Daniel R

References (50)

Title : Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern - Lu_2022_Front.Microbiol_13_851969
Author(s) : Lu M , Schneider D , Daniel R
Ref : Front Microbiol , 13 :851969 , 2022
Abstract : Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.
ESTHER : Lu_2022_Front.Microbiol_13_851969
PubMedSearch : Lu_2022_Front.Microbiol_13_851969
PubMedID: 35756004
Gene_locus related to this paper: 9bact-estC55.154 , 9bact-a0a0n9qch2 , pseth-a0a1m6y2k1 , rhom4-d0mhw6 , thet2-q72j75 , theth-TT1662 , 9bact-estC55.42 , 9bact-estC76.136 , 9bact-estC55.118 , 9bact-estC55.62 , 9bact-estC55.268 , 9bact-estC55.52 , 9bact-estC55.3 , 9bact-estC55.235 , 9bact-estC55.90 , 9bact-estC55.102 , 9bact-estC55.145 , 9bact-estC55.105 , 9bact-estC55.151 , 9bact-estC55.71 , 9bact-estC55.88 , 9bact-estC55.156 , 9bact-estC55.169 , 9bact-estC76.202 , 9bact-estC55.165 , 9bact-estC55.241 , 9bact-estC55.78 , 9bact-estC55.8n1 , 9bact-estC55.56 , 9bact-estC55.60 , 9bact-estC55.5 , 9bact-estC55.19n1 , 9bact-estC55.253 , 9bact-estC55.95 , 9bact-estC55.13 , 9bact-estC55.77 , 9bact-estC55.229 , 9bact-estC55.167 , 9bact-estC55.234 , 9bact-estC55.25 , 9bact-estC55.76 , 9bact-estC55.19n2 , 9bact-estC55.8n2 , 9bact-estC55.20 , 9bact-estC55.96 , 9bact-estC55.2 , 9bact-estC55.4n1 , 9bact-estC55.23 , 9bact-estC55.57 , 9bact-estC55.197 , 9bact-estC76.263 , 9bact-estC55.227 , 9bact-estC55.159 , 9bact-estC55.51 , 9bact-estC55.31 , 9bact-estC55.215 , 9bact-estC55.34 , 9bact-estC55.244 , 9bact-estC55.81 , 9bact-estC55.24 , 9bact-estC55.12 , 9bact-estC55.15 , 9bact-estC55.231 , 9bact-estC55.97 , 9bact-estC76.135 , 9bact-estC76.266n2 , 9bact-estC76.28n1 , 9bact-estC76.177 , 9bact-estC76.137 , 9bact-estC76.266n1 , 9bact-estC76.248 , 9bact-estC76.221

Title : A Novel Carboxylesterase Derived from a Compost Metagenome Exhibiting High Stability and Activity towards High Salinity - Lu_2021_Genes.(Basel)_12_E122
Author(s) : Lu M , Daniel R
Ref : Genes (Basel) , 12 : , 2021
Abstract : Halotolerant lipolytic enzymes have gained growing interest, due to potential applications under harsh conditions, such as hypersalinity and presence of organic solvents. In this study, a lipolytic gene, est56, encoding 287 amino acids was identified by functional screening of a compost metagenome. Subsequently, the gene was heterologously expressed, and the recombinant protein (Est56) was purified and characterized. Est56 is a mesophilic (T(opt) 50 degreesC) and moderate alkaliphilic (pH(opt) 8) enzyme, showing high thermostability at 30 and 40 degreesC. Strikingly, Est56 is halotolerant as it exhibited high activity and stability in the presence of up to 4 M NaCl or KCl. Est56 also displayed enhanced stability against high temperatures (50 and 60 degreesC) and urea (2, 4, and 6 M) in the presence of NaCl. In addition, the recently reported halotolerant lipolytic enzymes were summarized. Phylogenetic analysis grouped these enzymes into 13 lipolytic protein families. The majority (45%) including Est56 belonged to family IV. To explore the haloadaptation of halotolerant enzymes, the amino acid composition between halotolerant and halophilic enzymes was statistically compared. The most distinctive feature of halophilic from non-halophilic enzymes are the higher content of acidic residues (Asp and Glu), and a lower content of lysine, aliphatic hydrophobic (Leu, Met and Ile) and polar (Asn) residues. The amino acid composition and 3-D structure analysis suggested that the high content of acidic residues (Asp and Glu, 12.2%) and low content of lysine residues (0.7%), as well as the excess of surface-exposed acidic residues might be responsible for the haloadaptation of Est56.
ESTHER : Lu_2021_Genes.(Basel)_12_E122
PubMedSearch : Lu_2021_Genes.(Basel)_12_E122
PubMedID: 33478024
Gene_locus related to this paper: 9bact-a0a0n9qch2

Title : Biochemical profiles of two thermostable and organic solvent-tolerant esterases derived from a compost metagenome - Lu_2019_Appl.Microbiol.Biotechnol_103_3421
Author(s) : Lu M , Dukunde A , Daniel R
Ref : Applied Microbiology & Biotechnology , 103 :3421 , 2019
Abstract : Owing to the functional versatility and potential applications in industry, interest in lipolytic enzymes tolerant to organic solvents is increasing. In this study, functional screening of a compost soil metagenome resulted in identification of two lipolytic genes, est1 and est2, encoding 270 and 389 amino acids, respectively. The two genes were heterologously expressed and characterized. Est1 and Est2 are thermostable enzymes with optimal enzyme activities at 80 and 70 degrees C, respectively. A second-order rotatable design, which allows establishing the relationship between multiple variables with the obtained responses, was used to explore the combined effects of temperature and pH on esterase stability. The response curve indicated that Est1, and particularly Est2, retained high stability within a broad range of temperature and pH values. Furthermore, the effects of organic solvents on Est1 and Est2 activities and stabilities were assessed. Notably, Est2 activity was significantly enhanced (two- to tenfold) in the presence of ethanol, methanol, isopropanol, and 1-propanol over a concentration range between 6 and 30% (v/v). For the short-term stability (2 h of incubation), Est2 exhibited high tolerance against 60% (v/v) of ethanol, methanol, isopropanol, DMSO, and acetone, while Est1 activity resisted these solvents only at lower concentrations (below 30%, v/v). Est2 also displayed high stability towards some water-immiscible organic solvents, such as ethyl acetate, diethyl ether, and toluene. With respect to long-term stability, Est2 retained most of its activity after 26 days of incubation in the presence of 30% (v/v) ethanol, methanol, isopropanol, DMSO, or acetone. All of these features indicate that Est1 and Est2 possess application potential.
ESTHER : Lu_2019_Appl.Microbiol.Biotechnol_103_3421
PubMedSearch : Lu_2019_Appl.Microbiol.Biotechnol_103_3421
PubMedID: 30809711
Gene_locus related to this paper: 9bact-a0a0n9qma1

Title : Functional Metagenomics Reveals an Overlooked Diversity and Novel Features of Soil-Derived Bacterial Phosphatases and Phytases - Castillo Villamizar_2019_MBio_10_
Author(s) : Castillo Villamizar GA , Nacke H , Boehning M , Herz K , Daniel R
Ref : MBio , 10 : , 2019
Abstract : Phosphatases, including phytases, play a major role in cell metabolism, phosphorus cycle, biotechnology, and pathogenic processes. Nevertheless, their discovery by functional metagenomics is challenging. Here, soil metagenomic libraries were successfully screened for genes encoding phosphatase activity. In this context, we report the largest number and diversity of phosphatase genes derived from functional metagenome analysis. Two of the detected gene products carry domains which have never been associated with phosphatase activity before. One of these domains, the SNARE-associated domain DedA, harbors a so-far-overlooked motif present in numerous bacterial SNARE-associated proteins. Our analysis revealed a previously unreported phytase activity of the alkaline phosphatase and sulfatase superfamily (cl23718) and of purple acid phosphatases from nonvegetal origin. This suggests that the classical concept comprising four classes of phytases should be modified and indicates high performance of our screening method for retrieving novel types of phosphatases/phytases hidden in metagenomes of complex environments.IMPORTANCE Phosphorus (P) is a key element involved in numerous cellular processes and essential to meet global food demand. Phosphatases play a major role in cell metabolism and contribute to control the release of P from phosphorylated organic compounds, including phytate. Apart from the relationship with pathogenesis and the enormous economic relevance, phosphatases/phytases are also important for reduction of phosphorus pollution. Almost all known functional phosphatases/phytases are derived from cultured individual microorganisms. We demonstrate here for the first time the potential of functional metagenomics to exploit the phosphatase/phytase pools hidden in environmental soil samples. The recovered diversity of phosphatases/phytases comprises new types and proteins exhibiting largely unknown characteristics, demonstrating the potential of the screening method for retrieving novel target enzymes. The insights gained into the unknown diversity of genes involved in the P cycle highlight the power of function-based metagenomic screening strategies to study Earth's phosphatase pools.
ESTHER : Castillo Villamizar_2019_MBio_10_
PubMedSearch : Castillo Villamizar_2019_MBio_10_
PubMedID: 30696742
Gene_locus related to this paper: 9zzzz-a0a3g1qtk3

