Blocker H

References (15)

Title : Genome sequence, comparative analysis, and population genetics of the domestic horse - Wade_2009_Science_326_865
Author(s) : Wade CM , Giulotto E , Sigurdsson S , Zoli M , Gnerre S , Imsland F , Lear TL , Adelson DL , Bailey E , Bellone RR , Blocker H , Distl O , Edgar RC , Garber M , Leeb T , Mauceli E , MacLeod JN , Penedo MC , Raison JM , Sharpe T , Vogel J , Andersson L , Antczak DF , Biagi T , Binns MM , Chowdhary BP , Coleman SJ , Della Valle G , Fryc S , Guerin G , Hasegawa T , Hill EW , Jurka J , Kiialainen A , Lindgren G , Liu J , Magnani E , Mickelson JR , Murray J , Nergadze SG , Onofrio R , Pedroni S , Piras MF , Raudsepp T , Rocchi M , Roed KH , Ryder OA , Searle S , Skow L , Swinburne JE , Syvanen AC , Tozaki T , Valberg SJ , Vaudin M , White JR , Zody MC , Lander ES , Lindblad-Toh K
Ref : Science , 326 :865 , 2009
Abstract : We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.
ESTHER : Wade_2009_Science_326_865
PubMedSearch : Wade_2009_Science_326_865
PubMedID: 19892987
Gene_locus related to this paper: horse-1plip , horse-2plrp , horse-ACHE , horse-BCHE , horse-f6pri5 , horse-f6qlk6 , horse-f6qsc5 , horse-f6r958 , horse-f6sfg0 , horse-f6uif6 , horse-f6un85 , horse-f6vxp7 , horse-f6wfs9 , horse-f6wzv8 , horse-f6x0i7 , horse-f6x5e5 , horse-f6zmg7 , horse-f7afw6 , horse-f7agv7 , horse-f7bj10 , horse-f7bk45 , horse-f7bvl6 , horse-f7c7a8 , horse-f7cdt1 , horse-f7cxj0 , horse-f6ut17 , horse-f6svq9 , horse-f6xgj6 , horse-f6s101 , horse-f6wfa7 , horse-f7cpx3 , horse-f7adj7 , horse-f6r609 , horse-f6y0j2 , horse-f6zvb2 , horse-f7e4g0 , horse-f6ti02 , horse-f6re01 , horse-f6xmp6 , horse-f6vts1 , horse-f6quf7 , horse-f6tn81 , horse-f7bm46 , horse-f6q1u3 , horse-f6zna7 , horse-f6q208 , horse-f7cuh0 , horse-f6tq73 , horse-f6xa70 , horse-f6qj19 , horse-f6wgf3 , horse-f7d8t6 , horse-f6ul42 , horse-f7am73 , horse-f7dme2

Title : The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae - Gross_2008_BMC.Genomics_9_449
Author(s) : Gross R , Guzman CA , Sebaihia M , dos Santos VA , Pieper DH , Koebnik R , Lechner M , Bartels D , Buhrmester J , Choudhuri JV , Ebensen T , Gaigalat L , Herrmann S , Khachane AN , Larisch C , Link S , Linke B , Meyer F , Mormann S , Nakunst D , Ruckert C , Schneiker-Bekel S , Schulze K , Vorholter FJ , Yevsa T , Engle JT , Goldman WE , Puhler A , Gobel UB , Goesmann A , Blocker H , Kaiser O , Martinez-Arias R
Ref : BMC Genomics , 9 :449 , 2008
Abstract : BACKGROUND: Bordetella petrii is the only environmental species hitherto found among the otherwise host-restricted and pathogenic members of the genus Bordetella. Phylogenetically, it connects the pathogenic Bordetellae and environmental bacteria of the genera Achromobacter and Alcaligenes, which are opportunistic pathogens. B. petrii strains have been isolated from very different environmental niches, including river sediment, polluted soil, marine sponges and a grass root. Recently, clinical isolates associated with bone degenerative disease or cystic fibrosis have also been described. RESULTS: In this manuscript we present the results of the analysis of the completely annotated genome sequence of the B. petrii strain DSMZ12804. B. petrii has a mosaic genome of 5,287,950 bp harboring numerous mobile genetic elements, including seven large genomic islands. Four of them are highly related to the clc element of Pseudomonas knackmussii B13, which encodes genes involved in the degradation of aromatics. Though being an environmental isolate, the sequenced B. petrii strain also encodes proteins related to virulence factors of the pathogenic Bordetellae, including the filamentous hemagglutinin, which is a major colonization factor of B. pertussis, and the master virulence regulator BvgAS. However, it lacks all known toxins of the pathogenic Bordetellae. CONCLUSION: The genomic analysis suggests that B. petrii represents an evolutionary link between free-living environmental bacteria and the host-restricted obligate pathogenic Bordetellae. Its remarkable metabolic versatility may enable B. petrii to thrive in very different ecological niches.
ESTHER : Gross_2008_BMC.Genomics_9_449
PubMedSearch : Gross_2008_BMC.Genomics_9_449
PubMedID: 18826580
Gene_locus related to this paper: alceu-CBNC , borpd-a9hwh7 , borpd-a9hxw5 , borpd-a9hyr5 , borpd-a9hzm8 , borpd-a9i1l8 , borpd-a9i4f4 , borpd-a9i8i7 , borpd-a9icj9 , borpd-a9iec4 , borpd-a9iep7 , borpd-a9ih03 , borpd-a9iu09 , borpd-metx , bursp-tecF , borpd-a9i1v7

