DOCSLIB.ORG

Table S2 Genes Differentially Expressed in T. Reesei Strains Modulated in Lae1 Function*

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Table S2 Genes Differentially Expressed in T. Reesei Strains Modulated in Lae1 Function* Table S2 Genes differentially expressed in T. reesei strains modulated in lae1 function* ratio SEQ_ID wild-type S.D. ∆lae1 S.D. lae1OE S.D. ratio [∆lae1] p-value F- value Annotation [ae1OE] 1959 6.55 0.23 6.99 0.07 8.78 0.15 1.359 up 4.687 up 0.00 166.52 HaloaciD Dehalogenase-like hyDrolase 1977 12.71 0.03 12.57 0.04 11.58 0.14 1.106 DoWn 2.191 DoWn 0.00 89.50 PeptiDase_M28 1993 12.52 0.05 12.44 0.14 11.27 0.09 1.057 DoWn 2.381 DoWn 0.00 151.74 γ-glutamyl phosphate reductase GPR 2033 4.81 0.06 3.30 0.04 5.95 0.13 2.855 DoWn 2.205 up 0.00 404.26 unknown protein 2036 6.24 0.02 6.11 0.09 7.75 0.16 1.090 DoWn 2.856 up 0.00 142.94 cysteine peptiDase 2071 9.68 0.07 10.58 0.09 10.86 0.09 1.875 up 2.266 up 0.00 123.87 unknown protein. 5 TM 2076 9.84 0.10 6.09 0.11 6.75 0.45 13.496 DoWn 8.504 DoWn 0.00 67.36 malate permease 2091 12.79 0.03 12.11 0.17 11.37 0.08 1.604 DoWn 2.676 DoWn 0.00 136.90 6-phosphofructokinase 2096 9.25 0.02 9.96 0.15 7.47 0.31 1.637 up 3.429 DoWn 0.00 76.37 Zn2Cys6 transcriptional regulator 2125 12.16 0.01 12.35 0.05 11.13 0.10 1.146 up 2.029 DoWn 0.00 188.64 Fructose-2.6-bisphosphatase 2148 13.15 0.02 12.06 0.21 11.74 0.24 2.133 DoWn 2.651 DoWn 0.00 30.59 Zn2Cys6 transcriptional regulator 2185 5.85 0.02 6.67 0.15 8.71 0.36 1.764 up 7.251 up 0.00 76.38 GCN5-relateD N-acetyltransferase 2223 8.84 0.12 9.08 0.13 10.23 0.22 1.178 up 2.618 up 0.00 45.43 succinate-CoA ligase. alpha subunit 2316 12.36 0.10 10.37 0.27 10.33 0.10 3.965 DoWn 4.082 DoWn 0.00 141.24 unknown protein With caleosin domain 2322 9.61 0.01 9.18 0.14 8.22 0.17 1.344 DoWn 2.612 DoWn 0.00 65.81 unknown protein 2358 9.66 0.06 9.32 0.03 8.12 0.28 1.269 DoWn 2.915 DoWn 0.00 40.58 unknown protein With HIT domain 2392 14.29 0.09 14.02 0.04 12.19 0.23 1.209 DoWn 4.288 DoWn 0.00 117.02 peroxisomal hydratase-dehydrogenase-epimerase 2399 11.59 0.01 11.51 0.10 9.90 0.08 1.056 DoWn 3.210 DoWn 0.00 457.97 unknown protein 2489 6.70 0.04 5.83 0.06 8.45 0.38 1.820 DoWn 3.356 up 0.00 59.33 Ribonuclease T2 2492 10.31 0.17 9.44 0.02 8.18 0.24 1.832 DoWn 4.378 DoWn 0.00 78.04 PhosphatiDylinositol-4-phosphate 5-kinase 2499 7.61 0.09 7.85 0.04 5.36 0.27 1.182 up 4.741 DoWn 0.00 122.47 unknown protein 2517 4.72 0.08 4.23 0.05 5.82 0.41 1.399 DoWn 2.149 up 0.01 18.41 Flavoprotein monooxygenase. putative 2526 13.57 0.02 13.29 0.14 12.56 0.14 1.215 DoWn 2.010 DoWn 0.00 50.83 Protein kinase C 2570 3.28 0.07 3.82 0.24 4.83 0.08 1.448 up 2.929 up 0.00 105.25 short chain Dehydrogenase/reductase 2687 12.56 