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Li H.-W.,Yunnan University | Li H.-W.,Qujing Normal University | Zhi X.-Y.,Yunnan University | Zhi X.-Y.,CAS Institute of Microbiology | And 7 more authors.
PLoS ONE | Year: 2013

The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111T. The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins. © 2013 Li et al.

Scheuner C.,Deutsche Sammlung von Mikroorganismen und Zellkulturen | Goker M.,Deutsche Sammlung von Mikroorganismen und Zellkulturen | Porat I.,INEOS Bio | Klenk H.-P.,Deutsche Sammlung von Mikroorganismen und Zellkulturen
PLoS ONE | Year: 2011

Background: The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis. Methodology/Principal Findings: We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses. Conclusions: These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment. © 2011 Anderson et al.

Holmfeldt L.,St Jude Childrens Research Hospital | Wei L.,St Jude Childrens Research Hospital | Diaz-Flores E.,University of California at San Francisco | Walsh M.,St Jude Childrens Research Hospital | And 67 more authors.
Nature Genetics | Year: 2013

The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia. © 2013 Nature America, Inc. All rights reserved.

Ernst T.,University of Southampton | Ernst T.,Universitatsklinikum Jena | Chase A.J.,University of Southampton | Chase A.J.,Wessex Regional Genetics Laboratory | And 24 more authors.
Nature Genetics | Year: 2010

Abnormalities of chromosome 7q are common in myeloid malignancies, but no specific target genes have yet been identified. Here, we describe the finding of homozygous EZH2 mutations in 9 of 12 individuals with 7q acquired uniparental disomy. Screening of a total of 614 individuals with myeloid disorders revealed 49 monoallelic or biallelic EZH2 mutations in 42 individuals; the mutations were found most commonly in those with myelodysplastic/myeloproliferative neoplasms (27 out of 219 individuals, or 12%) and in those with myelofibrosis (4 out of 30 individuals, or 13%). EZH2 encodes the catalytic subunit of the polycomb repressive complex 2 (PRC2), a highly conserved histone H3 lysine 27 (H3K27) methyltransferase that influences stem cell renewal by epigenetic repression of genes involved in cell fate decisions. EZH2 has oncogenic activity, and its overexpression has previously been causally linked to differentiation blocks in epithelial tumors. Notably, the mutations we identified resulted in premature chain termination or direct abrogation of histone methyltransferase activity, suggesting that EZH2 acts as a tumor suppressor for myeloid malignancies. © 2010 Nature America, Inc. All rights reserved.

Young C.-C.,National Chung Hsing University | Busse H.-J.,University of Veterinary Medicine Vienna | Langer S.,University of Veterinary Medicine Vienna | Chu J.-N.,National Chung Hsing University | And 4 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2010

Three Gram-positive, rod-shaped bacteria (strains CC-SBCK-209T, CC-12309T and CC-5209T) were isolated from the stalk of the edible mushroom Agaricus blazei grown in the laboratory. 16S rRNA gene sequence analysis indicated that all three isolates clearly belonged to the genus Microbacterium. Strains CC-SBCK-209T and CC-12309T were most related closely to the type strain of Microbacterium halotolerans (95.9 and 96.1% 16S rRNA gene sequence similarity, respectively). These two novel strains shared 97.9 % 16S rRNA gene sequence similarity. Levels of similarity to the type strains of all other recognized Microbacterium species were lower than 95.5%. The third strain (CC-5209T) showed the highest 16S rRNA gene sequence similarity to the type strain of Microbacterium resistens (97.6 %); levels of similarity to the type strains of all other recognized Microbacterium species were lower than 96 %. The quinone systems of strains CC-SBCK-209T, CC-12309T and CC-5209T consisted of MK-11/MK-12, MK-11/MK-10 and MK-13 as major compounds, respectively. All three strains contained ornithine in their peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The polyamine pattern consisted of spermidine and spermine as predominant components. Fatty acid profiles (anteiso-C15:0, iso-C16:0 and anteiso-C17:0 as major components) supported the affiliation of all three strains to the genus Microbacterium. The results of physiological and biochemical tests and DNA-DNA hybridization experiments allowed the clear phenotypic and genotypic differentiation of strains CC-SBCK-209T and CC-12309T from M. halotolerans and other closely related Microbacterium species. Strain CC-5209T could be differentiated clearly from M. resistens both genotypically and phenotypically. Based on these data, the novel strains are considered to represent three novel species of the genus Microbacterium. The names proposed for these organisms are Microbacterium agarici sp. nov. [type strain CC-SBCK-209T (=DSM 21798T=CCM 7686T)], Microbacterium humi sp. nov. [type strain CC-12309T (=DSM 21799T=CCM 7687T)] and Microbacterium pseudoresistens sp. nov. [type strain CC-5209T (=DSM 22185v=CCM 7688T)]. © 2010 IUMS.

