Platzer M

References (11)

Title : The genome of the foraminiferan Reticulomyxa filosa - Glockner_2014_Curr.Biol_24_11
Author(s) : Glockner G , Hulsmann N , Schleicher M , Noegel AA , Eichinger L , Gallinger C , Pawlowski J , Sierra R , Euteneuer U , Pillet L , Moustafa A , Platzer M , Groth M , Szafranski K , Schliwa M
Ref : Current Biology , 24 :11 , 2014
Abstract : BACKGROUND: Rhizaria are a major branch of eukaryote evolution with an extensive microfossil record, but only scarce molecular data are available. The rhizarian species Reticulomyxa filosa, belonging to the Foraminifera, is free-living in freshwater environments. In culture, it thrives only as a plasmodium with thousands of haploid nuclei in one cell. The R. filosa genome is the first foraminiferal genome to be deciphered.
RESULTS: The genome is extremely repetitive, and the large amounts of identical sequences hint at frequent amplifications and homologous recombination events. Presumably, these mechanisms are employed to provide more gene copies for higher transcriptional activity and to build up a reservoir of gene diversification in certain gene families, such as the kinesin family. The gene repertoire indicates that it is able to switch to a single-celled, flagellated sexual state never observed in culture. Comparison to another rhizarian, the chlorarachniophyte alga Bigelowiella natans, reveals that proteins involved in signaling were likely drivers in establishing the Rhizaria lineage. Compared to some other protists, horizontal gene transfer is limited, but we found evidence of bacterial-to-eukaryote and eukaryote-to-eukaryote transfer events.
CONCLUSIONS: The R. filosa genome exhibits a unique architecture with extensive repeat homogenization and gene amplification, which highlights its potential for diverse life-cycle stages. The ability of R. filosa to rapidly transport matter from the pseudopodia to the cell body may be supported by the high diversification of actin and kinesin gene family members.
ESTHER : Glockner_2014_Curr.Biol_24_11
PubMedSearch : Glockner_2014_Curr.Biol_24_11
PubMedID: 24332546
Gene_locus related to this paper: retfi-x6m7c7 , retfi-x6nwc0

Title : A physical, genetic and functional sequence assembly of the barley genome - Mayer_2012_Nature_491_711
Author(s) : Mayer KF , Waugh R , Brown JW , Schulman A , Langridge P , Platzer M , Fincher GB , Muehlbauer GJ , Sato K , Close TJ , Wise RP , Stein N
Ref : Nature , 491 :711 , 2012
Abstract : Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.
ESTHER : Mayer_2012_Nature_491_711
PubMedSearch : Mayer_2012_Nature_491_711
PubMedID: 23075845
Gene_locus related to this paper: horvd-f2e504 , horvv-f2dwm7 , horvv-f2cwp1 , horvv-m0utz9 , wheat-a0a3b6c2m6 , horvv-a0a287g9l8 , horvv-a0a287p3b9 , horvv-a0a287k7y5 , horvv-a0a287k830 , horvv-a0a287uvs9 , horvv-a0a287uvt3 , horvv-a0a287vga7 , horvv-a0a287w0t8 , horvv-a0a287rem5 , horvv-f2dfe3 , horvv-f2db09 , horvv-a0a8i7b938 , horvv-a0a287hj26 , horvv-f2e0h1

Title : Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi - Burmester_2011_Genome.Biol_12_R7
Author(s) : Burmester A , Shelest E , Glockner G , Heddergott C , Schindler S , Staib P , Heidel A , Felder M , Petzold A , Szafranski K , Feuermann M , Pedruzzi I , Priebe S , Groth M , Winkler R , Li W , Kniemeyer O , Schroeckh V , Hertweck C , Hube B , White TC , Platzer M , Guthke R , Heitman J , Wostemeyer J , Zipfel PF , Monod M , Brakhage AA
Ref : Genome Biol , 12 :R7 , 2011
Abstract : BACKGROUND: Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans.
RESULTS: 97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species.