0.07 10.54 0.17 10.90 0.10 4.071 DoWn 3.173 DoWn 0.00 197.49 AAA ATPase 2703 11.87 0.14 11.97 0.04 10.62 0.24 1.074 up 2.372 DoWn 0.00 41.84 unknown protein 3 SI R. Karimi-Aghcheh et al. 2730 13.28 0.05 13.24 0.00 12.16 0.20 1.024 DoWn 2.171 DoWn 0.00 47.38 unknown protein 2745 12.92 0.02 12.76 0.13 11.80 0.12 1.115 DoWn 2.175 DoWn 0.00 91.93 fumarate hyDratase-like protein 2835 11.99 0.01 11.83 0.01 10.80 0.21 1.112 DoWn 2.275 DoWn 0.00 44.84 unknown protein 3043 3.23 0.03 3.71 0.18 5.11 0.18 1.393 up 3.664 up 0.00 105.89 SSCRP 3049 13.72 0.39 12.80 0.01 10.85 0.08 1.898 DoWn 7.341 DoWn 0.00 181.03 methionine aminopeptiDase 3055 12.48 0.15 7.97 0.14 11.17 0.12 22.757 DoWn 2.485 DoWn 0.00 651.11 short chain Dehydrogenase/reDuctase 3094 5.60 0.12 5.26 0.11 7.17 0.67 1.265 DoWn 2.986 up 0.02 11.46 GH30 glucan enDo 1.6-β-glucanase 3121 3.35 0.46 3.82 0.25 4.97 0.12 1.379 up 3.066 up 0.00 31.51 cytochrome P450 oxiDoreDuctase OrDA-like 3196 12.47 0.11 12.28 0.05 10.80 0.16 1.138 DoWn 3.171 DoWn 0.00 131.28 GH38 α-mannosiDase 3262 3.61 0.03 4.01 0.01 5.31 0.21 1.315 up 3.244 up 0.00 86.89 succinate semialDehyde Dehydrogenase (NADP) 3267 9.12 0.02 10.14 0.06 7.30 0.31 2.019 up 3.543 DoWn 0.00 100.17 MRSP1/expansin-like 3350 11.77 0.18 12.11 0.24 10.76 0.31 1.265 up 2.002 DoWn 0.01 18.73 phosphopantothenate-cysteine ligase 3364 11.25 0.06 10.43 0.11 9.12 0.17 1.768 DoWn 4.386 DoWn 0.00 156.98 Zinc-containing alcohol Dehydrogenase 3422 6.69 0.30 6.91 0.15 8.76 0.41 1.166 up 4.207 up 0.00 31.17 unknown protein With oxiDoreductase Domain 3462 12.11 0.15 12.22 0.06 11.06 0.24 1.083 up 2.060 DoWn 0.00 30.58 UreF urease accessory protein 3481 10.81 0.10 10.51 0.24 9.67 0.22 1.236 DoWn 2.211 DoWn 0.01 23.75 unknown protein 3488 11.29 0.09 9.77 0.05 9.93 0.21 2.876 DoWn 2.578 DoWn 0.00 55.13 unknown protein 3501 9.18 0.12 8.88 0.13 8.15 0.24 1.227 DoWn 2.035 DoWn 0.01 19.64 unknown protein 3529 10.62 0.10 11.31 0.32 11.99 0.16 1.613 up 2.586 up 0.00 33.87 unknown protein 3568 10.27 0.07 7.85 0.24 8.39 0.27 5.337 DoWn 3.682 DoWn 0.00 62.06 phospholipase A2 3579 7.68 0.00 7.74 0.19 9.71 0.27 1.046 up 4.104 up 0.00 79.80 ATP-dependent RNA helicases. 3596 7.86 0.25 7.31 0.09 8.90 0.43 1.470 DoWn 2.050 up 0.01 14.87 uroporphyrinogen synthase 3605 11.24 0.02 10.78 0.07 9.96 0.17 1.377 DoWn 2.431 DoWn 0.00 67.96 Zn2Cys6 transcriptional regulator 3835 10.40 0.27 10.40 0.01 8.73 0.33 1.002 DoWn 3.172 DoWn 0.00 34.15 3-ketoacyl-CoA thiolase 3889 13.56 0.12 13.42 0.01 12.31 0.33 1.099 DoWn 2.382 DoWn 0.01 21.19 unknown protein 3909 9.25 0.02 10.02 0.11 10.58 0.44 1.710 up 2.528 up 0.03 10.22 MitochonDrial ribosomal protein L43 3914 10.64 0.03 7.12 0.09 6.78 0.89 11.485 DoWn 14.492 DoWn 0.01 22.27 EnDoplasmic reticulum