Lehmann R

References (9)

Title : Structure of Drosophila Oskar reveals a novel RNA binding protein - Yang_2015_Proc.Natl.Acad.Sci.U.S.A_112_11541
Author(s) : Yang N , Yu Z , Hu M , Wang M , Lehmann R , Xu RM
Ref : Proc Natl Acad Sci U S A , 112 :11541 , 2015
Abstract : Oskar (Osk) protein plays critical roles during Drosophila germ cell development, yet its functions in germ-line formation and body patterning remain poorly understood. This situation contrasts sharply with the vast knowledge about the function and mechanism of osk mRNA localization. Osk is predicted to have an N-terminal LOTUS domain (Osk-N), which has been suggested to bind RNA, and a C-terminal hydrolase-like domain (Osk-C) of unknown function. Here, we report the crystal structures of Osk-N and Osk-C. Osk-N shows a homodimer of winged-helix-fold modules, but without detectable RNA-binding activity. Osk-C has a lipase-fold structure but lacks critical catalytic residues at the putative active site. Surprisingly, we found that Osk-C binds the 3'UTRs of osk and nanos mRNA in vitro. Mutational studies identified a region of Osk-C important for mRNA binding. These results suggest possible functions of Osk in the regulation of stability, regulation of translation, and localization of relevant mRNAs through direct interaction with their 3'UTRs, and provide structural insights into a novel protein-RNA interaction motif involving a hydrolase-related domain.
ESTHER : Yang_2015_Proc.Natl.Acad.Sci.U.S.A_112_11541
PubMedSearch : Yang_2015_Proc.Natl.Acad.Sci.U.S.A_112_11541
PubMedID: 26324911

Title : Direct action and modulating effect of (+)- and (-)-nicotine on ion channels expressed in trigeminal sensory neurons - Schreiner_2014_Eur.J.Pharmacol_728_48
Author(s) : Schreiner BS , Lehmann R , Thiel U , Ziemba PM , Beltran LR , Sherkheli MA , Jeanbourquin P , Hugi A , Werner M , Gisselmann G , Hatt H
Ref : European Journal of Pharmacology , 728 :48 , 2014
Abstract : Nicotine sensory perception is generally thought to be mediated by nicotinic acetylcholine (nACh) receptors. However, recent data strongly support the idea that other receptors (e.g., transient receptor potential A1 channel, TRPA1) and other pathways contribute to the detection mechanisms underlying the olfactory and trigeminal cell response to nicotine flavor. This is in accordance with the reported ability of humans to discriminate between (+)- and (-)- nicotine enantiomers. To get a more detailed understanding of the molecular and cellular basis underlying the sensory perception of nicotine, we studied the activity of (+)- and (-)-nicotine on cultured murine trigeminal sensory neurons and on a range of heterologously expressed receptors. The human TRPA1 channel is activated by (-)-nicotine. In this work, we show that (+)-nicotine is also an activator of this channel. Pharmacological experiments using nicotinic acetylcholine receptors and transient receptor potential blockers revealed that trigeminal neurons express one or more unidentified receptors that are sensitive to (+)- and/or (-)-nicotine. Results also indicate that the presence of extracellular calcium ions is required to elicit trigeminal neuron responses to (+)- and (-)-nicotine. Results also show that both (+)-nicotine and (-)-nicotine can block 5-hydroxytryptamine type 3 (5-HT3) receptor-mediated responses in recombinant expression systems and in cultured trigeminal neurons expressing 5-HT3 receptors. Our investigations broaden the spectra of receptors that are targets for nicotine enantiomers and give new insights into the physiological role of nicotine.
ESTHER : Schreiner_2014_Eur.J.Pharmacol_728_48
PubMedSearch : Schreiner_2014_Eur.J.Pharmacol_728_48
PubMedID: 24512725

Title : Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics - Gardebrecht_2012_ISME.J_6_766
Author(s) : Gardebrecht A , Markert S , Sievert SM , Felbeck H , Thurmer A , Albrecht D , Wollherr A , Kabisch J , Le Bris N , Lehmann R , Daniel R , Liesegang H , Hecker M , Schweder T
Ref : Isme J , 6 :766 , 2012
Abstract : The two closely related deep-sea tubeworms Riftia pachyptila and Tevnia jerichonana both rely exclusively on a single species of sulfide-oxidizing endosymbiotic bacteria for their nutrition. They do, however, thrive in markedly different geochemical conditions. A detailed proteogenomic comparison of the endosymbionts coupled with an in situ characterization of the geochemical environment was performed to investigate their roles and expression profiles in the two respective hosts. The metagenomes indicated that the endosymbionts are genotypically highly homogeneous. Gene sequences coding for enzymes of selected key metabolic functions were found to be 99.9% identical. On the proteomic level, the symbionts showed very consistent metabolic profiles, despite distinctly different geochemical conditions at the plume level of the respective hosts. Only a few minor variations were observed in the expression of symbiont enzymes involved in sulfur metabolism, carbon fixation and in the response to oxidative stress. Although these changes correspond to the prevailing environmental situation experienced by each host, our data strongly suggest that the two tubeworm species are able to effectively attenuate differences in habitat conditions, and thus to provide their symbionts with similar micro-environments.
ESTHER : Gardebrecht_2012_ISME.J_6_766
PubMedSearch : Gardebrecht_2012_ISME.J_6_766
PubMedID: 22011719
Gene_locus related to this paper: 9gamm-g2d8y1

