Genetic basis of metabolome variation in yeast.

Abstract:

:Metabolism, the conversion of nutrients into usable energy and biochemical building blocks, is an essential feature of all cells. The genetic factors responsible for inter-individual metabolic variability remain poorly understood. To investigate genetic causes of metabolome variation, we measured the concentrations of 74 metabolites across ~ 100 segregants from a Saccharomyces cerevisiae cross by liquid chromatography-tandem mass spectrometry. We found 52 quantitative trait loci for 34 metabolites. These included linkages due to overt changes in metabolic genes, e.g., linking pyrimidine intermediates to the deletion of ura3. They also included linkages not directly related to metabolic enzymes, such as those for five central carbon metabolites to ira2, a Ras/PKA pathway regulator, and for the metabolites, S-adenosyl-methionine and S-adenosyl-homocysteine to slt2, a MAP kinase involved in cell wall integrity. The variant of ira2 that elevates metabolite levels also increases glucose uptake and ethanol secretion. These results highlight specific examples of genetic variability, including in genes without prior known metabolic regulatory function, that impact yeast metabolism.

journal_name

PLoS Genet

journal_title

PLoS genetics

authors

Breunig JS,Hackett SR,Rabinowitz JD,Kruglyak L

doi

10.1371/journal.pgen.1004142

subject

Has Abstract

pub_date

2014-03-06 00:00:00

pages

e1004142

issue

3

eissn

1553-7390

issn

1553-7404

pii

PGENETICS-D-13-03062

journal_volume

10

pub_type

杂志文章
  • RAN-binding protein 9 is involved in alternative splicing and is critical for male germ cell development and male fertility.

    abstract::As a member of the large Ran-binding protein family, Ran-binding protein 9 (RANBP9) has been suggested to play a critical role in diverse cellular functions in somatic cell lineages in vitro, and this is further supported by the neonatal lethality phenotype in Ranbp9 global knockout mice. However, the exact molecular ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1004825

    authors: Bao J,Tang C,Li J,Zhang Y,Bhetwal BP,Zheng H,Yan W

    更新日期:2014-12-04 00:00:00

  • Socs36E Controls Niche Competition by Repressing MAPK Signaling in the Drosophila Testis.

    abstract::The Drosophila testis is a well-established system for studying stem cell self-renewal and competition. In this tissue, the niche supports two stem cell populations, germ line stem cells (GSCs), which give rise to sperm, and somatic stem cells called cyst stem cells (CySCs), which support GSCs and their descendants. I...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005815

    authors: Amoyel M,Anderson J,Suisse A,Glasner J,Bach EA

    更新日期:2016-01-25 00:00:00

  • Unintentional miRNA ablation is a risk factor in gene knockout studies: a short report.

    abstract::One of the most powerful techniques for studying the function of a gene is to disrupt the expression of that gene using genetic engineering strategies such as targeted recombination or viral integration of gene trap cassettes. The tremendous utility of these tools was recognized this year with the awarding of the Nobe...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.0040034

    authors: Osokine I,Hsu R,Loeb GB,McManus MT

    更新日期:2008-02-01 00:00:00

  • Mariner Transposons Contain a Silencer: Possible Role of the Polycomb Repressive Complex 2.

    abstract::Transposable elements are driving forces for establishing genetic innovations such as transcriptional regulatory networks in eukaryotic genomes. Here, we describe a silencer situated in the last 300 bp of the Mos1 transposase open reading frame (ORF) which functions in vertebrate and arthropod cells. Functional silenc...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005902

    authors: Bire S,Casteret S,Piégu B,Beauclair L,Moiré N,Arensbuger P,Bigot Y

    更新日期:2016-03-03 00:00:00

  • A cis-acting diversification activator both necessary and sufficient for AID-mediated hypermutation.

    abstract::Hypermutation of the immunoglobulin (Ig) genes requires Activation Induced cytidine Deaminase (AID) and transcription, but it remains unclear why other transcribed genes of B cells do not mutate. We describe a reporter transgene crippled by hypermutation when inserted into or near the Ig light chain (IgL) locus of the...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1000332

    authors: Blagodatski A,Batrak V,Schmidl S,Schoetz U,Caldwell RB,Arakawa H,Buerstedde JM

    更新日期:2009-01-01 00:00:00

  • Endogenous viral elements in animal genomes.

    abstract::Integration into the nuclear genome of germ line cells can lead to vertical inheritance of retroviral genes as host alleles. For other viruses, germ line integration has only rarely been documented. Nonetheless, we identified endogenous viral elements (EVEs) derived from ten non-retroviral families by systematic in si...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1001191

    authors: Katzourakis A,Gifford RJ

    更新日期:2010-11-18 00:00:00

  • Whole genome sequencing of experimental hybrids supports meiosis-like sexual recombination in Leishmania.

