Glockner FO

References (14)

Title : Determinants and prediction of esterase substrate promiscuity patterns - Martinez-Martinez_2018_ACS.Chem.Biol_13_225
Author(s) : Martinez-Martinez M , Coscolin C , Santiago G , Chow J , Stogios PJ , Bargiela R , Gertler C , Navarro-Fernandez J , Bollinger A , Thies S , Mendez-Garcia C , Popovic A , Brown G , Chernikova TN , Garcia-Moyano A , Bjergah GE , Perez-Garcia P , Hai T , Del Pozo MV , Stokke R , Steen IH , Cui H , Xu X , Nocek BP , Alcaide M , Distaso M , Mesa V , Pelaez AI , Sanchez J , Buchholz PCF , Pleiss J , Fernandez-Guerra A , Glockner FO , Golyshina OV , Yakimov MM , Savchenko A , Jaeger KE , Yakunin AF , Streit WR , Golyshin PN , Guallar V , Ferrer M
Ref : ACS Chemical Biology , 13 :225 , 2018
Abstract : Esterases receive special attention because their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others, remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps ranking (classifying) promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence datasets.
ESTHER : Martinez-Martinez_2018_ACS.Chem.Biol_13_225
PubMedSearch : Martinez-Martinez_2018_ACS.Chem.Biol_13_225
PubMedID: 29182315
Gene_locus related to this paper: 9zzzz-a0a2k8jn75 , 9zzzz-a0a2k8jt94 , 9zzzz-a0a0g3fj44 , 9zzzz-a0a0g3fh10 , 9zzzz-a0a0g3fh03 , 9bact-a0a1s5qkj8 , 9zzzz-a0a0g3feh5 , 9zzzz-a0a0g3fkz4 , 9zzzz-a0a0g3fh07 , 9zzzz-a0a0g3fh34 , 9zzzz-a0a0g3fh31 , 9bact-KY458167 , alcbs-q0vqa3 , 9bact-a0a1s5qki8 , 9zzzz-a0a0g3feq8 , 9zzzz-a0a0g3feh8 , 9zzzz-a0a0g3fh19 , 9bact-KY203037 , 9bact-a0a1s5ql22 , 9bact-a0a1s5qm34 , 9bact-KY203034 , 9bact-r9qzg0 , 9bact-a0a1s5qly8 , 9zzzz-a0a0g3fkz8 , 9zzzz-a0a0g3feg9 , 9zzzz-KY203033 , 9zzzz-a0a0g3fes4 , 9zzzz-a0a0g3fh42 , 9bact-a0a1s5qlx2 , 9zzzz-KY483651 , 9bact-a0a1s5qmh4 , 9zzzz-KY203032 , 9zzzz-EH87 , 9zzzz-a0a0g3fei1 , 9zzzz-a0a0g3fet2 , 9zzzz-KY483647 , 9zzzz-EH82 , 9zzzz-a0a0g3fe15 , 9bact-KY203031 , 9bact-t1w006 , 9zzzz-a0a0g3fet6 , 9bact-KY458164 , geoth-g8myf3 , 9bact-a0a1s5ql04 , 9gamm-a0a1y0ihk7 , 9bact-a0a1s5qly6 , 9bact-a0a1s5qkg4 , 9bact-a0a1s5qkm4 , 9gamm-s5tv80 , 9gamm-a0a0c4zhg2 , 9zzzz-t1b379 , 9gamm-KY483646 , 9bact-KY458160 , 9zzzz-a0a0g3fj57 , 9gamm-s5t8349 , 9arch-KY203036 , 9bact-KY458168 , 9zzzz-a0a0g3fes0 , 9zzzz-t1be47 , 9bact-KY458159 , 9zzzz-a0a0g3fh39 , 9bact-t1vzd5 , 9prot-EH41 , 9bact-Lip114 , alcbs-q0vt77 , 9bact-a0a1s5qke6 , 9bact-a0a1s5qkf3 , 9prot-SRP030024 , 9gamm-s5t532 , 9bact-a0a1s5qkl2 , 9bact-a0a1s5qkk8 , 9zzzz-KY203030 , 9zzzz-t1d4I7 , 9prot-KY019260 , 9bact-a0a1s5qm38 , 9arch-KY458161 , 9prot-KY010302 , 9zzzz-a0a0g3fl25 , 9actn-KY010298 , 9gamm-s5u059 , 9bact-a0a1s5qmi7 , 9bact-KY010297 , 9bact-KY483642 , 9bact-a0a1s5qkj1 , 9bact-KY010299 , 9bact-KY483648 , alcbs-q0vtl7 , 9bact-a0a1s5qf1 , 9bact-a0a1s5qkg0 , 9bact-a0a0h4tgu6 , 9bact-MilE3 , 9bact-LAE6 , 9alte-MGS-MT1 , 9bact-r9qzf7 , 9gamm-k0c6t6 , alcbs-q0vl36 , alcbs-q0vlq1 , alcbs-q0vq49 , bacsu-pnbae , canar-LipB , canan-lipasA , geost-lipas , marav-a1u5n0 , pseps-i7k8x5 , staep-GEHD , symth-q67mr3 , altma-s5cfn7 , cycsp-k0c2b8 , alcbs-q0vlk5 , 9bact-k7qe48 , 9bact-MGS-M1 , 9bact-MGS-M2 , 9bact-a0a0b5kns5 , 9zzzz-a0a0g3fej4 , 9zzzz-a0a0g3fj60 , 9zzzz-a0a0g3fej0 , 9zzzz-a0a0g3fj64 , 9bact-a0a0b5kc16 , 9zzzz-a0a0g3feg6 , 9zzzz-a0a0g3feu6

