Reconstruction of pathways associated with amino acid metabolism in human mitochondria

We have used a bioinformatics approach for the identification and reconstruction of metabolic pathways associated with amino acid metabolism in human mitochondria. Human mitochondrial proteins determined by experimental and computational methods have been superposed on the reference pathways from the KEGG database to identify mitochondrial pathways. Enzymes at the entry and exit points for each reconstructed pathway were identified, and mitochondrial solute carrier proteins were determined where applicable. Intermediate enzymes in the mitochondrial pathways were identified based on the annotations available from public databases, evidence in current literature, or our MITOPRED program, which predicts the mitochondrial localization of proteins. Through integration of the data derived from experimental, bibliographical, and computational sources, we reconstructed the amino acid metabolic pathways in human mitochondria, which could help better understand the mitochondrial metabolism and its role in human health.     

Small-molecule metabolism: an enzyme mosaic

Escherichia coli has been a popular organism for studying metabolic pathways. In an attempt to find out more about how these pathways are constructed, the enzymes were analysed by defining their protein domains. Structural assignments and sequence comparisons were used to show that 213 domain families constitute 90% of the enzymes in the small-molecule metabolic pathways. Catalytic or cofactor-binding properties between family members are often conserved, while recognition of the main substrate with change in catalytic mechanism is only observed in a few cases of consecutive enzymes in a pathway. Recruitment of domains across pathways is very common, but there is little regularity in the pattern of domains in metabolic pathways. This is analogous to a mosaic in which a stone of a certain colour is selected to fill a position in the picture.     

Specificity space,the structure and evolution of metabolic pathways: Part II of a general theory

Biomolecular structures are interacting in terms of their force fields. These force fields define the specificity surfaces of the molecules. Specificity surfaces are represented by specificity vectors in a multidimensional specificity space. A quantitative analytical expression is developed for biochemical reactions and the evolution of metabolic pathways in the specificity space. This leads to detailed identification of various biomolecular processes with individual terms in the equation. This theoretical analysis permits defining detailed function and resolution requirement of enzymes, as well as, how these fit into the overall metabolic pattern of the cell. This paper is Part II of a general theory of the physical basis of the biological state of matter.     

ADMET: ADipocyte METabolism mathematical model

White fat cells have an important physiological role in maintaining triglyceride and free fatty acid levels due to their fundamental storage property, as well as determining insulin resistance. ADipocyte METabolism is a mathematical model that mimics the main metabolic pathways of human white fat cell, connecting inputs (composition of culture medium) to outputs (glycerol and free fatty acid release). It is based on a set of nonlinear differential equations, implemented in Simulink® and controlled by cellular energetic state. The validation of this model is based on a comparison between the simulation results and a set of experimental data collected from the literature.     

HEMETβ: improvement of hepatocyte metabolism mathematical model

This article describes hepatocyte metabolism mathematical model (HEMETβ), which is an improved version of HEMET, an effective and versatile virtual cell model based on hepatic cell metabolism. HEMET is based on a set of non-linear differential equations, implemented in Simulink®, which describes the biochemical reactions and energetic cell state, and completely mimics the principal metabolic pathways in hepatic cells. The cell energy function and modular structure are the core of this model. HEMETβ as HEMET model describes hepatic cellular metabolism in standard conditions (cell culture in a plastic multi-well placed in an incubator at 37°C with 5% of CO₂) and with excess substrates concentration. The main improvements in HEMETβ are the introductions of Michaelis–Menten models for reversible reactions and enzymatic inhibition. In addition, we eliminated hard non-linearities and modelled cell proliferation and every single aminoacid degradation pathway. All these innovations, combined with a user-friendly aspect, allow researchers to create new cell types and validate new experimental protocols just varying ‘peripheral’ pathways or model inputs.     

