Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis.

Abstract:

:Identification of the underlying molecular mechanisms for a derived phenotype by adaptive evolution is difficult. Here, we performed a systems-level inquiry into the metabolic changes occurring in the yeast Saccharomyces cerevisiae as a result of its adaptive evolution to increase its specific growth rate on galactose and related these changes to the acquired phenotypic properties. Three evolved mutants (62A, 62B, and 62C) with higher specific growth rates and faster specific galactose uptake were isolated. The evolved mutants were compared with a reference strain and two engineered strains, SO16 and PGM2, which also showed higher galactose uptake rate in previous studies. The profile of intermediates in galactose metabolism was similar in evolved and engineered mutants, whereas reserve carbohydrates metabolism was specifically elevated in the evolved mutants and one evolved strain showed changes in ergosterol biosynthesis. Mutations were identified in proteins involved in the global carbon sensing Ras/PKA pathway, which is known to regulate the reserve carbohydrates metabolism. We evaluated one of the identified mutations, RAS2(Tyr112), and this mutation resulted in an increased specific growth rate on galactose. These results show that adaptive evolution results in the utilization of unpredicted routes to accommodate increased galactose flux in contrast to rationally engineered strains. Our study demonstrates that adaptive evolution represents a valuable alternative to rational design in bioengineering of improved strains and, that through systems biology, it is possible to identify mutations in evolved strain that can serve as unforeseen metabolic engineering targets for improving microbial strains for production of biofuels and chemicals.

authors

Hong KK,Vongsangnak W,Vemuri GN,Nielsen J

doi

10.1073/pnas.1103219108

subject

Has Abstract

pub_date

2011-07-19 00:00:00

pages

12179-84

issue

29

eissn

0027-8424

issn

1091-6490

pii

1103219108

journal_volume

108

pub_type

杂志文章
  • Heightened uterine mammalian target of rapamycin complex 1 (mTORC1) signaling provokes preterm birth in mice.

    abstract::Although preterm delivery is a major global health issue, its causes and underlying mechanism remain elusive. Using mutant mice, mimicking aspects of human preterm birth, we show here that uterine decidual senescence early in pregnancy via heightened mammalian target of rapamycin complex 1 (mTORC1) signaling is a sign...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1108180108

    authors: Hirota Y,Cha J,Yoshie M,Daikoku T,Dey SK

    更新日期:2011-11-01 00:00:00

  • Oxytocin regulates body composition.

    abstract::The primitive neurohypophyseal nonapeptide oxytocin (OXT) has established functions in parturition, lactation, appetite, and social behavior. We have shown that OXT has direct actions on the mammalian skeleton, stimulating bone formation by osteoblasts and modulating the genesis and function of bone-resorbing osteocla...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1913611116

    authors: Sun L,Lizneva D,Ji Y,Colaianni G,Hadelia E,Gumerova A,Ievleva K,Kuo TC,Korkmaz F,Ryu V,Rahimova A,Gera S,Taneja C,Khan A,Ahmad N,Tamma R,Bian Z,Zallone A,Kim SM,New MI,Iqbal J,Yuen T,Zaidi M

    更新日期:2019-12-16 00:00:00

  • Glucocorticoids locally disrupt an array of positioned nucleosomes on the rat tyrosine aminotransferase promoter in hepatoma cells.

    abstract::Transcriptional activation by steroid hormones is often associated with the appearance of a DNase I hypersensitive site resulting from a local alteration of the nucleoprotein structure of the promoter. For the mouse mammary tumor virus long terminal repeat, a viral promoter under glucocorticoid control, a model has be...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.23.9300

    authors: Carr KD,Richard-Foy H

    更新日期:1990-12-01 00:00:00

  • Sequence conservation in avian CR1: an interspersed repetitive DNA family evolving under functional constraints.

    abstract::CR1 is a short interspersed repetitive DNA element originally identified in the domestic chicken (Gallus gallus). However, unlike virtually all other such sequences described to date, CR1 is not confined to one or a few closely related species. It is probably a ubiquitous component of the avian genome, having been det...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.13.5814

    authors: Chen ZQ,Ritzel RG,Lin CC,Hodgetts RB

    更新日期:1991-07-01 00:00:00

  • An anatomy of normal and malignant gene expression.

    abstract::A gene's expression pattern provides clues to its role in normal physiology and disease. To provide quantitative expression levels on a genome-wide scale, the Cancer Genome Anatomy Project (CGAP) uses serial analysis of gene expression (SAGE). Over 5 million transcript tags from more than 100 human cell types have bee...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.152324199

    authors: Boon K,Osorio EC,Greenhut SF,Schaefer CF,Shoemaker J,Polyak K,Morin PJ,Buetow KH,Strausberg RL,De Souza SJ,Riggins GJ

