Global organization of metabolic fluxes in the bacterium, Escherichia coli

Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological organization of individual reactions into metabolic networks is increasingly well understood, the principles governing their global functional utilization under different growth conditions pose many open questions. We implement a flux balance analysis of the E. coli MG1655 metabolism, finding that the network utilization is highly uneven: while most metabolic reactions have small fluxes, the metabolism's activity is dominated by several reactions with very high fluxes. E. coli responds to changes in growth conditions by reorganizing the rates of selected fluxes predominantly within this high flux backbone. The identified behavior likely represents a universal feature of metabolic activity in all cells, with potential implications to metabolic engineering.Comment: 15 pages 4 figure

A New Role for Translation Initiation Factor 2 in Maintaining Genome Integrity

Escherichia coli translation initiation factor 2 (IF2) performs the unexpected function of promoting transition from recombination to replication during bacteriophage Mu transposition in vitro, leading to initiation by replication restart proteins. This function has suggested a role of IF2 in engaging cellular restart mechanisms and regulating the maintenance of genome integrity. To examine the potential effect of IF2 on restart mechanisms, we characterized its influence on cellular recovery following DNA damage by methyl methanesulfonate (MMS) and UV damage. Mutations that prevent expression of full-length IF2-1 or truncated IF2-2 and IF2-3 isoforms affected cellular growth or recovery following DNA damage differently, influencing different restart mechanisms. A deletion mutant (del1) expressing only IF2-2/3 was severely sensitive to growth in the presence of DNA-damaging agent MMS. Proficient as wild type in repairing DNA lesions and promoting replication restart upon removal of MMS, this mutant was nevertheless unable to sustain cell growth in the presence of MMS; however, growth in MMS could be partly restored by disruption of sulA, which encodes a cell division inhibitor induced during replication fork arrest. Moreover, such characteristics of del1 MMS sensitivity were shared by restart mutant priA300, which encodes a helicase-deficient restart protein. Epistasis analysis indicated that del1 in combination with priA300 had no further effects on cellular recovery from MMS and UV treatment; however, the del2/3 mutation, which allows expression of only IF2-1, synergistically increased UV sensitivity in combination with priA300. The results indicate that full-length IF2, in a function distinct from truncated forms, influences the engagement or activity of restart functions dependent on PriA helicase, allowing cellular growth when a DNA–damaging agent is present

The creatine kinase system and pleiotropic effects of creatine

The pleiotropic effects of creatine (Cr) are based mostly on the functions of the enzyme creatine kinase (CK) and its high-energy product phosphocreatine (PCr). Multidisciplinary studies have established molecular, cellular, organ and somatic functions of the CK/PCr system, in particular for cells and tissues with high and intermittent energy fluctuations. These studies include tissue-specific expression and subcellular localization of CK isoforms, high-resolution molecular structures and structure–function relationships, transgenic CK abrogation and reverse genetic approaches. Three energy-related physiological principles emerge, namely that the CK/PCr systems functions as (a) an immediately available temporal energy buffer, (b) a spatial energy buffer or intracellular energy transport system (the CK/PCr energy shuttle or circuit) and (c) a metabolic regulator. The CK/PCr energy shuttle connects sites of ATP production (glycolysis and mitochondrial oxidative phosphorylation) with subcellular sites of ATP utilization (ATPases). Thus, diffusion limitations of ADP and ATP are overcome by PCr/Cr shuttling, as most clearly seen in polar cells such as spermatozoa, retina photoreceptor cells and sensory hair bundles of the inner ear. The CK/PCr system relies on the close exchange of substrates and products between CK isoforms and ATP-generating or -consuming processes. Mitochondrial CK in the mitochondrial outer compartment, for example, is tightly coupled to ATP export via adenine nucleotide transporter or carrier (ANT) and thus ATP-synthesis and respiratory chain activity, releasing PCr into the cytosol. This coupling also reduces formation of reactive oxygen species (ROS) and inhibits mitochondrial permeability transition, an early event in apoptosis. Cr itself may also act as a direct and/or indirect anti-oxidant, while PCr can interact with and protect cellular membranes. Collectively, these factors may well explain the beneficial effects of Cr supplementation. The stimulating effects of Cr for muscle and bone growth and maintenance, and especially in neuroprotection, are now recognized and the first clinical studies are underway. Novel socio-economically relevant applications of Cr supplementation are emerging, e.g. for senior people, intensive care units and dialysis patients, who are notoriously Cr-depleted. Also, Cr will likely be beneficial for the healthy development of premature infants, who after separation from the placenta depend on external Cr. Cr supplementation of pregnant and lactating women, as well as of babies and infants are likely to be of benefit for child development. Last but not least, Cr harbours a global ecological potential as an additive for animal feed, replacing meat- and fish meal for animal (poultry and swine) and fish aqua farming. This may help to alleviate human starvation and at the same time prevent over-fishing of oceans

