Correlation of gene expression and protein production rate - a system wide study
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Mikko Arvas | Markku Saloheimo | Merja Penttilä | Erno Lindfors | Paula Jouhten | Jari Rautio | Tiina Pakula | Heini Koivistoinen | P. Jouhten | Mikko Arvas | M. Penttilä | M. Wiebe | T. Pakula | M. Saloheimo | B. Smit | J. Rautio | Marilyn Wiebe | Bart Smit | Heini Koivistoinen | Erno Lindfors
[1] R. Lahesmaa,et al. A comparative evaluation of software for the analysis of liquid chromatography‐tandem mass spectrometry data from isotope coded affinity tag experiments , 2005, Proteomics.
[2] A. Martín-Cuadrado,et al. The endo-β-1,3-glucanase eng1p is required for dissolution of the primary septum during cell separation in Schizosaccharomyces pombe , 2003, Journal of Cell Science.
[3] Megan F. Cole,et al. Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast , 2005, Cell.
[4] S. Zeilinger,et al. Crel, the carbon catabolite repressor protein from Trichoderma reesei , 1995, FEBS letters.
[5] J. Nielsen,et al. Metabolic model integration of the bibliome, genome, metabolome and reactome of Aspergillus niger , 2008, Molecular systems biology.
[6] A. Ohta,et al. Molecular cloning of a phospholipase D gene from Aspergillus nidulans and characterization of its deletion mutants. , 2003, FEMS microbiology letters.
[7] Mikko Arvas,et al. Array comparative genomic hybridization analysis of Trichoderma reesei strains with enhanced cellulase production properties , 2010, BMC Genomics.
[8] Cathryn J. Rehmeyer,et al. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae , 2006, Nucleic acids research.
[9] C. Kubicek,et al. The Snf1 kinase of the filamentous fungus Hypocrea jecorina phosphorylates regulation-relevant serine residues in the yeast carbon catabolite repressor Mig1 but not in the filamentous fungal counterpart Cre1. , 2003, Fungal genetics and biology : FG & B.
[10] Brandi L. Cantarel,et al. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics , 2008, Nucleic Acids Res..
[11] Mikko Arvas,et al. Detecting novel genes with sparse arrays. , 2010, Gene.
[12] G. L. Law,et al. The Transcriptional Coactivators SAGA, SWI/SNF, and Mediator Make Distinct Contributions to Activation of Glucose-repressed Genes* , 2008, Journal of Biological Chemistry.
[13] D. Archer,et al. Genomics of protein folding in the endoplasmic reticulum, secretion stress and glycosylation in the aspergilli , 2009 .
[14] T. Bosch,et al. More than just orphans: are taxonomically-restricted genes important in evolution? , 2009, Trends in genetics : TIG.
[15] M. Penttilä,et al. The protein disulphide isomerase gene of the fungus Trichoderma reesei is induced by endoplasmic reticulum stress and regulated by the carbon source , 1999, Molecular and General Genetics MGG.
[16] Jens Nielsen,et al. α-Amylase production in recombinant Aspergillus oryzae during fed-batch and continuous cultivations , 1998 .
[17] Judith B. Zaugg,et al. Bacterial adaptation through distributed sensing of metabolic fluxes , 2010, Molecular systems biology.
[18] Bernard Henrissat,et al. Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) , 2008, Nature Biotechnology.
[19] Rafael A Irizarry,et al. Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. , 2006, Molecular cell.
[20] Monika Schmoll,et al. Metabolic engineering strategies for the improvement of cellulase production by Hypocrea jecorina , 2009, Biotechnology for biofuels.
[21] B. Turcotte,et al. A Fungal Family of Transcriptional Regulators: the Zinc Cluster Proteins , 2006, Microbiology and Molecular Biology Reviews.
[22] M. Penttilä,et al. Transcriptional monitoring of steady state and effects of anaerobic phases in chemostat cultures of the filamentous fungus Trichoderma reesei , 2006, BMC Genomics.
