Goff S

References (3)

Title : Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution - Pope_2011_PLoS.One_6_e16329
Author(s) : Pope WH , Jacobs-Sera D , Russell DA , Peebles CL , Al-Atrache Z , Alcoser TA , Alexander LM , Alfano MB , Alford ST , Amy NE , Anderson MD , Anderson AG , Ang AA , Ares M, Jr. , Barber AJ , Barker LP , Barrett JM , Barshop WD , Bauerle CM , Bayles IM , Belfield KL , Best AA , Borjon A, Jr. , Bowman CA , Boyer CA , Bradley KW , Bradley VA , Broadway LN , Budwal K , Busby KN , Campbell IW , Campbell AM , Carey A , Caruso SM , Chew RD , Cockburn CL , Cohen LB , Corajod JM , Cresawn SG , Davis KR , Deng L , Denver DR , Dixon BR , Ekram S , Elgin SC , Engelsen AE , English BE , Erb ML , Estrada C , Filliger LZ , Findley AM , Forbes L , Forsyth MH , Fox TM , Fritz MJ , Garcia R , George ZD , Georges AE , Gissendanner CR , Goff S , Goldstein R , Gordon KC , Green RD , Guerra SL , Guiney-Olsen KR , Guiza BG , Haghighat L , Hagopian GV , Harmon CJ , Harmson JS , Hartzog GA , Harvey SE , He S , He KJ , Healy KE , Higinbotham ER , Hildebrandt EN , Ho JH , Hogan GM , Hohenstein VG , Holz NA , Huang VJ , Hufford EL , Hynes PM , Jackson AS , Jansen EC , Jarvik J , Jasinto PG , Jordan TC , Kasza T , Katelyn MA , Kelsey JS , Kerrigan LA , Khaw D , Kim J , Knutter JZ , Ko CC , Larkin GV , Laroche JR , Latif A , Leuba KD , Leuba SI , Lewis LO , Loesser-Casey KE , Long CA , Lopez AJ , Lowery N , Lu TQ , Mac V , Masters IR , McCloud JJ , McDonough MJ , Medenbach AJ , Menon A , Miller R , Morgan BK , Ng PC , Nguyen E , Nguyen KT , Nguyen ET , Nicholson KM , Parnell LA , Peirce CE , Perz AM , Peterson LJ , Pferdehirt RE , Philip SV , Pogliano K , Pogliano J , Polley T , Puopolo EJ , Rabinowitz HS , Resiss MJ , Rhyan CN , Robinson YM , Rodriguez LL , Rose AC , Rubin JD , Ruby JA , Saha MS , Sandoz JW , Savitskaya J , Schipper DJ , Schnitzler CE , Schott AR , Segal JB , Shaffer CD , Sheldon KE , Shepard EM , Shepardson JW , Shroff MK , Simmons JM , Simms EF , Simpson BM , Sinclair KM , Sjoholm RL , Slette IJ , Spaulding BC , Straub CL , Stukey J , Sughrue T , Tang TY , Tatyana LM , Taylor SB , Taylor BJ , Temple LM , Thompson JV , Tokarz MP , Trapani SE , Troum AP , Tsay J , Tubbs AT , Walton JM , Wang DH , Wang H , Warner JR , Weisser EG , Wendler SC , Weston-Hafer KA , Whelan HM , Williamson KE , Willis AN , Wirtshafter HS , Wong TW , Wu P , Yang Y , Yee BC , Zaidins DA , Zhang B , Zuniga MY , Hendrix RW , Hatfull GF
Ref : PLoS ONE , 6 :e16329 , 2011
Abstract : Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.
