Analysis of manganese-regulated gene expression in the ligninolytic basidiomycete Ceriporiopsis subvermispora

Current Genetics

Volumn 54, Issue 4, 2008, Pages 163-173

  Gutiérrez, Matías ^a,b,d   Rojas, Luis Alejandro ^a,b,e   Mancilla Villalobos, Rodrigo ^b,c   Seelenfreund, Daniela ^a   Vicuña, Rafael ^b   Lobos, Sergio ^a,b  

^a UNIVERSITY OF CHILE   (Chile)

^b UNIVERSIDAD ANDRÉS BELLO   (Chile)

^c PONTIFICIA UNIVERSIDAD CATÓLICA DE CHILE   (Chile)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

cDNA AFLP; Ceriporiopsis subvermispora; Manganese; Regulation; Transcription

Indexed keywords

ACYLTRANSFERASE; BINDING PROTEIN; COMPLEMENTARY DNA; ELONGATION FACTOR 3; FUNGAL RNA; HYDROLASE; MANGANESE; MANGANESE PEROXIDASE; OXIDOREDUCTASE;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; BASIDIOMYCETES; CERIPORIOPSIS SUBVERMISPORA; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DOWN REGULATION; ENZYME SUBUNIT; FUNGUS CULTURE; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC REGULATION; GENETIC TRANSCRIPTION; HOMEOSTASIS; MYCELIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FUNCTION; PROTEIN TARGETING; REAL TIME POLYMERASE CHAIN REACTION; REVIEW; RNA ISOLATION; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; UPREGULATION; WHITE ROT FUNGUS;

CORIOLACEAE; DNA, COMPLEMENTARY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENETIC TECHNIQUES; GENOME, FUNGAL; GLYCOSYLATION; IRON-SULFUR PROTEINS; MANGANESE; MICROSCOPY, ELECTRON, TRANSMISSION; MODELS, BIOLOGICAL; OLIGONUCLEOTIDES; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; TRANSCRIPTION, GENETIC;

CERIPORIOPSIS SUBVERMISPORA; FUNGI;

EID: 52549096148     PISSN: 01728083     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00294-008-0209-7     Document Type: Review

References (63)