protein EP58 4040 11.23 0.04 10.80 0.00 10.10 0.21 1.353 DoWn 2.187 DoWn 0.00 35.16 RNA polymerase Rpc34 subunit 4064 11.58 0.07 11.92 0.04 13.18 0.09 1.267 up 3.025 up 0.00 345.65 Threonine DehyDratase 4069 11.64 0.03 11.63 0.09 10.33 0.29 1.008 DoWn 2.480 DoWn 0.00 32.07 AMP-dependent synthetase anD ligase 4 SI R. Karimi-Aghcheh et al. 4109 9.86 0.05 10.13 0.00 8.71 0.20 1.204 up 2.228 DoWn 0.00 68.66 Aspartate/tyrosine/aromatic aminotransferase 4114 6.26 0.36 3.21 0.04 5.03 0.19 8.272 DoWn 2.337 DoWn 0.00 96.40 FAD linked oxiDase 4124 6.34 0.08 10.60 0.10 9.84 0.11 19.177 up 11.315 up 0.00 1042.30 myb transcriptional regulator 4171 9.30 0.15 6.01 0.14 7.97 0.19 9.788 DoWn 2.519 DoWn 0.00 177.10 calcium transporter 4240 11.22 0.06 8.06 0.05 8.02 0.08 8.960 DoWn 9.188 DoWn 0.00 1420.23 stress response protein RDs1; secreteD 4308 12.63 0.13 11.85 0.03 11.62 0.17 1.717 DoWn 2.021 DoWn 0.00 32.90 Aminopeptidase N 4428 10.26 0.15 9.95 0.05 9.19 0.25 1.234 DoWn 2.098 DoWn 0.01 20.69 unknown protein.
Load more

Recommended publications
  • Elb87.Pdf (3.312Mb)
    NONLINEAR CONSTRAINT-BASED MODELING OF THE FUNCTION AND EVOLUTION OF C4 PHOTOSYNTHESIS A Dissertation Presented to the Faculty of the Graduate School of Cornell University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Elijah Lane Bogart August 2015 © 2015 Elijah Lane Bogart ALL RIGHTS RESERVED NONLINEAR CONSTRAINT-BASED MODELING OF THE FUNCTION AND EVOLUTION OF C4 PHOTOSYNTHESIS Elijah Lane Bogart, Ph.D. Cornell University 2015 C4 plants, such as maize, concentrate carbon dioxide in a specialized compart- ment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. The C4 photosynthetic system is a key target of efforts to improve crop yield through biotechnology, and its independent development in dozens of plant species widely separated geographically and phylogenetically is an intriguing example of convergent evolution. The availability of extensive high-throughput experimental data from C4 and non-C4 plants, as well as the origin of the biochemical pathways of C4 photosynthesis in the recruitment of enzymatic reactions already present in the ancestral state, makes it natural to study the development, function and evolu- tion of the C4 system in the context of a plant’s complete metabolic network, but the essentially nonlinear relationship between rates of photosynthesis, rates of photorespiration, and carbon dioxide and oxygen levels prevents the appli- cation of conventional, linear methods for genome-scale metabolic modeling to these questions. I present an approach which incorporates nonlinear constraints on reaction rates arising from enzyme kinetics and diffusion laws into flux balance analysis problems, and software to enable it.
