Scharfe M

References (12)

Title : Genome sequence of the thermophilic strain Bacillus coagulans 2-6, an efficient producer of high-optical-purity L-lactic acid - Su_2011_J.Bacteriol_193_4563
Author(s) : Su F , Yu B , Sun J , Ou HY , Zhao B , Wang L , Qin J , Tang H , Tao F , Jarek M , Scharfe M , Ma C , Ma Y , Xu P
Ref : Journal of Bacteriology , 193 :4563 , 2011
Abstract : Bacillus coagulans 2-6 is an efficient producer of lactic acid. The genome of B. coagulans 2-6 has the smallest genome among the members of the genus Bacillus known to date. The frameshift mutation at the start of the d-lactate dehydrogenase sequence might be responsible for the production of high-optical-purity l-lactic acid.
ESTHER : Su_2011_J.Bacteriol_193_4563
PubMedSearch : Su_2011_J.Bacteriol_193_4563
PubMedID: 21705584
Gene_locus related to this paper: bacc6-f7z0w1 , bacco-c1p801 , bacco-g2tqg6

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 : 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 : 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

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome XII - Johnston_1997_Nature_387_87
Author(s) : Johnston M , Hillier L , Riles L , Albermann K , Andre B , Ansorge W , Benes V , Bruckner M , Delius H , Dubois E , Dusterhoft A , Entian KD , Floeth M , Goffeau A , Hebling U , Heumann K , Heuss-Neitzel D , Hilbert H , Hilger F , Kleine K , Kotter P , Louis EJ , Messenguy F , Mewes HW , Miosga T , Mostl D , Muller-Auer S , Nentwich U , Obermaier B , Piravandi E , Pohl TM , Portetelle D , Purnelle B , Rechmann S , Rieger M , Rinke M , Rose M , Scharfe M , Scherens B , Scholler P , Schwager C , Schwarz S , Underwood AP , Urrestarazu LA , Vandenbol M , Verhasselt P , Vierendeels F , Voet M , Volckaert G , Voss H , Wambutt , Wedler E , Wedler H , Zimmermann FK , Zollner A , Hani J , Hoheisel JD
Ref : Nature , 387 :87 , 1997
Abstract : The yeast Saccharomyces cerevisiae is the pre-eminent organism for the study of basic functions of eukaryotic cells. All of the genes of this simple eukaryotic cell have recently been revealed by an international collaborative effort to determine the complete DNA sequence of its nuclear genome. Here we describe some of the features of chromosome XII.
ESTHER : Johnston_1997_Nature_387_87
PubMedSearch : Johnston_1997_Nature_387_87
PubMedID: 9169871
Gene_locus related to this paper: yeast-ict1 , yeast-YLR118c

Title : The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI - Bussey_1997_Nature_387_103
Author(s) : Bussey H , Storms RK , Ahmed A , Albermann K , Allen E , Ansorge W , Araujo R , Aparicio A , Barrell B , Badcock K , Benes V , Botstein D , Bowman S , Bruckner M , Carpenter J , Cherry JM , Chung E , Churcher C , Coster F , Davis K , Davis RW , Dietrich FS , Delius H , DiPaolo T , Dubois E , Dusterhoft A , Duncan M , Floeth M , Fortin N , Friesen JD , Fritz C , Goffeau A , Hall J , Hebling U , Heumann K , Hilbert H , Hillier L , Hunicke-Smith S , Hyman R , Johnston M , Kalman S , Kleine K , Komp C , Kurdi O , Lashkari D , Lew H , Lin A , Lin D , Louis EJ , Marathe R , Messenguy F , Mewes HW , Mirtipati S , Moestl D , Muller-Auer S , Namath A , Nentwich U , Oefner P , Pearson D , Petel FX , Pohl TM , Purnelle B , Rajandream MA , Rechmann S , Rieger M , Riles L , Roberts D , Schafer M , Scharfe M , Scherens B , Schramm S , Schroder M , Sdicu AM , Tettelin H , Urrestarazu LA , Ushinsky S , Vierendeels F , Vissers S , Voss H , Walsh SV , Wambutt R , Wang Y , Wedler E , Wedler H , Winnett E , Zhong WW , Zollner A , Vo DH , Hani J
Ref : Nature , 387 :103 , 1997
Abstract : The nucleotide sequence of the 948,061 base pairs of chromosome XVI has been determined, completing the sequence of the yeast genome. Chromosome XVI was the last yeast chromosome identified, and some of the genes mapped early to it, such as GAL4, PEP4 and RAD1 (ref. 2) have played important roles in the development of yeast biology. The architecture of this final chromosome seems to be typical of the large yeast chromosomes, and shows large duplications with other yeast chromosomes. Chromosome XVI contains 487 potential protein-encoding genes, 17 tRNA genes and two small nuclear RNA genes; 27% of the genes have significant similarities to human gene products, and 48% are new and of unknown biological function. Systematic efforts to explore gene function have begun.
ESTHER : Bussey_1997_Nature_387_103
PubMedSearch : Bussey_1997_Nature_387_103
PubMedID: 9169875
Gene_locus related to this paper: yeast-MCFS1 , yeast-YPR147C