Title : The full-ORF clone resource of the German cDNA Consortium - Bechtel_2007_BMC.Genomics_8_399
Author(s) : Bechtel S , Rosenfelder H , Duda A , Schmidt CP , Ernst U , Wellenreuther R , Mehrle A , Schuster C , Bahr A , Blocker H , Heubner D , Hoerlein A , Michel G , Wedler H , Kohrer K , Ottenwalder B , Poustka A , Wiemann S , Schupp I
Ref : BMC Genomics , 8 :399 , 2007
Abstract : BACKGROUND: With the completion of the human genome sequence the functional analysis and characterization of the encoded proteins has become the next urging challenge in the post-genome era. The lack of comprehensive ORFeome resources has thus far hampered systematic applications by protein gain-of-function analysis. Gene and ORF coverage with full-length ORF clones thus needs to be extended. In combination with a unique and versatile cloning system, these will provide the tools for genome-wide systematic functional analyses, to achieve a deeper insight into complex biological processes. RESULTS: Here we describe the generation of a full-ORF clone resource of human genes applying the Gateway cloning technology (Invitrogen). A pipeline for efficient cloning and sequencing was developed and a sample tracking database was implemented to streamline the clone production process targeting more than 2,200 different ORFs. In addition, a robust cloning strategy was established, permitting the simultaneous generation of two clone variants that contain a particular ORF with as well as without a stop codon by the implementation of only one additional working step into the cloning procedure. Up to 92 % of the targeted ORFs were successfully amplified by PCR and more than 93 % of the amplicons successfully cloned. CONCLUSION: The German cDNA Consortium ORFeome resource currently consists of more than 3,800 sequence-verified entry clones representing ORFs, cloned with and without stop codon, for about 1,700 different gene loci. 177 splice variants were cloned representing 121 of these genes. The entry clones have been used to generate over 5,000 different expression constructs, providing the basis for functional profiling applications. As a member of the recently formed international ORFeome collaboration we substantially contribute to generating and providing a whole genome human ORFeome collection in a unique cloning system that is made freely available in the community.
ESTHER : Bechtel_2007_BMC.Genomics_8_399
PubMedSearch : Bechtel_2007_BMC.Genomics_8_399
PubMedID: 17974005
Gene_locus related to this paper: human-AFMID , human-MEST , human-TMCO4

