Stephanopoulos:Literature Reviewed

Literature Reviewed

The purpose of this page is to post the recent articles that we in the Stephanopoulos group review in our nearly-weekly literature review presentations. Sometimes the presenter focuses on a particular paper, and sometimes the roughly one-hour talk gives a brief overview of an important series of related papers.

2006

27 April 2006: Curt Fischer

Curt presented a recent PNAS article [1] which explicated a newly-discovered operon in E. coli. This operon encodes a previously unreported pathway for uracil degradation, which ends in the excretion of 3-hydroxypropionic acid in the medium. He also briefly mentioned two other recent high-profile papers on nitrogen metabolism--one reported the genome sequence of a anaerobic ammonium oxidizing bacterium and hypthesized the full structure of this metabolic pathway [2], and the other presents laborious and careful analysis carbon utilization of non-thermophilic archaea living in medium-depth oceanic waters[3]. These bacteria fix inorganic carbon and oxidize nitrogen, and are probably major players in the global nitrogen cycle.

1. Loh KD, Gyaneshwar P, Markenscoff Papadimitriou E, Fong R, Kim KS, Parales R, Zhou Z, Inwood W, and Kustu S. A previously undescribed pathway for pyrimidine catabolism. Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. DOI:10.1073/pnas.0600521103 |
2. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Médigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M, and Le Paslier D. Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature. 2006 Apr 6;440(7085):790-4. DOI:10.1038/nature04647 |
3. Ingalls AE, Shah SR, Hansman RL, Aluwihare LI, Santos GM, Druffel ER, and Pearson A. Quantifying archaeal community autotrophy in the mesopelagic ocean using natural radiocarbon. Proc Natl Acad Sci U S A. 2006 Apr 25;103(17):6442-7. DOI:10.1073/pnas.0510157103 |

4 May 2006: Joel Forrest Moxley

Joel gave an excellent overview of several landmark papers about new tools for high-throughput data collection in systems biology. The papers were made possible by advances in tiling DNA microarrays, protein arrays, and automated yeast transformation and colony characterization.

4. Pokholok DK, Harbison CT, Levine S, Cole M, Hannett NM, Lee TI, Bell GW, Walker K, Rolfe PA, Herbolsheimer E, Zeitlinger J, Lewitter F, Gifford DK, and Young RA. Genome-wide map of nucleosome acetylation and methylation in yeast. Cell. 2005 Aug 26;122(4):517-27. DOI:10.1016/j.cell.2005.06.026 |
5. Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, Botstein D, and Kruglyak L. Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science. 2006 Mar 31;311(5769):1932-6. DOI:10.1126/science.1123726 |
6. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney RR, Schmidt MC, Rachidi N, Lee SJ, Mah AS, Meng L, Stark MJ, Stern DF, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki PF, and Snyder M. Global analysis of protein phosphorylation in yeast. Nature. 2005 Dec 1;438(7068):679-84. DOI:10.1038/nature04187 |
7. Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder M, Oliver SG, Cyert M, Hughes TR, Boone C, and Andrews B. Mapping pathways and phenotypes by systematic gene overexpression. Mol Cell. 2006 Feb 3;21(3):319-30. DOI:10.1016/j.molcel.2005.12.011 |
8. Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrín-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilstone JJ, Gandi K, Thompson NJ, Musso G, St Onge P, Ghanny S, Lam MH, Butland G, Altaf-Ul AM, Kanaya S, Shilatifard A, O'Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, and Greenblatt JF. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature. 2006 Mar 30;440(7084):637-43. DOI:10.1038/nature04670 |

18 May 2006: José O. Alemán

José gave a brief overview of two papers looking at insulin resistance from a perspective of cellular and animal experiments. The first uses cellular and animal experiments addressing reactive oxygen species' role in insulin resistance, while the second carefully dissects insulin signaling in the liver to tease divergent metabolic control of glucose and lipid metabolism.

