Kube M

References (23)

Title : Analysis of the complete genomes of Acholeplasma brassicae, A. palmae and A. laidlawii and their comparison to the obligate parasites from 'Candidatus Phytoplasma' - Kube_2014_J.Mol.Microbiol.Biotechnol_24_19
Author(s) : Kube M , Siewert C , Migdoll AM , Duduk B , Holz S , Rabus R , Seemuller E , Mitrovic J , Muller I , Buttner C , Reinhardt R
Ref : J Molecular Microbiology Biotechnol , 24 :19 , 2014
Abstract : Analysis of the completely determined genomes of the plant-derived Acholeplasma brassicae strain O502 and A. palmae strain J233 revealed that the circular chromosomes are 1,877,792 and 1,554,229 bp in size, have a G + C content of 36 and 29%, and encode 1,690 and 1,439 proteins, respectively. Comparative analysis of these sequences and previously published genomes of A. laidlawii strain PG-8, 'Candidatus Phytoplasma asteris' strains, 'Ca. P. australiense' and 'Ca. P. mali' show a limited shared basic genetic repertoire. The acholeplasma genomes are characterized by a low number of rearrangements, duplication and integration events. Exceptions are the unusual duplication of rRNA operons in A. brassicae and an independently introduced second gene for a single-stranded binding protein in both genera. In contrast to phytoplasmas, the acholeplasma genomes differ by encoding the cell division protein FtsZ, a wide variety of ABC transporters, the F0F1 ATP synthase, the Rnf-complex, SecG of the Sec-dependent secretion system, a richly equipped repertoire for carbohydrate metabolism, fatty acid, isoprenoid and partial amino acid metabolism. Conserved metabolic proteins encoded in phytoplasma genomes such as the malate dehydrogenase SfcA, several transporters and proteins involved in host-interaction, and virulence-associated effectors were not predicted for the acholeplasmas.
ESTHER : Kube_2014_J.Mol.Microbiol.Biotechnol_24_19
PubMedSearch : Kube_2014_J.Mol.Microbiol.Biotechnol_24_19
PubMedID: 24158107
Gene_locus related to this paper: 9molu-u4krv5

Title : Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica - Kube_2013_Nat.Commun_4_2156
Author(s) : Kube M , Chernikova TN , Al-Ramahi Y , Beloqui A , Lopez-Cortez N , Guazzaroni ME , Heipieper HJ , Klages S , Kotsyurbenko OR , Langer I , Nechitaylo TY , Lunsdorf H , Fernandez M , Juarez S , Ciordia S , Singer A , Kagan O , Egorova O , Petit PA , Stogios P , Kim Y , Tchigvintsev A , Flick R , Denaro R , Genovese M , Albar JP , Reva ON , Martinez-Gomariz M , Tran H , Ferrer M , Savchenko A , Yakunin AF , Yakimov MM , Golyshina OV , Reinhardt R , Golyshin PN
Ref : Nat Commun , 4 :2156 , 2013
Abstract : Ubiquitous bacteria from the genus Oleispira drive oil degradation in the largest environment on Earth, the cold and deep sea. Here we report the genome sequence of Oleispira antarctica and show that compared with Alcanivorax borkumensis--the paradigm of mesophilic hydrocarbonoclastic bacteria--O. antarctica has a larger genome that has witnessed massive gene-transfer events. We identify an array of alkane monooxygenases, osmoprotectants, siderophores and micronutrient-scavenging pathways. We also show that at low temperatures, the main protein-folding machine Cpn60 functions as a single heptameric barrel that uses larger proteins as substrates compared with the classical double-barrel structure observed at higher temperatures. With 11 protein crystal structures, we further report the largest set of structures from one psychrotolerant organism. The most common structural feature is an increased content of surface-exposed negatively charged residues compared to their mesophilic counterparts. Our findings are relevant in the context of microbial cold-adaptation mechanisms and the development of strategies for oil-spill mitigation in cold environments.
ESTHER : Kube_2013_Nat.Commun_4_2156
PubMedSearch : Kube_2013_Nat.Commun_4_2156
PubMedID: 23877221
Gene_locus related to this paper: olean-olei00960 , olean-r4ym14 , olean-r4yv64 , olean-r4ys13

Title : Complete genome, catabolic sub-proteomes and key-metabolites of Desulfobacula toluolica Tol2, a marine, aromatic compound-degrading, sulfate-reducing bacterium - Wohlbrand_2013_Environ.Microbiol_15_1334
Author(s) : Wohlbrand L , Jacob JH , Kube M , Mussmann M , Jarling R , Beck A , Amann R , Wilkes H , Reinhardt R , Rabus R
Ref : Environ Microbiol , 15 :1334 , 2013
Abstract : Among the dominant deltaproteobacterial sulfate-reducing bacteria (SRB), members of the genus Desulfobacula are not only present in (hydrocarbon-rich) marine sediments, but occur also frequently in the anoxic water bodies encountered in marine upwelling areas. Here, we present the 5.2 Mbp genome of Desulfobacula toluolica Tol2, which is the first of an aromatic compound-degrading, marine SRB. The genome has apparently been shaped by viral attacks (e.g. CRISPRs) and its high plasticity is reflected by 163 detected genes related to transposases and integrases, a total of 494 paralogous genes and 24 group II introns. Prediction of the catabolic network of strain Tol2 was refined by differential proteome and metabolite analysis of substrate-adapted cells. Toluene and p-cresol are degraded by separate suites of specific enzymes for initial arylsuccinate formation via addition to fumarate (p-cresol-specific enzyme HbsA represents a new phylogenetic branch) as well as for subsequent modified beta-oxidation of arylsuccinates to the central intermediate benzoyl-CoA. Proteogenomic evidence suggests specific electron transfer (EtfAB) and membrane proteins to channel electrons from dehydrogenation of both arylsuccinates directly to the membrane redox pool. In contrast to the known anaerobic degradation pathways in other bacteria, strain Tol2 deaminates phenylalanine non-oxidatively to cinnamate by phenylalanine ammonia-lyase and subsequently forms phenylacetate (both metabolites identified in (13) C-labelling experiments). Benzoate degradation involves CoA activation, reductive dearomatization by a class II benzoyl-CoA reductase and hydrolytic ring cleavage as found in the obligate anaerobe Geobacter metallireducens GS-15. The catabolic sub-proteomes displayed high substrate specificity, reflecting the genomically predicted complex and fine-tuned regulatory network of strain Tol2. Despite the genetic equipment for a TCA cycle, proteomic evidence supports complete oxidation of acetyl-CoA to CO2 via the Wood-Ljungdahl pathway. Strain Tol2 possesses transmembrane redox complexes similar to that of other Desulfobacteraceae members. The multiple heterodisulfide reductase-like proteins (more than described for Desulfobacterium autotrophicum HRM2) may constitute a multifaceted cytoplasmic electron transfer network.
ESTHER : Wohlbrand_2013_Environ.Microbiol_15_1334
PubMedSearch : Wohlbrand_2013_Environ.Microbiol_15_1334
PubMedID: 23088741
Gene_locus related to this paper: destt-k0nmq2