Title : Complete genome sequence of the myxobacterium Sorangium cellulosum - Schneiker_2007_Nat.Biotechnol_25_1281
Author(s) : Schneiker S , Perlova O , Kaiser O , Gerth K , Alici A , Altmeyer MO , Bartels D , Bekel T , Beyer S , Bode E , Bode HB , Bolten CJ , Choudhuri JV , Doss S , Elnakady YA , Frank B , Gaigalat L , Goesmann A , Groeger C , Gross F , Jelsbak L , Kalinowski J , Kegler C , Knauber T , Konietzny S , Kopp M , Krause L , Krug D , Linke B , Mahmud T , Martinez-Arias R , McHardy AC , Merai M , Meyer F , Mormann S , Munoz-Dorado J , Perez J , Pradella S , Rachid S , Raddatz G , Rosenau F , Ruckert C , Sasse F , Scharfe M , Schuster SC , Suen G , Treuner-Lange A , Velicer GJ , Vorholter FJ , Weissman KJ , Welch RD , Wenzel SC , Whitworth DE , Wilhelm S , Wittmann C , Blocker H , Puhler A , Muller R
Ref : Nat Biotechnol , 25 :1281 , 2007
Abstract : The genus Sorangium synthesizes approximately half of the secondary metabolites isolated from myxobacteria, including the anti-cancer metabolite epothilone. We report the complete genome sequence of the model Sorangium strain S. cellulosum So ce56, which produces several natural products and has morphological and physiological properties typical of the genus. The circular genome, comprising 13,033,779 base pairs, is the largest bacterial genome sequenced to date. No global synteny with the genome of Myxococcus xanthus is apparent, revealing an unanticipated level of divergence between these myxobacteria. A large percentage of the genome is devoted to regulation, particularly post-translational phosphorylation, which probably supports the strain's complex, social lifestyle. This regulatory network includes the highest number of eukaryotic protein kinase-like kinases discovered in any organism. Seventeen secondary metabolite loci are encoded in the genome, as well as many enzymes with potential utility in industry.
ESTHER : Schneiker_2007_Nat.Biotechnol_25_1281
PubMedSearch : Schneiker_2007_Nat.Biotechnol_25_1281
PubMedID: 17965706
Gene_locus related to this paper: sorc5-a9en84 , sorc5-a9enf0 , sorc5-a9eu04 , sorc5-a9eur8 , sorc5-a9ev31 , sorc5-a9ewe7 , sorc5-a9f2w6 , sorc5-a9fd82 , sorc5-a9fec8 , sorc5-a9fg26 , sorc5-a9fjh7 , sorc5-a9fpe7 , sorc5-a9fvz2 , sorc5-a9fw17 , sorc5-a9fw70 , sorc5-a9fwe6 , sorc5-a9fya1 , sorc5-a9g9n9 , sorc5-a9g651 , sorc5-a9gj93 , sorc5-a9glc5 , sorc5-a9glv5 , sorc5-a9gqy4 , sorc5-a9grj0 , sorc5-a9grk3 , sorc5-a9grp4 , sorc5-a9grt6 , sorc5-a9guw3 , sorc5-a9gy73 , sorce-q2n3s7 , sorc5-a9fsu5 , sorc5-a9gq11 , sorc5-a9ev65 , sorc5-a9fcj4 , sorc5-a9gut3 , sorc5-a9env4 , sorc5-a9fai0 , sorc5-a9g908 , sorc5-a9gmg6 , sorc5-ce1

Title : Spiroketal polyketide formation in Sorangium: identification and analysis of the biosynthetic gene cluster for the highly cytotoxic spirangienes - Frank_2007_Chem.Biol_14_221
Author(s) : Frank B , Knauber J , Steinmetz H , Scharfe M , Blocker H , Beyer S , Muller R
Ref : Chemical Biology , 14 :221 , 2007
Abstract : Natural products constitute important lead structures in drug discovery. In bacteria, they are often synthesized by large, modular multienzyme complexes. Detailed analysis of the biosynthetic machinery should enable its directed engineering and production of desirable analogs. The myxobacterium Sorangium cellulosum So ce90 produces the cytotoxic spiroketal polyketide spirangien, for which we describe the identification and functional analysis of the biosynthetic pathway. The gene cluster spans 88 kb and encodes 7 type I polyketide synthases and additional enzymes such as a stand-alone thioesterase and 2 methyltransferases. Inactivation of two cytochrome P(450) monooxygenase genes resulted in the production of acyclic spirangien derivatives, providing direct evidence for the involvement of these enzymes in spiroketal formation. The presence of large DNA repeats is consistent with multiple rounds of gene duplication during the evolution of the biosynthetic gene locus.
ESTHER : Frank_2007_Chem.Biol_14_221
PubMedSearch : Frank_2007_Chem.Biol_14_221
PubMedID: 17317575
Gene_locus related to this paper: sorce-SPIJ

Title : Molecular and biochemical studies of chondramide formation-highly cytotoxic natural products from Chondromyces crocatus Cm c5 - Rachid_2006_Chem.Biol_13_667
Author(s) : Rachid S , Krug D , Kunze B , Kochems I , Scharfe M , Zabriskie TM , Blocker H , Muller R
Ref : Chemical Biology , 13 :667 , 2006
Abstract : The jaspamide/chondramide family of depsipeptides are mixed PKS/NRPS natural products isolated from marine sponges and a terrestrial myxobacterium that potently affect the function of the actin cytoskeleton. As a first step to improve production in heterologous host cells and permit genetic approaches to novel analogs, we have cloned and characterized the chondramide biosynthetic genes from the myxobacterium Chondromyces crocatus Cm c5. In addition to the expected PKS and NRPS genes, the cluster encodes a rare tyrosine aminomutase for beta-tyrosine formation and a previously unknown tryptophan-2-halogenase. Conditions for gene transfer into C. crocatus Cm c5 were developed, and inactivation of several genes corroborated their proposed function and served to define the boundaries of the cluster. Biochemical characterization of the final NRPS adenylation domain confirmed the direct activation of beta-tyrosine, and fluorinated chondramides were produced through precursor-directed biosynthesis.
ESTHER : Rachid_2006_Chem.Biol_13_667
PubMedSearch : Rachid_2006_Chem.Biol_13_667
PubMedID: 16793524
Gene_locus related to this paper: choco-chsad

