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Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway

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Synthetic and Systems Biotechnology 2022年第2期7卷 738-749页

作者： Francesca V.Gambacorta Ellen R.Wagner Tyler B.Jacobson Mary Tremaine laura k.muehlbauer Mick A.McGee Justin J.Baerwald Russell L.Wrobel John F.Wolters Mike Place Joshua J.Dietrich Dan Xie Jose Serate Shabda Gajbhiye Lisa Liu Maikayeng Vang-Smith Joshua J.Coon Yaoping Zhang Audrey P.Gasch Daniel Amador-Noguez Chris Todd Hittinger Trey k.Sato Brian F.Pfleger DOE Great Lakes Bioenergy Research Center University of Wisconsin-MadisonMadisonWIUSA Department of Chemical and Biological Engineering University of Wisconsin-MadisonMadisonWIUSA Laboratory of Genetics Center for Genomic Science InnovationUniversity of Wisconsin-MadisonMadisonWIUSA Department of Bacteriology University of Wisconsin-MadisonMadisonWIUSA Department of Chemistry University of Wisconsin-MadisonMadisonWIUSA Wisconsin Energy Institute J.F.Crow Institute for the Study of EvolutionUniversity of Wisconsin-MadisonMadisonWIUSA Department of Biomolecular Chemistry University of Wisconsin-MadisonMadisonWIUSA

Metabolic engineering strategies have been successfully implemented to improve the production of isobutanol,a next-generation biofuel,in Saccharomyces ***,we explore how two of these strategies,pathway re-localization and redox cofactor-balancing,affect the performance and physiology of isobutanol producing *** equipped yeast with isobutanol cassettes which had either a mitochondrial or cytosolic localized isobutanol pathway and used either a redox-imbalanced(NADPH-dependent)or redox-balanced(NADH-dependent)ketol-acid reductoisomerase *** then conducted transcriptomic,proteomic and metabolomic analyses to elucidate molecular differences between the engineered *** localization had a large effect on isobutanol production with the strain expressing the mitochondrial-localized enzymes producing 3.8-fold more isobutanol than strains expressing the cytosolic ***-balancing did not improve isobutanol titers and instead the strain with the redox-imbalanced pathway produced 1.5-fold more isobutanol than the balanced version,albeit at low overall pathway *** genomic analyses suggested that the poor performances of the cytosolic pathway strains were in part due to a shortage in cytosolic Fe-S clusters,which are required cofactors for the dihydroxyacid dehydratase *** then demonstrated that this cofactor limitation may be partially recovered by disrupting iron homeostasis with a fra2 mutation,thereby increasing cellular iron *** resulting isobutanol titer of the fra2 null strain harboring a cytosolic-localized isobutanol pathway outperformed the strain with the mitochondrial-localized pathway by 1.3-fold,demonstrating that both localizations can support flux to isobutanol.

关键词： Saccharomyces cerevisiae Isobutanol Functional genomics analysis Pathway localization Fe incorporation

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Reimagining large river management using the Resist-Accept-Direct(RAD)framework in the Upper Mississippi River

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Ecological Processes 2023年第1期12卷 645-664页

作者： Nicole k.Ward Abigail J.Lynch Erik A.Beever Joshua Booker kristen L.Bouska Holly Embke Jeffrey N.Houser John F.kocik Joshua kocik David J.Lawrence Mary Grace Lemon Doug Limpinsel Madeline R.Magee Bryan M.Maitland Owen Mckenna Andrew Meier John M.Morton Jeffrey D.muehlbauer Robert Newman Devon C.Oliver Heidi M.Rantala Greg G.Sass Aaron Shultz laura M.Thompson Jennifer L.Wilkening Minnesota Department of Natural Resources Lake CityMN 55041USA U.S.Geological Survey National Climate Adaptation Science CenterRestonVA 22041USA U.S.Geological Survey Northern Rocky Mountain Science CenterBozemanMT 59715USA Department of Ecology Montana State UniversityBozemanMT 59715USA U.S.Fish and Wildlife Service National Wildlife Refuge SystemOak HarborOH 43449USA U.S.Geological Survey Upper Midwest Environmental Sciences CenterLa CrosseWI 54603USA U.S.Geological Survey Midwest Climate Adaptation Science CenterSt.PaulMN 55108USA NOAA NEFSC OronoME 04473USA University of Nebraska-Lincoln LincolnNE 68503USA National Park Service Climate Change Response ProgramFort CollinsCO 80525USA U.S.Fish and Wild-life Service National Wildlife Refuge SystemBloomingtonMN 55437USA Habitat Conservation Division NOAAAlaska RegionAnchorageAK 99513USA Wisconsin Department of Natural Resources MadisonWI 53703USA Aquatic Sciences Center Center for LimnologyUW-MadisonMadisonWI 53706USA U.S.Geological Survey Northern Prairie Wildlife Research Center and Midwest Climate Adaptation Science CenterJamestownND 58401USA U.S.Army Corps of Engineers La CrescentMN 55947USA Alaska Wildlife Alliance AnchorageAK 99520USA U.S.Geological Survey Alaska Cooperative Fish and Wildlife Research UnitUniversity of Alaska FairbanksFairbanksAK 99775USA University of North Dakota Grand ForksND 58202USA Minnesota Department of Natural Resources DuluthMN 55804USA Wisconsin Department of Natural Resources Boulder JunctionWI 54512USA Great Lakes Indian Fish and Wildlife Commission(GLIFWC) OdanahWI 54861USA U.S.Geological Survey National Climate Adaptation Science Centerand School of Natural ResourcesUniversity of TennesseeKnoxvilleTN 37996USA U.S.Fish and Wildlife Service National Wildlife Refuge SystemFort CollinsCO 80526USA

Background Large-river decision-makers are charged with maintaining diverse ecosystem services through unprec-edented social-ecological transformations as climate change and other global stressors *** interconnected,dendritic habitats of rivers,which often demarcate jurisdictional boundaries,generate complex management ***,we explore how the Resist–Accept–Direct(RAD)framework may enhance large-river management by promoting coordinated and deliberate responses to social-ecological trajectories of *** RAD frame-work identifies the full decision space of potential management approaches,wherein managers may resist change to maintain historical conditions,accept change toward different conditions,or direct change to a specified future with novel *** the Upper Mississippi River System,managers are facing social-ecological transformations from more frequent and extreme high-water *** illustrate how RAD-informed basin-,reach-,and site-scale decisions could:(1)provide cross-spatial scale framing;(2)open the entire decision space of potential management approaches;and(3)enhance coordinated inter-jurisdictional management in response to the trajectory of the Upper Mississippi River *** The RAD framework helps identify plausible long-term trajectories in different reaches(or subbasins)of the river and how the associated social-ecological transformations could be managed by altering site-scale *** reach-scale objectives may reprioritize how,where,and when site conditions could be altered to contribute to the basin goal,given the basin’s plausible trajectories of change(e.g.,by coordinating action across sites to alter habitat connectivity,diversity,and redundancy in the river mosaic).Conclusions When faced with long-term systemic transformations(e.g.,>50 years),the RAD framework helps explicitly consider whether or when the basin vision or goals may no longer be achievable,and direct options may open y

关键词： Ecosystem Management Transformation Social-ecological system Anthropocene Climate change Basin planning Cross-scale interactions

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