CONCLUSIONS: Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens.
ESTHER : Burmester_2011_Genome.Biol_12_R7
PubMedSearch : Burmester_2011_Genome.Biol_12_R7
PubMedID: 21247460
Gene_locus related to this paper: artbc-d4ajq5 , artbc-d4an28 , artbc-d4aqa7 , artbc-d4aqb6 , artbc-d4av38 , artbc-d4ax63 , artbc-d4b5r3 , artbc-d4b5t7 , artbc-d4b465 , artbc-dapb , triec-f2pwm2 , trirc-f2sy06 , triru-q52h54 , trit1-f2rna8 , trivh-d4d5w1 , trivh-d4d8k1 , trivh-d4d228 , trivh-d4d960 , trivh-d4dbj6 , trivh-d4dbr9 , trivh-d4dct3 , trivh-d4dfu4 , trivh-d4dk34 , trivh-d4dkr7 , trivh-d4dlf5 , artbc-d4avu9 , artbc-d4aun9 , trivh-d4dkk1 , trivh-d4d3f3 , triru-a0a178f289 , artbc-scpe , artbc-kex1 , artbc-a1751 , artbc-scpd , artbc-scpf , artbc-fae1 , artbc-a6907

Title : Lack of association of genetic variants in genes of the endocannabinoid system with anorexia nervosa - Muller_2008_Child.Adolesc.Psychiatry.Ment.Health_2_33
Author(s) : Muller TD , Reichwald K , Bronner G , Kirschner J , Nguyen TT , Scherag A , Herzog W , Herpertz-Dahlmann B , Lichtner P , Meitinger T , Platzer M , Schafer H , Hebebrand J , Hinney A
Ref : Child Adolesc Psychiatry Ment Health , 2 :33 , 2008
Abstract : BACKGROUND: Several lines of evidence indicate that the central cannabinoid receptor 1 (CNR1) as well as the major endocannabinoid degrading enzymes fatty acid amide hydrolase (FAAH), N-acylethanolamine-hydrolyzing acid amidase (NAAA) and monoglyceride lipase (MGLL) are implicated in mediating the orexigenic effects of cannabinoids. The aim of this study was to analyse whether nucleotide sequence variations in the CNR1, FAAH, NAAA and MGLL genes are associated with anorexia nervosa (AN).
METHODS: We analysed the association of a previously described (AAT)n repeat in the 3' flanking region of CNR1 as well as a total of 15 single nucleotide polymorphisms (SNPs) representative of regions with restricted haplotype diversity in CNR1, FAAH, NAAA or MGLL in up to 91 German AN trios (patient with AN and both biological parents) using the transmission-disequilibrium-test (TDT). One SNP was additionally analysed in an independent case-control study comprising 113 patients with AN and 178 normal weight controls. Genotyping was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, ARMS-PCR or using 3730xl capillary sequencers.
RESULTS: The TDT revealed no evidence for association for any of the SNPs or the (AAT)n repeat with AN (all two-sided uncorrected p-values > 0.05). The lowest p-value of 0.11 was detected for the A-allele of the CNR1 SNP rs1049353 for which the transmission rate was 59% (95% confidence interval 47%...70%). Further genotyping of rs1049353 in 113 additional independent patients with AN and 178 normal weight controls could not substantiate the initial trend for association (p = 1.00).
CONCLUSION: As we found no evidence for an association of genetic variation in CNR1, FAAH, NAAA and MGLL with AN, we conclude that genetic variations in these genes do not play a major role in the etiology of AN in our study groups.