    [Show full text]
  • Supporting Information
    Supporting Information Figure S1. The functionality of the tagged Arp6 and Swr1 was confirmed by monitoring cell growth and sensitivity to hydeoxyurea (HU). Five-fold serial dilutions of each strain were plated on YPD with or without 50 mM HU and incubated at 30°C or 37°C for 3 days. Figure S2. Localization of Arp6 and Swr1 on chromosome 3. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 3L, Tel 3R, CEN3, and the RP gene are shown under the panels. Figure S3. Localization of Arp6 and Swr1 on chromosome 4. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) in the whole chromosome region are compared. The position of Tel 4L, Tel 4R, CEN4, SWR1, and RP genes are shown under the panels. Figure S4. Localization of Arp6 and Swr1 on the region including the SWR1 gene of chromosome 4. The binding of Arp6- FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position and orientation of the SWR1 gene is shown. Figure S5. Localization of Arp6 and Swr1 on chromosome 5. The binding of Arp6-FLAG (top), Swr1-FLAG (middle), and Arp6-FLAG in swr1 cells (bottom) are compared. The position of Tel 5L, Tel 5R, CEN5, and the RP genes are shown under the panels. Figure S6. Preferential localization of Arp6 and Swr1 in the 5′ end of genes. Vertical bars represent the binding ratio of proteins in each locus.
    [Show full text]
  • ( 12 ) Patent Application Publication
    US 20200199632A1 IN (19 ) United States (12 ) Patent Application Publication ( 10 ) Pub . No .: US 2020/0199632 A1 Toivari et al. (43 ) Pub . Date : Jun . 25 , 2020 ( 54 ) IMPROVED PRODUCTION OF C12N 9/14 (2006.01 ) OXALYL - COA , GLYOXYLATE AND /OR C12N 9/00 (2006.01 ) GLYCOLIC ACID C12N 9/88 (2006.01 ) (52 ) U.S. CI. ( 71 ) Applicant : Teknologian Tutkimuskeskus VTT CPC C12P 7/42 (2013.01 ) ; C12P 5/026 Oy , Espoo (FI ) ( 2013.01) ; C12N 9/14 (2013.01 ) ; C12N 9/88 (72 ) Inventors : Mervi Toivari , VTT (FI ) ; Marja ( 2013.01 ) ; C12N 9/93 (2013.01 ) ; C12Y Ilmén , VTT (FI ) ; Merja Penttilä , VTT 604/01001 ( 2013.01 ) ; C12 Y 602/01008 (FI ) ( 2013.01 ) ; C12Y 307/01001 (2013.01 ) (21 ) Appl. No.: 16 /633,608 (57 ) ABSTRACT ( 22 ) PCT Filed : Jul, 27 , 2018 The present invention relates to a method of converting ( 86 ) PCT No .: PCT/ FI2018 / 050557 oxalate to oxalyl - coA and /or oxalyl - coA to glyoxylate in a fungus and to a method of producing glycolic acid . Still , the $ 371 ( c ) ( 1 ) , present invention relates to a genetically modified fungus (2 ) Date : Jan. 24 , 2020 comprising increased enzyme activity associated with oxalyl- CoA . And furthermore , the present invention relates ( 30 ) Foreign Application Priority Data to use of the fungus of the present invention for producing oxalate , oxalyl- CoA , glyoxylate and /or glycolic acid from a Jul. 28 , 2017 (FI ) 20175703 carbon substrate . Still furthermore , the present invention Publication Classification relates to a method of producing specific products and to a (51 ) Int. Ci. method of preparing the genetically modified fungus of the C12P 7/42 ( 2006.01 ) present invention .