Title : Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus - Romano_2016_Front.Microbiol_7_387
Author(s) : Romano S , Fernandez-Guerra A , Reen FJ , Glockner FO , Crowley SP , O'Sullivan O , Cotter PD , Adams C , Dobson AD , O'Gara F
Ref : Front Microbiol , 7 :387 , 2016
Abstract : Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its microbiota. Our data suggest the presence of a sponge-specific lineage of Pseudovibrio. The reduction in genome size and the loss of some systems potentially used to successfully enter the host, leads to the hypothesis that P. axinellae strain AD2 may be a lineage that presents an ancient association with the host and that may be vertically transmitted to the progeny.
ESTHER : Romano_2016_Front.Microbiol_7_387
PubMedSearch : Romano_2016_Front.Microbiol_7_387
PubMedID: 27065959
Gene_locus related to this paper: 9rhob-a0a161uzs3 , 9rhob-a0a165mpu9 , 9rhob-a0a165u1y6 , 9rhob-a0a165rp54 , 9rhob-a0a165xcn8

Title : The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides - Mann_2013_Appl.Environ.Microbiol_79_6813
Author(s) : Mann AJ , Hahnke RL , Huang S , Werner J , Xing P , Barbeyron T , Huettel B , Stuber K , Reinhardt R , Harder J , Glockner FO , Amann RI , Teeling H
Ref : Applied Environmental Microbiology , 79 :6813 , 2013
Abstract : In recent years, representatives of the Bacteroidetes have been increasingly recognized as specialists for the degradation of macromolecules. Formosa constitutes a Bacteroidetes genus within the class Flavobacteria, and the members of this genus have been found in marine habitats with high levels of organic matter, such as in association with algae, invertebrates, and fecal pellets. Here we report on the generation and analysis of the genome of the type strain of Formosa agariphila (KMM 3901(T)), an isolate from the green alga Acrosiphonia sonderi. F. agariphila is a facultative anaerobe with the capacity for mixed acid fermentation and denitrification. Its genome harbors 129 proteases and 88 glycoside hydrolases, indicating a pronounced specialization for the degradation of proteins, polysaccharides, and glycoproteins. Sixty-five of the glycoside hydrolases are organized in at least 13 distinct polysaccharide utilization loci, where they are clustered with TonB-dependent receptors, SusD-like proteins, sensors/transcription factors, transporters, and often sulfatases. These loci play a pivotal role in bacteroidetal polysaccharide biodegradation and in the case of F. agariphila revealed the capacity to degrade a wide range of algal polysaccharides from green, red, and brown algae and thus a strong specialization of toward an alga-associated lifestyle. This was corroborated by growth experiments, which confirmed usage particularly of those monosaccharides that constitute the building blocks of abundant algal polysaccharides, as well as distinct algal polysaccharides, such as laminarins, xylans, and kappa-carrageenans.
ESTHER : Mann_2013_Appl.Environ.Microbiol_79_6813
PubMedSearch : Mann_2013_Appl.Environ.Microbiol_79_6813
PubMedID: 23995932
Gene_locus related to this paper: forag-t2ki26

