Author Report for: Kubicek CPNo contact information in database for Kubicek CP
Daly P, Cai F, Kubicek CP, Jiang S, Grujic M, Rahimi MJ, Sheteiwy MS, Giles R, Riaz A and Druzhinina IS <3 more author(s)> Daly P, Cai F, Kubicek CP, Jiang S, Grujic M, Rahimi MJ, Sheteiwy MS, Giles R, Riaz A, de Vries RP, Akcapinar GB, Wei L, Druzhinina IS (- 3) Ref: Biotechnol Adv, :107770, 2021 : PubMed ESTHER: Daly_2021_Biotechnol.Adv__107770 PubMedSearch: Daly 2021 Biotechnol.Adv 107770 PubMedID: 33989704 Abstract In this review, we argue that there is much to be learned by transferring knowledge from research on lignocellulose degradation to that on plastic. Plastic waste accumulates in the environment to hazardous levels, because it is inherently recalcitrant to biological degradation. Plants evolved lignocellulose to be resistant to degradation, but with time, fungi became capable of utilising it for their nutrition. Examples of how fungal strategies to degrade lignocellulose could be insightful for plastic degradation include how fungi overcome the hydrophobicity of lignin (e.g. production of hydrophobins) and crystallinity of cellulose (e.g. oxidative approaches). In parallel, knowledge of the methods for understanding lignocellulose degradation could be insightful such as advanced microscopy, genomic and post-genomic approaches (e.g. gene expression analysis). The known limitations of biological lignocellulose degradation, such as the necessity for physiochemical pretreatments for biofuel production, can be predictive of potential restrictions of biological plastic degradation. Taking lessons from lignocellulose degradation for plastic degradation is also important for biosafety as engineered plastic-degrading fungi could also have increased plant biomass degrading capabilities. Even though plastics are significantly different from lignocellulose because they lack hydrolysable C-C or C-O bonds and therefore have higher recalcitrance, there are apparent similarities, e.g. both types of compounds are mixtures of hydrophobic polymers with amorphous and crystalline regions, and both require hydrolases and oxidoreductases for their degradation. Thus, many lessons could be learned from fungal lignocellulose degradation. Title: Enhanced cutinase-catalyzed hydrolysis of polyethylene terephthalate by covalent fusion to hydrophobins Ribitsch D, Herrero Acero E, Przylucka A, Zitzenbacher S, Marold A, Gamerith C, Tscheliessnig R, Jungbauer A, Rennhofer H and Guebitz GM <5 more author(s)> Ribitsch D, Herrero Acero E, Przylucka A, Zitzenbacher S, Marold A, Gamerith C, Tscheliessnig R, Jungbauer A, Rennhofer H, Lichtenegger H, Amenitsch H, Bonazza K, Kubicek CP, Druzhinina IS, Guebitz GM (- 5) Ref: Applied Environmental Microbiology, 81:3586, 2015 : PubMed ESTHER: Ribitsch_2015_Appl.Environ.Microbiol_81_3586 PubMedSearch: Ribitsch 2015 Appl.Environ.Microbiol 81 3586 PubMedID: 25795674 Gene_locus related to this paper: thefu-q6a0i4 Abstract Cutinases have shown potential for hydrolysis of the recalcitrant synthetic polymer polyethylene terephthalate (PET). We have shown previously that the rate of this hydrolysis can be enhanced by the addition of hydrophobins, small fungal proteins that can alter the physicochemical properties of surfaces. Here we have investigated whether the PET-hydrolyzing activity of a bacterial cutinase from Thermobifida cellulosilytica (Thc_Cut1) would be further enhanced by fusion to one of three Trichoderma hydrophobins, i.e., the class II hydrophobins HFB4 and HFB7 and the pseudo-class I hydrophobin HFB9b. The