• Identification of an immune-regulated phagosomal Rab cascade in macrophages.

      Pei, Gang; Repnik, Urska; Griffiths, Gareth; Gutierrez, Maximiliano Gabriel; Helmholtz Centre for infection research, Inhoffenstr. 7 , D-38124 Braunschweig, Germany. (2014-05-01)
      Interferon-γ (IFN-γ) has been shown to regulate phagosome trafficking and function in macrophages, but the molecular mechanisms involved are poorly understood. Here, we identify Rab20 as part of the machinery by which IFN-γ controls phagosome maturation. We found that IFN-γ stimulates the association of Rab20 with early phagosomes in macrophages. By using imaging of single phagosomes in live cells, we found that Rab20 induces an early delay in phagosome maturation and extends the time for which Rab5a and phosphatidylinositol 3-phosphate (PI3P) remain associated with phagosomes. Moreover, Rab20 depletion in macrophages abrogates the delay in phagosome maturation induced by IFN-γ. Finally, we demonstrate that Rab20 interacts with the Rab5a guanine nucleotide exchange factor Rabex-5 (also known as RABGEF1) and that Rab20 knockdown impairs the IFN-γ-dependent recruitment of Rabex-5 and Rab5a into phagosomes. Taken together, here, we uncover Rab20 as a key player in the Rab cascade by which IFN-γ induces a delay in phagosome maturation in macrophages.
    • Complete genome sequence of Desulfarculus baarsii type strain (2st14).

      Sun, Hui; Spring, Stefan; Lapidus, Alla; Davenport, Karen; Del Rio, Tijana Glavina; Tice, Hope; Nolan, Matt; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; et al. (2010)
      Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO(2). The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14(T) was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Planctomyces limnophilus type strain (Mü 290).

      Labutti, Kurt; Sikorski, Johannes; Schneider, Susanne; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne; Pitluck, Sam; et al. (2010)
      Planctomyces limnophilus Hirsch and Müller 1986 belongs to the order Planctomycetales, which differs from other bacterial taxa by several distinctive features such as internal cell compartmentalization, multiplication by forming buds directly from the spherical, ovoid or pear-shaped mother cell and a cell wall which is stabilized by a proteinaceous layer rather than a peptidoglycan layer. Besides Pirellula staleyi, this is the second completed genome sequence of the family Planctomycetaceae. P. limnophilus is of interest because it differs from Pirellula by the presence of a stalk and its structure of fibril bundles, its cell shape and size, the formation of multicellular rosettes, low salt tolerance and red pigmented colonies. The 5,460,085 bp long genome with its 4,304 protein-coding and 66 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Nakamurella multipartita type strain (Y-104).

      Tice, Hope; Mayilraj, Shanmugam; Sims, David; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Copeland, Alex; Cheng, Jan-Fang; Meincke, Linda; et al. (2010)
      Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the monospecific genus Nakamurella in the actinobacterial suborder Frankineae. The nonmotile, coccus-shaped strain was isolated from activated sludge acclimated with sugar-containing synthetic wastewater, and is capable of accumulating large amounts of polysaccharides in its cells. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Geodermatophilus obscurus type strain (G-20).

      Ivanova, Natalia; Sikorski, Johannes; Jando, Marlen; Munk, Christine; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; et al. (2010)
      Geodermatophilus obscurus Luedemann 1968 is the type species of the genus, which is the type genus of the family Geodermatophilaceae. G. obscurus is of interest as it has frequently been isolated from stressful environments such as rock varnish in deserts, and as it exhibits interesting phenotypes such as lytic capability of yeast cell walls, UV-C resistance, strong production of extracellular functional amyloid (FuBA) and manganese oxidation. This is the first completed genome sequence of the family Geodermatophilaceae. The 5,322,497 bp long genome with its 5,161 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Brachyspira murdochii type strain (56-150).