[23] C. Kubicek,et al. The Trichoderma atroviride seb1 (stress response element binding) gene encodes an AGGGG-binding protein which is involved in the response to high osmolarity stress , 2002, Molecular Genetics and Genomics.
[24] U. Sauer,et al. Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics , 2011, Molecular systems biology.
[25] M. Gribskov,et al. The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion , 2009, PLoS genetics.
[26] A. Törrönen,et al. The Two Major Xylanases from Trichoderma Reesei: Characterization of Both Enzymes and Genes , 1992, Bio/Technology.
[27] T. Speed,et al. Summaries of Affymetrix GeneChip probe level data. , 2003, Nucleic acids research.
[28] J. Nielsen,et al. Uncovering transcriptional regulation of metabolism by using metabolic network topology. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[29] John D. Storey,et al. Strong control, conservative point estimation and simultaneous conservative consistency of false discovery rates: a unified approach , 2004 .
[30] Julian N. Selley,et al. Glucose depletion inhibits translation initiation via eIF4A loss and subsequent 48S preinitiation complex accumulation, while the pentose phosphate pathway is coordinately up-regulated , 2011, Molecular biology of the cell.
[31] M. Hynes,et al. ATP-Citrate Lyase Is Required for Production of Cytosolic Acetyl Coenzyme A and Development in Aspergillus nidulans , 2010, Eukaryotic Cell.
[32] M. Penttilä,et al. Physiological evaluation of the filamentous fungus Trichoderma reesei in production processes by marker gene expression analysis , 2007, BMC biotechnology.
[33] C. Kubicek,et al. Lactose metabolism in filamentous fungi: how to deal with an unknown substrate , 2007 .
[34] D. Hoyle,et al. Growth control of the eukaryote cell: a systems biology study in yeast , 2007, Journal of biology.
[35] Dong-Min Han,et al. Screening of growth- or development-related genes by using genomic library with inducible promoter in Aspergillus nidulans. , 2005, Journal of microbiology.
[36] Yasuji Koyama,et al. Transcriptional regulation of genes on the non-syntenic blocks of Aspergillus oryzae and its functional relationship to solid-state cultivation. , 2008, Fungal genetics and biology : FG & B.
[37] G. Robson,et al. Growth‐rate‐independent production of recombinant glucoamylase by Fusarium venenatum JeRS 325 , 2000, Biotechnology and bioengineering.
[38] K. Isono,et al. Genome sequencing and analysis of Aspergillus oryzae , 2005, Nature.
[39] Desmond S. Lun,et al. Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production , 2009, PLoS Comput. Biol..
[40] Justin R. Cross,et al. ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation , 2009, Science.
[41] D. Ussery,et al. Comparison of protein coding gene contents of the fungal phyla Pezizomycotina and Saccharomycotina , 2007, BMC Genomics.
[42] Corinna Lange,et al. Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. , 2007, Nature chemical biology.
[43] C. Ball,et al. Saccharomyces Genome Database. , 2002, Methods in enzymology.
[44] B. Barrell,et al. Life with 6000 Genes , 1996, Science.
[45] Gordon K Smyth,et al. Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .
[46] J. Cherry,et al. Directed evolution of industrial enzymes: an update. , 2003, Current opinion in biotechnology.
[47] M. Penttilä,et al. Cloning and Expression of a Fungal l-Arabinitol 4-Dehydrogenase Gene* , 2001, The Journal of Biological Chemistry.
[48] John E. Linz,et al. Volatile profiling reveals intracellular metabolic changes in Aspergillus parasiticus: veA regulates branched chain amino acid and ethanol metabolism , 2010, BMC Biochemistry.
[49] P. Kemmeren,et al. Monitoring global messenger RNA changes in externally controlled microarray experiments , 2003, EMBO reports.
[50] M. Penttilä,et al. Identification in the mold Hypocrea jecorina of the first fungal D-galacturonic acid reductase. , 2005, Biochemistry.
[51] F. Henrique-Silva,et al. Mitochondrial functions mediate cellulase gene expression in Trichoderma reesei. , 1995, Biochemistry.
[52] Kathryn S Lilley,et al. Nutrient control of eukaryote cell growth: a systems biology study in yeast , 2010, BMC Biology.