1. Aschner M, Guilarte TR, Schneider JS, Zheng W (2007) Manganese: Recent advances in understanding its transport and neurotoxicity. Toxicol Appl Pharmacol 221:131-147
2. Assman EM, Mariscal Ottoboni LM, Ferraz A, Rodriguez J, Palandi de Mello M (2003) Iron-responsive genes of Phanerochaete chrysosporium isolated by differential display reverse transcription polymerase chain reaction. Environ Microbiol 5:777-786
3. Bachem CW, van der Hoeven RS, de Bruijn SM, Vreugdenhil D, Zabeau M, Visser RG (1996) Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: Analysis of gene expression during potato tuber development. Plant J 9:745-753
4. Blanchette RA, Burnes TA, Eerdmans MM, Akhtar M (1992) Evaluating isolates of Phanerochaete chrysosporium and Ceriporiopsis subvermispora for use in biological pulping processes. Holzforschung 46:109-115
5. Brown JA, Alic M, Gold MH (1991) Manganese peroxidase gene transcription in Phanerochaete chrysosporium: Activation by manganese. J Bacteriol 173:4101-4106
6. Cochrane FC, Davin LB, Lewis NG (2004) The Arabidopsis phenylalanine ammonia lyase gene family: Kinetic characterization of the four PAL isoforms. Phytochemistry 65:1557-1564
7. Crowley JD, Traynor DA, Weatherburn DC (2000) Enzymes and proteins containing manganese: An overview. Met Ions Biol Syst 37:209-278
8. Culotta VC, Yang M, Hall MD (2005) Manganese transport and trafficking: lessons learned from Saccharomyces cerevisiae. Eukaryot Cell 4:1159-1165
9. Chakraburtty K (2001) Translational regulation by ABC systems. Res Microbiol 152:391-399
10. Chen JY, Tsao GC, Zhao Q, Zheng W (2001) Differential cytotoxicity of Mn(II) and Mn(III): Special reference to mitochondrial [Fe-S] containing enzymes. Toxicol Appl Pharmacol 175:160-168
11. Cho JH, Ko KM, Singaravelu G, Ahnn J (2005) Caenorhabditis elegans PMR1, a P-type calcium ATPase, is important for calcium/manganese homeostasis and oxidative stress response. FEBS Lett 579:778-782
12. 2-producing enzyme pyranose oxidase in Phanerochaete chrysosporium grown under liquid culture conditions. Appl Environ Microbiol 58:3667-3676
13. Driessen HP, de Jong WW, Tesser GI, Bloemendal H (1985) The mechanism of N-terminal acetylation of proteins. CRC Crit Rev Biochem 18:281-325
14. 2+ required for glycosylation, sorting, and endoplasmic reticulum-associated protein degradation. Mol Biol Cell 9:1149-1162
15. Eide DJ, Clark S, Nair TM, Gehl M, Gribskov M, Guerinot ML, Harper JF (2005) Characterization of the yeast ionome: A genome-wide analysis of nutrient mineral and trace element homeostasis in Saccharomyces cerevisiae. Genome Biol 6:R77
16. Gavin AC, Aloy P, Grandi P, Krause R, Boesche M, Marzioch M, Rau C, Jensen LJ, Bastuck S, Dumpelfeld B, Edelmann A, Heurtier MA, Hoffman V, Hoefert C, Klein K, Hudak M, Michon AM, Schelder M, Schirle M, Remor M, Rudi T, Hooper S, Bauer A, Bouwmeester T, Casari G, Drewes G, Neubauer G, Rick JM, Kuster B, Bork P, Russell RB, Superti-Furga G (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature 440:631-636
17. Gebhart D, Bahrami AK, Sil A (2006) Identification of a copper-inducible promoter for use in ectopic expression in the fungal pathogen Histoplasma capsulatum. Eukaryot Cell 5:935-944
18. Goossens A, de La Fuente N, Forment J, Serrano R, Portillo F (2000) Regulation of yeast H(+)-ATPase by protein kinases belonging to a family dedicated to activation of plasma membrane transporters. Mol Cell Biol 20:7654-7661
19. Ibeas JI, Yun DJ, Damsz B, Narasimhan ML, Uesono Y, Ribas JC, Lee H, Hasegawa PM, Bressan RA, Pardo JM (2001) Resistance to the plant PR-5 protein osmotin in the model fungus Saccharomyces cerevisiae is mediated by the regulatory effects of SSD1 on cell wall composition. Plant J 25:271-280
20. Kadota K, Araki R, Nakai Y, Abe M (2007) GOGOT: A method for the identification of differentially expressed fragments from cDNA-AFLP data. Algorithms Mol Biol 2:5