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 : DNA sequence and analysis of human chromosome 9 - Humphray_2004_Nature_429_369
Author(s) : Humphray SJ , Oliver K , Hunt AR , Plumb RW , Loveland JE , Howe KL , Andrews TD , Searle S , Hunt SE , Scott CE , Jones MC , Ainscough R , Almeida JP , Ambrose KD , Ashwell RI , Babbage AK , Babbage S , Bagguley CL , Bailey J , Banerjee R , Barker DJ , Barlow KF , Bates K , Beasley H , Beasley O , Bird CP , Bray-Allen S , Brown AJ , Brown JY , Burford D , Burrill W , Burton J , Carder C , Carter NP , Chapman JC , Chen Y , Clarke G , Clark SY , Clee CM , Clegg S , Collier RE , Corby N , Crosier M , Cummings AT , Davies J , Dhami P , Dunn M , Dutta I , Dyer LW , Earthrowl ME , Faulkner L , Fleming CJ , Frankish A , Frankland JA , French L , Fricker DG , Garner P , Garnett J , Ghori J , Gilbert JG , Glison C , Grafham DV , Gribble S , Griffiths C , Griffiths-Jones S , Grocock R , Guy J , Hall RE , Hammond S , Harley JL , Harrison ES , Hart EA , Heath PD , Henderson CD , Hopkins BL , Howard PJ , Howden PJ , Huckle E , Johnson C , Johnson D , Joy AA , Kay M , Keenan S , Kershaw JK , Kimberley AM , King A , Knights A , Laird GK , Langford C , Lawlor S , Leongamornlert DA , Leversha M , Lloyd C , Lloyd DM , Lovell J , Martin S , Mashreghi-Mohammadi M , Matthews L , Mclaren S , McLay KE , McMurray A , Milne S , Nickerson T , Nisbett J , Nordsiek G , Pearce AV , Peck AI , Porter KM , Pandian R , Pelan S , Phillimore B , Povey S , Ramsey Y , Rand V , Scharfe M , Sehra HK , Shownkeen R , Sims SK , Skuce CD , Smith M , Steward CA , Swarbreck D , Sycamore N , Tester J , Thorpe A , Tracey A , Tromans A , Thomas DW , Wall M , Wallis JM , West AP , Whitehead SL , Willey DL , Williams SA , Wilming L , Wray PW , Young L , Ashurst JL , Coulson A , Blocker H , Durbin R , Sulston JE , Hubbard T , Jackson MJ , Bentley DR , Beck S , Rogers J , Dunham I
Ref : Nature , 429 :369 , 2004
Abstract : Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.
ESTHER : Humphray_2004_Nature_429_369
PubMedSearch : Humphray_2004_Nature_429_369
PubMedID: 15164053
Gene_locus related to this paper: human-CEL

Title : Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs - Wiemann_2001_Genome.Res_11_422
Author(s) : Wiemann S , Weil B , Wellenreuther R , Gassenhuber J , Glassl S , Ansorge W , Boecher M , Bloecker H , Bauersachs S , Blum H , Lauber J , Duesterhoeft A , Beyer A , Koehrer K , Strack N , Mewes H-W , Ottenwaelder B , Obermaier B , Tampe J , Heubner D , Wambutt R , Korn B , Klein M , Poustka A , Bocher M , Blocker H , Dusterhoft A , Kohrer K , Mewes HW , Ottenwalder B
Ref : Genome Res , 11 :422 , 2001
Abstract : With the complete human genomic sequence being unraveled, the focus will shift to gene identification and to the functional analysis of gene products. The generation of a set of cDNAs, both sequences and physical clones, which contains the complete and noninterrupted protein coding regions of all human genes will provide the indispensable tools for the systematic and comprehensive analysis of protein function to eventually understand the molecular basis of man. Here we report the sequencing and analysis of 500 novel human cDNAs containing the complete protein coding frame. Assignment to functional categories was possible for 52% (259) of the encoded proteins, the remaining fraction having no similarities with known proteins. By aligning the cDNA sequences with the sequences of the finished chromosomes 21 and 22 we identified a number of genes that either had been completely missed in the analysis of the genomic sequences or had been wrongly predicted. Three of these genes appear to be present in several copies. We conclude that full-length cDNA sequencing continues to be crucial also for the accurate identification of genes. The set of 500 novel cDNAs, and another 1000 full-coding cDNAs of known transcripts we have identified, adds up to cDNA representations covering 2%--5 % of all human genes. We thus substantially contribute to the generation of a gene catalog, consisting of both full-coding cDNA sequences and clones, which should be made freely available and will become an invaluable tool for detailed functional studies.
ESTHER : Wiemann_2001_Genome.Res_11_422
PubMedSearch : Wiemann_2001_Genome.Res_11_422
PubMedID: 11230166
Gene_locus related to this paper: human-FAM135A , human-KANSL3 , human-NDRG2 , human-NDRG4