Title : A novel, versatile family IV carboxylesterase exhibits high stability and activity in a broad pH spectrum - Dukunde_2017_Biotechnol.Lett_39_577
Author(s) : Dukunde A , Schneider D , Lu M , Brady S , Daniel R
Ref : Biotechnol Lett , 39 :577 , 2017
Abstract : OBJECTIVES: To investigate the properties of a novel metagenome-derived member of the hormone-sensitive lipase family of lipolytic enzymes.
RESULTS: A forest soil metagenome-derived gene encoding an esterase (Est06) belonging to the hormone-sensitive lipase family of lipolytic enzymes was subcloned, heterologously expressed and characterized. Est06 is a polypeptide of 295 amino acids with a molecular mass of 31 kDa. The deduced protein sequence shares 61% similarity with a hypothetical protein from the marine symbiont Candidatus Entotheonella sp. TSY1. Purified Est06 exhibited high affinity for acyl esters with short-chain fatty acids, and showed optimum activity with p-nitrophenyl valerate (C5). Maximum enzymatic activity was at 50 degrees C and pH 7. Est06 exhibited high stability at moderate temperatures by retaining all of its catalytic activity below 30 degrees C over 13 days. Additionally, Est06 displayed high stability between pH 5 and 9. Esterase activity was not inhibited by metal ions or detergents, although organic solvents decreased activity.
CONCLUSIONS: The combination of Est06 properties place it among novel biocatalysts that have potential for industrial use including low temperature applications.
ESTHER : Dukunde_2017_Biotechnol.Lett_39_577
PubMedSearch : Dukunde_2017_Biotechnol.Lett_39_577
PubMedID: 28044227
Gene_locus related to this paper: 9zzzz-g3crd1

Title : First Insights into the Genome Sequence of Pseudomonas oleovorans DSM 1045 - Poehlein_2017_Genome.Announc_5_
Author(s) : Poehlein A , Daniel R , Thurmer A , Bollinger A , Thies S , Katzke N , Jaeger KE
Ref : Genome Announc , 5 : , 2017
Abstract : The Gram-negative proteobacterium Pseudomonas oleovorans DSM 1045 is considered a promising source for enzymes of biotechnological interest, e.g., hydrolases and transaminases. Here, we present a draft sequence of its 4.86-Mb genome, enabling the identification of novel biocatalysts.
ESTHER : Poehlein_2017_Genome.Announc_5_
PubMedSearch : Poehlein_2017_Genome.Announc_5_
PubMedID: 28798180

Title : Molecular Keys to the Janthinobacterium and Duganella spp. Interaction with the Plant Pathogen Fusarium graminearum - Haack_2016_Front.Microbiol_7_1668
Author(s) : Haack FS , Poehlein A , Kroger C , Voigt CA , Piepenbring M , Bode HB , Daniel R , Schafer W , Streit WR
Ref : Front Microbiol , 7 :1668 , 2016
Abstract : Janthinobacterium and Duganella are well-known for their antifungal effects. Surprisingly, almost nothing is known on molecular aspects involved in the close bacterium-fungus interaction. To better understand this interaction, we established the genomes of 11 Janthinobacterium and Duganella isolates in combination with phylogenetic and functional analyses of all publicly available genomes. Thereby, we identified a core and pan genome of 1058 and 23,628 genes. All strains encoded secondary metabolite gene clusters and chitinases, both possibly involved in fungal growth suppression. All but one strain carried a single gene cluster involved in the biosynthesis of alpha-hydroxyketone-like autoinducer molecules, designated JAI-1. Genome-wide RNA-seq studies employing the background of two isolates and the corresponding JAI-1 deficient strains identified a set of 45 QS-regulated genes in both isolates. Most regulated genes are characterized by a conserved sequence motif within the promoter region. Among the most strongly regulated genes were secondary metabolite and type VI secretion system gene clusters. Most intriguing, co-incubation studies of J. sp. HH102 or its corresponding JAI-1 synthase deletion mutant with the plant pathogen Fusarium graminearum provided first evidence of a QS-dependent interaction with this pathogen.
ESTHER : Haack_2016_Front.Microbiol_7_1668
PubMedSearch : Haack_2016_Front.Microbiol_7_1668
PubMedID: 27833590
Gene_locus related to this paper: 9burk-a0a1e7w6l2 , 9burk-a0a1e7wlu5

Title : Adaptation of an abundant Roseobacter RCA organism to pelagic systems revealed by genomic and transcriptomic analyses - Voget_2015_ISME.J_9_371
Author(s) : Voget S , Wemheuer B , Brinkhoff T , Vollmers J , Dietrich S , Giebel HA , Beardsley C , Sardemann C , Bakenhus I , Billerbeck S , Daniel R , Simon M
Ref : Isme J , 9 :371 , 2015
Abstract : The RCA (Roseobacter clade affiliated) cluster, with an internal 16S rRNA gene sequence similarity of >98%, is the largest cluster of the marine Roseobacter clade and most abundant in temperate to (sub)polar oceans, constituting up to 35% of total bacterioplankton. The genome analysis of the first described species of the RCA cluster, Planktomarina temperata RCA23, revealed that this phylogenetic lineage is deeply branching within the Roseobacter clade. It shares not >65.7% of homologous genes with any other organism of this clade. The genome is the smallest of all closed genomes of the Roseobacter clade, exhibits various features of genome streamlining and encompasses genes for aerobic anoxygenic photosynthesis (AAP) and CO oxidation. In order to assess the biogeochemical significance of the RCA cluster we investigated a phytoplankton spring bloom in the North Sea. This cluster constituted 5.1% of the total, but 10-31% (mean 18.5%) of the active bacterioplankton. A metatranscriptomic analysis showed that the genome of P. temperata RCA23 was transcribed to 94% in the bloom with some variations during day and night. The genome of P. temperata RCA23 was also retrieved to 84% from metagenomic data sets from a Norwegian fjord and to 82% from stations of the Global Ocean Sampling expedition in the northwestern Atlantic. In this region, up to 6.5% of the total reads mapped on the genome of P. temperata RCA23. This abundant taxon appears to be a major player in ocean biogeochemistry.
ESTHER : Voget_2015_ISME.J_9_371
PubMedSearch : Voget_2015_ISME.J_9_371
PubMedID: 25083934
Gene_locus related to this paper: 9rhob-a0a076k065 , 9rhob-a0a076k2s0 , 9rhob-a0a076k4p3

Title : Closed Genome Sequence of Octadecabacter temperatus SB1, the First Mesophilic Species of the Genus Octadecabacter - Voget_2015_Genome.Announc_3_e01051
Author(s) : Voget S , Billerbeck S , Simon M , Daniel R
Ref : Genome Announc , 3 : , 2015
Abstract : The Gram-negative alphaproteobacterium Octadecabacter temperatus SB1 (DSM 26878) belongs to the marine Roseobacter clade. The genome of this strain is the smallest closed genome of the Roseobacter clade. O. temperatus SB1 is the first described nonpolar mesophilic isolate of the genus Octadecabacter and the type strain of the species.
ESTHER : Voget_2015_Genome.Announc_3_e01051
PubMedSearch : Voget_2015_Genome.Announc_3_e01051
PubMedID: 26358607
Gene_locus related to this paper: 9rhob-a0a0k0y4u6

Title : Insights into the microbial degradation of rubber and gutta-percha by analysis of the complete genome of Nocardia nova SH22a - Luo_2014_Appl.Environ.Microbiol_80_3895
Author(s) : Luo Q , Hiessl S , Poehlein A , Daniel R , Steinbuchel A
Ref : Applied Environmental Microbiology , 80 :3895 , 2014
Abstract : The complete genome sequence of Nocardia nova SH22a was determined in light of the remarkable ability of rubber and gutta-percha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G+C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide- and/or nonribosomal peptide-type secondary metabolites, were detected. Based on in silico analyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include, inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid-AMP ligase and arabinofuranosyltransferase), beta-oxidation (alpha-methylacyl-coenzyme A [alpha-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genus Nocardia regarding metabolic diversity.
ESTHER : Luo_2014_Appl.Environ.Microbiol_80_3895
PubMedSearch : Luo_2014_Appl.Environ.Microbiol_80_3895
PubMedID: 24747905
Gene_locus related to this paper: 9noca-w5tsg4 , 9noca-w5trr8 , 9noca-w5thm0 , 9noca-w5thv4 , 9noca-w5tnu3 , 9noca-w5tqc7 , 9noca-w5tvt4 , 9noca-w5tpt0 , 9noca-w5tmm4 , 9noca-w5t815 , 9noca-w5t9a8 , 9noca-w5thn5 , 9noca-w5tky7 , 9noca-w5trn3 , 9noca-w5tk87

Title : Draft Genome Sequence of Serratia sp. Strain DD3, Isolated from the Guts of Daphnia magna - Poehlein_2014_Genome.Announc_2_e00903
Author(s) : Poehlein A , Freese HM , Daniel R , Simeonova DD
Ref : Genome Announc , 2 : , 2014
Abstract : We report the draft genome sequence of Serratia sp. strain DD3, a gammaproteobacterium from the family Enterobacteriaceae. It was isolated from homogenized guts of Daphnia magna. The genome size is 5,274 Mb.
ESTHER : Poehlein_2014_Genome.Announc_2_e00903
PubMedSearch : Poehlein_2014_Genome.Announc_2_e00903
PubMedID: 25212623
Gene_locus related to this paper: 9entr-a0a083zyd0