ESTHER : Muller_2008_Child.Adolesc.Psychiatry.Ment.Health_2_33
PubMedSearch : Muller_2008_Child.Adolesc.Psychiatry.Ment.Health_2_33
PubMedID: 19014633

Title : Widespread occurrence and genomic context of unusually small polyketide synthase genes in microbial consortia associated with marine sponges - Fieseler_2007_Appl.Environ.Microbiol_73_2144
Author(s) : Fieseler L , Hentschel U , Grozdanov L , Schirmer A , Wen G , Platzer M , Hrvatin S , Butzke D , Zimmermann K , Piel J
Ref : Applied Environmental Microbiology , 73 :2144 , 2007
Abstract : Numerous marine sponges harbor enormous amounts of as-yet-uncultivated bacteria in their tissues. There is increasing evidence that these symbionts play an important role in the synthesis of protective metabolites, many of which are of great pharmacological interest. In this study, genes for the biosynthesis of polyketides, one of the most important classes of bioactive natural products, were systematically investigated in 20 demosponge species from different oceans. Unexpectedly, the sponge metagenomes were dominated by a ubiquitously present, evolutionarily distinct, and highly sponge-specific group of polyketide synthases (PKSs). Open reading frames resembling animal fatty acid genes were found on three corresponding DNA regions isolated from the metagenomes of Theonella swinhoei and Aplysina aerophoba. Their architecture suggests that methyl-branched fatty acids are the metabolic product. According to a phylogenetic analysis of housekeeping genes, at least one of the PKSs belongs to a bacterium of the Deinococcus-Thermus phylum. The results provide new insights into the chemistry of sponge symbionts and allow inference of a detailed phylogeny of the diverse functional PKS types present in sponge metagenomes. Based on these qualitative and quantitative data, we propose a significantly simplified strategy for the targeted isolation of biomedically relevant PKS genes from complex sponge-symbiont associations.
ESTHER : Fieseler_2007_Appl.Environ.Microbiol_73_2144
PubMedSearch : Fieseler_2007_Appl.Environ.Microbiol_73_2144
PubMedID: 17293531

Title : DNA sequence and analysis of human chromosome 8 - Nusbaum_2006_Nature_439_331
Author(s) : Nusbaum C , Mikkelsen TS , Zody MC , Asakawa S , Taudien S , Garber M , Kodira CD , Schueler MG , Shimizu A , Whittaker CA , Chang JL , Cuomo CA , Dewar K , Fitzgerald MG , Yang X , Allen NR , Anderson S , Asakawa T , Blechschmidt K , Bloom T , Borowsky ML , Butler J , Cook A , Corum B , DeArellano K , Decaprio D , Dooley KT , Dorris L, 3rd , Engels R , Glockner G , Hafez N , Hagopian DS , Hall JL , Ishikawa SK , Jaffe DB , Kamat A , Kudoh J , Lehmann R , Lokitsang T , Macdonald P , Major JE , Matthews CD , Mauceli E , Menzel U , Mihalev AH , Minoshima S , Murayama Y , Naylor JW , Nicol R , Nguyen C , O'Leary SB , O'Neill K , Parker SC , Polley A , Raymond CK , Reichwald K , Rodriguez J , Sasaki T , Schilhabel M , Siddiqui R , Smith CL , Sneddon TP , Talamas JA , Tenzin P , Topham K , Venkataraman V , Wen G , Yamazaki S , Young SK , Zeng Q , Zimmer AR , Rosenthal A , Birren BW , Platzer M , Shimizu N , Lander ES
Ref : Nature , 439 :331 , 2006
Abstract : The International Human Genome Sequencing Consortium (IHGSC) recently completed a sequence of the human genome. As part of this project, we have focused on chromosome 8. Although some chromosomes exhibit extreme characteristics in terms of length, gene content, repeat content and fraction segmentally duplicated, chromosome 8 is distinctly typical in character, being very close to the genome median in each of these aspects. This work describes a finished sequence and gene catalogue for the chromosome, which represents just over 5% of the euchromatic human genome. A unique feature of the chromosome is a vast region of approximately 15 megabases on distal 8p that appears to have a strikingly high mutation rate, which has accelerated in the hominids relative to other sequenced mammals. This fast-evolving region contains a number of genes related to innate immunity and the nervous system, including loci that appear to be under positive selection--these include the major defensin (DEF) gene cluster and MCPH1, a gene that may have contributed to the evolution of expanded brain size in the great apes. The data from chromosome 8 should allow a better understanding of both normal and disease biology and genome evolution.