Title : Novel features in a combined polyketide synthase\/non-ribosomal peptide synthetase: the myxalamid biosynthetic gene cluster of the myxobacterium Stigmatella aurantiaca Sga15 - Silakowski_2001_Chem.Biol_8_59
Author(s) : Silakowski B , Nordsiek G , Kunze B , Blocker H , Muller R
Ref : Chemical Biology , 8 :59 , 2001
Abstract : BACKGROUND: Myxobacteria have been well established as a potent source for natural products with biological activity. They produce a considerable variety of compounds which represent typical polyketide structures with incorporated amino acids (e.g. the epothilons, the myxothiazols and the myxalamids). Several of these secondary metabolites are effective inhibitors of the electron transport via the respiratory chain and have been widely used. Molecular cloning and characterization of the genes governing the biosynthesis of these structures is of considerable interest, because such information adds to the limited knowledge as to how polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) interact and how they might be manipulated in order to form novel antibiotics.
RESULTS: A DNA region of approximately 50000 base pairs from Stigmatella aurantiaca Sga15 was sequenced and shown by gene disruption to be involved in myxalamid biosynthesis. Sequence analysis reveals that the myxalamids are formed by a combined PKS/NRPS system. The terminal NRPS MxaA extends the assembled polyketide chain of the myxalamids with alanine. MxaA contains an N-terminal domain with homology to NAD binding proteins, which is responsible during the biogenesis for a novel type of reductive chain release giving rise to the 2-amino-propanol moiety of the myxalamids. The last module of the PKS reveals an unprecedented genetic organization; it is encoded on two genes (mxaB1 and mxaB2), subdividing the domains of one module from each other. A sequence comparison of myxobacterial acyl-transferase domains with known systems from streptomycetes and bacilli reveals that consensus sequences proposed to be specific for methylmalonyl-CoA and malonyl-CoA are not always reliable.
CONCLUSIONS: The complete biosynthetic gene cluster of the myxalamid-type electron transport inhibitor from S. aurantiaca Sga15 has been cloned and analyzed. It represents one of the few examples of combined PKS/NRPS systems, the analysis and manipulation of which has the potential to generate novel hybrid structures via combinatorial biosynthesis (e.g. via module-swapping techniques). Additionally, a new type of reductive release from PKS/NRPS systems is described.
ESTHER : Silakowski_2001_Chem.Biol_8_59
PubMedSearch : Silakowski_2001_Chem.Biol_8_59
PubMedID: 11182319
Gene_locus related to this paper: stiau-Q93TW5