Title : Unravelling the complete genome sequence of Advenella mimigardefordensis strain DPN7T and novel insights in the catabolism of the xenobiotic polythioester precursor 3,3'-dithiodipropionate - Wubbeler_2014_Microbiology_160_1401
Author(s) : Wubbeler JH , Hiessl S , Schuldes J , Thurmer A , Daniel R , Steinbuchel A
Ref : Microbiology , 160 :1401 , 2014
Abstract : Advenella mimigardefordensis strain DPN7(T) is a remarkable betaproteobacterium because of its extraordinary ability to use the synthetic disulfide 3,3'-dithiodipropionic acid (DTDP) as the sole carbon source and electron donor for aerobic growth. One application of DTDP is as a precursor substrate for biotechnically synthesized polythioesters (PTEs), which are interesting non-degradable biopolymers applicable for plastics materials. Metabolic engineering for optimization of PTE production requires an understanding of DTDP conversion. The genome of A. mimigardefordensis strain DPN7(T) was sequenced and annotated. The circular chromosome was found to be composed of 4,740,516 bp and 4112 predicted ORFs, whereas the circular plasmid consisted of 23,610 bp and 24 predicted ORFs. The genes participating in DTDP catabolism had been characterized in detail previously, but knowing the complete genome sequence and with support of Tn5: :mob-induced mutants, putatively involved transporter proteins and a transcriptional regulator were also identified. Most probably, DTDP is transported into the cell by a specific tripartite tricarboxylate transport system and is then cleaved by the disulfide reductase LpdA, sulfoxygenated by the 3-mercaptopropionate dioxygenase Mdo, activated by the CoA ligase SucCD and desulfinated by the acyl-CoA dehydrogenase-like desulfinase AcdA. Regulation of this pathway is presumably performed by a transcriptional regulator of the xenobiotic response element family. The excessive sulfate that is inevitably produced is secreted by the cells by a unique sulfate exporter of the CPA (cation : proton antiporter) superfamily.
ESTHER : Wubbeler_2014_Microbiology_160_1401
PubMedSearch : Wubbeler_2014_Microbiology_160_1401
PubMedID: 24739217
Gene_locus related to this paper: 9burk-w0pji8 , 9burk-w0p6d7

Title : How to kill the honey bee larva: genomic potential and virulence mechanisms of Paenibacillus larvae - Djukic_2014_PLoS.One_9_e90914
Author(s) : Djukic M , Brzuszkiewicz E , Funfhaus A , Voss J , Gollnow K , Poppinga L , Liesegang H , Garcia-Gonzalez E , Genersch E , Daniel R
Ref : PLoS ONE , 9 :e90914 , 2014
Abstract : Paenibacillus larvae, a Gram positive bacterial pathogen, causes American Foulbrood (AFB), which is the most serious infectious disease of honey bees. In order to investigate the genomic potential of P. larvae, two strains belonging to two different genotypes were sequenced and used for comparative genome analysis. The complete genome sequence of P. larvae strain DSM 25430 (genotype ERIC II) consisted of 4,056,006 bp and harbored 3,928 predicted protein-encoding genes. The draft genome sequence of P. larvae strain DSM 25719 (genotype ERIC I) comprised 4,579,589 bp and contained 4,868 protein-encoding genes. Both strains harbored a 9.7 kb plasmid and encoded a large number of virulence-associated proteins such as toxins and collagenases. In addition, genes encoding large multimodular enzymes producing nonribosomally peptides or polyketides were identified. In the genome of strain DSM 25719 seven toxin associated loci were identified and analyzed. Five of them encoded putatively functional toxins. The genome of strain DSM 25430 harbored several toxin loci that showed similarity to corresponding loci in the genome of strain DSM 25719, but were non-functional due to point mutations or disruption by transposases. Although both strains cause AFB, significant differences between the genomes were observed including genome size, number and composition of transposases, insertion elements, predicted phage regions, and strain-specific island-like regions. Transposases, integrases and recombinases are important drivers for genome plasticity. A total of 390 and 273 mobile elements were found in strain DSM 25430 and strain DSM 25719, respectively. Comparative genomics of both strains revealed acquisition of virulence factors by horizontal gene transfer and provided insights into evolution and pathogenicity.
ESTHER : Djukic_2014_PLoS.One_9_e90914
PubMedSearch : Djukic_2014_PLoS.One_9_e90914
PubMedID: 24599066
Gene_locus related to this paper: 9bacl-v9wcv0

Title : First Insights into the Completely Annotated Genome Sequence of Bacillus licheniformis Strain 9945A - Rachinger_2013_Genome.Announc_1_e00525
Author(s) : Rachinger M , Volland S , Meinhardt F , Daniel R , Liesegang H
Ref : Genome Announc , 1 : , 2013
Abstract : Strains of the species Bacillus licheniformis are widely used in biotechnology for the production of enzymes and antibiotics (M. Schallmey, A. Singh, and O. P. Ward, Can. J. Microbiol. 50:1-17, 2004). However, research and application of B. licheniformis strains are adversely affected by poor genetic accessibility. Thus, for a closer inspection of natural competence in B. licheniformis, the genome of strain 9945A, of which derivatives are known to be naturally competent (C. B. Thorne and H. B. Stull, J. Bacteriol. 91:1012-1020, 1966), was completely sequenced and manually annotated.
ESTHER : Rachinger_2013_Genome.Announc_1_e00525
PubMedSearch : Rachinger_2013_Genome.Announc_1_e00525
PubMedID: 23908277
Gene_locus related to this paper: bacld-q65eq1 , bacld-q65my7 , bacld-q65n63

Title : Legionella oakridgensis ATCC 33761 genome sequence and phenotypic characterization reveals its replication capacity in amoebae - Brzuszkiewicz_2013_Int.J.Med.Microbiol_303_514
Author(s) : Brzuszkiewicz E , Schulz T , Rydzewski K , Daniel R , Gillmaier N , Dittmann C , Holland G , Schunder E , Lautner M , Eisenreich W , Luck C , Heuner K
Ref : Int J Med Microbiol , 303 :514 , 2013
Abstract : Legionella oakridgensis is able to cause Legionnaires' disease, but is less virulent compared to L. pneumophila strains and very rarely associated with human disease. L. oakridgensis is the only species of the family legionellae which is able to grow on media without additional cysteine. In contrast to earlier publications, we found that L. oakridgensis is able to multiply in amoebae. We sequenced the genome of L. oakridgensis type strain OR-10 (ATCC 33761). The genome is smaller than the other yet sequenced Legionella genomes and has a higher G+C-content of 40.9%. L. oakridgensis lacks a flagellum and it also lacks all genes of the flagellar regulon except of the alternative sigma-28 factor FliA and the anti-sigma-28 factor FlgM. Genes encoding structural components of type I, type II, type IV Lvh and type IV Dot/Icm, Sec- and Tat-secretion systems could be identified. Only a limited set of Dot/Icm effector proteins have been recognized within the genome sequence of L. oakridgensis. Like in L. pneumophila strains, various proteins with eukaryotic motifs and eukaryote-like proteins were detected. We could demonstrate that the Dot/Icm system is essential for intracellular replication of L. oakridgensis. Furthermore, we identified new putative virulence factors of Legionella.
ESTHER : Brzuszkiewicz_2013_Int.J.Med.Microbiol_303_514
PubMedSearch : Brzuszkiewicz_2013_Int.J.Med.Microbiol_303_514
PubMedID: 23932911
Gene_locus related to this paper: 9gamm-w2v1w4

Title : Complete Genome Sequence of Clostridium stercorarium subsp. stercorarium Strain DSM 8532, a Thermophilic Degrader of Plant Cell Wall Fibers - Poehlein_2013_Genome.Announc_1_e0007313
Author(s) : Poehlein A , Zverlov VV , Daniel R , Schwarz WH , Liebl W
Ref : Genome Announc , 1 :e0007313 , 2013
Abstract : Clostridium stercorarium strain DSM 8532 is a thermophilic bacterium capable of efficiently degrading polysaccharides in plant biomass and converting the resulting sugars to ethanol and acetate. The complete genome sequence of 2.96 Mbp reveals a multitude of genes for hydrolytic enzymes and enables further study of the organism and its enzymes, and their exploitation for biotechnological processes.
ESTHER : Poehlein_2013_Genome.Announc_1_e0007313
PubMedSearch : Poehlein_2013_Genome.Announc_1_e0007313
PubMedID: 23516204
Gene_locus related to this paper: closh-l7vmb2

Title : Poles apart: Arctic and Antarctic Octadecabacter strains share high genome plasticity and a new type of xanthorhodopsin - Vollmers_2013_PLoS.One_8_e63422
Author(s) : Vollmers J , Voget S , Dietrich S , Gollnow K , Smits M , Meyer K , Brinkhoff T , Simon M , Daniel R
Ref : PLoS ONE , 8 :e63422 , 2013
Abstract : The genus Octadecabacter is a member of the ubiquitous marine Roseobacter clade. The two described species of this genus, Octadecabacter arcticus and Octadecabacter antarcticus, are psychrophilic and display a bipolar distribution. Here we provide the manually annotated and finished genome sequences of the type strains O. arcticus 238 and O. antarcticus 307, isolated from sea ice of the Arctic and Antarctic, respectively. Both genomes exhibit a high genome plasticity caused by an unusually high density and diversity of transposable elements. This could explain the discrepancy between the low genome synteny and high 16S rRNA gene sequence similarity between both strains. Numerous characteristic features were identified in the Octadecabacter genomes, which show indications of horizontal gene transfer and may represent specific adaptations to the habitats of the strains. These include a gene cluster encoding the synthesis and degradation of cyanophycin in O. arcticus 238, which is absent in O. antarcticus 307 and unique among the Roseobacter clade. Furthermore, genes representing a new subgroup of xanthorhodopsins as an adaptation to icy environments are present in both Octadecabacter strains. This new xanthorhodopsin subgroup differs from the previously characterized xanthorhodopsins of Salinibacter ruber and Gloeobacter violaceus in phylogeny, biogeography and the potential to bind 4-keto-carotenoids. Biochemical characterization of the Octadecabacter xanthorhodopsins revealed that they function as light-driven proton pumps.
ESTHER : Vollmers_2013_PLoS.One_8_e63422
PubMedSearch : Vollmers_2013_PLoS.One_8_e63422
PubMedID: 23671678
Gene_locus related to this paper: 9rhob-m9rkw4 , 9rhob-m9r8t1

