Thermodynamic analysis of biodegradation pathways

Microorganisms provide a wealth of biodegradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental data for the thermodynamic properties of xenobiotics is scarce. The present work uses a group contribution method to study the thermodynamic properties of the University of Minnesota Biocatalysis/Biodegradation Database. The Gibbs free energies of formation and reaction are estimated for 914 compounds (81%) and 902 reactions (75%), respectively, in the database. The reactions are classified based on the minimum and maximum Gibbs free energy values, which accounts for uncertainty in the free energy estimates and a feasible concentration range relevant to biodegradation. Using the free energy estimates, the cumulative free energy change of 89 biodegradation pathways (51%) in the database could be estimated. A comparison of the likelihood of the biotransformation rules in the Pathway Prediction System and their thermodynamic feasibility was then carried out. This analysis revealed that when evaluating the feasibility of biodegradation pathways, it is important to consider the thermodynamic topology of the reactions in the context of the complete pathway. Group contribution is shown to be a viable tool for estimating, a priori, the thermodynamic feasibility and the relative likelihood of alternative biodegradation reactions. This work offers a useful tool to a broad range of researchers interested in estimating the feasibility of the reactions in existing or novel biodegradation pathways. Biotechnol. Bioeng. 2009;103: 532–541. © 2009 Wiley Periodicals, Inc.     

Metabolic networks: enzyme function and metabolite structure

Metabolism is one of the most complex cellular processes. Connections between biochemical reactions via substrate and product metabolites create complex metabolic networks that may be analyzed using network theory, stoichiometric analysis, and information on protein structure/function and metabolite properties. These frameworks take into consideration different aspects of enzyme chemistry, enzyme structure and metabolite structure, and demonstrate the impact of metabolic biochemistry on the systemic properties of metabolism. The integration of these approaches and the systematic classification of enzyme function and the chemical structure of metabolites will enhance our understanding of metabolism, and could improve our ability to predict enzyme function and novel metabolic pathways.     

Jay Bailey as mentor--the students' perspective

Professor James E. Bailey was not only a world-renowned leader and pioneer in biochemical engineering but also a mentor to the many graduate students and postdoctoral researchers in his group. To provide non-"Bailey-ites" with an impression of Jay as a mentor, we begin with a brief review of his career, focusing on the dynamics of the research group. Typical student experiences of being part of the Bailey group are then discussed, including the recognition of a particular research style and Jay's expectations for hard work. Finally, we provide some thoughts on Jay's mentoring style, which was marked by an ability to foster independence, a sense of quality, and passion for research. Jay's contributions as a mentor can perhaps be recognized as being as significant as his research achievements.     

Triplex targeting of a native gene in permeabilized intact cells: covalent modification of the gene for the chemokine receptor CCR5.

A 12 nucleotide oligodeoxyribopurine tract in the gene for the chemokine receptor CCR5 has been targeted and covalently modified in intact cells by a 12mer triplex forming oligonucleotide (TFO) bearing a reactive group. A nitrogen mustard placed on the 5'-end of the purine motif TFO modified a guanine on the DNA target with high efficiency and selectivity. A new use of a guanine analog in these TFOs significantly enhanced triplex formation and efficiency of modification, as did the use of the triplex-stabilizing intercalator coralyne. This site-directed modification of a native chromosomal gene in intact human cells under conditions where many limitations of triplex formation have been partially addressed underscores the potential of this approach for gene control via site-directed mutagenesis.     

Spatial and temporal variability in reproductive timing of Antarctic krill (Euphausia superba Dana)

Spawning dates of Antarctic krill, Euphausia superba Dana, were calculated from larval stage compositions, and corrected using data on maturity stage composition of the adult krill. Both original and literature data obtained from the Antarctic Peninsula-Bellingshausen Sea area and around the Antarctic continent were used. A time series (1975/76–1986/87) for several subareas of the Antarctic Peninsula-Bellingshausen Sea area indicates considerable variation in the krill spawning start, maxima and completion. In particular years (1975/76, 1980/81), krill spawning in the western Atlantic sector began relatively early, was intensive, and completed early. Some years (1977/78, 1981/82) were characterised by long and non-synchronised krill spawning. Compiled data sets for the Atlantic sector (1980/81), the entire Antarctic (1983/84) and the east Indian-west Pacific Antarctic waters (1981–85) reveal some spatial patterns in krill reproductive timing. In relation to spawning timing variation, the habitats of the krill population fall into five categories: (1) areas with an early beginning (late Novemberearly December) and a variable, but normally long, duration (3–3.5 months) of krill spawning; this is generally the southern boundary of the Antarctic Circumpolar Current, (2) areas with an early beginning, but a short duration of krill spawning (Gerlache Strait), (3) areas with a highly variable (within 1–1.5 months) beginning and a relatively long duration (ca. 3 months) of krill spawning (Bransfield Strait, Palmer Archipelago), (4) areas with a late beginning (late December–January) and a long duration of krill spawning (Bellingshausen Sea, D'Urville Sea, and Balleny Islands area), and (5) areas with a delayed beginning, but a very short duration (ca. 1.5 months) of krill spawning (Ross Sea slope, probably the Coastal Current area off the Lasarev Sea shelf and in the south-eastern Weddell Sea. These patterns can be partly explained by peculiarities of the ice regime in particular areas and by routes of krill movement within water circulation systems.     

Analysis of the maximum theoretical yield for the synthesis of erythromycin precursors in Escherichia coli

The heterologous biosynthesis of complex polyketides in Escherichia coli was recently achieved through metabolic engineering. However, it was observed that less than 10% of the propionate carbon source is transformed into the erythromycin precursor, 6-deoxyerythronolide B (6dEB), resulting in a 1.4% molar yield. Therefore, metabolic flux analysis was performed using a model of the Escherichia coli metabolism with the addition of the enzymes required for 6dEB synthesis. The analysis shows that the maximum theoretical yield for 6dEB synthesis in E. coli is 11%. The maintenance energy requirement of E. coli and limitations in the specific oxygen uptake rate can further decrease the yield, suggesting that the observed 6dEB yield of 1.4% can be the result of these two factors. In addition, the results suggest that an increase in the specific carbon and oxygen uptake rates will increase the yield of 6dEB. The use of glucose as an alternative carbon source was also evaluated using metabolic flux analysis and the results suggest that the choice of glucose as the carbon source will allow a small improvement in performance relative to a propionate-based process.