Title : Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis - Kalhoefer_2011_BMC.Genomics_12_324
Author(s) : Kalhoefer D , Thole S , Voget S , Lehmann R , Liesegang H , Wollher A , Daniel R , Simon M , Brinkhoff T
Ref : BMC Genomics , 12 :324 , 2011
Abstract : BACKGROUND: Roseobacter litoralis OCh149, the type species of the genus, and Roseobacter denitrificans OCh114 were the first described organisms of the Roseobacter clade, an ecologically important group of marine bacteria. Both species were isolated from seaweed and are able to perform aerobic anoxygenic photosynthesis.
RESULTS: The genome of R. litoralis OCh149 contains one circular chromosome of 4,505,211 bp and three plasmids of 93,578 bp (pRLO149_94), 83,129 bp (pRLO149_83) and 63,532 bp (pRLO149_63). Of the 4537 genes predicted for R. litoralis, 1122 (24.7%) are not present in the genome of R. denitrificans. Many of the unique genes of R. litoralis are located in genomic islands and on plasmids. On pRLO149_83 several potential heavy metal resistance genes are encoded which are not present in the genome of R. denitrificans. The comparison of the heavy metal tolerance of the two organisms showed an increased zinc tolerance of R. litoralis. In contrast to R. denitrificans, the photosynthesis genes of R. litoralis are plasmid encoded. The activity of the photosynthetic apparatus was confirmed by respiration rate measurements, indicating a growth-phase dependent response to light. Comparative genomics with other members of the Roseobacter clade revealed several genomic regions that were only conserved in the two Roseobacter species. One of those regions encodes a variety of genes that might play a role in host association of the organisms. The catabolism of different carbon and nitrogen sources was predicted from the genome and combined with experimental data. In several cases, e.g. the degradation of some algal osmolytes and sugars, the genome-derived predictions of the metabolic pathways in R. litoralis differed from the phenotype.
CONCLUSIONS: The genomic differences between the two Roseobacter species are mainly due to lateral gene transfer and genomic rearrangements. Plasmid pRLO149_83 contains predominantly recently acquired genetic material whereas pRLO149_94 was probably translocated from the chromosome. Plasmid pRLO149_63 and one plasmid of R. denitrifcans (pTB2) seem to have a common ancestor and are important for cell envelope biosynthesis. Several new mechanisms of substrate degradation were indicated from the combination of experimental and genomic data. The photosynthetic activity of R. litoralis is probably regulated by nutrient availability.
ESTHER : Kalhoefer_2011_BMC.Genomics_12_324
PubMedSearch : Kalhoefer_2011_BMC.Genomics_12_324
PubMedID: 21693016
Gene_locus related to this paper: rosdo-q161f4 , roslo-f7zm11 , roslo-f7zjk8

Title : Genome sequence of the polysaccharide-degrading, thermophilic anaerobe Spirochaeta thermophila DSM 6192 - Angelov_2010_J.Bacteriol_192_6492
Author(s) : Angelov A , Liebl S , Ballschmiter M , Bomeke M , Lehmann R , Liesegang H , Daniel R , Liebl W
Ref : Journal of Bacteriology , 192 :6492 , 2010
Abstract : Spirochaeta thermophila is a thermophilic, free-living anaerobe that is able to degrade various alpha- and beta-linked sugar polymers, including cellulose. We report here the complete genome sequence of S. thermophila DSM 6192, which is the first genome sequence of a thermophilic, free-living member of the Spirochaetes phylum. The genome data reveal a high density of genes encoding enzymes from more than 30 glycoside hydrolase families, a noncellulosomal enzyme system for (hemi)cellulose degradation, and indicate the presence of a novel carbohydrate-binding module.
ESTHER : Angelov_2010_J.Bacteriol_192_6492
PubMedSearch : Angelov_2010_J.Bacteriol_192_6492
PubMedID: 20935097
Gene_locus related to this paper: spitd-e0rq60 , spitd-e0rrc2 , spitd-e0rsy8

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 : 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

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