fusion enzymes exhibited decreased kcat values on soluble substrates (p-nitrophenyl acetate and p-nitrophenyl butyrate) and strongly decreased the hydrophilicity of glass but caused only small changes in the hydrophobicity of PET. When the enzyme was fused to HFB4 or HFB7, the hydrolysis of PET was enhanced >16-fold over the level with the free enzyme, while a mixture of the enzyme and the hydrophobins led only to a 4-fold increase at most. Fusion with the non-class II hydrophobin HFB9b did not increase the rate of hydrolysis over that of the enzyme-hydrophobin mixture, but HFB9b performed best when PET was preincubated with the hydrophobins before enzyme treatment. The pattern of hydrolysis by the fusion enzymes differed from that of Thc_Cut1 as the concentration of the product mono(2-hydroxyethyl) terephthalate relative to that of the main product, terephthalic acid, increased. Small-angle X-ray scattering (SAXS) analysis revealed an increased scattering contrast of the fusion proteins over that of the free proteins, suggesting a change in conformation or enhanced protein aggregation. Our data show that the level of hydrolysis of PET by cutinase can be significantly increased by fusion to hydrophobins. The data further suggest that this likely involves binding of the hydrophobins to the cutinase and changes in the conformation of its active center. Title: Genome Sequence and Annotation of Trichoderma parareesei, the Ancestor of the Cellulase Producer Trichoderma reesei Yang D, Pomraning K, Kopchinskiy A, Karimi Aghcheh R, Atanasova L, Chenthamara K, Baker SE, Zhang R, Shen Q and Druzhinina IS <2 more author(s)> Yang D, Pomraning K, Kopchinskiy A, Karimi Aghcheh R, Atanasova L, Chenthamara K, Baker SE, Zhang R, Shen Q, Freitag M, Kubicek CP, Druzhinina IS (- 2) Ref: Genome Announc, 3:e00885, 2015 : PubMed ESTHER: Yang_2015_Genome.Announc_3_e00885 PubMedSearch: Yang 2015 Genome.Announc 3 e00885 PubMedID: 26272569 Gene_locus related to this paper: hypjr-a0a024s1s9 Abstract The filamentous fungus Trichoderma parareesei is the asexually reproducing ancestor of Trichoderma reesei, the holomorphic industrial producer of cellulase and hemicellulase. Here, we present the genome sequence of the T. parareesei type strain CBS 125925, which contains genes for 9,318 proteins. Title: Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Duenas FJ, Held B and Cullen D <31 more author(s)> Hori C, Ishida T, Igarashi K, Samejima M, Suzuki H, Master E, Ferreira P, Ruiz-Duenas FJ, Held B, Canessa P, Larrondo LF, Schmoll M, Druzhinina IS, Kubicek CP, Gaskell JA, Kersten P, St John F, Glasner J, Sabat G, Splinter BonDurant S, Syed K, Yadav J, Mgbeahuruike AC, Kovalchuk A, Asiegbu FO, Lackner G, Hoffmeister D, Rencoret J, Gutierrez A, Sun H, Lindquist E, Barry K, Riley R, Grigoriev IV, Henrissat B, Kues U, Berka RM, Martinez AT, Covert SF, Blanchette RA, Cullen D (- 31) Ref: PLoS Genet, 10:e1004759, 2014 : PubMed ESTHER: Hori_2014_PLoS.Genet_10_E1004759 PubMedSearch: Hori 2014 PLoS.Genet 10 E1004759 PubMedID: 25474575 Gene_locus related to this paper: phlgi-a0a0c3nds0, phlgi-a0a0c3niq6, phlgi-a0a0c3pc91, phlgi-a0a0c3pv58, phlgi-a0a0c3rra0, phlgi-a0a0c3rvc4, phlgi-a0a0c3rvu0, phlgi-a0a0c3s394, phlgi-a0a0c3s606, phlgi-a0a0c3s673, phlgi-a0a0c3s8d3, phlgi-a0a0c3sce4, phlgi-a0a0c3sdt8 Abstract Collectively classified as white-rot fungi, certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls. A small subset of these Agaricomycetes, exemplified by Phlebiopsis gigantea, is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives, which