ESTHER : Pope_2011_PLoS.One_6_e16329
PubMedSearch : Pope_2011_PLoS.One_6_e16329
PubMedID: 21298013
Gene_locus related to this paper: 9caud-g1jvt5 , 9caud-e0ypf9

Title : Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium - Ma_2010_Nature_464_367
Author(s) : Ma LJ , van der Does HC , Borkovich KA , Coleman JJ , Daboussi MJ , Di Pietro A , Dufresne M , Freitag M , Grabherr M , Henrissat B , Houterman PM , Kang S , Shim WB , Woloshuk C , Xie X , Xu JR , Antoniw J , Baker SE , Bluhm BH , Breakspear A , Brown DW , Butchko RA , Chapman S , Coulson R , Coutinho PM , Danchin EG , Diener A , Gale LR , Gardiner DM , Goff S , Hammond-Kosack KE , Hilburn K , Hua-Van A , Jonkers W , Kazan K , Kodira CD , Koehrsen M , Kumar L , Lee YH , Li L , Manners JM , Miranda-Saavedra D , Mukherjee M , Park G , Park J , Park SY , Proctor RH , Regev A , Ruiz-Roldan MC , Sain D , Sakthikumar S , Sykes S , Schwartz DC , Turgeon BG , Wapinski I , Yoder O , Young S , Zeng Q , Zhou S , Galagan J , Cuomo CA , Kistler HC , Rep M
Ref : Nature , 464 :367 , 2010
Abstract : Fusarium species are among the most important phytopathogenic and toxigenic fungi. To understand the molecular underpinnings of pathogenicity in the genus Fusarium, we compared the genomes of three phenotypically diverse species: Fusarium graminearum, Fusarium verticillioides and Fusarium oxysporum f. sp. lycopersici. Our analysis revealed lineage-specific (LS) genomic regions in F. oxysporum that include four entire chromosomes and account for more than one-quarter of the genome. LS regions are rich in transposons and genes with distinct evolutionary profiles but related to pathogenicity, indicative of horizontal acquisition. Experimentally, we demonstrate the transfer of two LS chromosomes between strains of F. oxysporum, converting a non-pathogenic strain into a pathogen. Transfer of LS chromosomes between otherwise genetically isolated strains explains the polyphyletic origin of host specificity and the emergence of new pathogenic lineages in F. oxysporum. These findings put the evolution of fungal pathogenicity into a new perspective.
ESTHER : Ma_2010_Nature_464_367
PubMedSearch : Ma_2010_Nature_464_367
PubMedID: 20237561
Gene_locus related to this paper: fusox-a0a1d3s5h0 , gibf5-fus2 , fusof-f9f2k2 , fusof-f9f3l6 , fusof-f9f6t8 , fusof-f9f6v2 , fusof-f9f132 , fusof-f9f781 , fusof-f9fd72 , fusof-f9fd90 , fusof-f9fem0 , fusof-f9fhk2 , fusof-f9fj19 , fusof-f9fj20 , fusof-f9fki8 , fusof-f9fmx2 , fusof-f9fnt4 , fusof-f9fpy4 , fusof-f9fvs6 , fusof-f9fwu0 , fusof-f9fxz4 , fusof-f9fzy5 , fusof-f9g2a2 , fusof-f9g3b1 , fusof-f9g5h7 , fusof-f9g6e6 , fusof-f9g6y7 , fusof-f9g7b0 , fusof-f9g797 , fusof-f9g972 , fusof-f9ga50 , fusof-f9gck4 , fusof-f9gd15 , gibze-a8w610 , gibze-b1pdn0 , gibze-i1r9e6 , gibze-i1rda9 , gibze-i1rdk7 , gibze-i1rec8 , gibze-i1rgs0 , gibze-i1rgy0 , gibze-i1rh52 , gibze-i1rhi8 , gibze-i1rig9 , gibze-i1rip5 , gibze-i1rpg6 , gibze-i1rsg2 , gibze-i1rv36 , gibze-i1rxm5 , gibze-i1rxp8 , gibze-i1rxv5 , gibze-i1s1u3 , gibze-i1s3j9 , gibze-i1s6l7 , gibze-i1s8i8 , gibze-i1s9x4 , gibze-q4huy1 , gibze-i1rg17 , fuso4-j9mvr9 , fuso4-j9ngs6 , fuso4-j9niq8 , fuso4-j9nqm2 , gibze-i1rb76 , gibze-i1s1m7 , gibze-i1s3z6 , gibze-i1rd78 , gibze-i1rgl9 , gibze-i1rjp7 , gibze-i1s1q6 , gibze-i1ri35 , gibze-i1rf76 , gibze-i1rhp3 , fusc1-n4uj11 , fusc4-n1s9p6 , gibf5-s0dqr2 , gibm7-w7n1b5 , fusof-f9g6q0 , gibm7-w7n497 , fusox-x0bme4 , gibm7-w7mcf8 , gibm7-w7mak5 , fusox-x0a2c5 , gibm7-w7mum7 , fusox-w9iyc7 , gibm7-w7maw6 , gibm7-w7msi0 , gibm7-w7luf0 , gibm7-w7msa3 , gibm7-w7mna8 , gibm7-w7n8b7 , gibm7-w7n564 , fusox-w9jpi0 , gibm7-w7ngc3 , gibm7-w7m4v6 , gibm7-w7m4v2 , gibm7-w7lt61 , gibm7-w7mly6 , gibm7-w7ncn3 , fusox-w9ibd7 , fusof-f9fnm6 , gibm7-w7n526 , gibza-a0a016pda4 , gibza-a0a016pl96 , gibm7-w7muq1 , fusof-f9gfd3 , gibm7-w7mt52 , gibze-i1rjb5 , gibf5-s0ehu3 , fusox-w9hvf0 , gibze-i1rkc4 , gibm7-w7mv30 , gibze-a0a1c3ylb1 , fuso4-a0a0c4diy4 , gibm7-w7n4n0 , gibze-gra11 , gibze-fsl2 , gibf5-fub4 , gibf5-fub5 , gibf5-fus5 , gibm7-dlh1

Title : The biosynthetic gene cluster for the microtubule-stabilizing agents epothilones A and B from Sorangium cellulosum So ce90 - Molnar_2000_Chem.Biol_7_97
Author(s) : Molnar I , Schupp T , Ono M , Zirkle R , Milnamow M , Nowak-Thompson B , Engel N , Toupet C , Stratmann A , Cyr DD , Gorlach J , Mayo JM , Hu A , Goff S , Schmid J , Ligon JM
Ref : Chemical Biology , 7 :97 , 2000
Abstract : BACKGROUND: Epothilones are produced by the myxobacterium Sorangium cellulosum So ce90, and, like paclitaxel (Taxol((R))), they inhibit microtubule depolymerisation and arrest the cell cycle at the G2-M phase. They are effective against P-glycoprotein-expressing multiple-drug-resistant tumor cell lines and are more water soluble than paclitaxel. The total synthesis of epothilones has been achieved, but has not provided an economically viable alternative to fermentation. We set out to clone, sequence and analyze the gene cluster responsible for the biosynthesis of the epothilones in S. cellulosum So ce90.
RESULTS: A cluster of 22 open reading frames spanning 68,750 base pairs of the S. cellulosum So ce90 genome has been sequenced and found to encode nine modules of a polyketide synthase (PKS), one module of a nonribosomal peptide synthetase (NRPS), a cytochrome P450, and two putative antibiotic transport proteins. Disruptions in the genes encoding the PKS abolished epothilone production. The first PKS module and the NRPS module are proposed to co-operate in forming the thiazole heterocycle of epothilone from an acetate and a cysteine by condensation, cyclodehydration and subsequent dehydrogenation. The remaining eight PKS modules are responsible for the elaboration of the rest of the epothilone carbon skeleton.
CONCLUSIONS: The overall architecture of the gene cluster responsible for epothilone biosynthesis has been determined. The availability of the cluster should facilitate the generation of designer epothilones by combinatorial biosynthesis approaches, and the heterologous expression of epothilones in surrogate microbial hosts.
ESTHER : Molnar_2000_Chem.Biol_7_97
PubMedSearch : Molnar_2000_Chem.Biol_7_97
PubMedID: 10662695
Gene_locus related to this paper: sorce-EPOE