Sabat G

References (6)

Title : A tail of two voltages: Proteomic comparison of the three electric organs of the electric eel - Traeger_2017_Sci.Adv_3_e1700523
Author(s) : Traeger LL , Sabat G , Barrett-Wilt GA , Wells GB , Sussman MR
Ref : Sci Adv , 3 :e1700523 , 2017
Abstract : The electric eel (Electrophorus electricus) is unusual among electric fishes because it has three pairs of electric organs that serve multiple biological functions: For navigation and communication, it emits continuous pulses of weak electric discharge (<1 V), but for predation and defense, it intermittently emits lethal strong electric discharges (10 to 600 V). We hypothesized that these two electrogenic outputs have different energetic demands reflected by differences in their proteome and phosphoproteome. We report the use of isotope-assisted quantitative mass spectrometry to test this hypothesis. We observed novel phosphorylation sites in sodium transporters and identified a potassium channel with unique differences in protein concentration among the electric organs. In addition, we found transcription factors and protein kinases that show differential abundance in the strong versus weak electric organs. Our findings support the hypothesis that proteomic differences among electric organs underlie differences in energetic needs, reflecting a trade-off between generating weak voltages continuously and strong voltages intermittently.
ESTHER : Traeger_2017_Sci.Adv_3_e1700523
PubMedSearch : Traeger_2017_Sci.Adv_3_e1700523
PubMedID: 28695212
Gene_locus related to this paper: eleel-BCHE , eleel-a0a4w4gcb7 , eleel-a0a4w4dt57

Title : Analysis of the Phlebiopsis gigantea genome, transcriptome and secretome provides insight into its pioneer colonization strategies of wood - Hori_2014_PLoS.Genet_10_e1004759
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
Ref : PLoS Genet , 10 :e1004759 , 2014
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.
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

Title : The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes - Floudas_2012_Science_336_1715
Author(s) : Floudas D , Binder M , Riley R , Barry K , Blanchette RA , Henrissat B , Martinez AT , Otillar R , Spatafora JW , Yadav JS , Aerts A , Benoit I , Boyd A , Carlson A , Copeland A , Coutinho PM , de Vries RP , Ferreira P , Findley K , Foster B , Gaskell J , Glotzer D , Gorecki P , Heitman J , Hesse C , Hori C , Igarashi K , Jurgens JA , Kallen N , Kersten P , Kohler A , Kues U , Kumar TK , Kuo A , LaButti K , Larrondo LF , Lindquist E , Ling A , Lombard V , Lucas S , Lundell T , Martin R , McLaughlin DJ , Morgenstern I , Morin E , Murat C , Nagy LG , Nolan M , Ohm RA , Patyshakuliyeva A , Rokas A , Ruiz-Duenas FJ , Sabat G , Salamov A , Samejima M , Schmutz J , Slot JC , St John F , Stenlid J , Sun H , Sun S , Syed K , Tsang A , Wiebenga A , Young D , Pisabarro A , Eastwood DC , Martin F , Cullen D , Grigoriev IV , Hibbett DS
Ref : Science , 336 :1715 , 2012
Abstract : Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which also contains non-lignin-degrading brown rot and ectomycorrhizal species. Comparative analyses of 31 fungal genomes (12 generated for this study) suggest that lignin-degrading peroxidases expanded in the lineage leading to the ancestor of the Agaricomycetes, which is reconstructed as a white rot species, and then contracted in parallel lineages leading to brown rot and mycorrhizal species. Molecular clock analyses suggest that the origin of lignin degradation might have coincided with the sharp decrease in the rate of organic carbon burial around the end of the Carboniferous period.
ESTHER : Floudas_2012_Science_336_1715
PubMedSearch : Floudas_2012_Science_336_1715
PubMedID: 22745431
Gene_locus related to this paper: aurde-j0d098 , aurde-j0dc31 , glota-s7rlc1 , fompi-s8f7s4 , dacsp-m5fpg2 , dicsq-r7sm16 , dacsp-m5g7q5 , dacsp-m5fr12 , glota-s7q5w3 , fompi-s8f826.1 , fompi-s8f826.2 , dicsq-r7sy09 , glota-s7rt87 , dicsq-r7t032 , glota-s7rym7 , fompi-s8fiv2 , dacsp-m5gda3.2 , dicsq-r7swi6 , dacsp-m5frf2 , fompi-s8ebb6 , dicsq-r7sln3 , dicsq-r7sya6 , dacsp-m5g7g1 , dicsq-r7syx7 , dicsq-r7sx57 , dacsp-m5fps7 , glota-s7pwi7 , dicsq-r7swj6 , fompi-s8ejq6 , dicsq-r7spc3 , glota-s7q258 , dacsp-m5ft65 , glota-s7q3m7 , fompi-s8dkc7 , glota-s7q1z1 , fompi-s8eqi2 , glota-s7q1z8 , fompi-s8du50 , dacsp-m5gg33 , dacsp-m5g3a7 , fompi-s8ecd7 , fompi-s8dps1 , dacsp-m5fwr0 , dicsq-r7sub7 , glota-s7q8k9 , fompi-s8ffc3 , dacsp-m5g2f9 , fompi-s8ecc2 , dacsp-m5g868 , fompi-s8f890 , dicsq-r7t1a8 , fompi-s8ebx4 , fompi-s8eb97 , glota-s7q222 , glota-s7puf0 , fompi-s8f6v9 , dacsp-m5g0z2 , dacsp-m5gdh9 , fompi-s8fb37 , dacsp-m5fy91 , glota-s7q5v6 , fompi-s8fl44 , dicsq-r7stv9 , dicsq-r7szk3 , fompi-s8epq9 , glota-s7rh56 , dacsp-m5gbt1 , punst-r7s3x9 , punst-r7s0t5 , glota-s7q312 , glota-s7rhh6 , dicsq-r7t117 , dicsq-r7slz3