retards the establishment of other fungal species. The mechanism(s) by which P. gigantea tolerates and metabolizes resinous compounds have not been explored. Here, we report the annotated P. gigantea genome and compare profiles of its transcriptome and secretome when cultured on fresh-cut versus solvent-extracted loblolly pine wood. The P. gigantea genome contains a conventional repertoire of hydrolase genes involved in cellulose/hemicellulose degradation, whose patterns of expression were relatively unperturbed by the absence of extractives. The expression of genes typically ascribed to lignin degradation was also largely unaffected. In contrast, genes likely involved in the transformation and detoxification of wood extractives were highly induced in its presence. Their products included an ABC transporter, lipases, cytochrome P450s, glutathione S-transferase and aldehyde dehydrogenase. Other regulated genes of unknown function and several constitutively expressed genes are also likely involved in P. gigantea's extractives metabolism. These results contribute to our fundamental understanding of pioneer colonization of conifer wood and provide insight into the diverse chemistries employed by fungi in carbon cycling processes. Title: Two novel class II hydrophobins from Trichoderma spp. stimulate enzymatic hydrolysis of poly(ethylene terephthalate) when expressed as fusion proteins Espino-Rammer L, Ribitsch D, Przylucka A, Marold A, Greimel KJ, Herrero Acero E, Guebitz GM, Kubicek CP, Druzhinina IS Ref: Applied Environmental Microbiology, 79:4230, 2013 : PubMed ESTHER: Espino-Rammer_2013_Appl.Environ.Microbiol_79_4230 PubMedSearch: Espino-Rammer 2013 Appl.Environ.Microbiol 79 4230 PubMedID: 23645195 Gene_locus related to this paper: humin-cut Abstract Poly(ethylene terephthalate) (PET) can be functionalized and/or recycled via hydrolysis by microbial cutinases. The rate of hydrolysis is however low. Here, we tested whether hydrophobins (HFBs), small secreted fungal proteins containing eight positionally conserved cysteine residues, are able to enhance the rate of enzymatic hydrolysis of PET. Species of the fungal genus Trichoderma have the most proliferated arsenal of class II hydrophobin-encoding genes among fungi. To this end, we studied two novel class II HFBs (HFB4 and HFB7) of Trichoderma. HFB4 and HFB7, produced in Escherichia coli as fusions to the C terminus of glutathione S-transferase, exhibited subtle structural differences reflected in hydrophobicity plots that correlated with unequal hydrophobicity and hydrophily, respectively, of particular amino acid residues. Both proteins exhibited a dosage-dependent stimulation effect on PET hydrolysis by cutinase from Humicola insolens, with HFB4 displaying an adsorption isotherm-like behavior, whereas HFB7 was active only at very low concentrations and was inhibitory at higher concentrations. We conclude that class II HFBs can stimulate the activity of cutinases on PET, but individual HFBs can display different properties. The present findings suggest that hydrophobins can be used in the enzymatic hydrolysis of aromatic-aliphatic polyesters such as PET. Title: Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis Fernandez-Fueyo E, Ruiz-Duenas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D and Cullen D <55 more author(s)> Fernandez-Fueyo E, Ruiz-Duenas FJ, Ferreira P, Floudas D, Hibbett DS, Canessa P, Larrondo LF, James TY, Seelenfreund D, Lobos S, Polanco R, Tello M, Honda Y, Watanabe T, Ryu JS, Kubicek CP, Schmoll M, Gaskell J, Hammel