Title : Complete genome sequence of Methylocystis sp. strain SC2, an aerobic methanotroph with high-affinity methane oxidation potential - Dam_2012_J.Bacteriol_194_6008
Author(s) : Dam B , Dam S , Kube M , Reinhardt R , Liesack W
Ref : Journal of Bacteriology , 194 :6008 , 2012
Abstract : Methylocystis sp. strain SC2 is an aerobic type II methanotroph isolated from a highly polluted aquifer in Germany. A specific trait of the SC2 strain is the expression of two isozymes of particulate methane monooxygenase with different methane oxidation kinetics. Here we report the complete genome sequence of this methanotroph that contains not only a circular chromosome but also two large plasmids.
ESTHER : Dam_2012_J.Bacteriol_194_6008
PubMedSearch : Dam_2012_J.Bacteriol_194_6008
PubMedID: 23045511

Title : Structure and activity of the cold-active and anion-activated carboxyl esterase OLEI01171 from the oil-degrading marine bacterium Oleispira antarctica - Lemak_2012_Biochem.J_445_193
Author(s) : Lemak S , Tchigvintsev A , Petit P , Flick R , Singer AU , Brown G , Evdokimova E , Egorova O , Gonzalez CF , Chernikova TN , Yakimov MM , Kube M , Reinhardt R , Golyshin PN , Savchenko A , Yakunin AF
Ref : Biochemical Journal , 445 :193 , 2012
Abstract : The uncharacterized alpha/beta-hydrolase protein OLEI01171 from the psychrophilic marine bacterium Oleispira antarctica belongs to the PF00756 family of putative esterases, which also includes human esterase D. In the present paper we show that purified recombinant OLEI01171 exhibits high esterase activity against the model esterase substrate alpha-naphthyl acetate at 5-30 degrees C with maximal activity at 15-20 degrees C. The esterase activity of OLEI01171 was stimulated 3-8-fold by the addition of chloride or several other anions (0.1-1.0 M). Compared with mesophilic PF00756 esterases, OLEI01171 exhibited a lower overall protein thermostability. Two crystal structures of OLEI01171 were solved at 1.75 and 2.1 A resolution and revealed a classical serine hydrolase catalytic triad and the presence of a chloride or bromide ion bound in the active site close to the catalytic Ser148. Both anions were found to co-ordinate a potential catalytic water molecule located in the vicinity of the catalytic triad His257. The results of the present study suggest that the bound anion perhaps contributes to the polarization of the catalytic water molecule and increases the rate of the hydrolysis of an acyl-enzyme intermediate. Alanine replacement mutagenesis of OLEI01171 identified ten amino acid residues important for esterase activity. The replacement of Asn225 by lysine had no significant effect on the activity or thermostability of OLEI01171, but resulted in a detectable increase of activity at 35-45 degrees C. The present study has provided insight into the molecular mechanisms of activity of a cold-active and anion-activated carboxyl esterase.
ESTHER : Lemak_2012_Biochem.J_445_193
PubMedSearch : Lemak_2012_Biochem.J_445_193
PubMedID: 22519667
Gene_locus related to this paper: olean-d0vwz4

Title : Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation - Zedelius_2011_Environ.Microbiol.Rep_3_125
Author(s) : Zedelius J , Rabus R , Grundmann O , Werner I , Brodkorb D , Schreiber F , Ehrenreich P , Behrends A , Wilkes H , Kube M , Reinhardt R , Widdel F
Ref : Environ Microbiol Rep , 3 :125 , 2011
Abstract : Microorganisms can degrade saturated hydrocarbons (alkanes) not only under oxic but also under anoxic conditions. Three denitrifying isolates (strains HxN1, OcN1, HdN1) able to grow under anoxic conditions by coupling alkane oxidation to CO(2) with NO(3) (-) reduction to N(2) were compared with respect to their alkane metabolism. Strains HxN1 and OcN1, which are both Betaproteobacteria, utilized n-alkanes from C(6) to C(8) and C(8) to C(12) respectively. Both activate alkanes anaerobically in a fumarate-dependent reaction yielding alkylsuccinates, as suggested by present and previous metabolite and gene analyses. However, strain HdN1 was unique in several respects. It belongs to the Gammaproteobacteria and was more versatile towards alkanes, utilizing the range from C(6) to C(30). Neither analysis of metabolites nor analysis of genes in the complete genome sequence of strain HdN1 hinted at fumarate-dependent alkane activation. Moreover, whereas strains HxN1 and OcN1 grew with alkanes and NO(3) (-), NO(2) (-) or N(2)O added to the medium, strain HdN1 oxidized alkanes only with NO(3) (-) or NO(2) (-) but not with added N(2)O; but N(2)O was readily used for growth with long-chain alcohols or fatty acids. Results suggest that NO(2) (-) or a subsequently formed nitrogen compound other than N(2)O is needed for alkane activation in strain HdN1. From an energetic point of view, nitrogen-oxygen species are generally rather strong oxidants. They may enable enzymatic mechanisms that are not possible under conditions of sulfate reduction or methanogenesis and thus allow a special mode of alkane activation.
ESTHER : Zedelius_2011_Environ.Microbiol.Rep_3_125
PubMedSearch : Zedelius_2011_Environ.Microbiol.Rep_3_125
PubMedID: 21837252
Gene_locus related to this paper: 9gamm-e1vi37 , 9gamm-e1vjh4 , 9gamm-e1vli3 , 9gamm-e1vqy3 , 9gamm-e1vnt0 , 9gamm-e1vj65 , 9gamm-e1vpf8