Title : Expression of sulfatases in Rhodopirellula baltica and the diversity of sulfatases in the genus Rhodopirellula - Wegner_2013_Mar.Genomics_9_51
Author(s) : Wegner CE , Richter-Heitmann T , Klindworth A , Klockow C , Richter M , Achstetter T , Glockner FO , Harder J
Ref : Mar Genomics , 9 :51 , 2013
Abstract : The whole genome sequence of Rhodopirellula baltica SH1(T), published nearly 10years ago, already revealed a high amount of sulfatase genes. So far, little is known about the diversity and potential functions mediated by sulfatases in Planctomycetes. We combined in vivo and in silico techniques to gain insights into the ecophysiology of planktomycetal sulfatases. Comparative genomics of nine recently sequenced Rhodopirellula strains detected 1120 open reading frames annotated as sulfatases (Enzyme Commission number (EC) 3.1.6.*). These were clustered into 173 groups of orthologous and paralogous genes. To analyze the functional aspects, 708 sulfatase protein sequences from these strains were aligned with 67 sulfatase reference sequences of reviewed functionality. Our analysis yielded 22 major similarity clusters, but only five of these clusters contained Rhodopirellula sequences homologous to reference sequences, indicating a surprisingly high diversity. Exemplarily, R. baltica SH1(T) was grown on different sulfated polysaccharides, chondroitin sulfate, lambda-carrageenan and fucoidan. Subsequent gene expression analyses using whole genome microarrays revealed distinct sulfatase expression profiles based on substrates tested. This might be indicative for a high structural diversity of sulfated polysaccharides as potential substrates. The pattern of sulfatases in individual planctomycete species may reflect ecological niche adaptation.
ESTHER : Wegner_2013_Mar.Genomics_9_51
PubMedSearch : Wegner_2013_Mar.Genomics_9_51
PubMedID: 23273849
Gene_locus related to this paper: 9plan-m5rjx3

Title : Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones - Grote_2012_Proc.Natl.Acad.Sci.U.S.A_109_506
Author(s) : Grote J , Schott T , Bruckner CG , Glockner FO , Jost G , Teeling H , Labrenz M , Jurgens K
Ref : Proc Natl Acad Sci U S A , 109 :506 , 2012
Abstract : Eutrophication and global climate change lead to expansion of hypoxia in the ocean, often accompanied by the production of hydrogen sulfide, which is toxic to higher organisms. Chemoautotrophic bacteria are thought to buffer against increased sulfide concentrations by oxidizing hydrogen sulfide before its diffusion to oxygenated surface waters. Model organisms from such environments have not been readily available, which has contributed to a poor understanding of these microbes. We present here a detailed study of "Sulfurimonas gotlandica" str. GD1, an Epsilonproteobacterium isolated from the Baltic Sea oxic-anoxic interface, where it plays a key role in nitrogen and sulfur cycling. Whole-genome analysis and laboratory experiments revealed a high metabolic flexibility, suggesting a considerable capacity for adaptation to variable redox conditions. S. gotlandica str. GD1 was shown to grow chemolithoautotrophically by coupling denitrification with oxidation of reduced sulfur compounds and dark CO(2) fixation. Metabolic versatility was further suggested by the use of a range of different electron donors and acceptors and organic carbon sources. The number of genes involved in signal transduction and metabolic pathways exceeds those of other Epsilonproteobacteria. Oxygen tolerance and environmental-sensing systems combined with chemotactic responses enable this organism to thrive successfully in marine oxygen-depletion zones. We propose that S. gotlandica str. GD1 will serve as a model organism in investigations that will lead to a better understanding how members of the Epsilonproteobacteria are able to cope with water column anoxia and the role these microorganisms play in the detoxification of sulfidic waters.
ESTHER : Grote_2012_Proc.Natl.Acad.Sci.U.S.A_109_506
PubMedSearch : Grote_2012_Proc.Natl.Acad.Sci.U.S.A_109_506
PubMedID: 22203982
Gene_locus related to this paper: sulgg-b6bk50 , sulgg-b6bjr0