    [Show full text]
  • Enzymatic Mechanism of Oxalate Production in the TCA and Glyoxylate Pathways Using Various Isolates of Antrodia Radiculosa K.M
    AMERICAN WOOD PROTECTION ASSOCIATION Enzymatic Mechanism of Oxalate Production in the TCA and Glyoxylate Pathways using Various Isolates of Antrodia radiculosa K.M. Jenkins S.V. Diehl Mississippi State University Starkville, Mississippi C.A. Clausen F. Green, III USDA-FS Forest Products Laboratory Madison, Wisconsin ABSTRACT Brown-rot fungi produce oxalate in large amounts; however, levels of accumulation and function vary by species. Copper-tolerant fungi, like Antrodia radiculosa, produce and accumulate high levels of oxalate in response to copper. Oxalate biosynthesis in copper-tolerant fungi has been linked to the glyoxylate and tricarboxylic acid (TCA) cycles. Within these two cycles, it has been proposed that oxalate production relies on twelve specific enzymes. In this study, Antrodia radiculosa isolates causing decay of untreated and 1.2% copper citrate treated wood were used to evaluate oxalate concentration and enzyme activity in five of the twelve enzymes. The enzyme activity of fumarase, glyoxylate dehydrogenase, isocitrate lyase, malate synthase, and oxaloacetase, was determined. Future gene expression analysis will determine any variations in enzymatic activity, as well as attempt to establish a pathway involved in the direct production of oxalate. INTRODUCTION Oxalate is a metabolic byproduct of the decay process, and is also a major factor that leads to the tolerance of copper based preservatives (Arango et al. 2009). The role of oxalate tends to vary with the type of copper treatment and species. Most brown-rot fungi produce oxalate regularly; however, copper-tolerant fungi produce it in much higher quantities. Clausen and Green (2003) found that copper-tolerant fungi produce 2-17 times more oxalate in copper treated blocks when compared to untreated controls.
    [Show full text]
  • Nucleosome Assembly and Histone H3 Methylation During Dna Replication
    NUCLEOSOME ASSEMBLY AND HISTONE H3 METHYLATION DURING DNA REPLICATION TxrwTom Rolef Ben-Shahar A thesis submitted for the degree of Ph.D. at The University of London July, 2004 Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire, EN6 3LD and University College London, Gower Street, London, WC1 6BT ProQuest Number: 10014844 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest 10014844 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 ACKNOWLEDGEMENTS To begin with, I would like to acknowledge my mistakes, scientific and others. Hopefully the future will show that I have learned what I could from them. My work has been funded by Cancer Research UK and with a B’NAI BRITH scholarship, and for that I am grateful. I would like to thank Alain Verreault for his supervision, for our scientific conversations and for allowing me to make my own mistakes. My gratitude is given to Munah Abdul-Rauf for being a colleague, collaborator, friend and sister; to Michal Goldberg, Niki Hawks and to other friends and colleagues in Clare-Hall.
    [Show full text]
  • Advances in Selectable Marker Genes for Plant Transformation
    ARTICLE IN PRESS Journal of Plant Physiology 165 (2008) 1698—1716 www.elsevier.de/jplph Advances in selectable marker genes for plant transformation Isaac Kirubakaran Sundar, Natarajan Sakthivelà Department of Biotechnology, School of Life Sciences, Pondicherry University, Kalapet, Puducherry 605 014, India Received 1 March 2008; accepted 4 August 2008 KEYWORDS Summary Biosafety; Plant transformation systems for creating transgenics require separate process for Plant introducing cloned DNA into living plant cells. Identification or selection of those transformation; cells that have integrated DNA into appropriate plant genome is a vital step to Positive selection; regenerate fully developed plants from the transformed cells. Selectable marker Selectable marker; genes are pivotal for the development of plant transformation technologies because Transgenic plants marker genes allow researchers to identify or isolate the cells that are expressing the cloned DNA, to monitor and select the transformed progeny. As only a very small portion of cells are transformed in most experiments, the chances of recovering transgenic lines without selection are usually low. Since the selectable marker gene is expected to function in a range of cell types it is usually constructed as a chimeric gene using regulatory sequences that ensure constitutive expression throughout the plant. Advent of recombinant DNA technology and progress in plant molecular biology had led to a desire to introduce several genes into single transgenic plant line, necessitating the development of various types of selectable markers. This review article describes the developments made in the recent past on plant transformation systems using different selection methods adding a note on their importance as marker genes in transgenic crop plants.