Title : Comparative genomic analysis of fruiting body formation in Myxococcales - Huntley_2011_Mol.Biol.Evol_28_1083
Author(s) : Huntley S , Hamann N , Wegener-Feldbrugge S , Treuner-Lange A , Kube M , Reinhardt R , Klages S , Muller R , Ronning CM , Nierman WC , Sogaard-Andersen L
Ref : Molecular Biology Evolution , 28 :1083 , 2011
Abstract : Genetic programs underlying multicellular morphogenesis and cellular differentiation are most often associated with eukaryotic organisms, but examples also exist in bacteria such as the formation of multicellular, spore-filled fruiting bodies in the order Myxococcales. Most members of the Myxococcales undergo a multicellular developmental program culminating in the formation of spore-filled fruiting bodies in response to starvation. To gain insight into the evolutionary history of fruiting body formation in Myxococcales, we performed a comparative analysis of the genomes and transcriptomes of five Myxococcales species, four of these undergo fruiting body formation (Myxococcus xanthus, Stigmatella aurantiaca, Sorangium cellulosum, and Haliangium ochraceum) and one does not (Anaeromyxobacter dehalogenans). Our analyses show that a set of 95 known M. xanthus development-specific genes--although suffering from a sampling bias--are overrepresented and occur more frequently than an average M. xanthus gene in S. aurantiaca, whereas they occur at the same frequency as an average M. xanthus gene in S. cellulosum and in H. ochraceum and are underrepresented in A. dehalogenans. Moreover, genes for entire signal transduction pathways important for fruiting body formation in M. xanthus are conserved in S. aurantiaca, whereas only a minority of these genes are conserved in A. dehalogenans, S. cellulosum, and H. ochraceum. Likewise, global gene expression profiling of developmentally regulated genes showed that genes that upregulated during development in M. xanthus are overrepresented in S. aurantiaca and slightly underrepresented in A. dehalogenans, S. cellulosum, and H. ochraceum. These comparative analyses strongly indicate that the genetic programs for fruiting body formation in M. xanthus and S. aurantiaca are highly similar and significantly different from the genetic program directing fruiting body formation in S. cellulosum and H. ochraceum. Thus, our analyses reveal an unexpected level of plasticity in the genetic programs for fruiting body formation in the Myxococcales and strongly suggest that the genetic program underlying fruiting body formation in different Myxococcales is not conserved. The evolutionary implications of this finding are discussed.
ESTHER : Huntley_2011_Mol.Biol.Evol_28_1083
PubMedSearch : Huntley_2011_Mol.Biol.Evol_28_1083
PubMedID: 21037205
Gene_locus related to this paper: stiad-q08nm4 , stiad-q08xf5 , stiad-q08va0 , stiad-e3fgi9

Title : Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula - Jones_2011_Proc.Natl.Acad.Sci.U.S.A_108_8815
Author(s) : Jones AC , Monroe EA , Podell S , Hess WR , Klages S , Esquenazi E , Niessen S , Hoover H , Rothmann M , Lasken RS , Yates JR, 3rd , Reinhardt R , Kube M , Burkart MD , Allen EE , Dorrestein PC , Gerwick WH , Gerwick L
Ref : Proc Natl Acad Sci U S A , 108 :8815 , 2011
Abstract : Filamentous cyanobacteria of the genus Lyngbya are important contributors to coral reef ecosystems, occasionally forming dominant cover and impacting the health of many other co-occurring organisms. Moreover, they are extraordinarily rich sources of bioactive secondary metabolites, with 35% of all reported cyanobacterial natural products deriving from this single pantropical genus. However, the true natural product potential and life strategies of Lyngbya strains are poorly understood because of phylogenetic ambiguity, lack of genomic information, and their close associations with heterotrophic bacteria and other cyanobacteria. To gauge the natural product potential of Lyngbya and gain insights into potential microbial interactions, we sequenced the genome of Lyngbya majuscula 3L, a Caribbean strain that produces the tubulin polymerization inhibitor curacin A and the molluscicide barbamide, using a combination of Sanger and 454 sequencing approaches. Whereas approximately 293,000 nucleotides of the draft genome are putatively dedicated to secondary metabolism, this is far too few to encode a large suite of Lyngbya metabolites, suggesting Lyngbya metabolites are strain specific and may be useful in species delineation. Our analysis revealed a complex gene regulatory network, including a large number of sigma factors and other regulatory proteins, indicating an enhanced ability for environmental adaptation or microbial associations. Although Lyngbya species are reported to fix nitrogen, nitrogenase genes were not found in the genome or by PCR of genomic DNA. Subsequent growth experiments confirmed that L. majuscula 3L is unable to fix atmospheric nitrogen. These unanticipated life history characteristics challenge current views of the genus Lyngbya.
ESTHER : Jones_2011_Proc.Natl.Acad.Sci.U.S.A_108_8815
PubMedSearch : Jones_2011_Proc.Natl.Acad.Sci.U.S.A_108_8815
PubMedID: 21555588
Gene_locus related to this paper: 9cyan-f4xvi1 , 9cyan-f4xkf8 , 9cyan-f4y3s0

Title : Genome comparison of the epiphytic bacteria Erwinia billingiae and E. tasmaniensis with the pear pathogen E. pyrifoliae - Kube_2010_BMC.Genomics_11_393
Author(s) : Kube M , Migdoll AM , Gehring I , Heitmann K , Mayer Y , Kuhl H , Knaust F , Geider K , Reinhardt R
Ref : BMC Genomics , 11 :393 , 2010
Abstract : BACKGROUND: The genus Erwinia includes plant-associated pathogenic and non-pathogenic Enterobacteria. Important pathogens such as Erwinia amylovora, the causative agent of fire blight and E. pyrifoliae causing bacterial shoot blight of pear in Asia belong to this genus. The species E. tasmaniensis and E. billingiae are epiphytic bacteria and may represent antagonists for biocontrol of fire blight. The presence of genes that are putatively involved in virulence in E. amylovora and E. pyrifoliae is of special interest for these species in consequence.
RESULTS: Here we provide the complete genome sequences of the pathogenic E. pyrifoliae strain Ep1/96 with a size of 4.1 Mb and of the non-pathogenic species E. billingiae strain Eb661 with a size of 5.4 Mb, de novo determined by conventional Sanger sequencing and next generation sequencing techniques. Genome comparison reveals large inversions resulting from homologous recombination events. Furthermore, comparison of deduced proteins highlights a relation of E. billingiae strain Eb661 to E. tasmaniensis strain Et1/99 and a distance to E. pyrifoliae for the overall gene content as well as for the presence of encoded proteins representing virulence factors for the pathogenic species. Pathogenicity of E. pyrifoliae is supposed to have evolved by accumulation of potential virulence factors. E. pyrifoliae carries factors for type III secretion and cell invasion. Other genes described as virulence factors for E. amylovora are involved in the production of exopolysaccharides, the utilization of plant metabolites such as sorbitol and sucrose. Some virulence-associated genes of the pathogenic species are present in E. tasmaniensis but mostly absent in E. billingiae. CONCLUSION: The data of the genome analyses correspond to the pathogenic lifestyle of E. pyrifoliae and underlines the epiphytic localization of E. tasmaniensis and E. billingiae as a saprophyte.
ESTHER : Kube_2010_BMC.Genomics_11_393
PubMedSearch : Kube_2010_BMC.Genomics_11_393
PubMedID: 20565991
Gene_locus related to this paper: 9entr-d8mru2 , erwac-d4i3s4 , erwbe-d8mnk7 , erwbe-d8mus5 , erwp6-d2tb51 , erwpe-d0fv08 , erwpe-d0fwy1 , erwpe-d0fx20 , erwpy-d0fr69 , erwbe-d8mx29 , erwse-e3dex4 , erwbe-d8mqu3 , erwbe-d8mxb0 , erwbe-d8mmb0