ESTHER : Nusbaum_2006_Nature_439_331
PubMedSearch : Nusbaum_2006_Nature_439_331
PubMedID: 16421571
Gene_locus related to this paper: human-TG

Title : The genome of the social amoeba Dictyostelium discoideum - Eichinger_2005_Nature_435_43
Author(s) : Eichinger L , Pachebat JA , Glockner G , Rajandream MA , Sucgang R , Berriman M , Song J , Olsen R , Szafranski K , Xu Q , Tunggal B , Kummerfeld S , Madera M , Konfortov BA , Rivero F , Bankier AT , Lehmann R , Hamlin N , Davies R , Gaudet P , Fey P , Pilcher K , Chen G , Saunders D , Sodergren E , Davis P , Kerhornou A , Nie X , Hall N , Anjard C , Hemphill L , Bason N , Farbrother P , Desany B , Just E , Morio T , Rost R , Churcher C , Cooper J , Haydock S , van Driessche N , Cronin A , Goodhead I , Muzny D , Mourier T , Pain A , Lu M , Harper D , Lindsay R , Hauser H , James K , Quiles M , Madan Babu M , Saito T , Buchrieser C , Wardroper A , Felder M , Thangavelu M , Johnson D , Knights A , Loulseged H , Mungall K , Oliver K , Price C , Quail MA , Urushihara H , Hernandez J , Rabbinowitsch E , Steffen D , Sanders M , Ma J , Kohara Y , Sharp S , Simmonds M , Spiegler S , Tivey A , Sugano S , White B , Walker D , Woodward J , Winckler T , Tanaka Y , Shaulsky G , Schleicher M , Weinstock G , Rosenthal A , Cox EC , Chisholm RL , Gibbs R , Loomis WF , Platzer M , Kay RR , Williams J , Dear PH , Noegel AA , Barrell B , Kuspa A
Ref : Nature , 435 :43 , 2005
Abstract : The social amoebae are exceptional in their ability to alternate between unicellular and multicellular forms. Here we describe the genome of the best-studied member of this group, Dictyostelium discoideum. The gene-dense chromosomes of this organism encode approximately 12,500 predicted proteins, a high proportion of which have long, repetitive amino acid tracts. There are many genes for polyketide synthases and ABC transporters, suggesting an extensive secondary metabolism for producing and exporting small molecules. The genome is rich in complex repeats, one class of which is clustered and may serve as centromeres. Partial copies of the extrachromosomal ribosomal DNA (rDNA) element are found at the ends of each chromosome, suggesting a novel telomere structure and the use of a common mechanism to maintain both the rDNA and chromosomal termini. A proteome-based phylogeny shows that the amoebozoa diverged from the animal-fungal lineage after the plant-animal split, but Dictyostelium seems to have retained more of the diversity of the ancestral genome than have plants, animals or fungi.