[53] Y. Reyes-Domínguez,et al. Chromatin-level regulation of biosynthetic gene clusters. , 2009, Nature chemical biology.
[54] K. Gould,et al. Proteomics Analysis Reveals Stable Multiprotein Complexes in Both Fission and Budding Yeasts Containing Myb-Related Cdc5p/Cef1p, Novel Pre-mRNA Splicing Factors, and snRNAs , 2002, Molecular and Cellular Biology.
[55] M. Schmoll. The information highways of a biotechnological workhorse – signal transduction in Hypocrea jecorina , 2008, BMC Genomics.
[56] Peter Walter,et al. Gcn4p and Novel Upstream Activating Sequences Regulate Targets of the Unfolded Protein Response , 2004, PLoS biology.
[57] K. O’Donnell,et al. Ancestral polymorphism and adaptive evolution in the trichothecene mycotoxin gene cluster of phytopathogenic Fusarium , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[58] John E. Linz,et al. The initiation and pattern of spread of histone H4 acetylation parallel the order of transcriptional activation of genes in the aflatoxin cluster , 2007, Molecular microbiology.
[59] J. Kruszewska,et al. Cloning and functional analysis of the dpm2 and dpm3 genes from Trichoderma reesei expressed in a Saccharomyces cerevisiae dpm1Δ mutant strain , 2011, Biological chemistry.
[60] B. Seiboth,et al. Sequential gene deletions in Hypocrea jecorina using a single blaster cassette , 2005, Current Genetics.
[61] Yin-Won Lee,et al. ATP citrate lyase is required for normal sexual and asexual development in Gibberella zeae. , 2011, Fungal genetics and biology : FG & B.
[62] Jaideep P. Sundaram,et al. Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus , 2008, PLoS genetics.
[63] Søren Brunak,et al. Prediction of human protein function according to Gene Ontology categories , 2003, Bioinform..
[64] Andreas Beyer,et al. Posttranscriptional Expression Regulation: What Determines Translation Rates? , 2007, PLoS Comput. Biol..
[65] John R Yates,et al. Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator , 2009, Molecular systems biology.
[66] Ari J. S. Ferreira,et al. Elucidation of the Metabolic Fate of Glucose in the Filamentous Fungus Trichoderma reesei Using Expressed Sequence Tag (EST) Analysis and cDNA Microarrays* , 2002, The Journal of Biological Chemistry.
[67] J. Bennett,et al. Fungal secondary metabolism — from biochemistry to genomics , 2005, Nature Reviews Microbiology.
[68] M. Tribus,et al. Histone Deacetylase Activity Regulates Chemical Diversity in Aspergillus , 2007, Eukaryotic Cell.
[69] Rolf Apweiler,et al. InterProScan: protein domains identifier , 2005, Nucleic Acids Res..
[70] Sarah Calvo,et al. Insights from the genome of the biotrophic fungal plant pathogen Ustilago maydis , 2006, Nature.
[71] Kristiina Kruus,et al. Discovery of a new tyrosinase-like enzyme family lacking a C-terminally processed domain: production and characterization of an Aspergillus oryzae catechol oxidase , 2010, Applied Microbiology and Biotechnology.
[72] John E. Linz,et al. Clustered Pathway Genes in Aflatoxin Biosynthesis , 2004, Applied and Environmental Microbiology.
[73] C. Kubicek,et al. The Hypocrea jecorina gal10 (uridine 5'-diphosphate-glucose 4-epimerase-encoding) gene differs from yeast homologues in structure, genomic organization and expression. , 2002, Gene.
[74] M. Penttilä,et al. The Effects of Drugs Inhibiting Protein Secretion in the Filamentous Fungus Trichoderma reesei , 2003, Journal of Biological Chemistry.
[75] D. Bell-Pedersen,et al. Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. , 2004, Fungal genetics and biology : FG & B.
[76] J. Pronk,et al. Role of Transcriptional Regulation in Controlling Fluxes in Central Carbon Metabolism of Saccharomyces cerevisiae , 2004, Journal of Biological Chemistry.