KE, St John FJ, Vanden Wymelenberg A, Sabat G, Splinter BonDurant S, Syed K, Yadav JS, Doddapaneni H, Subramanian V, Lavin JL, Oguiza JA, Perez G, Pisabarro AG, Ramirez L, Santoyo F, Master E, Coutinho PM, Henrissat B, Lombard V, Magnuson JK, Kues U, Hori C, Igarashi K, Samejima M, Held BW, Barry KW, LaButti KM, Lapidus A, Lindquist EA, Lucas SM, Riley R, Salamov AA, Hoffmeister D, Schwenk D, Hadar Y, Yarden O, de Vries RP, Wiebenga A, Stenlid J, Eastwood D, Grigoriev IV, Berka RM, Blanchette RA, Kersten P, Martinez AT, Vicuna R, Cullen D (- 55) Ref: Proc Natl Acad Sci U S A, 109:5458, 2012 : PubMed ESTHER: Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458 PubMedSearch: Fernandez-Fueyo 2012 Proc.Natl.Acad.Sci.U.S.A 109 5458 PubMedID: 22434909 Gene_locus related to this paper: cers8-m2r3x2, cers8-m2qf37, cers8-m2pcy7, cers8-m2pcz3, cers8-m2qn26, cers8-m2r654, cers8-m2r8g9, cers8-m2ps90, cers8-m2qn44, cers8-m2q837, cers8-m2pjy6, cers8-m2r609, cers8-m2qy35, cers8-m2r1n1, cers8-m2rl22, cers8-m2qkx5, cers8-m2qib7, cers8-m2rgs8, cers8-m2rlx6, cers8-m2r4p3, cers8-m2rf62, cers8-m2qyx5, cers8-m2pcz2, cers8-m2rm22, cers8-m2qwb7, cers8-m2r9u3, cers8-m2pp23, cers8-m2r613, cers8-m2rup8, cers8-m2piv7, cers8-m2rch3, cers8-m2qvf7, cers8-m2qvb7, cers8-m2qvb2, cers8-m2pip7, cers8-m2rb73, cers8-m2qgd3, cers8-m2rcg8, cers8-m2rb68 Abstract Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium. Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium, respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli, the enzymes were shown to oxidize high redox potential substrates, but not Mn(2+). Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium. Title: Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88 Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R and Baker SE <37 more author(s)> Andersen MR, Salazar MP, Schaap PJ, van de Vondervoort PJ, Culley D, Thykaer J, Frisvad JC, Nielsen KF, Albang R, Albermann K, Berka RM, Braus GH, Braus-Stromeyer SA, Corrochano LM, Dai Z, van Dijck PW, Hofmann G, Lasure LL, Magnuson JK, Menke H, Meijer M, Meijer SL, Nielsen JB, Nielsen ML, van Ooyen AJ, Pel HJ, Poulsen L, Samson RA, Stam H, Tsang A, van den Brink JM, Atkins A, Aerts A, Shapiro H, Pangilinan J, Salamov A, Lou Y, Lindquist E, Lucas S, Grimwood J, Grigoriev IV, Kubicek CP, Martinez D, van Peij NN, Roubos JA, Nielsen J, Baker SE (- 37) Ref: Genome Res, 21:885, 2011 : PubMed ESTHER: Andersen_2011_Genome.Res_21_885 PubMedSearch: Andersen 2011 Genome.Res 21 885 PubMedID: 21543515 Gene_locus related to this paper: aspna-g3y4g9, aspna-g3yal2, aspna-g3ycq2, aspnc-a2qbh3, aspnc-a2qe77, aspnc-a2qf54, aspnc-a2qfe9, aspnc-a2qg33, aspnc-a2qh76, aspnc-a2qhe2, aspnc-a2qi32, aspnc-a2ql89, aspnc-a2ql90, aspnc-a2qla0, aspnc-a2qmk5, aspnc-a2qn56, aspnc-a2qs22, aspnc-a2qti9, aspnc-a2qtz0, aspnc-a2quc1, aspnc-a2qx92, aspnc-a2qyf0, aspnc-a2qys7, aspnc-a2qz72, aspnc-a2qzn6, aspnc-a2qzr0, aspnc-a2qzx0, aspnc-a2qzx4, aspnc-a2r0p4, aspnc-a2r1r5, aspnc-a2r2i5, aspnc-a2r5r4, aspnc-a2r6h5, aspnc-a2r8r3, aspnc-a2r8z3, aspnc-a2r273, aspnc-a2r496, aspnc-a2r502, aspnc-a5abe5, aspnc-a5abe8, aspnc-a5abh9, aspnc-a5abk1, aspnc-axe1, aspnc-cuti1, aspnc-cuti2, aspng-a2qs46, aspng-a2qv27, aspni-EstA, aspkw-g7y0v7, aspnc-a2qt47, aspnc-a2qt66, aspna-g3xpq9, aspnc-a2qqa1, aspna-g3xsl3, aspna-g3y5a6, aspna-g3xpw9, aspaw-a0a401kpx5, aspnc-a2qw57, aspaw-a0a401kcz4, aspna-alba, aspna-azac Abstract The filamentous fungus Aspergillus niger exhibits great diversity in its phenotype. It is found globally, both as marine and terrestrial strains, produces both