    更新日期:2002-08-20 00:00:00

  • The Vibrio cholerae O139 O-antigen polysaccharide is essential for Ca2+-dependent biofilm development in sea water.

    abstract::Vibrio cholerae is both an inhabitant of estuarine environments and the etiologic agent of the diarrheal disease cholera. Previous work has demonstrated that V. cholerae forms both an exopolysaccharide-dependent biofilm and a Ca2+-dependent biofilm. In this work, we demonstrate a role for the O-antigen polysaccharide ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2334614100

    authors: Kierek K,Watnick PI

    更新日期:2003-11-25 00:00:00

  • Inhibition of prostate carcinogenesis in TRAMP mice by oral infusion of green tea polyphenols.

    abstract::Development of effective chemopreventive agents against prostate cancer (CaP) for humans requires conclusive evidence of their efficacy in animal models that closely emulates human disease. The autochthonous transgenic adenocarcinoma of the mouse prostate (TRAMP) model, which spontaneously develops metastatic CaP, is ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.171326098

    authors: Gupta S,Hastak K,Ahmad N,Lewin JS,Mukhtar H

    更新日期:2001-08-28 00:00:00

  • A single polypeptide catalyzing the conversion of phytoene to zeta-carotene is transcriptionally regulated during tomato fruit ripening.

    abstract::The cDNA of the gene pds from tomato, encoding the carotenoid biosynthesis enzyme phytoene desaturase, was cloned, and its nucleotide sequence was determined. Cells of Escherichia coli that expressed the tomato pds gene could convert phytoene to zeta-carotene. This result suggests that one polypeptide, the product of ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.11.4962

    authors: Pecker I,Chamovitz D,Linden H,Sandmann G,Hirschberg J

    更新日期:1992-06-01 00:00:00

  • Structural dynamics and transient lipid binding of synaptobrevin-2 tune SNARE assembly and membrane fusion.

    abstract::Intrinsically disordered proteins (IDPs) and their conformational transitions play an important role in neurotransmitter release at the neuronal synapse. Here, the SNARE proteins are essential by forming the SNARE complex that drives vesicular membrane fusion. While it is widely accepted that the SNARE proteins are in...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1813194116

    authors: Lakomek NA,Yavuz H,Jahn R,Pérez-Lara Á

    更新日期:2019-04-30 00:00:00

  • Inhibition of acute in vivo human immunodeficiency virus infection by human interleukin 10 treatment of SCID mice implanted with human fetal thymus and liver.

    abstract::To improve the usefulness of in vivo mode for the investigation of the pathophysiology of human immunodeficiency virus (HIV) infection, we modified the construction of SCID mice implanted with human fetal thymus and liver (thy/liv-SCID-hu mice) so that the peripheral blood of the mice contained significant numbers of ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.7.3126

    authors: Kollmann TR,Pettoello-Mantovani M,Katopodis NF,Hachamovitch M,Rubinstein A,Kim A,Goldstein H

    更新日期:1996-04-02 00:00:00

  • Estradiol binds to a receptor-like cytosol binding protein and initiates a biological response in Paracoccidioides brasiliensis.

    abstract::Paracoccidioidomycosis, a disease caused by Paracoccidioides brasiliensis, which is endemic to Latin America, is much more common in men than women, suggesting a role for hormonal factors. We recently showed that two other yeasts possess steroid binding proteins and postulated that these receptor-like molecules repres...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.24.7659

    authors: Loose DS,Stover EP,Restrepo A,Stevens DA,Feldman D

    更新日期:1983-12-01 00:00:00

  • Isolation and characterization of a complementary DNA specific for human aromatase-system cytochrome P-450 mRNA.

    abstract::A cloned complementary DNA sequence has been isolated from a human placental cDNA library in the bacteriophage expression vector lambda gt11 after screening with polyclonal antibodies against human placental aromatase-system cytochrome P-450 (P-450Arom). A single recombinant clone, lambda hAROM1, was characterized by ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.17.6387

    authors: Evans CT,Ledesma DB,Schulz TZ,Simpson ER,Mendelson CR

    更新日期:1986-09-01 00:00:00

  • Diazonamide toxins reveal an unexpected function for ornithine delta-amino transferase in mitotic cell division.

    abstract::We have studied a naturally occurring small-molecule antimitotic called diazonamide A. Diazonamide A is highly effective at blocking spindle assembly in mammalian cell culture and does so through a unique mechanism. A biotinylated form of diazonamide A affinity purifies ornithine delta-amino transferase (OAT), a mitoc...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0610832104

    authors: Wang G,Shang L,Burgett AW,Harran PG,Wang X

    更新日期:2007-02-13 00:00:00

  • Functional anatomy of human eyeblink conditioning determined with regional cerebral glucose metabolism and positron-emission tomography.