Title : Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group - Meyerdierks_2010_Environ.Microbiol_12_422
Author(s) : Meyerdierks A , Kube M , Kostadinov I , Teeling H , Glockner FO , Reinhardt R , Amann R
Ref : Environ Microbiol , 12 :422 , 2010
Abstract : Microbial consortia mediating the anaerobic oxidation of methane with sulfate are composed of methanotrophic Archaea (ANME) and Bacteria related to sulfate-reducing Deltaproteobacteria. Cultured representatives are not available for any of the three ANME clades. Therefore, a metagenomic approach was applied to assess the genetic potential of ANME-1 archaea. In total, 3.4 Mbp sequence information was generated based on metagenomic fosmid libraries constructed directly from a methanotrophic microbial mat in the Black Sea. These sequence data represent, in 30 contigs, about 82-90% of a composite ANME-1 genome. The dataset supports the hypothesis of a reversal of the methanogenesis pathway. Indications for an assimilatory, but not for a dissimilatory sulfate reduction pathway in ANME-1, were found. Draft genome and expression analyses are consistent with acetate and formate as putative electron shuttles. Moreover, the dataset points towards downstream electron-accepting redox components different from the ones known from methanogenic archaea. Whereas catalytic subunits of [NiFe]-hydrogenases are lacking in the dataset, genes for an [FeFe]-hydrogenase homologue were identified, not yet described to be present in methanogenic archaea. Clustered genes annotated as secreted multiheme c-type cytochromes were identified, which have not yet been correlated with methanogenesis-related steps. The genes were shown to be expressed, suggesting direct electron transfer as an additional possible mode to shuttle electrons from ANME-1 to the bacterial sulfate-reducing partner.
ESTHER : Meyerdierks_2010_Environ.Microbiol_12_422
PubMedSearch : Meyerdierks_2010_Environ.Microbiol_12_422
PubMedID: 19878267
Gene_locus related to this paper: 9arch-d1j9b3 , 9arch-d1ja37 , 9arch-d1jaz1 , 9arch-q64ad0

Title : The genome of Erwinia tasmaniensis strain Et1\/99, a non-pathogenic bacterium in the genus Erwinia - Kube_2008_Environ.Microbiol_10_2211
Author(s) : Kube M , Migdoll AM , Muller I , Kuhl H , Beck A , Reinhardt R , Geider K
Ref : Environ Microbiol , 10 :2211 , 2008
Abstract : The complete genome of the bacterium Erwinia tasmaniensis strain Et1/99 consisting of a 3.9 Mb circular chromosome and five plasmids was sequenced. Strain Et1/99 represents an epiphytic plant bacterium related to Erwinia amylovora and E. pyrifoliae, which are responsible for the important plant diseases fire blight and Asian pear shoot blight, respectively. Strain Et1/99 is a non-pathogenic bacterium and is thought to compete with these and other bacteria when occupying the same habitat during initial colonization. Genome analysis revealed tools for colonization, cellular communication and defence modulation, as well as genes coding for the synthesis of levan and a not detected capsular exopolysaccharide. Strain Et1/99 may secrete indole-3-acetic acid to increase availability of nutrients provided on plant surfaces. These nutrients are subsequently accessed and metabolized. Secretion systems include the hypersensitive response type III pathway present in many pathogens. Differences or missing parts within the virulence-related factors distinguish strain Et1/99 from pathogens such as Pectobacterium atrosepticum and the related Erwinia spp. Strain Et1/99 completely lacks the sorbitol operon, which may also affect its inability to invade fire blight host plants. Erwinia amylovora in contrast depends for virulence on utilization of sorbitol, the dominant carbohydrate in rosaceous plants. The presence of other virulence-associated factors in strain Et1/99 indicates the ancestral genomic background of many plant-associated bacteria.
ESTHER : Kube_2008_Environ.Microbiol_10_2211
PubMedSearch : Kube_2008_Environ.Microbiol_10_2211
PubMedID: 18462403
Gene_locus related to this paper: erwt9-b2vih8 , erwt9-b2vjv8 , erwt9-b2vkk6 , erwt9-y2597 , erwt9-b2vgh9

Title : Genome analysis of the platypus reveals unique signatures of evolution - Warren_2008_Nature_453_175
Author(s) : Warren WC , Hillier LW , Marshall Graves JA , Birney E , Ponting CP , Grutzner F , Belov K , Miller W , Clarke L , Chinwalla AT , Yang SP , Heger A , Locke DP , Miethke P , Waters PD , Veyrunes F , Fulton L , Fulton B , Graves T , Wallis J , Puente XS , Lopez-Otin C , Ordonez GR , Eichler EE , Chen L , Cheng Z , Deakin JE , Alsop A , Thompson K , Kirby P , Papenfuss AT , Wakefield MJ , Olender T , Lancet D , Huttley GA , Smit AF , Pask A , Temple-Smith P , Batzer MA , Walker JA , Konkel MK , Harris RS , Whittington CM , Wong ES , Gemmell NJ , Buschiazzo E , Vargas Jentzsch IM , Merkel A , Schmitz J , Zemann A , Churakov G , Kriegs JO , Brosius J , Murchison EP , Sachidanandam R , Smith C , Hannon GJ , Tsend-Ayush E , McMillan D , Attenborough R , Rens W , Ferguson-Smith M , Lefevre CM , Sharp JA , Nicholas KR , Ray DA , Kube M , Reinhardt R , Pringle TH , Taylor J , Jones RC , Nixon B , Dacheux JL , Niwa H , Sekita Y , Huang X , Stark A , Kheradpour P , Kellis M , Flicek P , Chen Y , Webber C , Hardison R , Nelson J , Hallsworth-Pepin K , Delehaunty K , Markovic C , Minx P , Feng Y , Kremitzki C , Mitreva M , Glasscock J , Wylie T , Wohldmann P , Thiru P , Nhan MN , Pohl CS , Smith SM , Hou S , Nefedov M , de Jong PJ , Renfree MB , Mardis ER , Wilson RK
Ref : Nature , 453 :175 , 2008
Abstract : We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
ESTHER : Warren_2008_Nature_453_175
PubMedSearch : Warren_2008_Nature_453_175
PubMedID: 18464734
Gene_locus related to this paper: ornan-f6s0q0 , ornan-f6ty74 , ornan-f6u2k2 , ornan-f6uve1 , ornan-f6vpb6 , ornan-f6ybp3 , ornan-f7bgu8 , ornan-f7ct41 , ornan-f7cza1 , ornan-f7ejp8 , ornan-f7exu1 , ornan-f7f392 , ornan-f7f9y6 , ornan-f6ve87 , ornan-f7f1d9 , ornan-f6z3l1 , ornan-f6r3f9 , ornan-f6r3g8 , ornan-f6vs71 , ornan-f7g4v8