[77] C. Fanelli,et al. Natural functions of mycotoxins and control of their biosynthesis in fungi , 2010, Applied Microbiology and Biotechnology.
[78] M. Penttilä,et al. Activation mechanisms of the HACI‐mediated unfolded protein response in filamentous fungi , 2003, Molecular microbiology.
[79] J. Nielsen,et al. Glucoamylase production in batch, chemostat and fed-batch cultivations by an industrial strain of Aspergillus niger , 2000, Applied Microbiology and Biotechnology.
[80] C. Kubicek,et al. The fungal STRE-element-binding protein Seb1 is involved but not essential for glycerol dehydrogenase (gld1) gene expression and glycerol accumulation in Trichoderma atroviride during osmotic stress. , 2004, Fungal genetics and biology : FG & B.
[81] C. Kubicek,et al. The d‐xylose reductase of Hypocrea jecorina is the major aldose reductase in pentose and d‐galactose catabolism and necessary for β‐galactosidase and cellulase induction by lactose , 2007, Molecular microbiology.
[82] P. Goloboff. Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima , 1999, Cladistics : the international journal of the Willi Hennig Society.
[83] Wendy Schackwitz,et al. Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing , 2009, Proceedings of the National Academy of Sciences.
[84] R. D. de Vries,et al. The Hypocrea jecorina (syn. Trichoderma reesei) lxr1 gene encodes a d‐mannitol dehydrogenase and is not involved in l‐arabinose catabolism , 2009, FEBS letters.
[85] R. Contreras,et al. Cloning and Characterization of the Glucosidase II Alpha Subunit Gene of Trichoderma reesei: a Frameshift Mutation Results in the Aberrant Glycosylation Profile of the Hypercellulolytic Strain Rut-C30 , 2005, Applied and Environmental Microbiology.
[86] M. Penttilä,et al. Protein production and induction of the unfolded protein response in Trichoderma reesei strain Rut-C30 and its transformant expressing endoglucanase I with a hydrophobic tag. , 2005, Biotechnology and bioengineering.
[87] Jean YH Yang,et al. Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.
[88] D. Sinclair,et al. Nicotinamide and PNC1 govern lifespan extension by calorie restriction in Saccharomyces cerevisiae , 2003, Nature.
[89] W. Nierman,et al. Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis , 2008, PLoS pathogens.
[90] L. Hood,et al. Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in Saccharomyces cerevisiae*S , 2002, Molecular & Cellular Proteomics.
[91] K. Struhl,et al. Histone Acetylation at Promoters Is Differentially Affected by Specific Activators and Repressors , 2001, Molecular and Cellular Biology.
[92] U. Kück,et al. The fungal acl1 and acl2 genes encode two polypeptides with homology to the N- and C-terminal parts of the animal ATP citrate lyase polypeptide , 2000, Current Genetics.
[93] S. Brunak,et al. Locating proteins in the cell using TargetP, SignalP and related tools , 2007, Nature Protocols.
[94] M. Lorito,et al. The ThPG1 endopolygalacturonase is required for the trichoderma harzianum-plant beneficial interaction. , 2009, Molecular plant-microbe interactions : MPMI.
[95] G. Mannhaupt,et al. Relationship between Phylogenetic Distribution and Genomic Features in Neurospora crassa , 2009, PloS one.
[96] D. Kaback,et al. Meiotic Recombination at the Ends of Chromosomes in Saccharomyces cerevisiae , 2008, Genetics.
[97] Sarath Chandra Janga,et al. Interplay between posttranscriptional and posttranslational interactions of RNA-binding proteins. , 2011, Journal of molecular biology.
[98] James R Broach,et al. How Saccharomyces responds to nutrients. , 2008, Annual review of genetics.
[99] Kellen L. Olszewski,et al. Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network , 2010, Molecular systems biology.
[100] K. Myambo,et al. Molecular Cloning of Exo–Cellobiohydrolase I Derived from Trichoderma Reesei Strain L27 , 1983, Bio/Technology.