organic acids and hydrolytic enzymes in high amounts, and some isolates exhibit pathogenicity. Although the genome of an industrial enzyme-producing A. niger strain (CBS 513.88) has already been sequenced, the versatility and diversity of this species compel additional exploration. We therefore undertook whole-genome sequencing of the acidogenic A. niger wild-type strain (ATCC 1015) and produced a genome sequence of very high quality. Only 15 gaps are present in the sequence, and half the telomeric regions have been elucidated. Moreover, sequence information from ATCC 1015 was used to improve the genome sequence of CBS 513.88. Chromosome-level comparisons uncovered several genome rearrangements, deletions, a clear case of strain-specific horizontal gene transfer, and identification of 0.8 Mb of novel sequence. Single nucleotide polymorphisms per kilobase (SNPs/kb) between the two strains were found to be exceptionally high (average: 7.8, maximum: 160 SNPs/kb). High variation within the species was confirmed with exo-metabolite profiling and phylogenetics. Detailed lists of alleles were generated, and genotypic differences were observed to accumulate in metabolic pathways essential to acid production and protein synthesis. A transcriptome analysis supported up-regulation of genes associated with biosynthesis of amino acids that are abundant in glucoamylase A, tRNA-synthases, and protein transporters in the protein producing CBS 513.88 strain. Our results and data sets from this integrative systems biology analysis resulted in a snapshot of fungal evolution and will support further optimization of cell factories based on filamentous fungi. Title: Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA and Grigoriev IV <54 more author(s)> Kubicek CP, Herrera-Estrella A, Seidl-Seiboth V, Martinez DA, Druzhinina IS, Thon M, Zeilinger S, Casas-Flores S, Horwitz BA, Mukherjee PK, Mukherjee M, Kredics L, Alcaraz LD, Aerts A, Antal Z, Atanasova L, Cervantes-Badillo MG, Challacombe J, Chertkov O, McCluskey K, Coulpier F, Deshpande N, von Dohren H, Ebbole DJ, Esquivel-Naranjo EU, Fekete E, Flipphi M, Glaser F, Gomez-Rodriguez EY, Gruber S, Han C, Henrissat B, Hermosa R, Hernandez-Onate M, Karaffa L, Kosti I, Le Crom S, Lindquist E, Lucas S, Lubeck M, Lubeck PS, Margeot A, Metz B, Misra M, Nevalainen H, Omann M, Packer N, Perrone G, Uresti-Rivera EE, Salamov A, Schmoll M, Seiboth B, Shapiro H, Sukno S, Tamayo-Ramos JA, Tisch D, Wiest A, Wilkinson HH, Zhang M, Coutinho PM, Kenerley CM, Monte E, Baker SE, Grigoriev IV (- 54) Ref: Genome Biol, 12:R40, 2011 : PubMed ESTHER: Kubicek_2011_Genome.Biol_12_R40 PubMedSearch: Kubicek 2011 Genome.Biol 12 R40 PubMedID: 21501500 Gene_locus related to this paper: hypai-g9nem6, hypai-g9ng36, hypai-g9ngu2, hypai-g9nks5, hypai-g9nks6, hypai-g9nqe5, hypai-g9nqk5, hypai-g9nrx6, hypai-g9nsx1, hypai-g9ntn3, hypai-g9nzc9, hypai-g9nzd7, hypai-g9p1t1, hypai-g9p1v2, hypai-g9p2n8, hypai-g9p4z2, hypai-g9p878, hypai-g9pa17, hypai-g9pbz9, hypvg-g9mem8, hypvg-g9mg52, hypvg-g9mga2, hypvg-g9mhi3, hypvg-g9mjc7, hypvg-g9mk44, hypvg-g9mms1, hypvg-g9mnf0, hypvg-g9mng3, hypvg-g9mpt0, hypvg-g9mrp9, hypvg-g9ms16, hypvg-g9ms32, hypvg-g9msv5, hypvg-g9muh6, hypvg-g9muk0, hypvg-g9mwe2, hypvg-g9my79, hypvg-g9n0p7, hypvg-g9n2g3, hypvg-g9n2g4, hypvg-g9n4k5, hypvg-g9n9n0, hypvg-g9n561, hypvg-g9n988, hypvg-g9nb12, hypvg-g9nb54, hypvg-g9nbh8, hypai-g9npz7, hypai-g9njw6, hypvg-g9mx08, hypvg-g9mlt2, hypai-g9p4j3, hypvg-g9nbd3, hypai-g9nxf6, hypvg-g9n3y9, hypvg-g9mgs4, hypai-g9p6m2, hypvg-g9my62, hypvg-g9nbv2, hypvg-g9my22, hypai-g9p2e2, hypai-g9p596, hypai-g9nf87, hypvg-g9me87, hypvg-g9ndn9, hypai-g9niy5, hypai-g9ntx6, hypvg-g9n3e7, hypai-g9nu29, hypvg-g9n2z0, hypvg-g9ndf4, 