9. Houstis N, Rosen ED, and Lander ES. Reactive oxygen species have a causal role in multiple forms of insulin resistance. Nature. 2006 Apr 13;440(7086):944-8. DOI:10.1038/nature04634 |
10. Taniguchi CM, Kondo T, Sajan M, Luo J, Bronson R, Asano T, Farese R, Cantley LC, and Kahn CR. Divergent regulation of hepatic glucose and lipid metabolism by phosphoinositide 3-kinase via Akt and PKClambda/zeta. Cell Metab. 2006 May;3(5):343-53. DOI:10.1016/j.cmet.2006.04.005 |

14 Sep 2006: José O. Alemán

José presented a paper using deuterium and carbon labeling to elucidate the function of a redundant metabolic module for formaldehyde metabolism in Methylobacterium extorquens AM1.

11. Marx CJ, Van Dien SJ, and Lidstrom ME. Flux analysis uncovers key role of functional redundancy in formaldehyde metabolism. PLoS Biol. 2005 Feb;3(2):e16. DOI:10.1371/journal.pbio.0030016 |

21 Sep 2006: Jamey D. Young

Jamey presented a paper from the Nicholson group describing the effects of gut microbes on choline metabolism in the development of fatty liver disease.

12. Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A, Fearnside J, Tatoud R, Blanc V, Lindon JC, Mitchell SC, Holmes E, McCarthy MI, Scott J, Gauguier D, and Nicholson JK. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12511-6. DOI:10.1073/pnas.0601056103 |

12 Oct 2006: Curt Fischer

Curt presented a very recent paper from Nature Chemical Biology about isotopically instationary analysis of nitrogen assimilation in E. coli. Two notable things about this paper were 1) the invention of a technique for rapid metabolome quenching of E. coli while still obtaining some degree of intracellular/extracellular separation, and 2) the agreement of the measured net fluxes with net fluxes predicted by FBA.

13. Yuan J, Fowler WU, Kimball E, Lu W, and Rabinowitz JD. Kinetic flux profiling of nitrogen assimilation in Escherichia coli. Nat Chem Biol. 2006 Oct;2(10):529-30. DOI:10.1038/nchembio816 |

26 Oct 2006: Christine Santos

Christine presented two papers on cannibalism in Bacillus subtilis. In an effort to delay sporulation under conditions of extreme nutrient deprivation, B. subtilis cells with an activated sporulation regulatory protein, Spo0A, make use of two modes of killing to bring about the cell lysis of genetically identical sister cells and the subsequent release of nutrients.

14. González-Pastor JE, Hobbs EC, and Losick R. Cannibalism by sporulating bacteria. Science. 2003 Jul 25;301(5632):510-3. DOI:10.1126/science.1086462 |
15. Ellermeier CD, Hobbs EC, Gonzalez-Pastor JE, and Losick R. A three-protein signaling pathway governing immunity to a bacterial cannibalism toxin. Cell. 2006 Feb 10;124(3):549-59. DOI:10.1016/j.cell.2005.11.041 |

30 Nov 2006: José O. Alemán

José presented a paper documenting the effects of resveratrol, one of the active compounds in red wine and an effector of caloric restriction, in preventing disease progression associated with a high-calorie diet in mice.

16. Baur JA, Pearson KJ, Price NL, Jamieson HA, Lerin C, Kalra A, Prabhu VV, Allard JS, Lopez-Lluch G, Lewis K, Pistell PJ, Poosala S, Becker KG, Boss O, Gwinn D, Wang M, Ramaswamy S, Fishbein KW, Spencer RG, Lakatta EG, Le Couteur D, Shaw RJ, Navas P, Puigserver P, Ingram DK, de Cabo R, and Sinclair DA. Resveratrol improves health and survival of mice on a high-calorie diet. Nature. 2006 Nov 16;444(7117):337-42. DOI:10.1038/nature05354 |

2007

8 March 2007: Benjamin L. Wang

Ben presented a paper describing the use of a microfluidic device to measure transcription factor binding.