ESTHER : Eichinger_2005_Nature_435_43
PubMedSearch : Eichinger_2005_Nature_435_43
PubMedID: 15875012
Gene_locus related to this paper: dicdi-abhd , dicdi-ACHE , dicdi-apra , dicdi-cinbp , dicdi-CMBL , dicdi-crysp , dicdi-DPOA , dicdi-P90528 , dicdi-ppme1 , dicdi-Q8MYE7 , dicdi-q54cf7 , dicdi-q54cl7 , dicdi-q54cm0 , dicdi-q54ct5 , dicdi-q54cu1 , dicdi-q54d54 , dicdi-q54d66 , dicdi-q54dj5 , dicdi-q54dy7 , dicdi-q54ek1 , dicdi-q54eq6 , dicdi-q54et1 , dicdi-q54et7 , dicdi-q54f01 , dicdi-q54g24 , dicdi-q54g47 , dicdi-q54gi7 , dicdi-q54gw5 , dicdi-q54gx3 , dicdi-q54h23 , dicdi-q54h73 , dicdi-q54i38 , dicdi-q54ie5 , dicdi-q54in4 , dicdi-q54kz1 , dicdi-q54l36 , dicdi-q54li1 , dicdi-q54m29 , dicdi-q54n21 , dicdi-q54n35 , dicdi-q54n85 , dicdi-q54qe7 , dicdi-q54qi3 , dicdi-q54qk2 , dicdi-q54rl3 , dicdi-q54rl8 , dicdi-q54sy6 , dicdi-q54sz3 , dicdi-q54t49 , dicdi-q54t91 , dicdi-q54th2 , dicdi-q54u01 , dicdi-q54vc2 , dicdi-q54vw1 , dicdi-q54xe3 , dicdi-q54xl3 , dicdi-q54xu1 , dicdi-q54xu2 , dicdi-q54y48 , dicdi-q54yd0 , dicdi-q54ye0 , dicdi-q54yl1 , dicdi-q54yr8 , dicdi-q54z90 , dicdi-q55bx3 , dicdi-q55d01 , dicdi-q55d81 , dicdi-q55du6 , dicdi-q55eu1 , dicdi-q55eu8 , dicdi-q55fk4 , dicdi-q55gk7 , dicdi-Q54ZA6 , dicdi-q86h82 , dicdi-Q86HC9 , dicdi-Q86HM5 , dicdi-Q86HM6 , dicdi-q86iz7 , dicdi-q86jb6 , dicdi-Q86KU7 , dicdi-q550s3 , dicdi-q552c0 , dicdi-q553t5 , dicdi-q555e5 , dicdi-q555h0 , dicdi-q555h1 , dicdi-q557k5 , dicdi-q558u2 , dicdi-Q869Q8 , dicdi-u554 , dicdi-y9086 , dicdi-q54r44 , dicdi-f172a

Title : The DNA sequence of the human X chromosome - Ross_2005_Nature_434_325
Author(s) : Ross MT , Grafham DV , Coffey AJ , Scherer S , McLay K , Muzny D , Platzer M , Howell GR , Burrows C , Bird CP , Frankish A , Lovell FL , Howe KL , Ashurst JL , Fulton RS , Sudbrak R , Wen G , Jones MC , Hurles ME , Andrews TD , Scott CE , Searle S , Ramser J , Whittaker A , Deadman R , Carter NP , Hunt SE , Chen R , Cree A , Gunaratne P , Havlak P , Hodgson A , Metzker ML , Richards S , Scott G , Steffen D , Sodergren E , Wheeler DA , Worley KC , Ainscough R , Ambrose KD , Ansari-Lari MA , Aradhya S , Ashwell RI , Babbage AK , Bagguley CL , Ballabio A , Banerjee R , Barker GE , Barlow KF , Barrett IP , Bates KN , Beare DM , Beasley H , Beasley O , Beck A , Bethel G , Blechschmidt K , Brady N , Bray-Allen S , Bridgeman AM , Brown AJ , Brown MJ , Bonnin D , Bruford EA , Buhay C , Burch P , Burford D , Burgess J , Burrill W , Burton J , Bye JM , Carder C , Carrel L , Chako J , Chapman JC , Chavez D , Chen E , Chen G , Chen Y , Chen Z , Chinault C , Ciccodicola A , Clark SY , Clarke G , Clee CM , Clegg S , Clerc-Blankenburg K , Clifford K , Cobley V , Cole CG , Conquer JS , Corby N , Connor RE , David R , Davies J , Davis C , Davis J , Delgado O , Deshazo D , Dhami P , Ding Y , Dinh H , Dodsworth S , Draper H , Dugan-Rocha S , Dunham A , Dunn M , Durbin KJ , Dutta I , Eades T , Ellwood M , Emery-Cohen A , Errington H , Evans KL , Faulkner L , Francis F , Frankland J , Fraser AE , Galgoczy P , Gilbert J , Gill R , Glockner G , Gregory SG , Gribble S , Griffiths C , Grocock R , Gu Y , Gwilliam R , Hamilton C , Hart EA , Hawes A , Heath PD , Heitmann K , Hennig S , Hernandez J , Hinzmann B , Ho S , Hoffs M , Howden PJ , Huckle EJ , Hume J , Hunt PJ , Hunt AR , Isherwood J , Jacob L , Johnson D , Jones S , de Jong PJ , Joseph SS , Keenan S , Kelly S , Kershaw JK , Khan Z , Kioschis P , Klages S , Knights AJ , Kosiura A , Kovar-Smith C , Laird GK , Langford C , Lawlor S , Leversha M , Lewis L , Liu W , Lloyd C , Lloyd DM , Loulseged H , Loveland JE , Lovell JD , Lozado R , Lu J , Lyne R , Ma J , Maheshwari M , Matthews LH , McDowall J , Mclaren S , McMurray A , Meidl P , Meitinger T , Milne S , Miner G , Mistry SL , Morgan M , Morris S , Muller I , Mullikin JC , Nguyen N , Nordsiek G , Nyakatura G , O'Dell CN , Okwuonu G , Palmer S , Pandian R , Parker D , Parrish J , Pasternak S , Patel D , Pearce AV , Pearson DM , Pelan SE , Perez L , Porter KM , Ramsey Y , Reichwald K , Rhodes S , Ridler KA , Schlessinger D , Schueler MG , Sehra HK , Shaw-Smith C , Shen H , Sheridan EM , Shownkeen R , Skuce CD , Smith ML , Sotheran EC , Steingruber HE , Steward CA , Storey R , Swann RM , Swarbreck D , Tabor PE , Taudien S , Taylor T , Teague B , Thomas K , Thorpe A , Timms K , Tracey A , Trevanion S , Tromans AC , d'Urso M , Verduzco D , Villasana D , Waldron L , Wall M , Wang Q , Warren J , Warry GL , Wei X , West A , Whitehead SL , Whiteley MN , Wilkinson JE , Willey DL , Williams G , Williams L , Williamson A , Williamson H , Wilming L , Woodmansey RL , Wray PW , Yen J , Zhang J , Zhou J , Zoghbi H , Zorilla S , Buck D , Reinhardt R , Poustka A , Rosenthal A , Lehrach H , Meindl A , Minx PJ , Hillier LW , Willard HF , Wilson RK , Waterston RH , Rice CM , Vaudin M , Coulson A , Nelson DL , Weinstock G , Sulston JE , Durbin R , Hubbard T , Gibbs RA , Beck S , Rogers J , Bentley DR
Ref : Nature , 434 :325 , 2005
Abstract : The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise process that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence.
ESTHER : Ross_2005_Nature_434_325
PubMedSearch : Ross_2005_Nature_434_325
PubMedID: 15772651
Gene_locus related to this paper: human-NLGN3 , human-NLGN4X

Title : Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei - Piel_2004_Proc.Natl.Acad.Sci.U.S.A_101_16222
Author(s) : Piel J , Hui D , Wen G , Butzke D , Platzer M , Fusetani N , Matsunaga S
Ref : Proc Natl Acad Sci U S A , 101 :16222 , 2004
Abstract : Bacterial symbionts have long been suspected to be the true producers of many drug candidates isolated from marine invertebrates. Sponges, the most important marine source of biologically active natural products, have been frequently hypothesized to contain compounds of bacterial origin. This symbiont hypothesis, however, remained unproven because of a general inability to cultivate the suspected producers. However, we have recently identified an uncultured Pseudomonas sp. symbiont as the most likely producer of the defensive antitumor polyketide pederin in Paederus fuscipes beetles by cloning the putative biosynthesis genes. Here we report closely related genes isolated from the highly complex metagenome of the marine sponge Theonella swinhoei, which is the source of the onnamides and theopederins, a group of polyketides that structurally resemble pederin. Sequence features of the isolated genes clearly indicate that it belongs to a prokaryotic genome and should be responsible for the biosynthesis of almost the entire portion of the polyketide structure that is correlated with antitumor activity. Besides providing further proof for the role of the related beetle symbiont-derived genes, these findings raise intriguing ecological and evolutionary questions and have important general implications for the sustainable production of otherwise inaccessible marine drugs by using biotechnological strategies.