    abstract::Hybrid genotypes have been repeatedly described among natural isolates of Leishmania, and the recovery of experimental hybrids from sand flies co-infected with different strains or species of Leishmania has formally demonstrated that members of the genus possess the machinery for genetic exchange. As neither gamete st...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008042

    authors: Inbar E,Shaik J,Iantorno SA,Romano A,Nzelu CO,Owens K,Sanders MJ,Dobson D,Cotton JA,Grigg ME,Beverley SM,Sacks D

    更新日期:2019-05-15 00:00:00

  • DNA ligase III promotes alternative nonhomologous end-joining during chromosomal translocation formation.

    abstract::Nonhomologous end-joining (NHEJ) is the primary DNA repair pathway thought to underlie chromosomal translocations and other genomic rearrangements in somatic cells. The canonical NHEJ pathway, including DNA ligase IV (Lig4), suppresses genomic instability and chromosomal translocations, leading to the notion that a po...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1002080

    authors: Simsek D,Brunet E,Wong SY,Katyal S,Gao Y,McKinnon PJ,Lou J,Zhang L,Li J,Rebar EJ,Gregory PD,Holmes MC,Jasin M

    更新日期:2011-06-01 00:00:00

  • Analysis of the genetic basis of disease in the context of worldwide human relationships and migration.

    abstract::Genetic diversity across different human populations can enhance understanding of the genetic basis of disease. We calculated the genetic risk of 102 diseases in 1,043 unrelated individuals across 51 populations of the Human Genome Diversity Panel. We found that genetic risk for type 2 diabetes and pancreatic cancer d...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1003447

    authors: Corona E,Chen R,Sikora M,Morgan AA,Patel CJ,Ramesh A,Bustamante CD,Butte AJ

    更新日期:2013-05-01 00:00:00

  • The POU factor ventral veins lacking/Drifter directs the timing of metamorphosis through ecdysteroid and juvenile hormone signaling.

    abstract::Although endocrine changes are known to modulate the timing of major developmental transitions, the genetic mechanisms underlying these changes remain poorly understood. In insects, two developmental hormones, juvenile hormone (JH) and ecdysteroids, are coordinated with each other to induce developmental changes assoc...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1004425

    authors: Cheng C,Ko A,Chaieb L,Koyama T,Sarwar P,Mirth CK,Smith WA,Suzuki Y

    更新日期:2014-06-19 00:00:00

  • DNA Sequence Evolution and Rare Homoeologous Conversion in Tetraploid Cotton.

    abstract::Allotetraploid cotton species are a vital source of spinnable fiber for textiles. The polyploid nature of the cotton genome raises many evolutionary questions as to the relationships between duplicated genomes. We describe the evolution of the cotton genome (SNPs and structural variants) with the greatly improved reso...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1006012

    authors: Page JT,Liechty ZS,Alexander RH,Clemons K,Hulse-Kemp AM,Ashrafi H,Van Deynze A,Stelly DM,Udall JA

    更新日期:2016-05-11 00:00:00

  • BRCA1 and BRCA2 tumor suppressors in neural crest cells are essential for craniofacial bone development.

    abstract::Craniofacial abnormalities, including facial skeletal defects, comprise approximately one-third of all birth defects in humans. Since most bones in the face derive from cranial neural crest cells (CNCCs), which are multipotent stem cells, craniofacial bone disorders are largely attributed to defects in CNCCs. However,...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1007340

    authors: Kitami K,Kitami M,Kaku M,Wang B,Komatsu Y

    更新日期:2018-05-02 00:00:00

  • Knock-out of a mitochondrial sirtuin protects neurons from degeneration in Caenorhabditis elegans.

    abstract::Sirtuins are NAD⁺-dependent deacetylases, lipoamidases, and ADP-ribosyltransferases that link cellular metabolism to multiple intracellular pathways that influence processes as diverse as cell survival, longevity, and cancer growth. Sirtuins influence the extent of neuronal death in stroke. However, different sirtuins...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1006965

    authors: Sangaletti R,D'Amico M,Grant J,Della-Morte D,Bianchi L

    更新日期:2017-08-18 00:00:00

  • A candidate gene approach identifies the CHRNA5-A3-B4 region as a risk factor for age-dependent nicotine addiction.

    abstract::People who begin daily smoking at an early age are at greater risk of long-term nicotine addiction. We tested the hypothesis that associations between nicotinic acetylcholine receptor (nAChR) genetic variants and nicotine dependence assessed in adulthood will be stronger among smokers who began daily nicotine exposure...

    journal_title:PLoS genetics

    pub_type: 杂志文章,随机对照试验

    doi:10.1371/journal.pgen.1000125

    authors: Weiss RB,Baker TB,Cannon DS,von Niederhausern A,Dunn DM,Matsunami N,Singh NA,Baird L,Coon H,McMahon WM,Piper ME,Fiore MC,Scholand MB,Connett JE,Kanner RE,Gahring LC,Rogers SW,Hoidal JR,Leppert MF