21. Kaeberlein M, Guarente L (2002) Saccharomyces cerevisiae MPT5 and SSD1 function in parallel pathways to promote cell wall integrity. Genetics 160:83-95
22. Keen CL, Ensunsa JL, Clegg MS (2000) Manganese metabolism in animals and humans including the toxicity of manganese. Met Ions Biol Syst 37:89-121
23. Larrondo LF, Lobos S, Stewart P, Cullen D, Vicuña R (2001) Isoenzyme multiplicity and characterization of recombinant manganese peroxidases from Ceriporiopsis subvermispora and Phanerochaete chrysosporium. Appl Environ Microbiol 67:2070-2075
24. Lee JW, Helmann JD (2007) Functional specialization within the Fur family of metalloregulators. Biometals 20:485-499
25. Lei Y, Korpelainen H, Li C (2007) Physiological and biochemical responses to high Mn concentrations in two contrasting Populus cathayana populations. Chemosphere 68:686-694
26. Leymarie J, Bruneaux E, Gibot-Leclerc S, Corbineau F (2007) Identification of transcripts potentially involved in barley seed germination and dormancy using cDNA-AFLP. J Exp Bot 58:425-437
27. Lill R, Mühlenhoff U (2006) Iron-sulfur protein biogenesis in eukaryotes: Components and mechanisms. Annu Rev Cell Dev Biol 22:457-486
28. Liu XF, Culotta VC (1999) Post-translation control of Nramp metal transport in yeast. Role of metal ions and the BSD2 gene. J Biol Chem 274:4863-4868
29. Lobos S, Larraín J, Salas L, Cullen D, Vicuña R (1994) Isoenzymes of manganese-dependent peroxidase and laccase produced by the lignin-degrading basidiomycete Ceriporiopsis subvermispora. Microbiology 140(Pt 10):2691-2698
30. Lobos S, Larrondo L, Salas L, Karahanian E, Vicuña R (1998) Cloning and molecular analysis of a cDNA and the Cs-mnp1 gene encoding a manganese peroxidase isoenzyme from the lignin-degrading basidiomycete Ceriporiopsis subvermispora. Gene 206:185-193
31. Luk EE, Culotta VC (2001) Manganese superoxide dismutase in Saccharomyces cerevisiae acquires its metal co-factor through a pathway involving the Nramp metal transporter, Smf2p. J Biol Chem 276:47556-47562
32. Lussier M, White AM, Sheraton J, di Paolo T, Treadwell J, Southard SB, Horenstein CI, Chen-Weiner J, Ram AF, Kapteyn JC, Roemer TW, Vo DH, Bondoc DC, Hall J, Zhong WW, Sdicu AM, Davies J, Klis FM, Robbins PW, Bussey H (1997) Large scale identification of genes involved in cell surface biosynthesis and architecture in Saccharomyces cerevisiae. Genetics 147:435-450
33. Ma B, Mayfield MB, Godfrey BJ, Gold MH (2004) Novel promoter sequence required for manganese regulation of manganese peroxidase isozyme 1 gene expression in Phanerochaete chrysosporium. Eukaryot Cell 3:579-588
34. Malecki EA, Devenyi AG, Barron TF, Mosher TJ, Eslinger P, Flaherty-Craig CV, Rossaro L (1999) Iron and manganese homeostasis in chronic liver disease: Relationship to pallidal T1-weighted magnetic resonance signal hyperintensity. Neurotoxicology 20:647-652
35. Manubens A, Avila M, Canessa P, Vicuña R (2003) Differential regulation of genes encoding manganese peroxidase (MnP) in the basidiomycete Ceriporiopsis subvermispora. Curr Genet 43:433-438
36. Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, Gwadz M, Hao L, He S, Hurwitz DI, Jackson JD, Ke Z, Krylov D, Lanczycki CJ, Liebert CA, Liu C, Lu F, Lu S, Marchler GH, Mullokandov M, Song JS, Thanki N, Yamashita RA, Yin JJ, Zhang D, Bryant SH (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35:D237-D240
37. Moore CM, Helmann JD (2005) Metal ion homeostasis in Bacillus subtilis. Curr Opin Microbiol 8:188-195
38. Mullen JR, Kayne PS, Moerschell RP, Tsunasawa S, Gribskov M, Colavito-Shepanski M, Grunstein M, Sherman F, Sternglanz R (1989) Identification and characterization of genes and mutants for an N-terminal acetyltransferase from yeast. EMBO J 8:2067-2075
39. Nehls U, Ecke M, Hampp R (1999) Sugar- and nitrogen-dependent regulation of an Amanita muscaria phenylalanine ammonium lyase gene. J Bacteriol 181:1931-1933