Title : The linear chromosome of the plant-pathogenic mycoplasma 'Candidatus Phytoplasma mali' - Kube_2008_BMC.Genomics_9_306
Author(s) : Kube M , Schneider B , Kuhl H , Dandekar T , Heitmann K , Migdoll AM , Reinhardt R , Seemuller E
Ref : BMC Genomics , 9 :306 , 2008
Abstract : BACKGROUND: Phytoplasmas are insect-transmitted, uncultivable bacterial plant pathogens that cause diseases in hundreds of economically important plants. They represent a monophyletic group within the class Mollicutes (trivial name mycoplasmas) and are characterized by a small genome with a low GC content, and the lack of a firm cell wall. All mycoplasmas, including strains of 'Candidatus (Ca.) Phytoplasma asteris' and 'Ca. P. australiense', examined so far have circular chromosomes, as is the case for almost all walled bacteria. RESULTS: Our work has shown that 'Ca. Phytoplasma mali', the causative agent of apple proliferation disease, has a linear chromosome. Linear chromosomes were also identified in the closely related provisional species 'Ca. P. pyri' and 'Ca. P. prunorum'. The chromosome of 'Ca. P. mali' strain AT is 601,943 bp in size and has a GC content of 21.4%. The chromosome is further characterized by large terminal inverted repeats and covalently closed hairpin ends. Analysis of the protein-coding genes revealed that glycolysis, the major energy-yielding pathway supposed for 'Ca. P. asteris', is incomplete in 'Ca. P. mali'. Due to the apparent lack of other metabolic pathways present in mycoplasmas, it is proposed that maltose and malate are utilized as carbon and energy sources. However, complete ATP-yielding pathways were not identified. 'Ca. P. mali' also differs from 'Ca. P. asteris' by a smaller genome, a lower GC content, a lower number of paralogous genes, fewer insertions of potential mobile DNA elements, and a strongly reduced number of ABC transporters for amino acids. In contrast, 'Ca. P. mali' has an extended set of genes for homologous recombination, excision repair and SOS response than 'Ca. P. asteris'. CONCLUSION: The small linear chromosome with large terminal inverted repeats and covalently closed hairpin ends, the extremely low GC content and the limited metabolic capabilities reflect unique features of 'Ca. P. mali', not only within phytoplasmas, but all mycoplasmas. It is expected that the genome information obtained here will contribute to a better understanding of the reduced metabolism of phytoplasmas, their fastidious nutrition requirements that prevented axenic cultivation, and the mechanisms involved in pathogenicity.
ESTHER : Kube_2008_BMC.Genomics_9_306
PubMedSearch : Kube_2008_BMC.Genomics_9_306
PubMedID: 18582369
Gene_locus related to this paper: phymt-b3qzy9

Title : Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function - Richter_2007_J.Bacteriol_189_4899
Author(s) : Richter M , Kube M , Bazylinski DA , Lombardot T , Glockner FO , Reinhardt R , Schuler D
Ref : Journal of Bacteriology , 189 :4899 , 2007
Abstract : Magnetotactic bacteria (MTB) are a heterogeneous group of aquatic prokaryotes with a unique intracellular organelle, the magnetosome, which orients the cell along magnetic field lines. Magnetotaxis is a complex phenotype, which depends on the coordinate synthesis of magnetosomes and the ability to swim and orient along the direction caused by the interaction with the Earth's magnetic field. Although a number of putative magnetotaxis genes were recently identified within a conserved genomic magnetosome island (MAI) of several MTB, their functions have remained mostly unknown, and it was speculated that additional genes located outside the MAI might be involved in magnetosome formation and magnetotaxis. In order to identify genes specifically associated with the magnetotactic phenotype, we conducted comparisons between four sequenced magnetotactic Alphaproteobacteria including the nearly complete genome of Magnetospirillum gryphiswaldense strain MSR-1, the complete genome of Magnetospirillum magneticum strain AMB-1, the complete genome of the magnetic coccus MC-1, and the comparative-ready preliminary genome assembly of Magnetospirillum magnetotacticum strain MS-1 against an in-house database comprising 426 complete bacterial and archaeal genome sequences. A magnetobacterial core genome of about 891 genes was found shared by all four MTB. In addition to a set of approximately 152 genus-specific genes shared by the three Magnetospirillum strains, we identified 28 genes as group specific, i.e., which occur in all four analyzed MTB but exhibit no (MTB-specific genes) or only remote (MTB-related genes) similarity to any genes from nonmagnetotactic organisms and which besides various novel genes include nearly all mam and mms genes previously shown to control magnetosome formation. The MTB-specific and MTB-related genes to a large extent display synteny, partially encode previously unrecognized magnetosome membrane proteins, and are either located within (18 genes) or outside (10 genes) the MAI of M. gryphiswaldense. These genes, which represent less than 1% of the 4,268 open reading frames of the MSR-1 genome, as yet are mostly of unknown functions but are likely to be specifically involved in magnetotaxis and, thus, represent prime targets for future experimental analysis.
ESTHER : Richter_2007_J.Bacteriol_189_4899
PubMedSearch : Richter_2007_J.Bacteriol_189_4899
PubMedID: 17449609
Gene_locus related to this paper: 9prot-a4u2g1 , 9prot-a4u2n1 , 9prot-a4u4p5 , 9prot-a4u5l5 , 9prot-a4u049 , 9prot-a4u391