    [Show full text]
  • WO 2014/202616 A2 24 December 2014 (24.12.2014) P O P C T
    (12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2014/202616 A2 24 December 2014 (24.12.2014) P O P C T (51) International Patent Classification: 13 172714 1 I June 2013 (19.06.2013) EP C07K 14/37 (2006.01) 13 172724 0 I June 2013 (19.06.2013) EP 13 172685 3 I June 2013 (19.06.2013) EP (21) International Application Number: 13 172686 1 I S June 2013 (19.06.2013) EP PCT/EP2014/062737 13 172683 8 I S June 2013 (19.06.2013) EP (22) International Filing Date: 13 172672 1 I S June 2013 (19.06.2013) EP 17 June 2014 (17.06.2014) 13 172673 9 I S June 2013 (19.06.2013) EP 13 172675 4 I S June 2013 (19.06.2013) EP (25) Filing Language: English 13 172677 0 I S June 2013 (19.06.2013) EP (26) Publication Lan ua e: English 13 172681 2 I S June 2013 (19.06.2013) EP 13 172837 0 I S June 2013 (19.06.2013) EP (30) Priority Data: 13 17261 1 9 I S June 2013 (19.06.2013) EP 13 172700.0 19 June 2013 (19 .06.2013) EP 13 172784 4 I S June 2013 (19.06.2013) EP 13 172812.3 19 June 2013 (19 .06.2013) EP 13 172821 4 I S June 2013 (19.06.2013) EP 13 172758.8 19 June 2013 (19 .06.2013) EP 13 172615 0 I S June 2013 (19.06.2013) EP 13 172757.0 19 June 2013 (19 .06.2013) EP 13 172624 2 I S June 2013 (19.06.2013) EP 13 172842.0 19 June 2013 (19 .06.2013) EP 13 172680 4 I S June 2013 (19.06.2013) EP 13 172756.2 19 June 2013 (19 .06.2013) EP 13 172623 4 I S June 2013 (19.06.2013) EP 13 172759.6
    [Show full text]
  • Prospects for Bioprocess Development Based on Recent Genome Advances in Lignocellulose Degrading Basidiomycetes
    Prospects for Bioprocess Development Based on Recent Genome Advances in Lignocellulose Degrading Basidiomycetes Chiaki Hori and Daniel Cullen 1 Introduction Efficient and complete degradation of woody plant cell walls requires the concerted action of hydrolytic and oxidative systems possessed by a relatively small group of filamentous basidiomycetous fungi. Among these wood decay species, Phanerochaete chrysosporium was the first to be sequenced (Martinez et al. 2004). In the intervening 10 years, over 100 related saprophytes have been sequenced. There genomes have revealed impressive sequence diversity. and recent functional analyses are providing a deeper understanding of their roles in the deconstruction of plant cell walls and the transformation of xenobiotics. Wood cell walls are primarily composed of cellulose, hemicellulose and lignin. Many microbes are capable of hydrolyzing the linkages in cellulose and hemicel­ lulose, even though crystalline regions within cellulose can be rather challenging substrates (reviewed in Baldrian and Lopez-Mondejar 2014; van den Brink and de Vries 2011). In contrast, few microbes possess the oxidative enzymes required to efficiently degrade the recalcitrant lignin, a complex, amorphous, and insoluble phenylpropanoid polymer (Higuchi 1990; Ralph et al. 2004). These unusual wood decay fungi secrete extracellular peroxidases with impressive oxidative potential. Potential applications have focused primarily on lignocellulosic bioconversions to C. Hori, Ph.D. ( ) Riken Biomass Engineering Group, Yokohama, Japan e-mail: [email protected] D. Cullen, Ph.D USDA Forest Products Laboratory, Madison, WI. USA e-mail: [email protected] © Springer International Publishing Switzerland 2016 161 M. Schmoll, C. Dattenböck (eds.). Gene Expression Systems in Fungi: Advancements and Applications, Fungal Biology, DOI 10.1007/978-3-319-27951-0_6 162 C.