ESTHER : Piel_2004_Proc.Natl.Acad.Sci.U.S.A_101_16222
PubMedSearch : Piel_2004_Proc.Natl.Acad.Sci.U.S.A_101_16222
PubMedID: 15520376
Gene_locus related to this paper: 9bact-q5i686

Title : DNA sequence and comparative analysis of chimpanzee chromosome 22 - Watanabe_2004_Nature_429_382
Author(s) : Watanabe H , Fujiyama A , Hattori M , Taylor TD , Toyoda A , Kuroki Y , Noguchi H , BenKahla A , Lehrach H , Sudbrak R , Kube M , Taenzer S , Galgoczy P , Platzer M , Scharfe M , Nordsiek G , Blocker H , Hellmann I , Khaitovich P , Paabo S , Reinhardt R , Zheng HJ , Zhang XL , Zhu GF , Wang BF , Fu G , Ren SX , Zhao GP , Chen Z , Lee YS , Cheong JE , Choi SH , Wu KM , Liu TT , Hsiao KJ , Tsai SF , Kim CG , S OO , Kitano T , Kohara Y , Saitou N , Park HS , Wang SY , Yaspo ML , Sakaki Y
Ref : Nature , 429 :382 , 2004
Abstract : Human-chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.
ESTHER : Watanabe_2004_Nature_429_382
PubMedSearch : Watanabe_2004_Nature_429_382
PubMedID: 15164055
Gene_locus related to this paper: pantr-a0a2j8lmv7

Title : Sequence and analysis of chromosome 2 of Dictyostelium discoideum - Glockner_2002_Nature_418_79
Author(s) : Glockner G , Eichinger L , Szafranski K , Pachebat JA , Bankier AT , Dear PH , Lehmann R , Baumgart C , Parra G , Abril JF , Guigo R , Kumpf K , Tunggal B , Cox E , Quail MA , Platzer M , Rosenthal A , Noegel AA
Ref : Nature , 418 :79 , 2002
Abstract : The genome of the lower eukaryote Dictyostelium discoideum comprises six chromosomes. Here we report the sequence of the largest, chromosome 2, which at 8 megabases (Mb) represents about 25% of the genome. Despite an A + T content of nearly 80%, the chromosome codes for 2,799 predicted protein coding genes and 73 transfer RNA genes. This gene density, about 1 gene per 2.6 kilobases (kb), is surpassed only by Saccharomyces cerevisiae (one per 2 kb) and is similar to that of Schizosaccharomyces pombe (one per 2.5 kb). If we assume that the other chromosomes have a similar gene density, we can expect around 11,000 genes in the D. discoideum genome. A significant number of the genes show higher similarities to genes of vertebrates than to those of other fully sequenced eukaryotes. This analysis strengthens the view that the evolutionary position of D. discoideum is located before the branching of metazoa and fungi but after the divergence of the plant kingdom, placing it close to the base of metazoan evolution.
ESTHER : Glockner_2002_Nature_418_79
PubMedSearch : Glockner_2002_Nature_418_79
PubMedID: 12097910
Gene_locus related to this paper: dicdi-crd2p , dicdi-DPOA , dicdi-P90528 , dicdi-Q8MMX8 , dicdi-Q8MYE7 , dicdi-q54z90 , dicdi-Q75JJ5 , dicdi-Q54ZA6 , dicdi-q86h82 , dicdi-Q86HC9 , dicdi-Q86HM5 , dicdi-Q86HM6 , dicdi-Q86I88 , dicdi-q86iz7 , dicdi-Q86KU7 , dicdi-q552c0 , dicdi-q553t5 , dicdi-q555h0 , dicdi-q555h1 , dicdi-q557k5 , dicdi-Q869Q8 , dicdi-f172a