9hypo-a0a2p4zt82, hypvg-g9n0g0, hypvg-g9muj2, hypvg-g9mud0, hypai-g9nkx5 Abstract BACKGROUND: Mycoparasitism, a lifestyle where one fungus is parasitic on another fungus, has special relevance when the prey is a plant pathogen, providing a strategy for biological control of pests for plant protection. Probably, the most studied biocontrol agents are species of the genus Hypocrea/Trichoderma. Title: Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT and Cullen D <43 more author(s)> Martinez D, Challacombe J, Morgenstern I, Hibbett D, Schmoll M, Kubicek CP, Ferreira P, Ruiz-Duenas FJ, Martinez AT, Kersten P, Hammel KE, Vanden Wymelenberg A, Gaskell J, Lindquist E, Sabat G, Bondurant SS, Larrondo LF, Canessa P, Vicuna R, Yadav J, Doddapaneni H, Subramanian V, Pisabarro AG, Lavin JL, Oguiza JA, Master E, Henrissat B, Coutinho PM, Harris P, Magnuson JK, Baker SE, Bruno K, Kenealy W, Hoegger PJ, Kues U, Ramaiya P, Lucas S, Salamov A, Shapiro H, Tu H, Chee CL, Misra M, Xie G, Teter S, Yaver D, James T, Mokrejs M, Pospisek M, Grigoriev IV, Brettin T, Rokhsar D, Berka R, Cullen D (- 43) Ref: Proc Natl Acad Sci U S A, 106:1954, 2009 : PubMed ESTHER: Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954 PubMedSearch: Martinez 2009 Proc.Natl.Acad.Sci.U.S.A 106 1954 PubMedID: 19193860 Gene_locus related to this paper: pospm-b8p1f3, pospm-b8p2q7, pospm-b8p4n0, pospm-b8p4n9, pospm-b8p5g9, pospm-b8p5r9, pospm-b8p6h2, pospm-b8p7b1, pospm-b8p7c4, pospm-b8p8w7, pospm-b8p9j1, pospm-b8p164, pospm-b8p280, pospm-b8p423.1, pospm-b8p423.2, pospm-b8p858, pospm-b8pam2, pospm-b8pam5, pospm-b8pb68, pospm-b8pbm3, pospm-b8pc54, pospm-b8pc56, pospm-b8pce4, pospm-b8pd91, pospm-b8pdk6, pospm-b8ph32, pospm-b8ph43, pospm-b8phc9, pospm-b8php7, pospm-b8phy5, pospm-b8pjg8, pospm-b8pji9, pospm-b8plr5, pospm-b8pmk3, pospm-b8pfg0, pospm-b8pg35, pospm-b8pa20.1, pospm-b8pa20.2, pospm-b8p4g8, pospm-b8phn6 Abstract Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative beta-1-4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H(2)O(2). These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H(2)O(2) react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost. Title: The 2008 update of the Aspergillus nidulans genome annotation: a community effort Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR, Archer D, Bencina M, Braus G and Turner G <76 more author(s)> Wortman JR, Gilsenan JM, Joardar V, Deegan J, Clutterbuck J, Andersen MR, Archer D, Bencina M, Braus G, Coutinho P, von Dohren H, Doonan J, Driessen AJ, Durek P, Espeso E, Fekete E, Flipphi M, Estrada CG, Geysens S, Goldman G, de Groot PW, Hansen K, Harris SD, Heinekamp T, Helmstaedt K, Henrissat B, Hofmann G, Homan T, Horio T, Horiuchi H, James S, Jones M, Karaffa L, Karanyi Z, Kato M, Keller N, Kelly DE, Kiel JA, Kim JM, van der Klei IJ, Klis FM, Kovalchuk A, Krasevec N, Kubicek CP, Liu B, Maccabe A, Meyer V, Mirabito P, Miskei M, Mos M, Mullins J, Nelson DR, Nielsen J, Oakley BR, Osmani SA, Pakula T, Paszewski A, Paulsen I, Pilsyk S, Pocsi I, Punt PJ, Ram AF, Ren Q, Robellet X, Robson G, Seiboth B, van Solingen P, Specht T, Sun J, Taheri-Talesh N, Takeshita N, Ussery D, vanKuyk PA, Visser H, van de Vondervoort PJ, de Vries RP, Walton J, Xiang X, Xiong Y, Zeng AP, Brandt BW, Cornell MJ, van den Hondel CA, Visser J, Oliver SG, Turner G (- 76) Ref: Fungal Genet Biol, 46 Suppl 1:S2, 2009 : PubMed ESTHER: Wortman_2009_Fungal.Genet.Biol_46 