Title : The DNA sequence, annotation and analysis of human chromosome 3 - Muzny_2006_Nature_440_1194
Author(s) : Muzny DM , Scherer SE , Kaul R , Wang J , Yu J , Sudbrak R , Buhay CJ , Chen R , Cree A , Ding Y , Dugan-Rocha S , Gill R , Gunaratne P , Harris RA , Hawes AC , Hernandez J , Hodgson AV , Hume J , Jackson A , Khan ZM , Kovar-Smith C , Lewis LR , Lozado RJ , Metzker ML , Milosavljevic A , Miner GR , Morgan MB , Nazareth LV , Scott G , Sodergren E , Song XZ , Steffen D , Wei S , Wheeler DA , Wright MW , Worley KC , Yuan Y , Zhang Z , Adams CQ , Ansari-Lari MA , Ayele M , Brown MJ , Chen G , Chen Z , Clendenning J , Clerc-Blankenburg KP , Davis C , Delgado O , Dinh HH , Dong W , Draper H , Ernst S , Fu G , Gonzalez-Garay ML , Garcia DK , Gillett W , Gu J , Hao B , Haugen E , Havlak P , He X , Hennig S , Hu S , Huang W , Jackson LR , Jacob LS , Kelly SH , Kube M , Levy R , Li Z , Liu B , Liu J , Liu W , Lu J , Maheshwari M , Nguyen BV , Okwuonu GO , Palmeiri A , Pasternak S , Perez LM , Phelps KA , Plopper FJ , Qiang B , Raymond C , Rodriguez R , Saenphimmachak C , Santibanez J , Shen H , Shen Y , Subramanian S , Tabor PE , Verduzco D , Waldron L , Wang Q , Williams GA , Wong GK , Yao Z , Zhang J , Zhang X , Zhao G , Zhou J , Zhou Y , Nelson D , Lehrach H , Reinhardt R , Naylor SL , Yang H , Olson M , Weinstock G , Gibbs RA
Ref : Nature , 440 :1194 , 2006
Abstract : After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.
ESTHER : Muzny_2006_Nature_440_1194
PubMedSearch : Muzny_2006_Nature_440_1194
PubMedID: 16641997
Gene_locus related to this paper: human-AADAC , human-AADACL2 , human-ABHD5 , human-ABHD6 , human-ABHD10 , human-ABHD14A , human-APEH , human-BCHE , human-CIB , human-LIPH , human-MGLL , human-NLGN1 , human-PLA1A

Title : Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere - Erkel_2006_Science_313_370
Author(s) : Erkel C , Kube M , Reinhardt R , Liesack W
Ref : Science , 313 :370 , 2006
Abstract : Rice fields are a global source of the greenhouse gas methane, which is produced by methanogenic archaea, and by methanogens of Rice Cluster I (RC-I) in particular. RC-I methanogens are not yet available in pure culture, and the mechanistic reasons for their prevalence in rice fields are unknown. We reconstructed a complete RC-I genome (3.18 megabases) using a metagenomic approach. Sequence analysis demonstrated an aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for carbohydrate metabolism and assimilatory sulfate reduction, hitherto unknown among methanogens. These capacities and a unique set of antioxidant enzymes and DNA repair mechanisms as well as oxygen-insensitive enzymes provide RC-I with a selective advantage over other methanogens in its habitats, thereby explaining the prevalence of RC-I methanogens in the rice rhizosphere.
ESTHER : Erkel_2006_Science_313_370
PubMedSearch : Erkel_2006_Science_313_370
PubMedID: 16857943
Gene_locus related to this paper: uncma-q0w2a8 , uncma-q0w2n6 , uncma-q0w6n9 , uncma-q0w8i3 , uncma-q0w8x7 , uncma-q0w484 , uncma-q0w562

Title : Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter - Bauer_2006_Environ.Microbiol_8_2201
Author(s) : Bauer M , Kube M , Teeling H , Richter M , Lombardot T , Allers E , Wurdemann CA , Quast C , Kuhl H , Knaust F , Woebken D , Bischof K , Mussmann M , Choudhuri JV , Meyer F , Reinhardt R , Amann RI , Glockner FO
Ref : Environ Microbiol , 8 :2201 , 2006
Abstract : Members of the Bacteroidetes, formerly known as the Cytophaga-Flavobacteria-Bacteroides (CFB) phylum, are among the major taxa of marine heterotrophic bacterioplankton frequently found on macroscopic organic matter particles (marine snow). In addition, they have been shown to also represent a significant part of free-living microbial assemblages in nutrient-rich microenvironments. Their abundance and distribution pattern in combination with enzymatic activity studies has led to the notion that organisms of this group are specialists for degradation of high molecular weight compounds in both the dissolved and particulate fraction of the marine organic matter pool, implying a major role of Bacteroidetes in the marine carbon cycle. Despite their ecological importance, comprehensive molecular data on organisms of this group have been scarce so far. Here we report on the first whole genome analysis of a marine Bacteroidetes representative, 'Gramella forsetii' KT0803. Functional analysis of the predicted proteome disclosed several traits which in joint consideration suggest a clear adaptation of this marine Bacteroidetes representative to the degradation of high molecular weight organic matter, such as a substantial suite of genes encoding hydrolytic enzymes, a predicted preference for polymeric carbon sources and a distinct capability for surface adhesion.
ESTHER : Bauer_2006_Environ.Microbiol_8_2201
PubMedSearch : Bauer_2006_Environ.Microbiol_8_2201
PubMedID: 17107561
Gene_locus related to this paper: grafk-a0ly58 , grafk-a0lyb1 , grafk-a0lzl9 , grafk-a0lzn2 , grafk-a0m3f2 , grafk-a0m3h3 , grafk-a0m3u0 , grafk-a0m4n9 , grafk-a0m5m4 , grafk-a0m6x9 , grafk-a0m6z1 , grafk-a0m243 , grafk-a0m536 , grafk-a0m641 , grafk-a0m784 , grafk-a0m4i1