    abstract::Relative cerebral glucose metabolism was examined with positron-emission tomography (PET) as a measure of neuronal activation during performance of the classically conditioned eyeblink response in 12 young adult subjects. Each subject received three sessions: (i) a control session with PET scan in which unpaired prese...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 临床试验,杂志文章

    doi:10.1073/pnas.92.16.7500

    authors: Logan CG,Grafton ST

    更新日期:1995-08-01 00:00:00

  • Resonance-induced multimodal body-size distributions in ecosystems.

    abstract::The size of an organism reflects its metabolic rate, growth rate, mortality, and other important characteristics; therefore, the distribution of body size is a major determinant of ecosystem structure and function. Body-size distributions often are multimodal, with several peaks of abundant sizes, and previous studies...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1211761110

    authors: Lampert A,Tlusty T

    更新日期:2013-01-02 00:00:00

  • Protonation of interacting residues in a protein by a Monte Carlo method: application to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides.

    abstract::We used Monte Carlo methods to treat statistical problem of electrostatic interactions among many titrating amino acids and applied these methods to lysozyme and the photosynthetic reaction center of Rhodobacter sphaeroides, including all titrating sites. We computed the average protonation of residues as a function o...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.13.5804

    authors: Beroza P,Fredkin DR,Okamura MY,Feher G

    更新日期:1991-07-01 00:00:00

  • Hypersensitivity of Ku80-deficient cell lines and mice to DNA damage: the effects of ionizing radiation on growth, survival, and development.

    abstract::We recently have shown that mice deficient for the 86-kDa component (Ku80) of the DNA-dependent protein kinase exhibit growth retardation and a profound deficiency in V(D)J (variable, diversity, and joining) recombination. These defects may be related to abnormalities in DNA metabolism that arise from the inability of...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.25.13588

    authors: Nussenzweig A,Sokol K,Burgman P,Li L,Li GC

    更新日期:1997-12-09 00:00:00

  • Tropical amphibian populations experience higher disease risk in natural habitats.

    abstract::Habitat loss and disease are main drivers of global amphibian declines, yet the interaction between them remains largely unexplored. Here we show that paradoxically, habitat loss is negatively associated with occurrence, prevalence, and infection intensity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1014497108

    authors: Becker CG,Zamudio KR

    更新日期:2011-06-14 00:00:00

  • Self/nonself recognition in ascidian fertilization: vitelline coat protein HrVC70 is a candidate allorecognition molecule.

    abstract::Ascidians are hermaphrodites releasing sperm and eggs simultaneously, but many species are self-sterile because of a self/nonself-recognition system in spermegg interaction. Here, we show that a 70-kDa vitelline coat protein, HrVC70, consisting of 12 epidermal growth factor-like repeats, plays a key role in self/nonse...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0401928101

    authors: Sawada H,Tanaka E,Ban S,Yamasaki C,Fujino J,Ooura K,Abe Y,Matsumoto K,Yokosawa H

    更新日期:2004-11-02 00:00:00

  • Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments.

    abstract::Intrinsically disordered proteins (IDPs) are involved in a wide range of regulatory processes in the cell. Owing to their flexibility, their conformations are expected to be particularly sensitive to the crowded cellular environment. Here we use single-molecule Förster resonance energy transfer to quantify the effect ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1322611111

    authors: Soranno A,Koenig I,Borgia MB,Hofmann H,Zosel F,Nettels D,Schuler B

    更新日期:2014-04-01 00:00:00

  • Signaling by N- and C-terminal sequences of parathyroid hormone-related protein in hippocampal neurons.

    abstract::Parathyroid hormone-related protein (PTHrP) is synthesized in the brain, and a single type of cloned receptor for the N-terminal portion of PTHrP and PTH is present in the central nervous system. Nothing is known about the physiological actions or signaling pathways used by PTHrP in the brain. Using cultured rat hippo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.22.10182

    authors: Fukayama S,Tashjian AH Jr,Davis JN,Chisholm JC

    更新日期:1995-10-24 00:00:00

  • Conservation of nodulation genes between Rhizobium meliloti and a slow-growing Rhizobium strain that nodulates a nonlegume host.

    abstract::Parasponia, a woody member of the elm family, is the only nonlegume genus whose members are known to form an effective nitrogen-fixing symbiosis with a Rhizobium species. The bacterial strain RP501 is a slow-growing strain of Rhizobium isolated from Parasponia nodules. Strain RP501 also nodulates the legumes siratro (...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.82.17.5841

    authors: Marvel DJ,Kuldau G,Hirsch A,Richards E,Torrey JG,Ausubel FM

    更新日期:1985-09-01 00:00:00

  • Transgenic cotton and sterile insect releases synergize eradication of pink bollworm a century after it invaded the United States.