Insights into the molecular mechanism of glucose metabolism regulation under stress in chicken skeletal muscle tissues

As substantial progress has been achieved in modern poultry production with large-scale and intensive feeding and farming in recent years, stress becomes a vital factor affecting chicken growth, development, and production yield, especially the quality and quantity of skeletal muscle mass. The review was aimed to outline and understand the stress-related genetic regulatory mechanism, which significantly affects glucose metabolism regulation in chicken skeletal muscle tissues. Progress in current studies was summarized relevant to the molecular mechanism and regulatory pathways of glucose metabolism regulation under stress in chicken skeletal muscle tissues. Particularly, the elucidation of those concerned pathways promoted by insulin and insulin receptors would give key clues to the understanding of biological processes of stress response and glucose metabolism regulation under stress, as well as their later effects on chicken muscle development.     

Molecular evolution of the histidine biosynthetic pathway

The available sequences of genes encoding the enzymes associated with histidine biosynthesis suggest that this is an ancient metabolic pathway that was assembled prior to the diversification of the Bacteria, Archaea, and Eucarya. Paralogous duplications, gene elongation, and fusion events involving different his genes have played a major role in shaping this biosynthetic route. Evidence that the hisA and the hisF genes and their homologues are the result of two successive duplication events that apparently took place before the separation of the three cellular lineages is extended. These two successive gene duplication events as well as the homology between the hisH genes and the sequences encoding the TrpG-type amidotransferases support the idea that during the early stages of metabolic evolution at least parts of the histidine biosynthetic pathway were mediated by enzymes of broader substrate specificities. Maximum likelihood trees calculated for the available sequences of genes encoding these enzymes have been obtained. Their topologies support the possibility of an evolutionary proximity of archaebacteria with low GC Gram-positive bacteria. This observation is consistent with those detected by other workers using the sequences of heat-shock proteins (HSP70), glutamine synthetases, glutamate dehydrogenases, and carbamoylphosphate synthetases.Abbreviations as amino acid - ORF open reading frame - bp base pair - kb 10³ bp - CarA carbamoyl phosphate synthetase (EC 6.3.5.5) - GAT glutamine amidotransferase - GuaA GMP synthetase (EC 6.3.4.1) - PabA 4-amino-4-deoxychorismate synthase (EC 4.1.3-) - PyrG GTP synthetase (EC 6.3.4.2) - AICAR 5-aminoimidazole-4-carboxamide-l--d ribofuranosyl 5-monophosphate - HAL l-histidinal - HOL l-histidinol - HP histidinol phosphate - IAP imidazole acetol-phosphate - IGP imidazole glycerol phosphate - PR phosphoribosyl - PRFAR N-[(5-phosphoribulosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide - 5-ProFAR N ¹-[(5-phosphoribosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide - PRPP phosphoribosyl-pyrophosphate - RFLP restriction fragment length polymorphism Correspondence to: R. Fani     

Reconstruction of Pathways Associated with Amino Acid Metabolism in Human Mitochondria

We have used a bioinformatics approach for the identification and reconstruction of metabolic pathways associated with amino acid metabolism in human mitochon- dria. Human mitochondrial proteins determined by experimental and computa- tional methods have been superposed on the reference pathways from the KEGG database to identify mitochondrial pathways. Enzymes at the entry and exit points for each reconstructed pathway were identified, and mitochondrial solute carrier proteins were determined where applicable. Intermediate enzymes in the mito- chondrial pathways were identified based on the annotations available from public databases, evidence in current literature, or our MITOPRED program, which pre- dicts the mitochondrial localization of proteins. Through integration of the data derived from experimental, bibliographical, and computational sources, we recon- structed the amino acid metabolic pathways in human mitochondria, which could help better understand the mitochondrial metabolism and its role in human health.     

Integrating ecology into macroevolutionary research

On 9 March, over 150 biologists gathered in London for the Centre for Ecology and Evolution spring symposium, 'Integrating Ecology into Macroevolutionary Research'. The event brought together researchers from London-based institutions alongside others from across the UK, Europe and North America for a day of talks. The meeting highlighted methodological advances and recent analyses of exemplar datasets focusing on the exploration of the role of ecological processes in shaping macroevolutionary patterns.     