Suppl 1_S2 PubMedSearch: Wortman 2009 Fungal.Genet.Biol 46 Suppl 1 S2 PubMedID: 19146970 Gene_locus related to this paper: emeni-axe1, emeni-c8v4m7, emeni-faec, emeni-ppme1, emeni-q5ara9, emeni-q5arf0, emeni-q5as30, emeni-q5ase8, emeni-q5av79, emeni-q5aw09, emeni-q5awc3, emeni-q5awc7, emeni-q5awu9, emeni-q5aww4, emeni-q5ax50, emeni-q5ay37, emeni-q5ay57, emeni-q5ay59, emeni-q5ayk9, emeni-q5ays5, emeni-q5az32, emeni-q5az91, emeni-q5az97, emeni-q5azp1, emeni-q5b0i6, emeni-q5b1h2, emeni-q5b2a9, emeni-q5b2p7, emeni-q5b3d2, emeni-q5b4q7, emeni-q5b5u7, emeni-q5b5y4, emeni-q5b9e7, emeni-q5b9i0, emeni-q5b364, emeni-q5b446, emeni-q5b938, emeni-q5ba78, emeni-q5bcd1, emeni-q5bcd2, emeni-q5bde7, emeni-q5bdr0, emeni-q5bf92, emeni-q7si80, emeni-q5bdv9, emeni-c8vu15, 9euro-a0a3d8t644, emeni-q5b719, emeni-q5ax97, emeni-tdia, emeni-afoc, emeni-dbae Abstract The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology. Title: Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina) Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM and Brettin TS <35 more author(s)> Martinez D, Berka RM, Henrissat B, Saloheimo M, Arvas M, Baker SE, Chapman J, Chertkov O, Coutinho PM, Cullen D, Danchin EG, Grigoriev IV, Harris P, Jackson M, Kubicek CP, Han CS, Ho I, Larrondo LF, de Leon AL, Magnuson JK, Merino S, Misra M, Nelson B, Putnam N, Robbertse B, Salamov AA, Schmoll M, Terry A, Thayer N, Westerholm-Parvinen A, Schoch CL, Yao J, Barabote R, Nelson MA, Detter C, Bruce D, Kuske CR, Xie G, Richardson P, Rokhsar DS, Lucas SM, Rubin EM, Dunn-Coleman N, Ward M, Brettin TS (- 35) Ref: Nat Biotechnol, 26:553, 2008 : PubMed ESTHER: Martinez_2008_Nat.Biotechnol_26_553 PubMedSearch: Martinez 2008 Nat.Biotechnol 26 553 PubMedID: 18454138 Gene_locus related to this paper: hypjq-g0rh85, hypjq-cip2, hypjq-g0r9d1, hypjq-g0r810, hypjq-g0rbm4, hypjq-g0rez4, hypjq-g0rfr3, hypjq-g0rg60, hypjq-g0rij9, hypjq-g0riu1, hypjq-g0rl87, hypjq-g0rlh4, hypjq-g0rme5, hypjq-g0rwy5, hypje-axylest, hypje-q7z9m3, hypjq-g0r6x2, hypje-a0a024s1b8, hypjr-a0a024s1s9, hypjq-g0rxi5 Abstract Trichoderma reesei is the main industrial source of cellulases and hemicellulases used to depolymerize biomass to simple sugars that are converted to chemical intermediates and biofuels, such as ethanol. We assembled 89 scaffolds (sets of ordered and oriented contigs) to generate 34 Mbp of nearly contiguous T. reesei genome sequence comprising 9,129 predicted gene models. Unexpectedly, considering the industrial utility and effectiveness of the carbohydrate-active enzymes of T. reesei, its genome encodes fewer cellulases and hemicellulases than any other sequenced fungus able to hydrolyze plant cell wall polysaccharides. Many T. reesei genes encoding carbohydrate-active enzymes are distributed nonrandomly in clusters that lie between regions of synteny with other Sordariomycetes. Numerous genes encoding biosynthetic pathways for secondary metabolites may promote survival of T. reesei in its competitive soil habitat, but genome analysis provided little mechanistic insight into its extraordinary capacity for protein secretion. Our analysis, coupled with the genome sequence data, provides a roadmap for constructing enhanced T. reesei strains for industrial applications such as biofuel production. Title: Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88 Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R and Stam H <59 more author(s)> Pel HJ, de Winde JH, Archer DB, Dyer PS, Hofmann G, Schaap PJ, Turner G, de Vries RP, Albang R, Albermann K, Andersen MR, Bendtsen JD, Benen