Title : The DNA sequence of human chromosome 21 - Hattori_2000_Nature_405_311
Author(s) : Hattori M , Fujiyama A , Taylor TD , Watanabe H , Yada T , Park HS , Toyoda A , Ishii K , Totoki Y , Choi DK , Groner Y , Soeda E , Ohki M , Takagi T , Sakaki Y , Taudien S , Blechschmidt K , Polley A , Menzel U , Delabar J , Kumpf K , Lehmann R , Patterson D , Reichwald K , Rump A , Schillhabel M , Schudy A , Zimmermann W , Rosenthal A , Kudoh J , Schibuya K , Kawasaki K , Asakawa S , Shintani A , Sasaki T , Nagamine K , Mitsuyama S , Antonarakis SE , Minoshima S , Shimizu N , Nordsiek G , Hornischer K , Brant P , Scharfe M , Schon O , Desario A , Reichelt J , Kauer G , Blocker H , Ramser J , Beck A , Klages S , Hennig S , Riesselmann L , Dagand E , Haaf T , Wehrmeyer S , Borzym K , Gardiner K , Nizetic D , Francis F , Lehrach H , Reinhardt R , Yaspo ML
Ref : Nature , 405 :311 , 2000
Abstract : Chromosome 21 is the smallest human autosome. An extra copy of chromosome 21 causes Down syndrome, the most frequent genetic cause of significant mental retardation, which affects up to 1 in 700 live births. Several anonymous loci for monogenic disorders and predispositions for common complex disorders have also been mapped to this chromosome, and loss of heterozygosity has been observed in regions associated with solid tumours. Here we report the sequence and gene catalogue of the long arm of chromosome 21. We have sequenced 33,546,361 base pairs (bp) of DNA with very high accuracy, the largest contig being 25,491,867 bp. Only three small clone gaps and seven sequencing gaps remain, comprising about 100 kilobases. Thus, we achieved 99.7% coverage of 21q. We also sequenced 281,116 bp from the short arm. The structural features identified include duplications that are probably involved in chromosomal abnormalities and repeat structures in the telomeric and pericentromeric regions. Analysis of the chromosome revealed 127 known genes, 98 predicted genes and 59 pseudogenes.
ESTHER : Hattori_2000_Nature_405_311
PubMedSearch : Hattori_2000_Nature_405_311
PubMedID: 10830953
Gene_locus related to this paper: human-LIPI

Title : Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana - Salanoubat_2000_Nature_408_820
Author(s) : Salanoubat M , Lemcke K , Rieger M , Ansorge W , Unseld M , Fartmann B , Valle G , Blocker H , Perez-Alonso M , Obermaier B , Delseny M , Boutry M , Grivell LA , Mache R , Puigdomenech P , de Simone V , Choisne N , Artiguenave F , Robert C , Brottier P , Wincker P , Cattolico L , Weissenbach J , Saurin W , Quetier F , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Benes V , Wurmbach E , Drzonek H , Erfle H , Jordan N , Bangert S , Wiedelmann R , Kranz H , Voss H , Holland R , Brandt P , Nyakatura G , Vezzi A , D'Angelo M , Pallavicini A , Toppo S , Simionati B , Conrad A , Hornischer K , Kauer G , Lohnert TH , Nordsiek G , Reichelt J , Scharfe M , Schon O , Bargues M , Terol J , Climent J , Navarro P , Collado C , Perez-Perez A , Ottenwalder B , Duchemin D , Cooke R , Laudie M , Berger-Llauro C , Purnelle B , Masuy D , de Haan M , Maarse AC , Alcaraz JP , Cottet A , Casacuberta E , Monfort A , Argiriou A , Flores M , Liguori R , Vitale D , Mannhaupt G , Haase D , Schoof H , Rudd S , Zaccaria P , Mewes HW , Mayer KF , Kaul S , Town CD , Koo HL , Tallon LJ , Jenkins J , Rooney T , Rizzo M , Walts A , Utterback T , Fujii CY , Shea TP , Creasy TH , Haas B , Maiti R , Wu D , Peterson J , Van Aken S , Pai G , Militscher J , Sellers P , Gill JE , Feldblyum TV , Preuss D , Lin X , Nierman WC , Salzberg SL , White O , Venter JC , Fraser CM , Kaneko T , Nakamura Y , Sato S , Kato T , Asamizu E , Sasamoto S , Kimura T , Idesawa K , Kawashima K , Kishida Y , Kiyokawa C , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Tabata S
Ref : Nature , 408 :820 , 2000
Abstract : Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
ESTHER : Salanoubat_2000_Nature_408_820
PubMedSearch : Salanoubat_2000_Nature_408_820
PubMedID: 11130713
Gene_locus related to this paper: arath-MES17 , arath-AT3G12150 , arath-At3g61680 , arath-AT3g62590 , arath-CXE12 , arath-eds1 , arath-SCP25 , arath-F1P2.110 , arath-F1P2.140 , arath-F11F8.28 , arath-F14D17.80 , arath-F16B3.4 , arath-SCP27 , arath-At3g50790 , arath-At3g05600 , arath-PAD4 , arath-At3g51000 , arath-SCP16 , arath-gid1 , arath-GID1B , arath-Q9LUG8 , arath-Q84JS1 , arath-Q9SFF6 , arath-q9m236 , arath-q9sr22 , arath-q9sr23 , arath-SCP7 , arath-SCP14 , arath-SCP15 , arath-SCP17 , arath-SCP36 , arath-SCP37 , arath-SCP39 , arath-SCP40 , arath-SCP49 , arath-T19F11.2