40. Otjen L, Blanchette R (1987) Assessment of 30 white rot basidiomycetes for selective lignin degradation. Holzforschung 41:343-349
41. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45
42. Pittman JK (2005) Managing the manganese: Molecular mechanisms of manganese transport and homeostasis. New Phytol 167:733-742
43. Polevoda B, Sherman F (2003) N-terminal acetyltransferases and sequence requirements for N-terminal acetylation of eukaryotic proteins. J Mol Biol 325:595-622
44. Portnoy ME, Liu XF, Culotta VC (2000) Saccharomyces cerevisiae expresses three functionally distinct homologues of the nramp family of metal transporters. Mol Cell Biol 20:7893-7902
45. Reynolds ES (1963) The use of lead citrate at high pH as an electron-opaque stain in electron microscopy. J Cell Biol 17:208-212
46. Rodionov DA, Gelfland MS, Todd JD, Curson ARJ, Johnston AWB (2006) Computational reconstruction of iron- and manganese-responsive transcriptional networks in α-proteobacteria. PLoS Comput Biol 2:1568-1585
47. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365-386
48. Rüttimann C, Schwember E, Salas L, Cullen D, Vicuña R (1992) Ligninolytic enzymes of the white rot basidiomycetes Phlebia brevispora and Ceriporiopsis subvermispora. Biotechnol Appl Biochem 16:64-76
49. Sarosh BR, Meijer J (2007) Transcriptional profiling by cDNA-AFLP reveals novel insights during methyl jasmonate, wounding and insect attack in Brassica napus. Plant Mol Biol 64:425-438
50. Semenza JC, Hardwick KG, Dean N, Pelham HR (1990) ERD2, a yeast gene required for the receptor-mediated retrieval of luminal ER proteins from the secretory pathway. Cell 61:1349-1357
51. Supek F, Supekova L, Nelson H, Nelson N (1996) A yeast manganese transporter related to the macrophage protein involved in conferring resistance to mycobacteria. Proc Natl Acad Sci USA 93:5105-5110
52. Tello M, Corsini G, Larrondo LF, Salas L, Lobos S, Vicuña R (2000) Characterization of three new manganese peroxidase genes from the ligninolytic basidiomycete Ceriporiopsis subvermispora. Biochim Biophys Acta 1490:137-144
53. Thiele DJ (1992) Metal-regulated transcription in eukaryotes. Nucleic Acids Res 20:1183-1191
54. Thomas D, Surdin-Kerjan Y (1997) Metabolism of sulfur amino acids in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 61:503-532
55. Tsuchiya E, Matsuzaki G, Kurano K, Fukuchi T, Tsukao A, Miyakawa T (1996) The Saccharomyces cerevisiae SSD1 gene is involved in the tolerance to high concentration of Ca2 + with the participation of HST1/ NRC1/BFR1. Gene 176:35-38
56. Uesono Y, Toh-e A, Kikuchi Y (1997) Ssd1p of Saccharomyces cerevisiae associates with RNA. J Biol Chem 272:16103-16109
57. Urzúa U, Larrondo LF, Lobos S, Larraín J, Vicuña R (1995) Oxidation reactions catalyzed by manganese peroxidase isoenzymes from Ceriporiopsis subvermispora. FEBS Lett 371:132-136
58. Urzúa U, Kersten PJ, Vicuña R (1998) Manganese peroxidase-dependent oxidation of glyoxylic and oxalic acids synthesized by Ceriporiopsis subvermispora produces extracellular hydrogen peroxide. Appl Environ Microbiol 64:68-73
59. Wanders RJ (2004) Peroxisomes, lipid metabolism, and peroxisomal disorders. Mol Genet Metab 83:16-27
60. Xie X, Lun J, Kulbokas EJ, Golub TR, Mootha V, Lindblad-Toh K, Lander ES, Kellis M (2005) Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 434:338-345
61. Yamamoto K, Hamada H, Shinkai H, Kohno Y, Koseki H, Aoe T (2003) The KDEL receptor modulates the endoplasmic reticulum stress response through mitogen-activated protein kinase signaling cascades. J Biol Chem 278:34525-34532
62. Yao YX, Li M, Liu Z, Hao YJ, Zhai H (2007) A novel gene, screened by cDNA-AFLP approach, contributes to lowering the acidity of fruit in apple. Plant Physiol Biochem 45:139-145
63. Yuan DS (2000) Zinc-regulated genes in Saccharomyces cerevisiae revealed by transposon tagging. Genetics 156:45-58