JA, van den Berg M, Breestraat S, Caddick MX, Contreras R, Cornell M, Coutinho PM, Danchin EG, Debets AJ, Dekker P, van Dijck PW, van Dijk A, Dijkhuizen L, Driessen AJ, d'Enfert C, Geysens S, Goosen C, Groot GS, de Groot PW, Guillemette T, Henrissat B, Herweijer M, van den Hombergh JP, van den Hondel CA, van der Heijden RT, van der Kaaij RM, Klis FM, Kools HJ, Kubicek CP, van Kuyk PA, Lauber J, Lu X, van der Maarel MJ, Meulenberg R, Menke H, Mortimer MA, Nielsen J, Oliver SG, Olsthoorn M, Pal K, van Peij NN, Ram AF, Rinas U, Roubos JA, Sagt CM, Schmoll M, Sun J, Ussery D, Varga J, Vervecken W, van de Vondervoort PJ, Wedler H, Wosten HA, Zeng AP, van Ooyen AJ, Visser J, Stam H (- 59) Ref: Nat Biotechnol, 25:221, 2007 : PubMed ESTHER: Pel_2007_Nat.Biotechnol_25_221 PubMedSearch: Pel 2007 Nat.Biotechnol 25 221 PubMedID: 17259976 Gene_locus related to this paper: aspna-g3yal2, aspnc-a2q8r7, aspnc-a2q814, aspnc-a2qb93, aspnc-a2qbd3, aspnc-a2qbh3, aspnc-a2qbx7, aspnc-a2qdj6, aspnc-a2qe77, aspnc-a2qf54, aspnc-a2qfe9, aspnc-a2qg33, aspnc-a2qgj6, aspnc-a2qgm6, aspnc-a2qh52, aspnc-a2qh76, aspnc-a2qh85, aspnc-a2qhe2, aspnc-a2qi32, aspnc-a2qib2, aspnc-a2qk14, aspnc-a2ql23, aspnc-a2ql89, aspnc-a2ql90, aspnc-a2qla0, aspnc-a2qlz0, aspnc-a2qm14, aspnc-a2qmk5, aspnc-a2qms0, aspnc-a2qn29, aspnc-a2qn56, aspnc-a2qn70, aspnc-a2qnw9, aspnc-a2qr21, aspnc-a2qs22, aspnc-a2qt50, aspnc-a2qti9, aspnc-a2qtz0, aspnc-a2quc1, aspnc-a2qw06, aspnc-a2qwz6, aspnc-a2qx92, aspnc-a2qyf0, aspnc-a2qys7, aspnc-a2qz72, aspnc-a2qzn6, aspnc-a2qzr0, aspnc-a2qzs1, aspnc-a2qzx0, aspnc-a2qzx4, aspnc-a2r0p4, aspnc-a2r0u0, aspnc-a2r1p3, aspnc-a2r1r5, aspnc-a2r2i5, aspnc-a2r2l0, aspnc-a2r3s8, aspnc-a2r4c0, aspnc-a2r4j8, aspnc-a2r5r4, aspnc-a2r6g3, aspnc-a2r6h5, aspnc-a2r6h8, aspnc-a2r7q1, aspnc-a2r8r3, aspnc-a2r8z3, aspnc-a2r9y8, aspnc-a2r032, aspnc-a2r040, aspnc-a2r273, aspnc-a2r496, aspnc-a2r502, aspnc-a2ra07, aspnc-a2rap4, aspnc-a2raq2, aspnc-a2rav1, aspnc-a5aaf4, aspnc-a5ab63, aspnc-a5abc6, aspnc-a5abe5, aspnc-a5abe8, aspnc-a5abf0, aspnc-a5abh9, aspnc-a5abk1, aspnc-a5abt2, aspnc-a5abz1, aspnc-atg15, aspnc-axe1, aspnc-cuti1, aspnc-cuti2, aspnc-faec, aspng-a2q8w0, aspng-a2qs46, aspng-a2qst4, aspng-a2qv27, aspng-a2qzk9, aspng-a2r0p8, aspng-a2r225, aspng-DAPB, aspng-DPP5, aspng-faeb, aspni-APSC, aspni-EstA, aspni-FAEA, aspni-PAPA, aspkw-g7y0v7, aspnc-a2qt47, aspnc-a2qt66, aspnc-a2r199, aspnc-a2r871, aspnc-a2qbp6, aspnc-a2qqa1, aspnc-a2qt70, aspna-g3y5a6, aspna-g3xpw9, aspnc-a2qw57, aspaw-a0a401kcz4, aspna-alba, aspnc-kex1, aspnc-cbpya, aspnc-a2qbg8 Abstract The filamentous fungus Aspergillus niger is widely exploited by the fermentation industry for the production of enzymes and organic acids, particularly citric acid. We sequenced the 33.9-megabase genome of A. niger CBS 513.88, the ancestor of currently used enzyme production strains. A high level of synteny was observed with other aspergilli sequenced. Strong function predictions were made for 6,506 of the 14,165 open reading frames identified. A detailed description of the components of the protein secretion pathway was made and striking differences in the hydrolytic enzyme spectra of aspergilli were observed. A reconstructed metabolic network comprising 1,069 unique reactions illustrates the versatile metabolism of A. niger. Noteworthy is the large number of major facilitator superfamily transporters and fungal zinc binuclear cluster transcription factors, and the presence of putative gene clusters for fumonisin and ochratoxin A synthesis. | |||||||
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