Title : Characterization and optimization of Bacillus subtilis ATCC 6051 as an expression host - Kabisch_2013_J.Biotechnol_163_97
Author(s) : Kabisch J , Thurmer A , Hubel T , Popper L , Daniel R , Schweder T
Ref : J Biotechnol , 163 :97 , 2013
Abstract : The genome sequence of Bacillus subtilis ATCC 6051 and its suitability as an expression host for recombinant protein production was determined. The comparison of this undomesticated wild type with the widely used laboratory strain B. subtilis 168 reveals a high degree of congruency between the two strains. Differences could only be detected on the level of point mutations or small insertions. B. subtilis ATCC 6051 shows none of the auxotrophies known for B. subtilis 168 and is able to produce polyketides. It exhibits better use of complex media and higher genomic stability through reduced natural competence. Consequently, B. subtilis ATCC 6051 was genetically modified to yield an optimized strain for the production of heterologously expressed proteins under control of an acetoin-inducible promoter.
ESTHER : Kabisch_2013_J.Biotechnol_163_97
PubMedSearch : Kabisch_2013_J.Biotechnol_163_97
PubMedID: 22789474
Gene_locus related to this paper: bacsu-pnbae , bacsu-YBAC

Title : Complete Genome Sequence of Geobacillus sp. Strain GHH01, a Thermophilic Lipase-Secreting Bacterium - Wiegand_2013_Genome.Announc_1_e0009213
Author(s) : Wiegand S , Rabausch U , Chow J , Daniel R , Streit WR , Liesegang H
Ref : Genome Announc , 1 :e0009213 , 2013
Abstract : Geobacillus sp. strain GHH01 was isolated during a screening for producers of extracellular thermostable lipases. The completely sequenced and annotated 3.6-Mb genome encodes 3,478 proteins. The strain is genetically equipped to utilize a broad range of different substrates and might develop natural competence.
ESTHER : Wiegand_2013_Genome.Announc_1_e0009213
PubMedSearch : Wiegand_2013_Genome.Announc_1_e0009213
PubMedID: 23618712
Gene_locus related to this paper: geoka-q5l3h0 , geosc-d7d055 , geotn-a4isp0 , geos2-a0a0e0tby6

Title : Complete Genome Sequence of Staphylococcus aureus 6850, a Highly Cytotoxic and Clinically Virulent Methicillin-Sensitive Strain with Distant Relatedness to Prototype Strains - Fraunholz_2013_Genome.Announc_1_e00775
Author(s) : Fraunholz M , Bernhardt J , Schuldes J , Daniel R , Hecker M , Sinha B
Ref : Genome Announc , 1 :e00775 , 2013
Abstract : Staphylococcus aureus is a frequent human commensal bacterium and pathogen. Here we report the complete genome sequence of strain 6850 (spa type t185; sequence type 50 [ST50]), a highly cytotoxic and clinically virulent methicillin-sensitive strain from a patient with complicated S. aureus bacteremia associated with osteomyelitis and septic arthritis.
ESTHER : Fraunholz_2013_Genome.Announc_1_e00775
PubMedSearch : Fraunholz_2013_Genome.Announc_1_e00775
PubMedID: 24072870

Title : Draft Genome Sequence of Desulfotignum phosphitoxidans DSM 13687 Strain FiPS-3 - Poehlein_2013_Genome.Announc_1_e00227
Author(s) : Poehlein A , Daniel R , Simeonova DD
Ref : Genome Announc , 1 : , 2013
Abstract : We report the 5.008-Mbp assembled draft genome sequence of Desulfotignum phosphitoxidans strain FiPS-3 (DSM 13687), which gains metabolic energy from the oxidation of phosphite to phosphate. Its genome provides insights into the composition and architecture of the phosphite-utilizing and energy-transducing systems required to live with phosphite as electron donor.
ESTHER : Poehlein_2013_Genome.Announc_1_e00227
PubMedSearch : Poehlein_2013_Genome.Announc_1_e00227
PubMedID: 23704177
Gene_locus related to this paper: 9delt-s0fu60

Title : First Insights into the Genome of the Gram-Negative, Endospore-Forming Organism Sporomusa ovata Strain H1 DSM 2662 - Poehlein_2013_Genome.Announc_1_e00734
Author(s) : Poehlein A , Gottschalk G , Daniel R
Ref : Genome Announc , 1 : , 2013
Abstract : The genome of Sporomusa ovata strain H1 DSM 2662, an anaerobic, Gram-negative endospore-forming bacterium, was sequenced. S. ovata uses N-methyl compounds, primary alcohols, fatty acids, and H2 and CO2 as energy and carbon sources to produce acetate. The genome harbors one chromosome, which encodes proteins typical for sporulation.
ESTHER : Poehlein_2013_Genome.Announc_1_e00734
PubMedSearch : Poehlein_2013_Genome.Announc_1_e00734
PubMedID: 24029766
Gene_locus related to this paper: 9firm-t0iev1 , 9firm-t0ikb0

Title : Draft Genome Sequence of the Methanotrophic Gammaproteobacterium Methyloglobulus morosus DSM 22980 Strain KoM1 - Poehlein_2013_Genome.Announc_1_e01078
Author(s) : Poehlein A , Deutzmann JS , Daniel R , Simeonova DD
Ref : Genome Announc , 1 : , 2013
Abstract : Here, we report the draft genome sequence of the methanotrophic gammaproteobacterium Methyloglobulus morosus DSM 22980 strain KoM1, which is proposed to be the type species for the novel genus Methyloglobulus. The genome (4.143 Mb) consists of a single circular chromosome and harbors genes for 2-aminoethylphosphonate (ciliatine) biosynthesis.
ESTHER : Poehlein_2013_Genome.Announc_1_e01078
PubMedSearch : Poehlein_2013_Genome.Announc_1_e01078
PubMedID: 24356841

Title : Novel organic solvent-tolerant esterase isolated by metagenomics: insights into the lipase\/esterase classification - Berlemont_2013_Rev.Argent.Microbiol_45_3
Author(s) : Berlemont R , Spee O , Delsaute M , Lara Y , Schuldes J , Simon C , Power P , Daniel R , Galleni M
Ref : Rev Argent Microbiol , 45 :3 , 2013
Abstract : in order to isolate novel organic solvent-tolerant (OST) lipases, a metagenomic library was built using DNA derived from a temperate forest soil sample. A two-step activity-based screening allowed the isolation of a lipolytic clone active in the presence of organic solvents. Sequencing of the plasmid pRBest recovered from the positive clone revealed the presence of a putative lipase/esterase encoding gene. The deduced amino acid sequence (RBest1) contains the conserved lipolytic enzyme signature and is related to the previously described OST lipase from Lysinibacillus sphaericus 205y, which is the sole studied prokaryotic enzyme belonging to the 4.4 alpha/beta hydrolase subgroup (abH04.04). Both in vivo and in vitro studies of the substrate specificity of RBest1, using triacylglycerols or nitrophenyl-esters, respectively, revealed that the enzyme is highly specific for butyrate (C4) compounds, behaving as an esterase rather than a lipase. The RBest1 esterase was purified and biochemically characterized. The optimal esterase activity was observed at pH 6.5 and at temperatures ranging from 38 to 45 degrees C. Enzymatic activity, determined by hydrolysis of p-nitrophenyl esters, was found to be affected by the presence of different miscible and non-miscible organic solvents, and salts. Noteworthy, RBest1 remains significantly active at high ionic strength. These findings suggest that RBest1 possesses the ability of OST enzymes to molecular adaptation in the presence of organic compounds and resistance of halophilic proteins.
ESTHER : Berlemont_2013_Rev.Argent.Microbiol_45_3
PubMedSearch : Berlemont_2013_Rev.Argent.Microbiol_45_3
PubMedID: 23560782