      Pati, Amrita; Sikorski, Johannes; Gronow, Sabine; Munk, Christine; Lapidus, Alla; Copeland, Alex; Glavina Del Tio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; et al. (2010)
      Brachyspira murdochii Stanton et al. 1992 is a non-pathogenic, host-associated spirochete of the family Brachyspiraceae. Initially isolated from the intestinal content of a healthy swine, the 'group B spirochaetes' were first described as Serpulina murdochii. Members of the family Brachyspiraceae are of great phylogenetic interest because of the extremely isolated location of this family within the phylum 'Spirochaetes'. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a type strain of a member of the family Brachyspiraceae and only the second genome sequence from a member of the genus Brachyspira. The 3,241,804 bp long genome with its 2,893 protein-coding and 40 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).

      Glavina Del Rio, Tijana; Abt, Birte; Spring, Stefan; Lapidus, Alla; Nolan, Matt; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; et al. (2010)
      Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is the type species of the rapidly growing genus Chitinophaga in the sphingobacterial family 'Chitinophagaceae'. Members of the genus Chitinophaga vary in shape between filaments and spherical bodies without the production of a fruiting body, produce myxospores, and are of special interest for their ability to degrade chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family 'Chitinophagaceae', and the 9,127,347 bp long single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Thermaerobacter marianensis type strain (7p75a).

      Han, Cliff; Gu, Wei; Zhang, Xiaojing; Lapidus, Alla; Nolan, Matt; Copeland, Alex; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; et al. (2010)
      Thermaerobacter marianensis Takai et al. 1999 is the type species of the genus Thermaerobacter, which belongs to the Clostridiales family Incertae Sedis XVII. The species is of special interest because T. marianensis is an aerobic, thermophilic marine bacterium, originally isolated from the deepest part in the western Pacific Ocean (Mariana Trench) at the depth of 10.897m. Interestingly, the taxonomic status of the genus has not been clarified until now. The genus Thermaerobacter may represent a very deep group within the Firmicutes or potentially a novel phylum. The 2,844,696 bp long genome with its 2,375 protein-coding and 60 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Thermocrinis albus type strain (HI 11/12).

      Wirth, Reinhard; Sikorski, Johannes; Brambilla, Evelyne; Misra, Monica; Lapidus, Alla; Copeland, Alex; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; et al. (2010)
      Thermocrinis albus Eder and Huber 2002 is one of three species in the genus Thermocrinis in the family Aquificaceae. Members of this family have become of significant interest because of their involvement in global biogeochemical cycles in high-temperature ecosystems. This interest had already spurred several genome sequencing projects for members of the family. We here report the first completed genome sequence a member of the genus Thermocrinis and the first type strain genome from a member of the family Aquificaceae. The 1,500,577 bp long genome with its 1,603 protein-coding and 47 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Sulfurimonas autotrophica type strain (OK10).

      Sikorski, Johannes; Munk, Christine; Lapidus, Alla; Ngatchou Djao, Olivier Duplex; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Han, Cliff; Cheng, Jan-Fang; et al. (2010)
      Sulfurimonas autotrophica Inagaki et al. 2003 is the type species of the genus Sulfurimonas. This genus is of interest because of its significant contribution to the global sulfur cycle as it oxidizes sulfur compounds to sulfate and by its apparent habitation of deep-sea hydrothermal and marine sulfidic environments as potential ecological niche. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second complete genome sequence of the genus Sulfurimonas and the 15(th) genome in the family Helicobacteraceae. The 2,153,198 bp long genome with its 2,165 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Methanoplanus petrolearius type strain (SEBR 4847).

      Brambilla, Evelyne; Djao, Olivier Duplex Ngatchou; Daligault, Hajnalka; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; et al. (2010)
      Methanoplanus petrolearius Ollivier et al. 1998 is the type strain of the genus Methanoplanus. The strain was originally isolated from an offshore oil field from the Gulf of Guinea. Members of the genus Methanoplanus are of interest because they play an important role in the carbon cycle and also because of their significant contribution to the global warming by methane emission in the atmosphere. Like other archaea of the family Methanomicrobiales, the members of the genus Methanoplanus are able to use CO(2) and H(2) as a source of carbon and energy; acetate is required for growth and probably also serves as carbon source. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Methanomicrobiaceae and the sixth complete genome sequence from the order Methanomicrobiales. The 2,843,290 bp long genome with its 2,824 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Spirosoma linguale type strain (1).