    abstract::Invasive organisms pose a global threat and are exceptionally difficult to eradicate after they become abundant in their new habitats. We report a successful multitactic strategy for combating the pink bollworm (Pectinophora gossypiella), one of the world's most invasive pests. A coordinated program in the southwester...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2019115118

    authors: Tabashnik BE,Liesner LR,Ellsworth PC,Unnithan GC,Fabrick JA,Naranjo SE,Li X,Dennehy TJ,Antilla L,Staten RT,Carrière Y

    更新日期:2021-01-05 00:00:00

  • The biomass distribution on Earth.

    abstract::A census of the biomass on Earth is key for understanding the structure and dynamics of the biosphere. However, a global, quantitative view of how the biomass of different taxa compare with one another is still lacking. Here, we assemble the overall biomass composition of the biosphere, establishing a census of the ≈5...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1711842115

    authors: Bar-On YM,Phillips R,Milo R

    更新日期:2018-06-19 00:00:00

  • Genetic confirmation for a central role for TNFα in the direct action of thyroid stimulating hormone on the skeleton.

    abstract::Clinical data showing correlations between low thyroid-stimulating hormone (TSH) levels and high bone turnover markers, low bone mineral density, and an increased risk of osteoporosis-related fractures are buttressed by mouse genetic and pharmacological studies identifying a direct action of TSH on the skeleton. Here ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1308336110

    authors: Sun L,Zhu LL,Lu P,Yuen T,Li J,Ma R,Baliram R,Moonga SS,Liu P,Zallone A,New MI,Davies TF,Zaidi M

    更新日期:2013-06-11 00:00:00

  • Targeted disruption of the galanin gene reduces the number of sensory neurons and their regenerative capacity.

    abstract::The neuropeptide galanin is expressed developmentally in the dorsal root ganglion (DRG) and is rapidly up-regulated 120-fold after peripheral nerve section in the adult. Here we report that adult mice carrying a loss-of-function mutation in the galanin gene have a 13% reduction in the number of cells in the DRG associ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.210221897

    authors: Holmes FE,Mahoney S,King VR,Bacon A,Kerr NC,Pachnis V,Curtis R,Priestley JV,Wynick D

    更新日期:2000-10-10 00:00:00

  • Karrikins enhance light responses during germination and seedling development in Arabidopsis thaliana.

    abstract::Karrikins are a class of seed germination stimulants identified in smoke from wildfires. Microarray analysis of imbibed Arabidopsis thaliana seeds was performed to identify transcriptional responses to KAR(1) before germination. A small set of genes that are regulated by KAR(1), even when germination is prevented by t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0911635107

    authors: Nelson DC,Flematti GR,Riseborough JA,Ghisalberti EL,Dixon KW,Smith SM

    更新日期:2010-04-13 00:00:00

  • Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs.

    abstract::Two decades after the discovery of the first animal microRNA (miRNA), the number of miRNAs in animal genomes remains a vexing question. Here, we report findings from analyzing 1,323 short RNA sequencing samples (RNA-seq) from 13 different human tissue types. Using stringent thresholding criteria, we identified 3,707 s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1420955112

    authors: Londin E,Loher P,Telonis AG,Quann K,Clark P,Jing Y,Hatzimichael E,Kirino Y,Honda S,Lally M,Ramratnam B,Comstock CE,Knudsen KE,Gomella L,Spaeth GL,Hark L,Katz LJ,Witkiewicz A,Rostami A,Jimenez SA,Hollingsworth MA,

    更新日期:2015-03-10 00:00:00

  • Excitation transfer spectroscopy with two metastable 138Ba+ ions in same trap.

    abstract::In the absence of lasers approaching trapped ion clock transitions in sharpness we propose to replace the 12.49 m laser field exciting the D3/2-D5/2 transition of the single Ba+ ion A in D3/2 with the near-field of a close by identical ion B in the excited D5/2 state. We tune the frequency of the near-field by the dif...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.14.6861

    authors: Dehmelt H,Zhao X,Yu N,Nagourney W

    更新日期:1996-07-09 00:00:00

  • Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.

    abstract::Angiosperms are the largest and most successful clade of land plants with >250,000 species distributed in nearly every terrestrial habitat. Many phylogenetic studies have been based on DNA sequences of one to several genes, but, despite decades of intensive efforts, relationships among early diverging lineages and sev...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0709121104

    authors: Jansen RK,Cai Z,Raubeson LA,Daniell H,Depamphilis CW,Leebens-Mack J,Müller KF,Guisinger-Bellian M,Haberle RC,Hansen AK,Chumley TW,Lee SB,Peery R,McNeal JR,Kuehl JV,Boore JL

    更新日期:2007-12-04 00:00:00