Title : The Janthinobacterium sp. HH01 genome encodes a homologue of the V. cholerae CqsA and L. pneumophila LqsA autoinducer synthases - Hornung_2013_PLoS.One_8_e55045
Author(s) : Hornung C , Poehlein A , Haack FS , Schmidt M , Dierking K , Pohlen A , Schulenburg H , Blokesch M , Plener L , Jung K , Bonge A , Krohn-Molt I , Utpatel C , Timmermann G , Spieck E , Pommerening-Roser A , Bode E , Bode HB , Daniel R , Schmeisser C , Streit WR
Ref : PLoS ONE , 8 :e55045 , 2013
Abstract : Janthinobacteria commonly form biofilms on eukaryotic hosts and are known to synthesize antibacterial and antifungal compounds. Janthinobacterium sp. HH01 was recently isolated from an aquatic environment and its genome sequence was established. The genome consists of a single chromosome and reveals a size of 7.10 Mb, being the largest janthinobacterial genome so far known. Approximately 80% of the 5,980 coding sequences (CDSs) present in the HH01 genome could be assigned putative functions. The genome encodes a wealth of secretory functions and several large clusters for polyketide biosynthesis. HH01 also encodes a remarkable number of proteins involved in resistance to drugs or heavy metals. Interestingly, the genome of HH01 apparently lacks the N-acylhomoserine lactone (AHL)-dependent signaling system and the AI-2-dependent quorum sensing regulatory circuit. Instead it encodes a homologue of the Legionella- and Vibrio-like autoinducer (lqsA/cqsA) synthase gene which we designated jqsA. The jqsA gene is linked to a cognate sensor kinase (jqsS) which is flanked by the response regulator jqsR. Here we show that a jqsA deletion has strong impact on the violacein biosynthesis in Janthinobacterium sp. HH01 and that a jqsA deletion mutant can be functionally complemented with the V. cholerae cqsA and the L. pneumophila lqsA genes.
ESTHER : Hornung_2013_PLoS.One_8_e55045
PubMedSearch : Hornung_2013_PLoS.One_8_e55045
PubMedID: 23405110
Gene_locus related to this paper: 9burk-l9pl81 , 9burk-l9pql3 , 9burk-l9pc92 , 9burk-l9pf07 , 9burk-l9pgi7 , 9burk-l9p8t0 , 9burk-l9pl28

Title : Phaeobacter gallaeciensis genomes from globally opposite locations reveal high similarity of adaptation to surface life - Thole_2012_ISME.J_6_2229
Author(s) : Thole S , Kalhoefer D , Voget S , Berger M , Engelhardt T , Liesegang H , Wollherr A , Kjelleberg S , Daniel R , Simon M , Thomas T , Brinkhoff T
Ref : Isme J , 6 :2229 , 2012
Abstract : Phaeobacter gallaeciensis, a member of the abundant marine Roseobacter clade, is known to be an effective colonizer of biotic and abiotic marine surfaces. Production of the antibiotic tropodithietic acid (TDA) makes P. gallaeciensis a strong antagonist of many bacteria, including fish and mollusc pathogens. In addition to TDA, several other secondary metabolites are produced, allowing the mutualistic bacterium to also act as an opportunistic pathogen. Here we provide the manually annotated genome sequences of the P. gallaeciensis strains DSM 17395 and 2.10, isolated at the Atlantic coast of north western Spain and near Sydney, Australia, respectively. Despite their isolation sites from the two different hemispheres, the genome comparison demonstrated a surprisingly high level of synteny (only 3% nucleotide dissimilarity and 88% and 93% shared genes). Minor differences in the genomes result from horizontal gene transfer and phage infection. Comparison of the P. gallaeciensis genomes with those of other roseobacters revealed unique genomic traits, including the production of iron-scavenging siderophores. Experiments supported the predicted capacity of both strains to grow on various algal osmolytes. Transposon mutagenesis was used to expand the current knowledge on the TDA biosynthesis pathway in strain DSM 17395. This first comparative genomic analysis of finished genomes of two closely related strains belonging to one species of the Roseobacter clade revealed features that provide competitive advantages and facilitate surface attachment and interaction with eukaryotic hosts.
ESTHER : Thole_2012_ISME.J_6_2229
PubMedSearch : Thole_2012_ISME.J_6_2229
PubMedID: 22717884

Title : Genome sequence of Paenibacillus alvei DSM 29, a secondary invader during European foulbrood outbreaks - Djukic_2012_J.Bacteriol_194_6365
Author(s) : Djukic M , Becker D , Poehlein A , Voget S , Daniel R
Ref : Journal of Bacteriology , 194 :6365 , 2012
Abstract : Paenibacillus alvei is known as a secondary invader during European foulbrood of honeybees. Here, we announce the 6.83-Mb draft genome sequence of P. alvei type strain DSM 29. Putative genes encoding an antimicrobial peptide, a binary toxin, a mosquitocidal toxin, alveolysin, and different polyketides and nonribosomal peptides were identified.
ESTHER : Djukic_2012_J.Bacteriol_194_6365
PubMedSearch : Djukic_2012_J.Bacteriol_194_6365
PubMedID: 23105091
Gene_locus related to this paper: paeal-k4zdd1

Title : Complete genome sequence of the broad-host-range strain Sinorhizobium fredii USDA257 - Schuldes_2012_J.Bacteriol_194_4483
Author(s) : Schuldes J , Rodriguez Orbegoso M , Schmeisser C , Krishnan HB , Daniel R , Streit WR
Ref : Journal of Bacteriology , 194 :4483 , 2012
Abstract : Here we announce the complete genome sequence of the symbiotic and nitrogen-fixing bacterium Sinorhizobium fredii USDA257. The genome shares a high degree of sequence similarity with the closely related broad-host-range strains S. fredii NGR234 and HH103. Most strikingly, the USDA257 genome encodes a wealth of secretory systems.
ESTHER : Schuldes_2012_J.Bacteriol_194_4483
PubMedSearch : Schuldes_2012_J.Bacteriol_194_4483
PubMedID: 22843606
Gene_locus related to this paper: rhifr-i3x2k3 , rhifr-i3x2s5 , rhifr-i3xe25

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

Title : Complete genome sequence and metabolic potential of the quinaldine-degrading bacterium Arthrobacter sp. Rue61a - Niewerth_2012_BMC.Genomics_13_534
Author(s) : Niewerth H , Schuldes J , Parschat K , Kiefer P , Vorholt JA , Daniel R , Fetzner S
Ref : BMC Genomics , 13 :534 , 2012
Abstract : BACKGROUND: Bacteria of the genus Arthrobacter are ubiquitous in soil environments and can be considered as true survivalists. Arthrobacter sp. strain Rue61a is an isolate from sewage sludge able to utilize quinaldine (2-methylquinoline) as sole carbon and energy source. The genome provides insight into the molecular basis of the versatility and robustness of this environmental Arthrobacter strain.
RESULTS: The genome of Arthrobacter sp. Rue61a consists of a single circular chromosome of 4,736,495 bp with an average G + C content of 62.32%, the circular 231,551-bp plasmid pARUE232, and the linear 112,992-bp plasmid pARUE113 that was already published. Plasmid pARUE232 is proposed to contribute to the resistance of Arthrobacter sp. Rue61a to arsenate and Pb2+, whereas the linear plasmid confers the ability to convert quinaldine to anthranilate. Remarkably, degradation of anthranilate exclusively proceeds via a CoA-thioester pathway. Apart from quinaldine utilization, strain Rue61a has a limited set of aromatic degradation pathways, enabling the utilization of 4-hydroxy-substituted aromatic carboxylic acids, which are characteristic products of lignin depolymerization, via ortho cleavage of protocatechuate. However, 4-hydroxyphenylacetate degradation likely proceeds via meta cleavage of homoprotocatechuate. The genome of strain Rue61a contains numerous genes associated with osmoprotection, and a high number of genes coding for transporters. It encodes a broad spectrum of enzymes for the uptake and utilization of various sugars and organic nitrogen compounds. A. aurescens TC-1 is the closest sequenced relative of strain Rue61a.
CONCLUSIONS: The genome of Arthrobacter sp. Rue61a reflects the saprophytic lifestyle and nutritional versatility of the organism and a strong adaptive potential to environmental stress. The circular plasmid pARUE232 and the linear plasmid pARUE113 contribute to heavy metal resistance and to the ability to degrade quinaldine, respectively.
ESTHER : Niewerth_2012_BMC.Genomics_13_534
PubMedSearch : Niewerth_2012_BMC.Genomics_13_534
PubMedID: 23039946
Gene_locus related to this paper: artat-a1r5d9 , artat-a1r6c9 , 9micc-j7lr62 , 9micc-j7lsz4

Title : The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations - Spang_2012_Environ.Microbiol_14_3122
Author(s) : Spang A , Poehlein A , Offre P , Zumbragel S , Haider S , Rychlik N , Nowka B , Schmeisser C , Lebedeva EV , Rattei T , Bohm C , Schmid M , Galushko A , Hatzenpichler R , Weinmaier T , Daniel R , Schleper C , Spieck E , Streit WR , Wagner M
Ref : Environ Microbiol , 14 :3122 , 2012
Abstract : The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.
ESTHER : Spang_2012_Environ.Microbiol_14_3122
PubMedSearch : Spang_2012_Environ.Microbiol_14_3122
PubMedID: 23057602
Gene_locus related to this paper: nitgg-k0im51

Title : Complete genome sequence of the B12-producing Shimwellia blattae strain DSM 4481, isolated from a cockroach - Brzuszkiewicz_2012_J.Bacteriol_194_4436
Author(s) : Brzuszkiewicz E , Waschkowitz T , Wiezer A , Daniel R
Ref : Journal of Bacteriology , 194 :4436 , 2012
Abstract : Here we announce the complete genome sequence of the coenzyme B(12)-producing enteric bacterium Shimwellia blattae (formerly Escherichia blattae). The genome consists of a single chromosome (4,158,636 bp). The genome size is smaller than that of most other enteric bacteria. Genome comparison revealed significant differences from the Escherichia coli genome.
ESTHER : Brzuszkiewicz_2012_J.Bacteriol_194_4436
PubMedSearch : Brzuszkiewicz_2012_J.Bacteriol_194_4436
PubMedID: 22843577
Gene_locus related to this paper: shibc-i2b9b6 , shibc-i2b577 , shibc-i2bac8 , shibc-i2b8p9