Title : Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana - Mayer_1999_Nature_402_769
Author(s) : Mayer K , Schuller C , Wambutt R , Murphy G , Volckaert G , Pohl T , Dusterhoft A , Stiekema W , Entian KD , Terryn N , Harris B , Ansorge W , Brandt P , Grivell L , Rieger M , Weichselgartner M , de Simone V , Obermaier B , Mache R , Muller M , Kreis M , Delseny M , Puigdomenech P , Watson M , Schmidtheini T , Reichert B , Portatelle D , Perez-Alonso M , Boutry M , Bancroft I , Vos P , Hoheisel J , Zimmermann W , Wedler H , Ridley P , Langham SA , McCullagh B , Bilham L , Robben J , Van der Schueren J , Grymonprez B , Chuang YJ , Vandenbussche F , Braeken M , Weltjens I , Voet M , Bastiaens I , Aert R , Defoor E , Weitzenegger T , Bothe G , Ramsperger U , Hilbert H , Braun M , Holzer E , Brandt A , Peters S , van Staveren M , Dirske W , Mooijman P , Klein Lankhorst R , Rose M , Hauf J , Kotter P , Berneiser S , Hempel S , Feldpausch M , Lamberth S , Van den Daele H , De Keyser A , Buysshaert C , Gielen J , Villarroel R , De Clercq R , van Montagu M , Rogers J , Cronin A , Quail M , Bray-Allen S , Clark L , Doggett J , Hall S , Kay M , Lennard N , McLay K , Mayes R , Pettett A , Rajandream MA , Lyne M , Benes V , Rechmann S , Borkova D , Blocker H , Scharfe M , Grimm M , Lohnert TH , Dose S , de Haan M , Maarse A , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Fartmann B , Granderath K , Dauner D , Herzl A , Neumann S , Argiriou A , Vitale D , Liguori R , Piravandi E , Massenet O , Quigley F , Clabauld G , Mundlein A , Felber R , Schnabl S , Hiller R , Schmidt W , Lecharny A , Aubourg S , Chefdor F , Cooke R , Berger C , Montfort A , Casacuberta E , Gibbons T , Weber N , Vandenbol M , Bargues M , Terol J , Torres A , Perez-Perez A , Purnelle B , Bent E , Johnson S , Tacon D , Jesse T , Heijnen L , Schwarz S , Scholler P , Heber S , Francs P , Bielke C , Frishman D , Haase D , Lemcke K , Mewes HW , Stocker S , Zaccaria P , Bevan M , Wilson RK , de la Bastide M , Habermann K , Parnell L , Dedhia N , Gnoj L , Schutz K , Huang E , Spiegel L , Sehkon M , Murray J , Sheet P , Cordes M , Abu-Threideh J , Stoneking T , Kalicki J , Graves T , Harmon G , Edwards J , Latreille P , Courtney L , Cloud J , Abbott A , Scott K , Johnson D , Minx P , Bentley D , Fulton B , Miller N , Greco T , Kemp K , Kramer J , Fulton L , Mardis E , Dante M , Pepin K , Hillier L , Nelson J , Spieth J , Ryan E , Andrews S , Geisel C , Layman D , Du H , Ali J , Berghoff A , Jones K , Drone K , Cotton M , Joshu C , Antonoiu B , Zidanic M , Strong C , Sun H , Lamar B , Yordan C , Ma P , Zhong J , Preston R , Vil D , Shekher M , Matero A , Shah R , Swaby IK , O'Shaughnessy A , Rodriguez M , Hoffmann J , Till S , Granat S , Shohdy N , Hasegawa A , Hameed A , Lodhi M , Johnson A , Chen E , Marra M , Martienssen R , McCombie WR
Ref : Nature , 402 :769 , 1999
Abstract : The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.
ESTHER : Mayer_1999_Nature_402_769
PubMedSearch : Mayer_1999_Nature_402_769
PubMedID: 10617198
Gene_locus related to this paper: arath-AT4G00500 , arath-AT4G16690 , arath-AT4G17480 , arath-AT4G24380 , arath-AT4g30610 , arath-o65513 , arath-o65713 , arath-LPAAT , arath-f4jt64

