Lombardot T

References (5)

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 : 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 : 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 : The genome of Desulfotalea psychrophila, a sulfate-reducing bacterium from permanently cold Arctic sediments - Rabus_2004_Environ.Microbiol_6_887
Author(s) : Rabus R , Ruepp A , Frickey T , Rattei T , Fartmann B , Stark M , Bauer M , Zibat A , Lombardot T , Becker I , Amann J , Gellner K , Teeling H , Leuschner WD , Glockner FO , Lupas AN , Amann R , Klenk HP
Ref : Environ Microbiol , 6 :887 , 2004
Abstract : Desulfotalea psychrophila is a marine sulfate-reducing delta-proteobacterium that is able to grow at in situ temperatures below 0 degrees C. As abundant members of the microbial community in permanently cold marine sediments, D. psychrophila-like bacteria contribute to the global cycles of carbon and sulfur. Here, we describe the genome sequence of D. psychrophila strain LSv54, which consists of a 3 523 383 bp circular chromosome with 3118 predicted genes and two plasmids of 121 586 bp and 14 663 bp. Analysis of the genome gave insight into the metabolic properties of the organism, e.g. the presence of TRAP-T systems as a major route for the uptake of C(4)-dicarboxylates, the unexpected presence of genes from the TCA cycle, a TAT secretion system, the lack of a beta-oxidation complex and typical Desulfovibrio cytochromes, such as c(553), c(3) and ncc. D. psychrophila encodes more than 30 two-component regulatory systems, including a new Ntr subcluster of hybrid kinases, nine putative cold shock proteins and nine potentially cold shock-inducible proteins. A comparison of D. psychrophila's genome features with those of the only other published genome from a sulfate reducer, the hyperthermophilic archaeon Archaeoglobus fulgidus, revealed many striking differences, but only a few shared features.
ESTHER : Rabus_2004_Environ.Microbiol_6_887
PubMedSearch : Rabus_2004_Environ.Microbiol_6_887
PubMedID: 15305914
Gene_locus related to this paper: desps-q6ajw5 , desps-q6ak51 , desps-q6ak75 , desps-q6akv7 , desps-q6and7 , desps-q6anv2 , desps-q6ar42 , desps-q6ara4

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