    更新日期:2008-07-11 00:00:00

  • Transcriptional mutagenesis induced by 8-oxoguanine in mammalian cells.

    abstract::Most of the somatic cells of adult metazoans, including mammals, do not undergo continuous cycles of replication. Instead, they are quiescent and devote most of their metabolic activity to gene expression. The mutagenic consequences of exposure to DNA-damaging agents are well documented, but less is known about the im...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1000577

    authors: Brégeon D,Peignon PA,Sarasin A

    更新日期:2009-07-01 00:00:00

  • Correction: The Epigenomic Landscape of Prokaryotes.

    abstract::[This corrects the article DOI: 10.1371/journal.pgen.1005854.]. ...

    journal_title:PLoS genetics

    pub_type: 已发布勘误

    doi:10.1371/journal.pgen.1006064

    authors: PLOS Genetics Staff.

    更新日期:2016-05-12 00:00:00

  • Canonical Poly(A) Polymerase Activity Promotes the Decay of a Wide Variety of Mammalian Nuclear RNAs.

    abstract::The human nuclear poly(A)-binding protein PABPN1 has been implicated in the decay of nuclear noncoding RNAs (ncRNAs). In addition, PABPN1 promotes hyperadenylation by stimulating poly(A)-polymerases (PAPα/γ), but this activity has not previously been linked to the decay of endogenous transcripts. Moreover, the mechani...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005610

    authors: Bresson SM,Hunter OV,Hunter AC,Conrad NK

    更新日期:2015-10-20 00:00:00

  • The protein quality control machinery regulates its misassembled proteasome subunits.

    abstract::Cellular toxicity introduced by protein misfolding threatens cell fitness and viability. Failure to eliminate these polypeptides is associated with various aggregation diseases. In eukaryotes, the ubiquitin proteasome system (UPS) plays a vital role in protein quality control (PQC), by selectively targeting misfolded ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005178

    authors: Peters LZ,Karmon O,David-Kadoch G,Hazan R,Yu T,Glickman MH,Ben-Aroya S

    更新日期:2015-04-28 00:00:00

  • The C-terminal of CASY-1/Calsyntenin regulates GABAergic synaptic transmission at the Caenorhabditis elegans neuromuscular junction.

    abstract::The C. elegans ortholog of mammalian calsyntenins, CASY-1, is an evolutionarily conserved type-I transmembrane protein that is highly enriched in the nervous system. Mammalian calsyntenins are strongly expressed at inhibitory synapses, but their role in synapse development and function is still elusive. Here, we repor...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1007263

    authors: Thapliyal S,Vasudevan A,Dong Y,Bai J,Koushika SP,Babu K

    更新日期:2018-03-12 00:00:00

  • Dietary restriction in Drosophila: delayed aging or experimental artefact?

    abstract::Lifespan can be extended by reduction of dietary intake. This practice is referred to as dietary restriction (DR), and extension of lifespan by DR is evolutionarily conserved in taxonomically diverse organisms including yeast, invertebrates, and mammals. Although these two often-stated facts carry the implication that...

    journal_title:PLoS genetics

    pub_type: 杂志文章,评审

    doi:10.1371/journal.pgen.0030057

    authors: Piper MD,Partridge L

    更新日期:2007-04-27 00:00:00

  • Common genetic variants and modification of penetrance of BRCA2-associated breast cancer.

    abstract::The considerable uncertainty regarding cancer risks associated with inherited mutations of BRCA2 is due to unknown factors. To investigate whether common genetic variants modify penetrance for BRCA2 mutation carriers, we undertook a two-staged genome-wide association study in BRCA2 mutation carriers. In stage 1 using ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1001183

    authors: Gaudet MM,Kirchhoff T,Green T,Vijai J,Korn JM,Guiducci C,Segrè AV,McGee K,McGuffog L,Kartsonaki C,Morrison J,Healey S,Sinilnikova OM,Stoppa-Lyonnet D,Mazoyer S,Gauthier-Villars M,Sobol H,Longy M,Frenay M,GEMO Study

    更新日期:2010-10-28 00:00:00

  • A genome-wide characterization of microRNA genes in maize.

    abstract::MicroRNAs (miRNAs) are small, non-coding RNAs that play essential roles in plant growth, development, and stress response. We conducted a genome-wide survey of maize miRNA genes, characterizing their structure, expression, and evolution. Computational approaches based on homology and secondary structure modeling ident...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1000716

    authors: Zhang L,Chia JM,Kumari S,Stein JC,Liu Z,Narechania A,Maher CA,Guill K,McMullen MD,Ware D