Young C.-C.,National Chung Hsing University | Busse H.-J.,University of Veterinary Medicine Vienna | Chu J.-N.,National Chung Hsing University | Schumann P.,Deutsche Sammlung von Mikroorganismen und Zellkulturen | And 3 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2010

A Gram-stain-positive, coccoid, non-endospore-forming actinobacterium (strain CC-12602T) was isolated from a spawn used for growing the edible mushroom Agaricus brasiliensis in the laboratory. On the basis of 16S rRNA gene sequence analysis, strain CC-12602T was shown to belong to the genus Microlunatus and was related most closely to the type strains of Microlunatus ginsengisoli (96.1 % similarity), M. phosphovorus (95.9 %), M. panaciterrae (95.8%) and M. aurantiacus (95.5 %). The quinone system comprised menaquinone MK-9(H4) as the major component and the polyamine pattern consisted of spermidine and spermine as major compounds. The predominant polar lipids were phosphatidylglycerol and unknown phospholipid PL3. Moderate amounts of diphosphatidylglycerol, an unknown glycolipid and three unknown phospholipids and minor amounts of an unknown phospholipid and a polar lipid were detected. The peptidoglycan type was A3γ', based on LL-2,6-diaminopimelic acid with an interpeptide bridge consisting of a single glycine residue and a second glycine residue at position 1 of the peptide subunit. Peptidoglycan structure and major fatty acids (anteiso-C15:0, iso-C16:0 and iso-C15:0) supported the affiliation of strain CC-12602T to the genus Microlunatus. The results of physiological and biochemical tests allowed strain CC-12602T to be differentiated phenotypically from recognized Microlunatus species. Strain CC-12602T is therefore considered to represent a novel species of the genus Microlunatus, for which the name Microlunatus soli sp. nov. is proposed. The type strain is CC-12602 T (=DSM 21800T =CCM 7685T). © 2010 IUMS.

Mwirichia R.,Jomo Kenyatta University of Agriculture and Technology | Muigai A.W.,Jomo Kenyatta University of Agriculture and Technology | Tindall B.,Deutsche Sammlung von Mikroorganismen und Zellkulturen | Boga H.I.,Jomo Kenyatta University of Agriculture and Technology | Stackebrandt E.,Deutsche Sammlung von Mikroorganismen und Zellkulturen
Extremophiles | Year: 2010

Culture-independent studies show that soda lake environments harbour diverse groups of bacteria and archaea. In this study different enrichment and isolation media were used in an attempt to isolate novel groups of bacteria from Lake Elmenteita. Different media were prepared using filter-sterilised water from the lake. The isolates recovered were purified on tryptic soy agar supplemented with 1% sodium carbonate and 4% sodium chloride. Phylogenetic analysis of 181 partial 16S rRNA gene sequences with excellent quality showed that the majority of the isolates were affiliated to the class Gammaproteobacteria and to the genus Bacillus. Isolates from the genus Halomonas and Bacillus constituted 37 and 31% of the total sequenced isolates, respectively. Other groups recovered were related to Marinospirillum, Idiomarina, Vibrio, Enterococcus, Alkalimonas, Alkalibacterium, Amphibacillus, Marinilactibacillus and the actinobacteria Nocardiopsis and Streptomyces. Fifty-one different genera were represented with 31 and 15 cultures scoring with their nearest neighbour similarities below 98 and 97%, respectively. Some novel taxa were identified which had not been isolated previously from the soda environment. The results show that the use of different media with varying compositions can help retrieve novel bacterial diversity from the soda lake environment. © 2010 Springer.