[101] J. Visser,et al. Mannitol Is Required for Stress Tolerance in Aspergillus niger Conidiospores , 2003, Eukaryotic Cell.
[102] Andrew J. Millar,et al. Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus , 2011, BMC Systems Biology.
[103] E. Halperin,et al. Detection of Molecular Paths Associated with Insulitis and Type 1 Diabetes in Non-Obese Diabetic Mouse , 2009, PloS one.
[104] M. Penttilä,et al. The glucose repressor genecre1 ofTrichoderma: Isolation and expression of a full-length and a truncated mutant form , 1996, Molecular and General Genetics MGG.
[105] Merja Penttilä,et al. The effect of specific growth rate on protein synthesis and secretion in the filamentous fungus Trichoderma reesei. , 2005, Microbiology.
[106] Mikko Arvas,et al. Common features and interesting differences in transcriptional responses to secretion stress in the fungi Trichoderma reesei and Saccharomyces cerevisiae , 2006, BMC Genomics.
[107] Mam Riess Jones. Color Coding , 1962, Human factors.
[108] R. Toledo,et al. Cellulase production in continuous culture by Trichoderma reesei on xylose‐based media , 1992, Biotechnology and bioengineering.
[109] P. Sunnerhagen,et al. Mkp1 and Mkp2, two MAPKAP-kinase homologues in Schizosaccharomyces pombe, interact with the MAP kinase Sty1 , 2003, Molecular Genetics and Genomics.
[110] M. Penttilä,et al. Use of matrix-assisted laser desorption/ionization time-of-flight mass mapping and nanospray liquid chromatography/electrospray ionization tandem mass spectrometry sequence tag analysis for high sensitivity identification of yeast proteins separated by two-dimensional gel electrophoresis. , 2001, Rapid communications in mass spectrometry : RCM.
[111] R. Contreras,et al. Cloning and Characterization of the Glucosidase II Alpha Subunit Gene of Trichoderma reesei : a Frameshift Mutation Results in the Aberrant Glycosylation Profile of the Hypercellulolytic Strain Rut-C 30 , 2005 .
[112] Marcel JT Reinders,et al. Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: A quantitative analysis of a compendium of chemostat-based transcriptome data , 2009, BMC Genomics.
[113] Osamu Akita,et al. Transcriptional analysis of genes for energy catabolism and hydrolytic enzymes in the filamentous fungus Aspergillus oryzae using cDNA microarrays and expressed sequence tags , 2004, Applied Microbiology and Biotechnology.
[114] H. Blanch,et al. Lactase production in continuous culture by Trichoderma reesei Rut-C30 , 1984, Biotechnology Letters.
[115] M. Penttilä,et al. Rapid and multiplexed transcript analysis of microbial cultures using capillary electophoresis-detectable oligonucleotide probe pools. , 2006, Journal of microbiological methods.
[116] Q. Zeng,et al. Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) , 2010, Proceedings of the National Academy of Sciences.
[117] John E. Linz,et al. Compartmentalization and molecular traffic in secondary metabolism: a new understanding of established cellular processes. , 2011, Fungal genetics and biology : FG & B.
[118] M. Rep,et al. The genomic organization of plant pathogenicity in Fusarium species. , 2010, Current opinion in plant biology.
[119] B. Dujon,et al. Genome evolution in yeasts , 2004, Nature.
[120] C. Kubicek,et al. d-Xylose Metabolism in Hypocrea jecorina: Loss of the Xylitol Dehydrogenase Step Can Be Partially Compensated for by lad1-Encoded l-Arabinitol-4-Dehydrogenase , 2003, Eukaryotic Cell.
[121] V. Sahai,et al. Comparison of growth and maintenance parameters for cellulase biosynthesis by Trichoderma reesei-C5 with some published data , 1994 .
[122] Rainer Breitling,et al. Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor , 2010, BMC Genomics.
[123] H. Mewes,et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. , 2004, Nucleic acids research.
[124] D. Eveleigh,et al. SELECTIVE SCREENING METHODS FOR THE ISOLATION OF HIGH YIELDING CELLULASE MUTANTS OF TRICHODERMA REESEI , 1979 .