杀螟硫磷暴露对大鼠肝细胞的代谢毒性及机制研究

为了研究低剂量杀螟硫磷(fenitrothion-O-analog, FNT)暴露对大鼠肝细胞(buffalo rat liver cells,BRL)的代谢毒性,并通过作用于体外的一系列指标分析其作用机制,分别对空白对照组和杀螟硫磷暴露组(13.78、27.55、55.10 μg·mL^-1)暴露48 h,观察其对BRL内糖代谢、胰岛素敏感和糖原合成信号通路中蛋白表达的影响。实验结果表明,杀螟硫磷暴露能够显著抑制BRL细胞的活力,半数抑制浓度（IC₅₀）为275.5 μg·mL^-1。杀螟硫磷暴露使超氧化物歧化酶（superoxide dismutase,SOD）和乙酰胆碱酯酶AchE活力显著降低(P<0.01),其体内丙二醛（malonaldehyde,MDA）含量显著增加(P<0.01),引起细胞氧化损伤。杀螟硫磷暴露使其细胞内糖原、胰岛素和葡萄糖激酶含量显著降低(P<0.01),增加胰岛素抵抗。杀螟硫磷暴露显著下调胰岛素敏感信号通路中IRS的表达,抑制IRS的磷酸化,并显著上调AKT和PI3K的表达,显著上调糖原合成信号通路中GSK-3α和GSK-3β的表达。因此,杀螟硫磷暴露使BRL产生糖代谢毒性的机制是通过氧化应激诱发胰岛素抵抗,从而改变糖代谢相关信号通路中蛋白的表达而实现的。     

Insights into the evolution of sorbitol metabolism: phylogenetic analysis of SDR196C family

ABSTRACT: BACKGROUND: Short chain dehydrogenases/reductases (SDR) are NAD(P)(H)-dependent oxidoreductases with a highly conserved 3D structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities. The SDR196C family (http://www.sdr-enzymes.org) groups bacterial sorbitol dehydrogenases (SDH), which are of great industrial interest. In this study, we examine the phylogenetic relationship between the members of this family, and based on the findings and some sequence conserved blocks, a new and a more accurate classification is proposed. RESULTS: The distribution of the 66 bacterial SDH species analyzed was limited to Gram-negative bacteria. Six different bacterial families were found, encompassing alpha-, beta- and gamma-proteobacteria. This broad distribution in terms of bacteria and niches agrees with that of SDR, which are found in all forms of life. A cluster analysis of sorbitol dehydrogenase revealed different types of gene organization, although with a common pattern in which the SDH gene is surrounded by sugar ABC transporter proteins, another SDR, a kinase, and several gene regulators.According to the obtained trees, six different lineages and three sublineages can be discerned. The phylogenetic analysis also suggested two different origins for SDH in beta-proteobacteria and four origins for gamma-proteobacteria.Finally, this subdivision was further confirmed by the differences observed in the sequence of the conserved blocks described for SDR and some specific blocks of SDH, and by a functional divergence analysis, which made it possible to establish new consensus sequences and specific fingerprints for the lineages and sub lineages. CONCLUSION: SDH distribution agrees with that observed for SDR, indicating the importance of the polyol metabolism, as an alternative source of carbon and energy. The phylogenetic analysis pointed to six clearly defined lineages and three sub lineages, and great variability in the origin of this gene, despite its well conserved 3D structure. This suggests that SDH are very old and emerged early during the evolution. This study also opens up a new and more accurate classification of SDR196C family, introducing two numbers at the end of the family name, which indicate the lineage and the sublineage of each member, i.e, SDR196C6.3.     

Determination of volatile products of human colon cell line metabolism by GC/MS analysis

Colon cancer is one of the most reasons for cancer death worldwide. Thus, it is important to find new prognostic and diagnostic marker, as well as to throw light on the special metabolic pathways of colon cancer cells. This paper highlights for the first time some qualitative differences in the profiles of the volatile metabolites of colon cancer cell lines SW 480 (grade IV, Duke B) and SW 1116 (grade II, Duke A) among themselves and in comparison to the normal colon cell line NCM460, which are mostly represented by ketones and alcohols. These results, which were obtained by applying solid phase micro extraction (SPME) and combined gas chromatography/mass spectrometry (GC/MS), are consistent with Warburg’s hypothesis because the found reaction products may indicate that the cancer cells show the Crabtree’s effect. Furthermore, compounds like undecan-2-ol and pentadecan-2-one were associated for the first time with the human metabolism. In summary, these findings indicate that the metabolism of colon cancer cells differs extremely from the metabolism of healthy cells and it changes during the progress of the disease. Compounds that are present in the breath, the blood and the tissue of patients represent the differences and they can serve as new biomarker for colon cancer in future.     