Title : Involvement of two latex-clearing proteins during rubber degradation and insights into the subsequent degradation pathway revealed by the genome sequence of Gordonia polyisoprenivorans strain VH2 - Hiessl_2012_Appl.Environ.Microbiol_78_2874
Author(s) : Hiessl S , Schuldes J , Thurmer A , Halbsguth T , Broker D , Angelov A , Liebl W , Daniel R , Steinbuchel A
Ref : Applied Environmental Microbiology , 78 :2874 , 2012
Abstract : The increasing production of synthetic and natural poly(cis-1,4-isoprene) rubber leads to huge challenges in waste management. Only a few bacteria are known to degrade rubber, and little is known about the mechanism of microbial rubber degradation. The genome of Gordonia polyisoprenivorans strain VH2, which is one of the most effective rubber-degrading bacteria, was sequenced and annotated to elucidate the degradation pathway and other features of this actinomycete. The genome consists of a circular chromosome of 5,669,805 bp and a circular plasmid of 174,494 bp with average GC contents of 67.0% and 65.7%, respectively. It contains 5,110 putative protein-coding sequences, including many candidate genes responsible for rubber degradation and other biotechnically relevant pathways. Furthermore, we detected two homologues of a latex-clearing protein, which is supposed to be a key enzyme in rubber degradation. The deletion of these two genes for the first time revealed clear evidence that latex-clearing protein is essential for the microbial utilization of rubber. Based on the genome sequence, we predict a pathway for the microbial degradation of rubber which is supported by previous and current data on transposon mutagenesis, deletion mutants, applied comparative genomics, and literature search.
ESTHER : Hiessl_2012_Appl.Environ.Microbiol_78_2874
PubMedSearch : Hiessl_2012_Appl.Environ.Microbiol_78_2874
PubMedID: 22327575
Gene_locus related to this paper: gorpv-h6mtj1 , gorpv-h6mzw9 , gorpv-h6n0e3 , gorpv-h6n0g6 , gorpv-h6n0p7 , gorpv-h6mts4 , 9acto-h0rbp9 , 9acto-h0rc96 , gorpv-h6mu09 , gorpv-h6mtj7 , gorpv-h6n352 , gorpv-h6mui9 , gorpv-h6n4w7

Title : ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer - Michael_2012_J.Antimicrob.Chemother_67_91
Author(s) : Michael GB , Kadlec K , Sweeney MT , Brzuszkiewicz E , Liesegang H , Daniel R , Murray RW , Watts JL , Schwarz S
Ref : J Antimicrob Chemother , 67 :91 , 2012
Abstract : BACKGROUND: Integrative and conjugative elements (ICEs) have not been detected in Pasteurella multocida. In this study the multiresistance ICEPmu1 from bovine P. multocida was analysed for its core genes and its ability to conjugatively transfer into strains of the same and different genera.
METHODS: ICEPmu1 was identified during whole genome sequencing. Coding sequences were predicted by bioinformatic tools and manually curated using the annotation software ERGO. Conjugation into P. multocida, Mannheimia haemolytica and Escherichia coli recipients was performed by mating assays. The presence of ICEPmu1 and its circular intermediate in the recipient strains was confirmed by PCR and sequence analysis. Integration sites were sequenced. Susceptibility testing of the ICEPmu1-carrying recipients was conducted by broth microdilution.
RESULTS: The 82 214 bp ICEPmu1 harbours 88 genes. The core genes of ICEPmu1, which are involved in excision/integration and conjugative transfer, resemble those found in a 66 641 bp ICE from Histophilus somni. ICEPmu1 integrates into a tRNA(Leu) and is flanked by 13 bp direct repeats. It is able to conjugatively transfer to P. multocida, M. haemolytica and E. coli, where it also uses a tRNA(Leu) for integration and produces closely related 13 bp direct repeats. PCR assays and susceptibility testing confirmed the presence and the functional activity of the ICEPmu1-associated resistance genes in the recipient strains.
CONCLUSIONS: The observation that the multiresistance ICEPmu1 is present in a bovine P. multocida and can easily spread across strain and genus boundaries underlines the risk of a rapid dissemination of multiple resistance genes, which will distinctly decrease the therapeutic options.
ESTHER : Michael_2012_J.Antimicrob.Chemother_67_91
PubMedSearch : Michael_2012_J.Antimicrob.Chemother_67_91
PubMedID: 22001176
Gene_locus related to this paper: pasmu-PM0055

Title : The purine-utilizing bacterium Clostridium acidurici 9a: a genome-guided metabolic reconsideration - Hartwich_2012_PLoS.One_7_e51662
Author(s) : Hartwich K , Poehlein A , Daniel R
Ref : PLoS ONE , 7 :e51662 , 2012
Abstract : Clostridium acidurici is an anaerobic, homoacetogenic bacterium, which is able to use purines such as uric acid as sole carbon, nitrogen, and energy source. Together with the two other known purinolytic clostridia C. cylindrosporum and C. purinilyticum, C. acidurici serves as a model organism for investigation of purine fermentation. Here, we present the first complete sequence and analysis of a genome derived from a purinolytic Clostridium. The genome of C. acidurici 9a consists of one chromosome (3,105,335 bp) and one small circular plasmid (2,913 bp). The lack of candidate genes encoding glycine reductase indicates that C. acidurici 9a uses the energetically less favorable glycine-serine-pyruvate pathway for glycine degradation. In accordance with the specialized lifestyle and the corresponding narrow substrate spectrum of C. acidurici 9a, the number of genes involved in carbohydrate transport and metabolism is significantly lower than in other clostridia such as C. acetobutylicum, C. saccharolyticum, and C. beijerinckii. The only amino acid that can be degraded by C. acidurici is glycine but growth on glycine only occurs in the presence of a fermentable purine. Nevertheless, the addition of glycine resulted in increased transcription levels of genes encoding enzymes involved in the glycine-serine-pyruvate pathway such as serine hydroxymethyltransferase and acetate kinase, whereas the transcription levels of formate dehydrogenase-encoding genes decreased. Sugars could not be utilized by C. acidurici but the full genetic repertoire for glycolysis was detected. In addition, genes encoding enzymes that mediate resistance against several antimicrobials and metals were identified. High resistance of C. acidurici towards bacitracin, acriflavine and azaleucine was experimentally confirmed.
ESTHER : Hartwich_2012_PLoS.One_7_e51662
PubMedSearch : Hartwich_2012_PLoS.One_7_e51662
PubMedID: 23240052
Gene_locus related to this paper: gota9-k0aw45

Title : Genome sequence of Brevibacillus laterosporus LMG 15441, a pathogen of invertebrates - Djukic_2011_J.Bacteriol_193_5535
Author(s) : Djukic M , Poehlein A , Thurmer A , Daniel R
Ref : Journal of Bacteriology , 193 :5535 , 2011
Abstract : Here we announce the genome sequence of the bacterium Brevibacillus laterosporus LMG 15441, which is a pathogen of invertebrates. The genome consists of one chromosome and two circular plasmids. Sequence analysis revealed a large potential to produce polyketides, nonribosomal peptides, and toxins.
ESTHER : Djukic_2011_J.Bacteriol_193_5535
PubMedSearch : Djukic_2011_J.Bacteriol_193_5535
PubMedID: 21914864
Gene_locus related to this paper: brela-a0a075r7b1 , brela-a0a075r8m9 , brela-a0a075rfd2

Title : Comparative genomics and transcriptomics of Propionibacterium acnes - Brzuszkiewicz_2011_PLoS.One_6_e21581
Author(s) : Brzuszkiewicz E , Weiner J , Wollherr A , Thurmer A , Hupeden J , Lomholt HB , Kilian M , Gottschalk G , Daniel R , Mollenkopf HJ , Meyer TF , Bruggemann H
Ref : PLoS ONE , 6 :e21581 , 2011
Abstract : The anaerobic gram-positive bacterium Propionibacterium acnes is a human skin commensal that is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with maintenance of skin homeostasis. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits differ between phylotypes, as judged from PCR analysis of a collection of P. acnes strains. Comparative transcriptome analysis of strains KPA171202 (type I-2) and 266 during exponential growth revealed inter-strain differences in gene expression of transport systems and metabolic pathways. In addition, transcript levels of genes encoding possible virulence factors such as dermatan-sulphate adhesin, polyunsaturated fatty acid isomerase, iron acquisition protein HtaA and lipase GehA were upregulated in strain 266. We investigated differential gene expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by upregulation of genes involved in stress responses and amino acid metabolism. Our data highlight the genomic basis for strain diversity and identify, for the first time, the actively transcribed part of the genome, underlining the important role growth status plays in the inflammation-inducing activity of P. acnes. We argue that the disease-causing potential of different P. acnes strains is not only determined by the phylotype-specific genome content but also by variable gene expression.
ESTHER : Brzuszkiewicz_2011_PLoS.One_6_e21581
PubMedSearch : Brzuszkiewicz_2011_PLoS.One_6_e21581
PubMedID: 21738717
Gene_locus related to this paper: proac-q6a5t3 , proac-q6a5w7 , proac-q6a981

