylate contributes substantially to the cumulative inhibition of the Krebs cycle by salicylates. Uncoupling of oxidative phosphorylation has little effect and coenzyme A consumption in salicylates transformation processes has an insignificant effect on the rate of substrate oxidation in the Krebs cycle. It is found that the salicylate-inhibited Krebs cycle flux can be increased by flux redirection through addition of external glutamate and malate, and depletion in external α-ketoglutarate and glycine concentrations.