Title : The genome sequence of an anaerobic aromatic-degrading denitrifying bacterium, strain EbN1 - Rabus_2005_Arch.Microbiol_183_27
Author(s) : Rabus R , Kube M , Heider J , Beck A , Heitmann K , Widdel F , Reinhardt R
Ref : Arch Microbiol , 183 :27 , 2005
Abstract : Recent research on microbial degradation of aromatic and other refractory compounds in anoxic waters and soils has revealed that nitrate-reducing bacteria belonging to the Betaproteobacteria contribute substantially to this process. Here we present the first complete genome of a metabolically versatile representative, strain EbN1, which metabolizes various aromatic compounds, including hydrocarbons. A circular chromosome (4.3 Mb) and two plasmids (0.21 and 0.22 Mb) encode 4603 predicted proteins. Ten anaerobic and four aerobic aromatic degradation pathways were recognized, with the encoding genes mostly forming clusters. The presence of paralogous gene clusters (e.g., for anaerobic phenylacetate oxidation), high sequence similarities to orthologs from other strains (e.g., for anaerobic phenol metabolism) and frequent mobile genetic elements (e.g., more than 200 genes for transposases) suggest high genome plasticity and extensive lateral gene transfer during metabolic evolution of strain EbN1. Metabolic versatility is also reflected by the presence of multiple respiratory complexes. A large number of regulators, including more than 30 two-component and several FNR-type regulators, indicate a finely tuned regulatory network able to respond to the fluctuating availability of organic substrates and electron acceptors in the environment. The absence of genes required for nitrogen fixation and specific interaction with plants separates strain EbN1 ecophysiologically from the closely related nitrogen-fixing plant symbionts of the Azoarcus cluster. Supplementary material on sequence and annotation are provided at the Web page http://www.micro-genomes.mpg.de/ebn1/.
ESTHER : Rabus_2005_Arch.Microbiol_183_27
PubMedSearch : Rabus_2005_Arch.Microbiol_183_27
PubMedID: 15551059
Gene_locus related to this paper: aroae-metx , aroae-q5nz38 , aroae-q5nzf6 , aroae-q5nzt3 , aroae-q5nzz6 , aroae-q5p0p4 , aroae-q5p0w7 , aroae-q5p1d0 , aroae-q5p1l8 , aroae-q5p3d9 , aroae-q5p3m7 , aroae-q5p3t3 , aroae-q5p4k6 , aroae-q5p4m0 , aroae-q5p4u0 , aroae-q5p6k3 , aroae-q5p8f6 , aroae-q5p072 , aroae-q5p115 , aroae-q5p962 , aroae-q5p966 , aroae-q5p2a5 , aroae-q5p2a4

Title : The genome of the kinetoplastid parasite, Leishmania major - Ivens_2005_Science_309_436
Author(s) : Ivens AC , Peacock CS , Worthey EA , Murphy L , Aggarwal G , Berriman M , Sisk E , Rajandream MA , Adlem E , Aert R , Anupama A , Apostolou Z , Attipoe P , Bason N , Bauser C , Beck A , Beverley SM , Bianchettin G , Borzym K , Bothe G , Bruschi CV , Collins M , Cadag E , Ciarloni L , Clayton C , Coulson RM , Cronin A , Cruz AK , Davies RM , De Gaudenzi J , Dobson DE , Duesterhoeft A , Fazelina G , Fosker N , Frasch AC , Fraser A , Fuchs M , Gabel C , Goble A , Goffeau A , Harris D , Hertz-Fowler C , Hilbert H , Horn D , Huang Y , Klages S , Knights A , Kube M , Larke N , Litvin L , Lord A , Louie T , Marra M , Masuy D , Matthews K , Michaeli S , Mottram JC , Muller-Auer S , Munden H , Nelson S , Norbertczak H , Oliver K , O'Neil S , Pentony M , Pohl TM , Price C , Purnelle B , Quail MA , Rabbinowitsch E , Reinhardt R , Rieger M , Rinta J , Robben J , Robertson L , Ruiz JC , Rutter S , Saunders D , Schafer M , Schein J , Schwartz DC , Seeger K , Seyler A , Sharp S , Shin H , Sivam D , Squares R , Squares S , Tosato V , Vogt C , Volckaert G , Wambutt R , Warren T , Wedler H , Woodward J , Zhou S , Zimmermann W , Smith DF , Blackwell JM , Stuart KD , Barrell B , Myler PJ
Ref : Science , 309 :436 , 2005
Abstract : Leishmania species cause a spectrum of human diseases in tropical and subtropical regions of the world. We have sequenced the 36 chromosomes of the 32.8-megabase haploid genome of Leishmania major (Friedlin strain) and predict 911 RNA genes, 39 pseudogenes, and 8272 protein-coding genes, of which 36% can be ascribed a putative function. These include genes involved in host-pathogen interactions, such as proteolytic enzymes, and extensive machinery for synthesis of complex surface glycoconjugates. The organization of protein-coding genes into long, strand-specific, polycistronic clusters and lack of general transcription factors in the L. major, Trypanosoma brucei, and Trypanosoma cruzi (Tritryp) genomes suggest that the mechanisms regulating RNA polymerase II-directed transcription are distinct from those operating in other eukaryotes, although the trypanosomatids appear capable of chromatin remodeling. Abundant RNA-binding proteins are encoded in the Tritryp genomes, consistent with active posttranscriptional regulation of gene expression.
ESTHER : Ivens_2005_Science_309_436
PubMedSearch : Ivens_2005_Science_309_436
PubMedID: 16020728
Gene_locus related to this paper: leima-e9ady6 , leima-L2464.12 , leima-L2802.02 , leima-OPB , leima-q4fw33 , leima-q4fwg8 , leima-q4fwj0 , leima-q4fya7 , leima-q4q0a1 , leima-q4q0t5 , leima-q4q0v0 , leima-q4q1h9 , leima-q4q2c9 , leima-q4q4j7 , leima-q4q4t6 , leima-q4q5j1 , leima-q4q6e9 , leima-q4q7v8 , leima-q4q8a8 , leima-q4q9g9 , leima-q4q080 , leima-q4q398 , leima-q4q615 , leima-q4q819 , leima-q4q871 , leima-q4q942 , leima-q4qae7 , leima-q4qb85 , leima-q4qdz7 , leima-q4qe26 , leima-q4qe31 , leima-q4qe85 , leima-q4qe86 , leima-q4qe87 , leima-q4qe90 , leima-q4qec8 , leima-q4qgz4 , leima-q4qgz5 , leima-q4qhs0 , leima-q4qj45