Wintertime organic and inorganic aerosols in Lanzhou, China: sources, processes, and comparison with the results during summer

Lanzhou, which is located in a steep alpine valley in western China, is one of the most polluted cities in China during the wintertime. In this study, an Aerodyne high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS), a seven-wavelength aethalometer, and a scanning mobility particle sizer (SMPS) were deployed during 10 January to 4 February 2014 to study the mass concentrations, chemical processes, and sources of submicrometer particulate matter (PM₁). The average PM₁ concentration during this study was 57.3 µg m⁻³ (ranging from 2.1 to 229.7 µg m⁻³ for hourly averages), with organic aerosol (OA) accounting for 51.2 %, followed by nitrate (16.5 %), sulfate (12.5 %), ammonium (10.3 %), black carbon (BC, 6.4 %), and chloride (3.0 %). The mass concentration of PM₁ during winter was more than twice the average value observed at the same site in summer 2012 (24.5 µg m⁻³), but the mass fraction of OA was similar in the two seasons. Nitrate contributed a significantly higher fraction to the PM₁ mass in winter than summer (16.5 % vs. 10 %), largely due to more favored partitioning to the particle phase at low air temperature. The mass fractions of both OA and nitrate increased by  ∼  5 % (47 to 52 for OA and 13 to 18 % for nitrate) with the increase of the total PM₁ mass loading, while the average sulfate fraction decreased by 6 % (17 to 11 %), indicating the importance of OA and nitrate for the heavy air pollution events in Lanzhou. The size distributions of OA, nitrate, sulfate, ammonium, and chloride all peaked at  ∼  500 nm, with OA being slightly broader, suggesting that aerosol particles were internally mixed during winter, likely due to frequently calm and stagnant air conditions during wintertime in Lanzhou (average wind speed: 0.82 m s⁻¹).<br><br>The average mass spectrum of OA showed a medium oxidation degree (average O ∕ C ratio of 0.28), which was lower than that during summer 2012 (O ∕ C  =  0.33). This is consistent with weaker photochemical processing during winter. Positive matrix factorization (PMF) with the multi-linear engine (ME-2) solver identified six OA sources, i.e., a hydrocarbon-like OA (HOA), a biomass burning OA (BBOA), a cooking-emitted OA (COA), a coal combustion OA (CCOA), and two oxygenated OA (OOA) factors. One of the OOAs was less oxidized (LO-OOA), and the other one more oxidized (MO-OOA). LO-OOA was the most abundant OA component (22.3 % of OA mass), followed by CCOA (22.0 %), COA (20.2 %), MO-OOA (14.9 %), BBOA (10.8 %), and HOA (9.8 %). The mass fraction of primary OA ( =  HOA + BBOA + COA + CCOA) increased during high PM pollution periods, indicating that local primary emissions were a main reason for the formation of air pollution events in Lanzhou during winter. Radiocarbon (¹⁴C) measurement was conducted on four PM_2.5 filter samples from this study, which allowed for a quantitative source apportionment of organic carbon (OC). The non-fossil sources on average accounted for 55 ± 3 % of OC, which could be mainly from biomass burning and cooking activities, suggesting the importance of non-fossil sources for the PM pollution in Lanzhou. Together with the PMF results, we also found that a large fraction (66 ± 10 %) of the secondary OC was from non-fossil OC