Title : Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories - Nacke_2011_FEMS.Microbiol.Ecol_78_188
Author(s) : Nacke H , Will C , Herzog S , Nowka B , Engelhaupt M , Daniel R
Ref : FEMS Microbiol Ecol , 78 :188 , 2011
Abstract : Microbial metagenomes derived from soils are rich sources for the discovery of novel genes and biocatalysts. Fourteen environmental plasmid and seven fosmid libraries obtained from 10 German forest soils (A horizons) and six grassland soils (A and B horizons) were screened for genes conferring lipolytic activity. The libraries comprised approximately 29.3 Gb of cloned soil DNA. Partial activity-based screening of the constructed libraries resulted in the identification of 37 unique lipolytic clones. The amino acid sequences of the 37 corresponding lipolytic gene products shared 29-90% identity to other lipolytic enzymes, which were mainly uncharacterized or derived from uncultured microorganisms. Multiple sequence alignments and phylogenetic tree analysis revealed that 35 of the predicted proteins were new members of known families of lipolytic enzymes. The remaining two gene products represent two putatively new families. In addition, sequence analysis indicated that two genes encode true lipases, whereas the other genes encode esterases. The determination of substrate specificity and chain-length selectivity using different triacylglycerides and p-nitrophenyl esters of fatty acids as substrates supported the classification of the esterases.
ESTHER : Nacke_2011_FEMS.Microbiol.Ecol_78_188
PubMedSearch : Nacke_2011_FEMS.Microbiol.Ecol_78_188
PubMedID: 21395625
Gene_locus related to this paper: 9zzzz-g3crf3 , 9zzzz-g3crg0 , 9zzzz-g3crd1 , 9zzzz-g3crg3 , 9zzzz-g3crf0 , 9zzzz-g3crf7 , 9zzzz-g3crf4 , 9zzzz-g3cre9 , 9zzzz-g3crf5 , 9zzzz-g3crf8 , 9zzzz-g3crc8 , 9zzzz-g3crg1 , 9zzzz-g3cre0 , 9zzzz-g3cre6 , 9zzzz-g3cre1 , 9zzzz-g3cre2 , 9zzzz-g3cre8 , 9zzzz-g3cre4 , 9zzzz-g3crd0 , 9zzzz-g3crc9 , 9zzzz-g3crf6 , 9zzzz-g3crf9 , 9zzzz-g3crg2 , 9zzzz-g3crd8 , 9zzzz-g3crd6 , 9zzzz-g3cre3 , 9zzzz-g3crd2 , 9zzzz-g3crf1 , 9zzzz-g3crc7 , 9zzzz-g3crc6

Title : Genomic features and insights into the biology of Mycoplasma fermentans - Rechnitzer_2011_Microbiology_157_760
Author(s) : Rechnitzer H , Brzuszkiewicz E , Strittmatter A , Liesegang H , Lysnyansky I , Daniel R , Gottschalk G , Rottem S
Ref : Microbiology , 157 :760 , 2011
Abstract : We present the complete genomic sequence of Mycoplasma fermentans, an organism suggested to be associated with the pathogenesis of rheumatoid arthritis in humans. The genome is composed of 977,524 bp and has a mean G+C content of 26.95 mol%. There are 835 predicted protein-coding sequences and a mean coding density of 87.6 %. Functions have been assigned to 58.8 % of the predicted protein-coding sequences, while 18.4 % of the proteins are conserved hypothetical proteins and 22.8 % are hypothetical proteins. In addition, there are two complete rRNA operons and 36 tRNA coding sequences. The largest gene families are the ABC transporter family (42 members), and the functionally heterogeneous group of lipoproteins (28 members), which encode the characteristic prokaryotic cysteine 'lipobox'. Protein secretion occurs through a pathway consisting of SecA, SecD, SecE, SecG, SecY and YidC. Some highly conserved eubacterial proteins, such as GroEL and GroES, are notably absent. The genes encoding DnaK-DnaJ-GrpE and Tig, forming the putative complex of chaperones, are intact, providing the only known control over protein folding. Eighteen nucleases and 17 proteases and peptidases were detected as well as three genes for the thioredoxin-thioreductase system. Overall, this study presents insights into the physiology of M. fermentans, and provides several examples of the genetic basis of systems that might function as virulence factors in this organism.
ESTHER : Rechnitzer_2011_Microbiology_157_760
PubMedSearch : Rechnitzer_2011_Microbiology_157_760
PubMedID: 21109561
Gene_locus related to this paper: mycfe-c4xfu4 , mycfp-c4xfg3

Title : Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5 - Volland_2011_J.Bacteriol_193_5043
Author(s) : Volland S , Rachinger M , Strittmatter A , Daniel R , Gottschalk G , Meyer O
Ref : Journal of Bacteriology , 193 :5043 , 2011
Abstract : We report on genome sequencing of Oligotropha carboxidovorans strain OM4 and resequencing of strain OM5. The genomes of both are composed of one chromosome and two plasmids. The presence of two plasmids in the OM5 genome is inconsistent with the previously published sequence, for which only one plasmid was described (D. Paul, S. Bridges, S. Burgess, Y. Dandass, and M. Lawrence, BMC Genomics 11:511, 2010).
ESTHER : Volland_2011_J.Bacteriol_193_5043
PubMedSearch : Volland_2011_J.Bacteriol_193_5043
PubMedID: 21742883
Gene_locus related to this paper: olico-b6jb07 , olico-b6jhe6

Title : Complete genome sequence of the type strain Cupriavidus necator N-1 - Poehlein_2011_J.Bacteriol_193_5017
Author(s) : Poehlein A , Kusian B , Friedrich B , Daniel R , Bowien B
Ref : Journal of Bacteriology , 193 :5017 , 2011
Abstract : Here we announce the complete genome sequence of the copper-resistant bacterium Cupriavidus necator N-1, the type strain of the genus Cupriavidus. The genome consists of two chromosomes and two circular plasmids. Based on genome comparison, the chromosomes of C. necator N-1 share a high degree of similarity with the two chromosomal replicons of the bioplastic-producing hydrogen bacterium Ralstonia eutropha H16. The two strains differ in their plasmids and the presence of hydrogenase genes, which are absent in strain N-1.
ESTHER : Poehlein_2011_J.Bacteriol_193_5017
PubMedSearch : Poehlein_2011_J.Bacteriol_193_5017
PubMedID: 21742890
Gene_locus related to this paper: alceu-catD1 , cupne-f8gup4 , cupnn-f8gp18 , cupnh-q0kd51 , cupnn-g0ewh7 , cupnn-f8gs82

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

Title : Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8 - Farnbacher_2010_BMC.Genomics_11_335
Author(s) : Farnbacher M , Jahns T , Willrodt D , Daniel R , Haas R , Goesmann A , Kurtz S , Rieder G
Ref : BMC Genomics , 11 :335 , 2010
Abstract : BACKGROUND: The Mongolian gerbils are a good model to mimic the Helicobacter pylori-associated pathogenesis of the human stomach. In the current study the gerbil-adapted strain B8 was completely sequenced, annotated and compared to previous genomes, including the 73 supercontigs of the parental strain B128.
RESULTS: The complete genome of H. pylori B8 was manually curated gene by gene, to assign as much function as possible. It consists of a circular chromosome of 1,673,997 bp and of a small plasmid of 6,032 bp carrying nine putative genes. The chromosome contains 1,711 coding sequences, 293 of which are strain-specific, coding mainly for hypothetical proteins, and a large plasticity zone containing a putative type-IV-secretion system and coding sequences with unknown function. The cag-pathogenicity island is rearranged such that the cagA-gene is located 13,730 bp downstream of the inverted gene cluster cagB-cag1. Directly adjacent to the cagA-gene, there are four hypothetical genes and one variable gene with a different codon usage compared to the rest of the H. pylori B8-genome. This indicates that these coding sequences might be acquired via horizontal gene transfer.The genome comparison of strain B8 to its parental strain B128 delivers 425 unique B8-proteins. Due to the fact that strain B128 was not fully sequenced and only automatically annotated, only 12 of these proteins are definitive singletons that might have been acquired during the gerbil-adaptation process of strain B128. CONCLUSION: Our sequence data and its analysis provide new insight into the high genetic diversity of H. pylori-strains. We have shown that the gerbil-adapted strain B8 has the potential to build, possibly by a high rate of mutation and recombination, a dynamic pool of genetic variants (e.g. fragmented genes and repetitive regions) required for the adaptation-processes. We hypothesize that these variants are essential for the colonization and persistence of strain B8 in the gerbil stomach during in ammation.
ESTHER : Farnbacher_2010_BMC.Genomics_11_335
PubMedSearch : Farnbacher_2010_BMC.Genomics_11_335
PubMedID: 20507619
Gene_locus related to this paper: helpy-o25061