    [Show full text]
  • 12) United States Patent (10
    US007635572B2 (12) UnitedO States Patent (10) Patent No.: US 7,635,572 B2 Zhou et al. (45) Date of Patent: Dec. 22, 2009 (54) METHODS FOR CONDUCTING ASSAYS FOR 5,506,121 A 4/1996 Skerra et al. ENZYME ACTIVITY ON PROTEIN 5,510,270 A 4/1996 Fodor et al. MICROARRAYS 5,512,492 A 4/1996 Herron et al. 5,516,635 A 5/1996 Ekins et al. (75) Inventors: Fang X. Zhou, New Haven, CT (US); 5,532,128 A 7/1996 Eggers Barry Schweitzer, Cheshire, CT (US) 5,538,897 A 7/1996 Yates, III et al. s s 5,541,070 A 7/1996 Kauvar (73) Assignee: Life Technologies Corporation, .. S.E. al Carlsbad, CA (US) 5,585,069 A 12/1996 Zanzucchi et al. 5,585,639 A 12/1996 Dorsel et al. (*) Notice: Subject to any disclaimer, the term of this 5,593,838 A 1/1997 Zanzucchi et al. patent is extended or adjusted under 35 5,605,662 A 2f1997 Heller et al. U.S.C. 154(b) by 0 days. 5,620,850 A 4/1997 Bamdad et al. 5,624,711 A 4/1997 Sundberg et al. (21) Appl. No.: 10/865,431 5,627,369 A 5/1997 Vestal et al. 5,629,213 A 5/1997 Kornguth et al. (22) Filed: Jun. 9, 2004 (Continued) (65) Prior Publication Data FOREIGN PATENT DOCUMENTS US 2005/O118665 A1 Jun. 2, 2005 EP 596421 10, 1993 EP 0619321 12/1994 (51) Int. Cl. EP O664452 7, 1995 CI2O 1/50 (2006.01) EP O818467 1, 1998 (52) U.S.
    [Show full text]
  • Global Response of Saccharomyces Cerevisiae to an Alkylating Agent
    Proc. Natl. Acad. Sci. USA Vol. 96, pp. 1486–1491, February 1999 Genetics Global response of Saccharomyces cerevisiae to an alkylating agent SCOTT A. JELINSKY AND LEONA D. SAMSON* Department of Cancer Cell Biology, Division of Toxicology, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115 Edited by David Botstein, Stanford University School of Medicine, Stanford, CA, and approved December 7, 1998 (received for review September 16, 1998) ABSTRACT DNA chip technology enables simultaneous CUPr) was used in this study and was grown in 1% yeast examination of how '6,200 Saccharomyces cerevisiae gene tran- extracty2% peptoney2% glucose at 30°C. Cells were grown to a script levels, representing the entire genome, respond to envi- density of 5 3 106 cells per ml as measured by counting duplicated ronmental change. By using chips bearing oligonucleotide ar- dilutions. Cultures were split into two; MMS (0.1%) was added rays, we show that, after exposure to the alkylating agent methyl directly to one culture, and both cultures were incubated at 30°C ' methanesulfonate, 325 gene transcript levels are increased and for 1 h. Cells were pelleted and washed once in distilled H2O and '76 are decreased. Of the 21 genes that already were known to once in AE buffer (50 mM NaOAc, pH 5.2y10 mM EDTA) be induced by a DNA-damaging agent, 18 can be scored as immediately before RNA extraction. inducible in this data set, and surprisingly, most of the newly RNA Extraction. Total RNA was isolated by using a hot-phenol identified inducible genes are induced even more strongly than method (15).