Title : Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains - Pena_2010_ISME.J_4_882
Author(s) : Pena A , Teeling H , Huerta-Cepas J , Santos F , Yarza P , Brito-Echeverria J , Lucio M , Schmitt-Kopplin P , Meseguer I , Schenowitz C , Dossat C , Barbe V , Dopazo J , Rossello-Mora R , Schuler M , Glockner FO , Amann R , Gabaldon T , Anton J
Ref : Isme J , 4 :882 , 2010
Abstract : Genomic and metagenomic data indicate a high degree of genomic variation within microbial populations, although the ecological and evolutive meaning of this microdiversity remains unknown. Microevolution analyses, including genomic and experimental approaches, are so far very scarce for non-pathogenic bacteria. In this study, we compare the genomes, metabolomes and selected ecological traits of the strains M8 and M31 of the hyperhalophilic bacterium Salinibacter ruber that contain ribosomal RNA (rRNA) gene and intergenic regions that are identical in sequence and were simultaneously isolated from a Mediterranean solar saltern. Comparative analyses indicate that S. ruber genomes present a mosaic structure with conserved and hypervariable regions (HVRs). The HVRs or genomic islands, are enriched in transposases, genes related to surface properties, strain-specific genes and highly divergent orthologous. However, the many indels outside the HVRs indicate that genome plasticity extends beyond them. Overall, 10% of the genes encoded in the M8 genome are absent from M31 and could stem from recent acquisitions. S. ruber genomes also harbor 34 genes located outside HVRs that are transcribed during standard growth and probably derive from lateral gene transfers with Archaea preceding the M8/M31 divergence. Metabolomic analyses, phage susceptibility and competition experiments indicate that these genomic differences cannot be considered neutral from an ecological perspective. The results point to the avoidance of competition by micro-niche adaptation and response to viral predation as putative major forces that drive microevolution within these Salinibacter strains. In addition, this work highlights the extent of bacterial functional diversity and environmental adaptation, beyond the resolution of the 16S rRNA and internal transcribed spacers regions.
ESTHER : Pena_2010_ISME.J_4_882
PubMedSearch : Pena_2010_ISME.J_4_882
PubMedID: 20164864
Gene_locus related to this paper: salrd-q2rzy1 , salrd-q2s0e4 , salrd-q2s1i8