      Lail, Kathleen; Sikorski, Johannes; Saunders, Elizabeth; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Nolan, Matt; et al. (2010)
      Spirosoma linguale Migula 1894 is the type species of the genus. S. linguale is a free-living and non-pathogenic organism, known for its peculiar ringlike and horseshoe-shaped cell morphology. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is only the third completed genome sequence of a member of the family Cytophagaceae. The 8,491,258 bp long genome with its eight plasmids, 7,069 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Thermobispora bispora type strain (R51).

      Liolios, Konstantinos; Sikorski, Johannes; Jando, Marlen; Lapidus, Alla; Copeland, Alex; Glavina, Tijana; Del Rio; Nolan, Matt; Lucas, Susan; Tice, Hope; et al. (2010)
      Thermobispora bispora (Henssen 1957) Wang et al. 1996 is the type species of the genus Thermobispora. This genus is of great interest because it is strictly thermophilic and because it has been shown for several of its members that the genome contains substantially distinct (6.4% sequence difference) and transcriptionally active 16S rRNA genes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member from the suborder Streptosporangineae and the first genome sequence of a member of the genus Thermobispora. The 4,189,976 bp long genome with its 3,596 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)).

      Spring, Stefan; Nolan, Matt; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Land, Miriam; Chen, Feng; et al. (2010)
      Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Methanothermus fervidus type strain (V24S).

      Anderson, Iain; Djao, Olivier Duplex Ngatchou; Misra, Monica; Chertkov, Olga; Nolan, Matt; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; et al. (2010)
      Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature (97°C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24S(T) is of interest because of its very low substrate ranges, it grows only on H(2) + CO(2). This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Sulfurospirillum deleyianum type strain (5175).

      Sikorski, Johannes; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Saunders, Elizabeth; et al. (2010)
      Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as an energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of cytochrome c nitrite reductase. Here, we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA).

      Mavromatis, Konstantinos; Sikorski, Johannes; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; et al. (2010)
      Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family 'Alicyclobacillaceae'. A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family 'Alicyclobacillaceae'. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Veillonella parvula type strain (Te3).

      Gronow, Sabine; Welnitz, Sabine; Lapidus, Alla; Nolan, Matt; Ivanova, Natalia; Glavina Del Rio, Tijana; Copeland, Alex; Chen, Feng; Tice, Hope; Pitluck, Sam; et al. (2010)
      Veillonella parvula (Veillon and Zuber 1898) Prévot 1933 is the type species of the genus Veillonella in the family Veillonellaceae within the order Clostridiales. The species V. parvula is of interest because it is frequently isolated from dental plaque in the human oral cavity and can cause opportunistic infections. The species is strictly anaerobic and grows as small cocci which usually occur in pairs. Veillonellae are characterized by their unusual metabolism which is centered on the activity of the enzyme methylmalonyl-CoA decarboxylase. Strain Te3(T), the type strain of the species, was isolated from the human intestinal tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large clostridial family Veillonellaceae, and the 2,132,142 bp long single replicon genome with its 1,859 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Streptosporangium roseum type strain (NI 9100).

      Nolan, Matt; Sikorski, Johannes; Jando, Marlen; Lucas, Susan; Lapidus, Alla; Glavina Del Rio, Tijana; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; et al. (2010)
      Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The 'pinkish coiled Streptomyces-like organism with a spore case' was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
    • Complete genome sequence of Kribbella flavida type strain (IFO 14399).

      Pukall, Rüdiger; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Labutti, Kurt; et al. (2010)
      The genus Kribbella consists of 15 species, with Kribbella flavida (Park et al. 1999) as the type species. The name Kribbella was formed from the acronym of the Korea Research Institute of Bioscience and Biotechnology, KRIBB. Strains of the various Kribbella species were originally isolated from soil, potato, alum slate mine, patinas of catacombs or from horse racecourses. Here we describe the features of K. flavida together with the complete genome sequence and annotation. In addition to the 5.3 Mbp genome of Nocardioides sp. JS614, this is only the second completed genome sequence of the family Nocardioidaceae. The 7,579,488 bp long genome with its 7,086 protein-coding and 60 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.