Title : New lessons for combinatorial biosynthesis from myxobacteria. The myxothiazol biosynthetic gene cluster of Stigmatella aurantiaca DW4\/3-1 - Silakowski_1999_J.Biol.Chem_274_37391
Author(s) : Silakowski B , Schairer HU , Ehret H , Kunze B , Weinig S , Nordsiek G , Brandt P , Blocker H , Hofle G , Beyer S , Muller R
Ref : Journal of Biological Chemistry , 274 :37391 , 1999
Abstract : The biosynthetic mta gene cluster responsible for myxothiazol formation from the fruiting body forming myxobacterium Stigmatella aurantiaca DW4/3-1 was sequenced and analyzed. Myxothiazol, an inhibitor of the electron transport via the bc(1)-complex of the respiratory chain, is biosynthesized by a unique combination of several polyketide synthases (PKS) and nonribosomal peptide synthetases (NRPS), which are activated by the 4'-phosphopantetheinyl transferase MtaA. Genomic replacement of a fragment of mtaB and insertion of a kanamycin resistance gene into mtaA both impaired myxothiazol synthesis. Genes mtaC and mtaD encode the enzymes for bis-thiazol(ine) formation and chain extension on one pure NRPS (MtaC) and on a unique combination of PKS and NRPS (MtaD). The genes mtaE and mtaF encode PKSs including peptide fragments with homology to methyltransferases. These methyltransferase modules are assumed to be necessary for the formation of the proposed methoxy- and beta-methoxy-acrylate intermediates of myxothiazol biosynthesis. The last gene of the cluster, mtaG, again resembles a NRPS and provides insight into the mechanism of the formation of the terminal amide of myxothiazol. The carbon backbone of an amino acid added to the myxothiazol-acid is assumed to be removed via an unprecedented module with homology to monooxygenases within MtaG.
ESTHER : Silakowski_1999_J.Biol.Chem_274_37391
PubMedSearch : Silakowski_1999_J.Biol.Chem_274_37391
PubMedID: 10601310
Gene_locus related to this paper: stiau-MTAG

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome IV - Jacq_1997_Nature_387_75
Author(s) : Jacq C , Alt-Morbe J , Andre B , Arnold W , Bahr A , Ballesta JP , Bargues M , Baron L , Becker A , Biteau N , Blocker H , Blugeon C , Boskovic J , Brandt P , Bruckner M , Buitrago MJ , Coster F , Delaveau T , del Rey F , Dujon B , Eide LG , Garcia-Cantalejo JM , Goffeau A , Gomez-Peris AC , Granotier C , Hanemann V , Hankeln T , Hoheisel JD , Jager W , Jimenez A , Jonniaux JL , Kramer C , Kuster H , Laamanen P , Legros Y , Louis E , Muller-Rieker S , Monnet A , Moro M , Muller-Auer S , Nussbaumer B , Paricio N , Paulin L , Perea J , Perez-Alonso M , Perez-Ortin JE , Pohl TM , Prydz H , Purnelle B , Rasmussen SW , Remacha M , Revuelta JL , Rieger M , Salom D , Saluz HP , Saiz JE , Saren AM , Schafer M , Scharfe M , Schmidt ER , Schneider C , Scholler P , Schwarz S , Soler-Mira A , Urrestarazu LA , Verhasselt P , Vissers S , Voet M , Volckaert G , Wagner G , Wambutt R , Wedler E , Wedler H , Wolfl S , Harris DE , Bowman S , Brown D , Churcher CM , Connor R , Dedman K , Gentles S , Hamlin N , Hunt S , Jones L , McDonald S , Murphy L , Niblett D , Odell C , Oliver K , Rajandream MA , Richards C , Shore L , Walsh SV , Barrell BG , Dietrich FS , Mulligan J , Allen E , Araujo R , Aviles E , Berno A , Carpenter J , Chen E , Cherry JM , Chung E , Duncan M , Hunicke-Smith S , Hyman R , Komp C , Lashkari D , Lew H , Lin D , Mosedale D , Nakahara K , Namath A , Oefner P , Oh C , Petel FX , Roberts D , Schramm S , Schroeder M , Shogren T , Shroff N , Winant A , Yelton M , Botstein D , Davis RW , Johnston M , Hillier L , Riles L , Albermann K , Hani J , Heumann K , Kleine K , Mewes HW , Zollner A , Zaccaria P
Ref : Nature , 387 :75 , 1997
Abstract : The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1-2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin.
ESTHER : Jacq_1997_Nature_387_75
PubMedSearch : Jacq_1997_Nature_387_75
PubMedID: 9169867
Gene_locus related to this paper: yeast-dlhh , yeast-ECM18 , yeast-YDL109C , yeast-YDR428C , yeast-YDR444W