Title : The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea - Wagner-Dobler_2010_Isme.J_4_61
Author(s) : Wagner-Dobler I , Ballhausen B , Berger M , Brinkhoff T , Buchholz I , Bunk B , Cypionka H , Daniel R , Drepper T , Gerdts G , Hahnke S , Han C , Jahn D , Kalhoefer D , Kiss H , Klenk HP , Kyrpides N , Liebl W , Liesegang H , Meincke L , Pati A , Petersen J , Piekarski T , Pommerenke C , Pradella S , Pukall R , Rabus R , Stackebrandt E , Thole S , Thompson L , Tielen P , Tomasch J , von Jan M , Wanphrut N , Wichels A , Zech H , Simon M
Ref : Isme J , 4 :61 , 2010
Abstract : Dinoroseobacter shibae DFL12(T), a member of the globally important marine Roseobacter clade, comprises symbionts of cosmopolitan marine microalgae, including toxic dinoflagellates. Its annotated 4 417 868 bp genome sequence revealed a possible advantage of this symbiosis for the algal host. D. shibae DFL12(T) is able to synthesize the vitamins B(1) and B(12) for which its host is auxotrophic. Two pathways for the de novo synthesis of vitamin B(12) are present, one requiring oxygen and the other an oxygen-independent pathway. The de novo synthesis of vitamin B(12) was confirmed to be functional, and D. shibae DFL12(T) was shown to provide the growth-limiting vitamins B(1) and B(12) to its dinoflagellate host. The Roseobacter clade has been considered to comprise obligate aerobic bacteria. However, D. shibae DFL12(T) is able to grow anaerobically using the alternative electron acceptors nitrate and dimethylsulfoxide; it has the arginine deiminase survival fermentation pathway and a complex oxygen-dependent Fnr (fumarate and nitrate reduction) regulon. Many of these traits are shared with other members of the Roseobacter clade. D. shibae DFL12(T) has five plasmids, showing examples for vertical recruitment of chromosomal genes (thiC) and horizontal gene transfer (cox genes, gene cluster of 47 kb) possibly by conjugation (vir gene cluster). The long-range (80%) synteny between two sister plasmids provides insights into the emergence of novel plasmids. D. shibae DFL12(T) shows the most complex viral defense system of all Rhodobacterales sequenced to date.
ESTHER : Wagner-Dobler_2010_Isme.J_4_61
PubMedSearch : Wagner-Dobler_2010_Isme.J_4_61
PubMedID: 19741735
Gene_locus related to this paper: dinsh-a8lqy2 , dinsh-a8luk0 , dinsh-a8lpz7

Title : Host imprints on bacterial genomes--rapid, divergent evolution in individual patients - Zdziarski_2010_PLoS.Pathog_6_e1001078
Author(s) : Zdziarski J , Brzuszkiewicz E , Wullt B , Liesegang H , Biran D , Voigt B , Gronberg-Hernandez J , Ragnarsdottir B , Hecker M , Ron EZ , Daniel R , Gottschalk G , Hacker J , Svanborg C , Dobrindt U
Ref : PLoS Pathog , 6 :e1001078 , 2010
Abstract : Bacteria lose or gain genetic material and through selection, new variants become fixed in the population. Here we provide the first, genome-wide example of a single bacterial strain's evolution in different deliberately colonized patients and the surprising insight that hosts appear to personalize their microflora. By first obtaining the complete genome sequence of the prototype asymptomatic bacteriuria strain E. coli 83972 and then resequencing its descendants after therapeutic bladder colonization of different patients, we identified 34 mutations, which affected metabolic and virulence-related genes. Further transcriptome and proteome analysis proved that these genome changes altered bacterial gene expression resulting in unique adaptation patterns in each patient. Our results provide evidence that, in addition to stochastic events, adaptive bacterial evolution is driven by individual host environments. Ongoing loss of gene function supports the hypothesis that evolution towards commensalism rather than virulence is favored during asymptomatic bladder colonization.
ESTHER : Zdziarski_2010_PLoS.Pathog_6_e1001078
PubMedSearch : Zdziarski_2010_PLoS.Pathog_6_e1001078
PubMedID: 20865122
Gene_locus related to this paper: ecoli-rutD , ecoli-bioh , ecoli-yafa , ecoli-ybff , ecoli-ycfp , ecoli-YFBB , ecoli-yqia , ecoli-YfhR

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

Title : Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms - Streit_2004_Curr.Opin.Biotechnol_15_285
Author(s) : Streit WR , Daniel R , Jaeger KE
Ref : Curr Opin Biotechnol , 15 :285 , 2004
Abstract : Modern biotechnology has a steadily increasing demand for vitamins, antibiotics and, in particular, novel biocatalysts for use in the production of flavors, agrochemicals, pharmaceuticals and high-value fine chemicals. Novel experimental approaches are being developed in attempts to identify such molecules. However, it is known that up to 99.8% of the microbes present in many environments are not readily culturable; hence, they cannot be exploited for biotechnology. The 'metagenome technology' offers a solution to this problem by developing culture-independent methods to isolate, clone and express environmental DNA. So far, metagenome-based approaches have led to the isolation of many novel biocatalysts and a variety of other molecules with a high potential for downstream applications.
ESTHER : Streit_2004_Curr.Opin.Biotechnol_15_285
PubMedSearch : Streit_2004_Curr.Opin.Biotechnol_15_285
PubMedID: 15296926

Title : Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli - Knietsch_2003_J.Mol.Microbiol.Biotechnol_5_46
Author(s) : Knietsch A , Waschkowitz T , Bowien S , Henne A , Daniel R
Ref : J Molecular Microbiology Biotechnol , 5 :46 , 2003
Abstract : Metagenomic DNA libraries from three different soil samples (meadow, sugar beet field, cropland) were constructed. The three unamplified libraries comprised approximately 1267000 independent clones and harbored approximately 4.05 Gbp of environmental DNA. Approximately 300000 recombinant Escherichia coli strains of each library per test substrate were screened for the production of carbonyls from short-chain (C2 to C4) polyols such as 1,2-ethanediol, 2,3-butanediol, and a mixture of glycerol and 1,2-propanediol on indicator agar. Twenty-four positive E. COLI clones were obtained during the initial screen. Fifteen of them contained recombinant plasmids, designated pAK201-215, which conferred a stable carbonyl-forming phenotype on E. coli Sequencing revealed that the inserts of pAK201-215 encoded 26 complete and 14 incomplete predicted protein-encoding genes. Most of these genes were similar to genes with unknown functions from other microorganisms or unrelated to any other known gene. The further analysis was focused on the 7 plasmids (pAK204, pAK206, pAK208, and pAK210-213) recovered from the positive clones, which exhibited an NAD(H)-dependent alcohol oxidoreductase activity with polyols or the correlating carbonyls as substrates in crude extracts. Three genes (ORF6, ORF24, and ORF25) conferring this activity were identified during subcloning of the inserts of pAK204, pAK211, and pAK212. The sequences of the three deduced gene products revealed no significant similarities to known alcohol oxidoreductases, but contained putative glycine-rich regions, which are characteristic for binding of nicotinamide cofactors.
ESTHER : Knietsch_2003_J.Mol.Microbiol.Biotechnol_5_46
PubMedSearch : Knietsch_2003_J.Mol.Microbiol.Biotechnol_5_46
PubMedID: 12673061
Gene_locus related to this paper: gamho-Q84CW1

Title : Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli - Knietsch_2003_Appl.Environ.Microbiol_69_1408
Author(s) : Knietsch A , Waschkowitz T , Bowien S , Henne A , Daniel R
Ref : Applied Environmental Microbiology , 69 :1408 , 2003
Abstract : Enrichment of microorganisms with special traits and the construction of metagenomic libraries by direct cloning of environmental DNA have great potential for identifying genes and gene products for biotechnological purposes. We have combined these techniques to isolate novel genes conferring oxidation of short-chain (C(2) to C(4)) polyols or reduction of the corresponding carbonyls. In order to favor the growth of microorganisms containing the targeted genes, samples collected from four different environments were incubated in the presence of glycerol and 1,2-propanediol. Subsequently, the DNA was extracted from the four samples and used to construct complex plasmid libraries. Approximately 100,000 Escherichia coli strains of each library per test substrate were screened for the production of carbonyls from polyols on indicator agar. Twenty-four positive E. coli clones were obtained during the initial screen. Sixteen of them contained a plasmid (pAK101 to pAK116) which conferred a stable carbonyl-forming phenotype. Eight of the positive clones exhibited NAD(H)-dependent alcohol oxidoreductase activity with polyols or carbonyls as the substrates in crude extracts. Sequencing revealed that the inserts of pAK101 to pAK116 encoded 36 complete and 17 incomplete presumptive protein-encoding genes. Fifty of these genes showed similarity to sequenced genes from a broad collection of different microorganisms. The genes responsible for the carbonyl formation of E. coli were identified for nine of the plasmids (pAK101, pAK102, pAK105, pAK107 to pAK110, pAK115, and pAK116). Analyses of the amino acid sequences deduced from these genes revealed that three (orf12, orf14, and orf22) encoded novel alcohol dehydrogenases of different types, four (orf5, sucB, fdhD, and yabF) encoded novel putative oxidoreductases belonging to groups distinct from alcohol dehydrogenases, one (glpK) encoded a putative glycerol kinase, and one (orf1) encoded a protein which showed no similarity to any other known gene product.
ESTHER : Knietsch_2003_Appl.Environ.Microbiol_69_1408
PubMedSearch : Knietsch_2003_Appl.Environ.Microbiol_69_1408
PubMedID: 12620823
Gene_locus related to this paper: uncba-Q848M3

Title : Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli - Henne_2000_Appl.Environ.Microbiol_66_3113
Author(s) : Henne A , Schmitz RA , Bomeke M , Gottschalk G , Daniel R
Ref : Applied Environmental Microbiology , 66 :3113 , 2000
Abstract : Environmental DNA libraries prepared from three different soil samples were screened for genes conferring lipolytic activity on Escherichia coli clones. Screening on triolein agar revealed 1 positive clone out of 730,000 clones, and screening on tributyrin agar revealed 3 positive clones out of 286,000 E. coli clones. Substrate specificity analysis revealed that one recombinant strain harbored a lipase and the other three contained esterases. The genes responsible for the lipolytic activity were identified and characterized.
ESTHER : Henne_2000_Appl.Environ.Microbiol_66_3113
PubMedSearch : Henne_2000_Appl.Environ.Microbiol_66_3113
PubMedID: 10877816
Gene_locus related to this paper: bacte-ester , gamho-LIPA , uncba-Q9KIU0 , uncba-Q9KIU2