    [Show full text]
  • POLSKIE TOWARZYSTWO BIOCHEMICZNE Postępy Biochemii
    POLSKIE TOWARZYSTWO BIOCHEMICZNE Postępy Biochemii http://rcin.org.pl WSKAZÓWKI DLA AUTORÓW Kwartalnik „Postępy Biochemii” publikuje artykuły monograficzne omawiające wąskie tematy, oraz artykuły przeglądowe referujące szersze zagadnienia z biochemii i nauk pokrewnych. Artykuły pierwszego typu winny w sposób syntetyczny omawiać wybrany temat na podstawie możliwie pełnego piśmiennictwa z kilku ostatnich lat, a artykuły drugiego typu na podstawie piśmiennictwa z ostatnich dwu lat. Objętość takich artykułów nie powinna przekraczać 25 stron maszynopisu (nie licząc ilustracji i piśmiennictwa). Kwartalnik publikuje także artykuły typu minireviews, do 10 stron maszynopisu, z dziedziny zainteresowań autora, opracowane na podstawie najnow­ szego piśmiennictwa, wystarczającego dla zilustrowania problemu. Ponadto kwartalnik publikuje krótkie noty, do 5 stron maszynopisu, informujące o nowych, interesujących osiągnięciach biochemii i nauk pokrewnych, oraz noty przybliżające historię badań w zakresie różnych dziedzin biochemii. Przekazanie artykułu do Redakcji jest równoznaczne z oświadczeniem, że nadesłana praca nie była i nie będzie publikowana w innym czasopiśmie, jeżeli zostanie ogłoszona w „Postępach Biochemii”. Autorzy artykułu odpowiadają za prawidłowość i ścisłość podanych informacji. Autorów obowiązuje korekta autorska. Koszty zmian tekstu w korekcie (poza poprawieniem błędów drukarskich) ponoszą autorzy. Artykuły honoruje się według obowiązujących stawek. Autorzy otrzymują bezpłatnie 25 odbitek swego artykułu; zamówienia na dodatkowe odbitki (płatne) należy zgłosić pisemnie odsyłając pracę po korekcie autorskiej. Redakcja prosi autorów o przestrzeganie następujących wskazówek: Forma maszynopisu: maszynopis pracy i wszelkie załączniki należy nadsyłać w dwu egzem­ plarzach. Maszynopis powinien być napisany jednostronnie, z podwójną interlinią, z marginesem ok. 4 cm po lewej i ok. 1 cm po prawej stronie; nie może zawierać więcej niż 60 znaków w jednym wierszu nie więcej niż 30 wierszy na stronie zgodnie z Normą Polską.
    [Show full text]
  • Omics Analyses and Biochemical Study of Phlebiopsis Gigantea Elucidate Its Degradation Strategy of Wood Extractives
    www.nature.com/scientificreports OPEN Omics analyses and biochemical study of Phlebiopsis gigantea elucidate its degradation strategy of wood extractives Mana Iwata1, Ana Gutiérrez2, Gisela Marques2, Grzegorz Sabat3, Philip J. Kersten4, Daniel Cullen4, Jennifer M. Bhatnagar5, Jagjit Yadav6, Anna Lipzen7, Yuko Yoshinaga7, Aditi Sharma7, Catherine Adam7, Christopher Daum7, Vivian Ng7, Igor V. Grigoriev7,8 & Chiaki Hori9* Wood extractives, solvent-soluble fractions of woody biomass, are considered to be a factor impeding or excluding fungal colonization on the freshly harvested conifers. Among wood decay fungi, the basidiomycete Phlebiopsis gigantea has evolved a unique enzyme system to efciently transform or degrade conifer extractives but little is known about the mechanism(s). In this study, to clarify the mechanism(s) of softwood degradation, we examined the transcriptome, proteome, and metabolome of P. gigantea when grown on defned media containing microcrystalline cellulose and pine sapwood extractives. Beyond the conventional enzymes often associated with cellulose, hemicellulose and lignin degradation, an array of enzymes implicated in the metabolism of softwood lipophilic extractives such as fatty and resin acids, steroids and glycerides was signifcantly up-regulated. Among these, a highly expressed and inducible lipase is likely responsible for lipophilic extractive degradation, based on its extracellular location and our characterization of the recombinant enzyme. Our results provide insight into physiological roles of extractives in the interaction between wood and fungi. Te most abundant source of terrestrial carbon is woody plant biomass. Te cell wall largely consists of cellulose, hemicellulose and lignin, the proportions of which difer between hardwood and sofwood species 1,2. In addition to these structural components, a solvent-soluble fraction, commonly referred to as extractives, constitute up to 10 w/w% of the total plant biomass, though the chemical compounds vary with tree species, age and position, i.e.
    [Show full text]