Title : Insights into the genomes of archaea mediating the anaerobic oxidation of methane - Meyerdierks_2005_Environ.Microbiol_7_1937
Author(s) : Meyerdierks A , Kube M , Lombardot T , Knittel K , Bauer M , Glockner FO , Reinhardt R , Amann R
Ref : Environ Microbiol , 7 :1937 , 2005
Abstract : The anaerobic oxidation of methane is a globally significant process which is mediated by consortia of yet uncultivated methanotrophic archaea (ANME) and sulfate-reducing bacteria. In order to gain deeper insights into genome characteristics of the different ANME groups, large-insert genomic libraries were constructed using DNA extracted from a methanotrophic microbial mat growing in the anoxic part of the Black Sea, and from sediments above gas hydrates at the Hydrate Ridge off the coast of Oregon. Analysis of these fosmid libraries with respect to archaeal 16S rRNA gene diversity revealed a single ANME-1b ribotype for the Black Sea libraries, whereas the sequences derived from the Hydrate Ridge library phylogenetically affiliated with the ANME-2a, ANME-2c and ANME-3 group. Genome walking for ANME-1b resulted in a contiguous 155 kb composite genome fragment. The comparison of a set of four genomic fragments belonging to the different ANME groups revealed differences in the rRNA operon structure and the average G+C content, with the ANME-2c contig showing the highest divergence within the set. A detailed analysis of the ANME contigs with respect to genes putatively involved in the anaerobic oxidation of methane led to the identification of: (i) a putative N5,N10-methenyltetrahydromethanopterin cyclohydrolase gene, (ii) a gene cluster supposedly encoding a novel type of heterodisulfide reductase/dehydrogenase complex and (iii) a gene cluster putatively encoding a new type of CO dehydrogenase/acetyl-CoA synthase enzyme complex.
ESTHER : Meyerdierks_2005_Environ.Microbiol_7_1937
PubMedSearch : Meyerdierks_2005_Environ.Microbiol_7_1937
PubMedID: 16309392

Title : Genome sequence of the chlorinated compound-respiring bacterium Dehalococcoides species strain CBDB1 - Kube_2005_Nat.Biotechnol_23_1269
Author(s) : Kube M , Beck A , Zinder SH , Kuhl H , Reinhardt R , Adrian L
Ref : Nat Biotechnol , 23 :1269 , 2005
Abstract : Dehalococcoides species are strictly anaerobic bacteria, which catabolize many of the most toxic and persistent chlorinated aromatics and aliphatics by reductive dechlorination and are used for in situ bioremediation of contaminated sites. Our sequencing of the complete 1,395,502 base pair genome of Dehalococcoides strain CBDB1 has revealed the presence of 32 reductive-dehalogenase-homologous (rdh) genes, possibly conferring on the bacteria an immense dehalogenating potential. Most rdh genes were associated with genes encoding transcription regulators such as two-component regulatory systems or transcription regulators of the MarR-type. Four new paralog groups of rdh-associated genes without known function were detected. Comparison with the recently sequenced genome of Dehalococcoides ethenogenes strain 195 reveals a high degree of gene context conservation (synteny) but exceptionally high plasticity in all regions containing rdh genes, suggesting that these regions are under intense evolutionary pressure.
ESTHER : Kube_2005_Nat.Biotechnol_23_1269
PubMedSearch : Kube_2005_Nat.Biotechnol_23_1269
PubMedID: 16116419
Gene_locus related to this paper: dehsc-q3zxf2 , dehsc-q3zy55 , dehsc-q3zyd4 , dehsc-q3zyk7 , dehmv-d2bg80

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 : Complete genome sequence of the marine planctomycete Pirellula sp. strain 1 - Glockner_2003_Proc.Natl.Acad.Sci.U.S.A_100_8298
Author(s) : Glockner FO , Kube M , Bauer M , Teeling H , Lombardot T , Ludwig W , Gade D , Beck A , Borzym K , Heitmann K , Rabus R , Schlesner H , Amann R , Reinhardt R
Ref : Proc Natl Acad Sci U S A , 100 :8298 , 2003
Abstract : Pirellula sp. strain 1 ("Rhodopirellula baltica") is a marine representative of the globally distributed and environmentally important bacterial order Planctomycetales. Here we report the complete genome sequence of a member of this independent phylum. With 7.145 megabases, Pirellula sp. strain 1 has the largest circular bacterial genome sequenced so far. The presence of all genes required for heterolactic acid fermentation, key genes for the interconversion of C1 compounds, and 110 sulfatases were unexpected for this aerobic heterotrophic isolate. Although Pirellula sp. strain 1 has a proteinaceous cell wall, remnants of genes for peptidoglycan synthesis were found. Genes for lipid A biosynthesis and homologues to the flagellar L- and P-ring protein indicate a former Gram-negative type of cell wall. Phylogenetic analysis of all relevant markers clearly affiliates the Planctomycetales to the domain Bacteria as a distinct phylum, but a deepest branching is not supported by our analyses.
ESTHER : Glockner_2003_Proc.Natl.Acad.Sci.U.S.A_100_8298
PubMedSearch : Glockner_2003_Proc.Natl.Acad.Sci.U.S.A_100_8298
PubMedID: 12835416
Gene_locus related to this paper: rhoba-DHLA , rhoba-EPHA , rhoba-pepx , rhoba-PLDB , rhoba-q7tty3 , rhoba-q7ufy7 , rhoba-q7ug04 , rhoba-q7uh76 , rhoba-q7uhj7 , rhoba-q7uik0 , rhoba-q7uit3 , rhoba-q7ujb6 , rhoba-q7ujc7.1 , rhoba-q7ujc7.2 , rhoba-q7ujd0 , rhoba-q7ujp7 , rhoba-q7ujv7 , rhoba-q7uk55 , rhoba-q7uk83 , rhoba-q7ul52 , rhoba-q7ule9 , rhoba-q7umh7 , rhoba-q7upt9 , rhoba-q7uq60 , rhoba-q7uqf1 , rhoba-q7uqr5 , rhoba-q7uqz0 , rhoba-q7ur17 , rhoba-q7ur85 , rhoba-q7urv6 , rhoba-q7us57 , rhoba-q7usu9 , rhoba-q7ut87 , rhoba-q7ut89 , rhoba-q7utj6 , rhoba-q7uua2 , rhoba-q7uvu6 , rhoba-q7uw49 , rhoba-q7uw53 , rhoba-q7uwf0 , rhoba-q7uwf1 , rhoba-q7uxn0 , rhoba-q7uyb7 , rhoba-q7uyh2 , rhoba-q7uz96 , rhoba-RB3694 , rhoba-RB4467 , rhoba-RB7907 , rhoba-RB9080 , rhoba-RB9565 , rhoba-RB13257