    更新日期:2009-11-01 00:00:00

  • A trans-acting Variant within the Transcription Factor RIM101 Interacts with Genetic Background to Determine its Regulatory Capacity.

    abstract::Most genetic variants associated with disease occur within regulatory regions of the genome, underscoring the importance of defining the mechanisms underlying differences in regulation of gene expression between individuals. We discovered a pair of co-regulated, divergently oriented transcripts, AQY2 and ncFRE6, that ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005746

    authors: Read T,Richmond PA,Dowell RD

    更新日期:2016-01-11 00:00:00

  • Simultaneous SNP selection and adjustment for population structure in high dimensional prediction models.

    abstract::Complex traits are known to be influenced by a combination of environmental factors and rare and common genetic variants. However, detection of such multivariate associations can be compromised by low statistical power and confounding by population structure. Linear mixed effects models (LMM) can account for correlati...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008766

    authors: Bhatnagar SR,Yang Y,Lu T,Schurr E,Loredo-Osti JC,Forest M,Oualkacha K,Greenwood CMT

    更新日期:2020-05-04 00:00:00

  • The abnormal phenotypes of cartilage and bone in calcium-sensing receptor deficient mice are dependent on the actions of calcium, phosphorus, and PTH.

    abstract::Patients with neonatal severe hyperparathyroidism (NSHPT) are homozygous for the calcium-sensing receptor (CaR) mutation and have very high circulating PTH, abundant parathyroid hyperplasia, and severe life-threatening hypercalcemia. Mice with homozygous deletion of CaR mimic the syndrome of NSHPT. To determine effect...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1002294

    authors: Liu J,Lv F,Sun W,Tao C,Ding G,Karaplis A,Brown E,Goltzman D,Miao D

    更新日期:2011-09-01 00:00:00

  • PNUTS/PP1 regulates RNAPII-mediated gene expression and is necessary for developmental growth.

    abstract::In multicellular organisms, tight regulation of gene expression ensures appropriate tissue and organismal growth throughout development. Reversible phosphorylation of the RNA Polymerase II (RNAPII) C-terminal domain (CTD) is critical for the regulation of gene expression states, but how phosphorylation is actively mod...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1003885

    authors: Ciurciu A,Duncalf L,Jonchere V,Lansdale N,Vasieva O,Glenday P,Rudenko A,Vissi E,Cobbe N,Alphey L,Bennett D

    更新日期:2013-10-01 00:00:00

  • Abnormal type I collagen post-translational modification and crosslinking in a cyclophilin B KO mouse model of recessive osteogenesis imperfecta.

    abstract::Cyclophilin B (CyPB), encoded by PPIB, is an ER-resident peptidyl-prolyl cis-trans isomerase (PPIase) that functions independently and as a component of the collagen prolyl 3-hydroxylation complex. CyPB is proposed to be the major PPIase catalyzing the rate-limiting step in collagen folding. Mutations in PPIB cause re...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1004465

    authors: Cabral WA,Perdivara I,Weis M,Terajima M,Blissett AR,Chang W,Perosky JE,Makareeva EN,Mertz EL,Leikin S,Tomer KB,Kozloff KM,Eyre DR,Yamauchi M,Marini JC

    更新日期:2014-06-26 00:00:00

  • Signalling crosstalk during early tumorigenesis in the absence of Polycomb silencing.

    abstract::In response to stress and injury a coordinated activation of conserved signalling modules, such as JNK and JAK/STAT, is critical to trigger regenerative tissue restoration. While these pathways rebuild homeostasis and promote faithful organ recovery, it is intriguing that they also become activated in various tumour c...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1007187

    authors: Beira JV,Torres J,Paro R

    更新日期:2018-01-22 00:00:00

  • An Africa-wide genomic evolution of insecticide resistance in the malaria vector Anopheles funestus involves selective sweeps, copy number variations, gene conversion and transposons.

    abstract::Insecticide resistance in malaria vectors threatens to reverse recent gains in malaria control. Deciphering patterns of gene flow and resistance evolution in malaria vectors is crucial to improving control strategies and preventing malaria resurgence. A genome-wide survey of Anopheles funestus genetic diversity Africa...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008822

    authors: Weedall GD,Riveron JM,Hearn J,Irving H,Kamdem C,Fouet C,White BJ,Wondji CS

    更新日期:2020-06-04 00:00:00

  • C. elegans CLASP/CLS-2 negatively regulates membrane ingression throughout the oocyte cortex and is required for polar body extrusion.

    abstract::The requirements for oocyte meiotic cytokinesis during polar body extrusion are not well understood. In particular, the relationship between the oocyte meiotic spindle and polar body contractile ring dynamics remains largely unknown. We have used live cell imaging and spindle assembly defective mutants lacking the fun...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008751

    authors: Schlientz AJ,Bowerman B

    更新日期:2020-10-07 00:00:00