Characterization and phylogenetic analysis of a cnidarian LMP X-like cDNA

Proteasomes are multisubunit protease complexes which are partly responsible for metabolism of intracellular, ubiquitinylated proteins. Vertebrates have adapted a second and specialized structure responsible for the generation of peptides presented to the adaptive immune system and is thus, commonly referred to as the immunoproteasome. This complex is assembled from paralogous copies of subunits belonging to the constitutive, housekeeping proteasome. The immunoproteasome is more efficient in the generation of peptides for display on major histocompatibility complex (MHC) molecules. Important components of this complex are the paralogous members, LMP X and 7; where the latter replaces the former in the assembly of the immunoproteasome of vertebrates. In this report, we describe an LMP X-like cDNA from an endosymbiont-free gorgonian coral, Swiftia exserta. Cnidarians predate the phylogenetic divergence of protostomes and deuterostomes (P–D split), and are becoming an essential model for our comprehension of immune system evolution. Phylogenetic analyses of available sequences indicates that invertebrate LMP X-like sequences are outgroups to vertebrate LMP X and LMP 7, and is in agreement with previous observations that the duplication event giving rise to the two rapidly diverging lineages of proteasomal subunits occurred before jawed fished divergence.     

Pathway analysis of Pichia pastoris to elucidate methanol metabolism and its regulation for production of recombinant proteins

This research rationally analyzes metabolic pathways of Pichia pastoris to study the metabolic flux responses of this yeast under methanol metabolism. A metabolic model of P. pastoris was constructed and analyzed by elementary mode analysis (EMA). EMA was used to comprehensively identify the cell's metabolic flux profiles and its underlying regulation mechanisms for the production of recombinant proteins from methanol. Change in phenotypes and flux profiles during methanol adaptation with varying feed mixture of glycerol and methanol was examined. EMA identified increasing and decreasing fluxes during the glycerol–methanol metabolic shift, which well agreed with experimental observations supporting the validity of the metabolic network model. Analysis of all the identified pathways also led to the determination of the metabolic capacities as well as the optimum metabolic pathways for recombinant protein synthesis during methanol induction. The network sensitivity analysis revealed that the production of proteins can be improved by manipulating the flux ratios at the pyruvate branch point. In addition, EMA suggested that protein synthesis is optimum under hypoxic culture conditions. The metabolic modeling and analysis presented in this study could potentially form a valuable knowledge base for future research on rational design and optimization of P. pastoris by determining target genes, pathways, and culture conditions for enhanced recombinant protein synthesis. The metabolic pathway analysis is also of considerable value for production of therapeutic proteins by P. pastoris in biopharmaceutical applications. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 30:28–37, 2014     

Regulation of energy metabolism in liver

Energy metabolism in liver has to cope with the special tasks of this organ in intermediary metabolism. Main ATP-generating processes in the liver cell are the respiratory chain and glycolysis, whereas main ATP-consuming processes are gluconeogenesis, urea synthesis, protein synthesis, ATPases and mitochondrial proton leak. Mitochondrial respiratory chain in the intact liver cell is subject to control mainly by substrate (hydrogen donors, ADP, oxygen) transport and supply and proton leak/slip. Whereas hormonal control is mainly on substrate supply to mitochondria, proton leak/slip is supposed to play an important role in the modulation of the efficiency of oxidative phosphorylation.     

Bacterial evolution and metabolism

This article examines the relationship between (or dependence of) bacterial evolution in prokaryotes and metabolism, and the changing physical-chemical conditions present during early evolution.