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 : Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide - Strittmatter_2009_Environ.Microbiol_11_1038
Author(s) : Strittmatter AW , Liesegang H , Rabus R , Decker I , Amann J , Andres S , Henne A , Fricke WF , Martinez-Arias R , Bartels D , Goesmann A , Krause L , Puhler A , Klenk HP , Richter M , Schuler M , Glockner FO , Meyerdierks A , Gottschalk G , Amann R
Ref : Environ Microbiol , 11 :1038 , 2009
Abstract : Sulfate-reducing bacteria (SRB) belonging to the metabolically versatile Desulfobacteriaceae are abundant in marine sediments and contribute to the global carbon cycle by complete oxidation of organic compounds. Desulfobacterium autotrophicum HRM2 is the first member of this ecophysiologically important group with a now available genome sequence. With 5.6 megabasepairs (Mbp) the genome of Db. autotrophicum HRM2 is about 2 Mbp larger than the sequenced genomes of other sulfate reducers (SRB). A high number of genome plasticity elements (> 100 transposon-related genes), several regions of GC discontinuity and a high number of repetitive elements (132 paralogous genes Mbp(-1)) point to a different genome evolution when comparing with Desulfovibrio spp. The metabolic versatility of Db. autotrophicum HRM2 is reflected in the presence of genes for the degradation of a variety of organic compounds including long-chain fatty acids and for the Wood-Ljungdahl pathway, which enables the organism to completely oxidize acetyl-CoA to CO(2) but also to grow chemolithoautotrophically. The presence of more than 250 proteins of the sensory/regulatory protein families should enable Db. autotrophicum HRM2 to efficiently adapt to changing environmental conditions. Genes encoding periplasmic or cytoplasmic hydrogenases and formate dehydrogenases have been detected as well as genes for the transmembrane TpII-c(3), Hme and Rnf complexes. Genes for subunits A, B, C and D as well as for the proposed novel subunits L and F of the heterodisulfide reductases are present. This enzyme is involved in energy conservation in methanoarchaea and it is speculated that it exhibits a similar function in the process of dissimilatory sulfate reduction in Db. autotrophicum HRM2.
ESTHER : Strittmatter_2009_Environ.Microbiol_11_1038
PubMedSearch : Strittmatter_2009_Environ.Microbiol_11_1038
PubMedID: 19187283
Gene_locus related to this paper: desah-c0q9m7 , desah-c0qb70 , desah-c0qf45 , desah-c0qhm8

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 : Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis - Fuchs_2007_Proc.Natl.Acad.Sci.U.S.A_104_2891
Author(s) : Fuchs BM , Spring S , Teeling H , Quast C , Wulf J , Schattenhofer M , Yan S , Ferriera S , Johnson J , Glockner FO , Amann R
Ref : Proc Natl Acad Sci U S A , 104 :2891 , 2007
Abstract : Members of the gammaproteobacterial clade NOR5/OM60 regularly form an abundant part, up to 11%, of the bacterioplankton community in coastal systems during the summer months. Here, we report the nearly complete genome sequence of one cultured representative, Congregibacter litoralis strain KT71, isolated from North Sea surface water. Unexpectedly, a complete photosynthesis superoperon, including genes for accessory pigments, was discovered. It has a high sequence similarity to BAC clones from Monterey Bay [Beja O, Suzuki MT, Heidelberg JF, Nelson WC, Preston CM, et al. (2002) Nature 415:630-633], which also share a nearly identical gene arrangement. Although cultures of KT71 show no obvious pigmentation, bacteriochlorophyll a and spirilloxanthin-like carotenoids could be detected by HPLC analysis in cell extracts. The presence of two potential BLUF (blue light using flavin adenine dinucleotide sensors), one of which was found adjacent to the photosynthesis operon in the genome, indicates a light- and redox-dependent regulation of gene expression. Like other aerobic anoxygenic phototrophs (AAnPs), KT71 is able to grow neither anaerobically nor photoautotrophically. Cultivation experiments and genomic evidence show that KT71 needs organic substrates like carboxylic acids, oligopeptides, or fatty acids for growth. The strain grows optimally under microaerobic conditions and actively places itself in a zone of approximately 10% oxygen saturation. The genome analysis of C. litoralis strain KT71 identifies the gammaproteobacterial marine AAnPs, postulated based on BAC sequences, as members of the NOR5/OM60 clade. KT71 enables future experiments investigating the importance of this group of gammaproteobacterial AAnPs in coastal environments.
ESTHER : Fuchs_2007_Proc.Natl.Acad.Sci.U.S.A_104_2891
PubMedSearch : Fuchs_2007_Proc.Natl.Acad.Sci.U.S.A_104_2891
PubMedID: 17299055
Gene_locus related to this paper: 9gamm-a4a7a9 , 9gamm-a4a9u6 , 9gamm-a4a440 , 9gamm-a4a484 , 9gamm-a4a590 , 9gamm-a4a746 , 9gamm-a4a758 , 9gamm-a4aa23 , 9gamm-a4acc1 , 9gamm-a4ada0 , 9gamm-a4ae00 , 9gamm-a4acf4 , 9gamm-a4acr9

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