Citron C.A.,TU Braunschweig | Gleitzmann J.,TU Braunschweig | Laurenzano G.,TU Braunschweig | Pukall R.,Deutsche Sammlung von Mikroorganismen und Zellkulturen | Dickschat J.S.,TU Braunschweig
ChemBioChem | Year: 2012

The genomes of all bacteria with publicly available sequenced genomes have been screened for the presence of sesquiterpene cyclase homologues, resulting in the identification of 55 putative geosmin synthases, 23 homologues of 2-methylisoborneol synthases, and 98 other sesquiterpene cyclase homologues. Most of these enzymes by far were found in actinomycetes. The terpenoid volatiles from 35 strains, including 31 actinomycetes and four strains from other taxa, were collected by using a closed-loop stripping apparatus and identified by GC-MS. All of these bacteria apart from one strain encode sesquiterpene cyclase homologues in their genomes. The identified volatile terpenoids were grouped according to structural similarities and their biosynthetic relationship, and the results of these analyses were correlated to the available genome information, resulting in valuable new insights into bacterial terpene biosynthesis. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chen Y.-G.,JiShou University | Zhang Y.-Q.,Chinese Academy of Sciences | Chen Q.-H.,JiShou University | Klenk H.-P.,Deutsche Sammlung von Mikroorganismen und Zellkulturen | And 5 more authors.
International Journal of Systematic and Evolutionary Microbiology | Year: 2011

A novel Gram-stain-positive, slightly halophilic, catalase-positive, oxidase-negative, endosporeforming, motile, facultatively anaerobic, rod-shaped bacterium, designated strain JSM 081004 T, was isolated from non-saline forest soil in Xiaoxi National Natural Reserve, China. Growth occurred with 0.5-20% (w/v) NaCl (optimum 2-4%), at pH 6.0-10.5 (optimum pH 8.0) and at 5-40 °C (optimum 25-30 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The major cellular fatty acids were iso-C 15:0 and anteiso-C 15:0. Strain JSM 081004 T contained MK-7 as the predominant respiratory quinone, and diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as the major polar lipids. The genomic DNA G+C content of strain JSM 081004 T was 40.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 081004 T should be assigned to the genus Bacillus and was most closely related to the type strains of Bacillus lehensis (sequence similarity 97.8%), Bacillus oshimensis (97.8%) and Bacillus patagoniensis (97.3%). Phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data all support the proposal of strain JSM 081004 T as a representative of a novel species of the genus Bacillus, for which the name Bacillus xiaoxiensis sp. nov. is proposed; the type strain is JSM 081004 T (=CCTCC AA 208057 T=DSM 21943 T). © 2011 IUMS.

Martin E.,Justus Liebig University | Lodders N.,Justus Liebig University | Jackel U.,Bundesanstalt fur Arbeitschutz und Arbeitsmedizin | Schumann P.,Deutsche Sammlung Von Mikroorganismen und Zellkulturen | Kampfer P.,Justus Liebig University
International Journal of Systematic and Evolutionary Microbiology | Year: 2010

A Gram-positive, non-spore-forming actinobacterium (Sj 10T) was isolated on tryptone soy agar from the air of a duck barn after filter sampling. Based on 16S rRNA gene sequence similarity studies, strain Sj 10T was shown to belong to the genus Leucobacter and was closely related to Leucobacter chromiireducens subsp. chromiireducens L-1T (97.8 %), Leucobacter tardus DSM 19811T (97.3 %) and Leucobacter luti RF6 T (97.3 %). The peptidoglycan of strain Sj 10T contained 2,4-diaminobutyric acid in combination with a lower amount of lysine as diagnostic diamino acids. In addition, threonine, glycine, alanine and glutamic acid were found. Menaquinone MK-11 was the major respiratory quinone; MK-12 and MK-10 were detected in minor amounts. The polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol and one unknown component each of a phospholipid, glycolipid and aminoglycolipid. Strain Sj 10T contained the major fatty acids anteiso-C15 : 0, iso-C 16 : 0 and anteiso-C17 : 0, like other members of the genus Leucobacter. Results of DNA-DNA hybridization, physiological and biochemical tests enabled strain Sj 10T to be differentiated genotypically and phenotypically from the most closely related Leucobacter species. Strain Sj 10T represents a novel species of the genus Leucobacter, for which the name Leucobacter aerolatus sp. nov. is proposed, with Sj 10T (=DSM 22806T =CCM 7705T) as the type strain. © 2010 IUMS.

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