Title : Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis - Fernandez-Fueyo_2012_Proc.Natl.Acad.Sci.U.S.A_109_5458
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
Ref : Proc Natl Acad Sci U S A , 109 :5458 , 2012
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.
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

Title : Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion - Martinez_2009_Proc.Natl.Acad.Sci.U.S.A_106_1954
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
Ref : Proc Natl Acad Sci U S A , 106 :1954 , 2009
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.
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

Title : Cloning, nucleotide sequencing, and functional analysis of a novel, mobile cluster of biodegradation genes from Pseudomonas aeruginosa strain JB2 - Hickey_2001_Appl.Environ.Microbiol_67_4603
Author(s) : Hickey WJ , Sabat G , Yuroff AS , Arment AR , Perez-Lesher J
Ref : Applied Environmental Microbiology , 67 :4603 , 2001
Abstract : We have identified in Pseudomonas aeruginosa strain JB2 a novel cluster of mobile genes encoding degradation of hydroxy- and halo-aromatic compounds. Nineteen open reading frames were located and, based on sequence similarities, were putatively identified as encoding a ring hydroxylating oxygenase (hybABCD), an ATP-binding cassette-type transporter, an extradiol ring-cleavage dioxygenase, transcriptional regulatory proteins, enzymes mediating chlorocatechol degradation, and transposition functions. Expression of hybABCD in Escherichia coli cells effected stoichiometric transformation of 2-hydroxybenzoate (salicylate) to 2,5-dihydroxybenzoate (gentisate). This activity was predicted from sequence similarity to functionally characterized genes, nagAaGHAb from Ralstonia sp. strain U2 (S. L. Fuenmayor, M. Wild, A. L. Boyes, and P. A. Williams, J. Bacteriol. 180:2522-2530, 1998), and is the second confirmed example of salicylate 5-hydroxylase activity effected by an oxygenase outside the flavoprotein group. Growth of strain JB2 or Pseudomonas huttiensis strain D1 (an organism that had acquired the 2-chlorobenzoate degradation phenotype from strain JB2) on benzoate yielded mutants that were unable to grow on salicylate or 2-chlorobenzoate and that had a deletion encompassing hybABCD and the region cloned downstream. The mutants' inability to grow on 2-chlorobenzoate suggested the loss of additional genes outside of, but contiguous with, the characterized region. Pulsed-field gel electrophoresis revealed a plasmid of >300 kb in strain D1, but no plasmids were detected in strain JB2. Hybridization analyses confirmed that the entire 26-kb region characterized here was acquired by strain D1 from strain JB2 and was located in the chromosome of both organisms. Further studies to delineate the element's boundaries and functional characteristics could provide new insights into the mechanisms underlying evolution of bacterial genomes in general and of catabolic pathways for anthropogenic pollutants in particular.
ESTHER : Hickey_2001_Appl.Environ.Microbiol_67_4603
PubMedSearch : Hickey_2001_Appl.Environ.Microbiol_67_4603
PubMedID: 11571162
Gene_locus related to this paper: pseae-CLCD