17. Maerkl SJ and Quake SR. A systems approach to measuring the binding energy landscapes of transcription factors. Science. 2007 Jan 12;315(5809):233-7. DOI:10.1126/science.1131007 |

3 May 2007: Jamey D. Young

Jamey presented a paper on reducing photorespiration and improving growth in C[math]\displaystyle{ _3 }[/math] plants. This was accomplished by introducing the glycolate catabolic pathway from E. coli into A. thaliana.

18. Kebeish R, Niessen M, Thiruveedhi K, Bari R, Hirsch HJ, Rosenkranz R, Stäbler N, Schönfeld B, Kreuzaler F, and Peterhänsel C. Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana. Nat Biotechnol. 2007 May;25(5):593-9. DOI:10.1038/nbt1299 |

13 December 2007: Benjamin L. Wang

Ben presented a paper describing a model relating mRNA, protein, enzymatic activity, and flux levels. The model system used was the glycolytic pathway in Saccharomyces cerevisiae.

19. Daran-Lapujade P, Rossell S, van Gulik WM, Luttik MA, de Groot MJ, Slijper M, Heck AJ, Daran JM, de Winde JH, Westerhoff HV, Pronk JT, and Bakker BM. The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15753-8. DOI:10.1073/pnas.0707476104 |

2008

7 February 2008: Curt R. Fischer

Curt discussed the two high-profile papers from the J. Craig Venter Institute on genome transplantation and genome synthesis. The lab debated if the popular press's treatment of the two articles was consistent with their actual scientific impact.

13. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, and Smith HO. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science. 2008 Feb 29;319(5867):1215-20. DOI:10.1126/science.1151721 |
20. Lartigue C, Glass JI, Alperovich N, Pieper R, Parmar PP, Hutchison CA 3rd, Smith HO, and Venter JC. Genome transplantation in bacteria: changing one species to another. Science. 2007 Aug 3;317(5838):632-8. DOI:10.1126/science.1144622 |

20 March 2008: Mitchell Tai

Mitchell presented a paper on a method for genome-scale analysis and tracking of library population under selective pressure. The technique, named SCALEs, utilizes microarrays to determine distribution of gene fragements in plasmids in a population. It is useful for determining genes which have beneficial (or deleterious) effects on cell fitness.

21. Bonomo J, Lynch MD, Warnecke T, Price JV, and Gill RT. Genome-scale analysis of anti-metabolite directed strain engineering. Metab Eng. 2008 Mar;10(2):109-20. DOI:10.1016/j.ymben.2007.10.002 |
22. Gill RT, Wildt S, Yang YT, Ziesman S, and Stephanopoulos G. Genome-wide screening for trait conferring genes using DNA microarrays. Proc Natl Acad Sci U S A. 2002 May 14;99(10):7033-8. DOI:10.1073/pnas.102154799 |

11 September 2008: Mitchell Tai

Mitchell presented two papers relating to future metabolic engineering tasks for biodiesel production: conversion of fatty acids to fatty acid alkyl esters, and secretion of fatty acids/triglycerides. The former is performed using a wax ester synthase/diglyceride acyltransferase enzyme from Acinetobacter sp. which transesterifies alcohols with acyl-coA. The latter has been found from a knockout of the FAA (acyl-CoA synthetase) enzymes in S. cerevisiae.

23. Kalscheuer R, Stölting T, and Steinbüchel A. Microdiesel: Escherichia coli engineered for fuel production. Microbiology (Reading). 2006 Sep;152(Pt 9):2529-2536. DOI:10.1099/mic.0.29028-0 |
24. Nojima Y, Kibayashi A, Matsuzaki H, Hatano T, and Fukui S. Isolation and characterization of triacylglycerol-secreting mutant strain from yeast, Saccharomyces cerevisiae. J Gen Appl Microbiol. 1999 Feb;45(1):1-6. DOI:10.2323/jgam.45.1 |

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