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Asset Tag: Microbiology

July 7, 2019

A novel type pathway-specific regulator and dynamic genome environments of solanapyrone biosynthesis gene cluster in the fungus Ascochyta rabiei.

Secondary metabolite genes are often clustered together and situated in particular genomic regions, like the subtelomere, that can facilitate niche adaptation in fungi. Solanapyrones are toxic secondary metabolites produced by fungi occupying different ecological niches. Full-genome sequencing of the ascomycete Ascochyta rabiei revealed a solanapyrone biosynthesis gene cluster embedded in an AT-rich region proximal to a telomere end and surrounded by Tc1/Mariner-type transposable elements. The highly AT-rich environment of the solanapyrone cluster is likely the product of repeat-induced point mutations. Several secondary metabolism-related genes were found in the flanking regions of the solanapyrone cluster. Although the solanapyrone cluster appears to be resistant to repeat-induced point mutations, a P450 monooxygenase gene adjacent to the cluster has been degraded by such mutations. Among the six solanapyrone cluster genes (sol1 to sol6), sol4 encodes a novel type of Zn(II)2Cys6 zinc cluster transcription factor. Deletion of sol4 resulted in the complete loss of solanapyrone production but did not compromise growth, sporulation, or virulence. Gene expression studies with the sol4 deletion and sol4-overexpressing mutants delimited the boundaries of the solanapyrone gene cluster and revealed that sol4 is likely a specific regulator of solanapyrone biosynthesis and appears to be necessary and sufficient for induction of the solanapyrone cluster genes. Despite the dynamic surrounding genomic regions, the solanapyrone gene cluster has maintained its integrity, suggesting important roles of solanapyrones in fungal biology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

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July 7, 2019

Dual functions of Macpiwi1 in transposon silencing and stem cell maintenance in the flatworm Macrostomum lignano.

PIWI proteins and piRNA pathways are essential for transposon silencing and some aspects of gene regulation during animal germline development. In contrast to most animal species, some flatworms also express PIWIs and piRNAs in somatic stem cells, where they are required for tissue renewal and regeneration. Here, we have identified and characterized piRNAs and PIWI proteins in the emerging model flatworm Macrostomum lignano. We found that M. lignano encodes at least three PIWI proteins. One of these, Macpiwi1, acts as a key component of the canonical piRNA pathway in the germline and in somatic stem cells. Knockdown of Macpiwi1 dramatically reduces piRNA levels, derepresses transposons, and severely impacts stem cell maintenance. Knockdown of the piRNA biogenesis factor Macvasa caused an even greater reduction in piRNA levels with a corresponding increase in transposons. Yet, in Macvasa knockdown animals, we detected no major impact on stem cell self-renewal. These results may suggest stem cell maintenance functions of PIWI proteins in flatworms that are distinguishable from their impact on transposons and that might function independently of what are considered canonical piRNA populations.© 2015 Zhou et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

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July 7, 2019

Complex population structure and virulence differences among serotype 2 Streptococcus suis strains belonging to sequence type 28.

Streptococcus suis is a major swine pathogen and a zoonotic agent. Serotype 2 strains are the most frequently associated with disease. However, not all serotype 2 lineages are considered virulent. Indeed, sequence type (ST) 28 serotype 2 S. suis strains have been described as a homogeneous group of low virulence. However, ST28 strains are often isolated from diseased swine in some countries, and at least four human ST28 cases have been reported. Here, we used whole-genome sequencing and animal infection models to test the hypothesis that the ST28 lineage comprises strains of different genetic backgrounds and different virulence. We used 50 S. suis ST28 strains isolated in Canada, the United States and Japan from diseased pigs, and one ST28 strain from a human case isolated in Thailand. We report a complex population structure among the 51 ST28 strains. Diversity resulted from variable gene content, recombination events and numerous genome-wide polymorphisms not attributable to recombination. Phylogenetic analysis using core genome single-nucleotide polymorphisms revealed four discrete clades with strong geographic structure, and a fifth clade formed by US, Thai and Japanese strains. When tested in experimental animal models, strains from this latter clade were significantly more virulent than a Canadian ST28 reference strain, and a closely related Canadian strain. Our results highlight the limitations of MLST for both phylogenetic analysis and virulence prediction and raise concerns about the possible emergence of ST28 strains in human clinical cases.

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July 7, 2019

A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose.

Thermophilic Campylobacter species colonize the intestine of agricultural and domestic animals commensally but cause severe gastroenteritis in humans. In contrast to other enteropathogenic bacteria, Campylobacter has been considered to be non-glycolytic, a metabolic property originally used for their taxonomic classification. Contrary to this dogma, we demonstrate that several Campylobacter coli strains are able to utilize glucose as a growth substrate. Isotopologue profiling experiments with (13) C-labeled glucose suggested that these strains catabolize glucose via the pentose phosphate and Entner-Doudoroff (ED) pathways and use glucose efficiently for de novo synthesis of amino acids and cell surface carbohydrates. Whole genome sequencing of glycolytic C.?coli isolates identified a genomic island located within a ribosomal RNA gene cluster that encodes for all ED pathway enzymes and a glucose permease. We could show in vitro that a non-glycolytic C.?coli strain could acquire glycolytic activity through natural transformation with chromosomal DNA of C.?coli and C.?jejuni subsp. doylei strains possessing the ED pathway encoding plasticity region. These results reveal for the first time the ability of a Campylobacter species to catabolize glucose and provide new insights into how genetic macrodiversity through intra- and interspecies gene transfer expand the metabolic capacity of this food-borne pathogen. © 2015 John Wiley & Sons Ltd.

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July 7, 2019

Complete genome sequences of two Bordetella hinzii strains isolated from humans.

Bordetella hinzii is primarily recovered from poultry but can also colonize mammalian hosts and immunocompromised humans. Here, we report the first complete genome sequences of B. hinzii in two isolates recovered from humans. The availability of these sequences will hopefully aid in identifying host-specific determinants variably present within this species. Copyright © 2015 Weigand et al.

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July 7, 2019

Complete genome sequence of Streptomyces sp. strain CFMR 7, a natural rubber degrading actinomycete isolated from Penang, Malaysia.

Streptomyces sp. strain CFMR 7, which naturally degrades rubber, was isolated from a rubber plantation. Whole genome sequencing and assembly resulted in 2 contigs with total genome size of 8.248 Mb. Two latex clearing protein (lcp) genes which are responsible for rubber degrading activities were identified. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Lactobacillus paracasei CAUH35, a new strain isolated from traditional fermented dairy product koumiss in China.

Lactobacillus paracasei CAUH35 was isolated from homemade koumiss, a traditional fermented dairy product with beneficial effects on human health. The genome consists of a circular 2,770,411bp chromosome and four plasmids. Genome analysis revealed the presence of gene clusters involved in the production of exopolysaccharides and bacteriocin. The complete genome sequence of L. paracasei CAUH35 will provide genetic basis for further comparative and functional genomic analyses. Copyright © 2015. Published by Elsevier B.V.

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July 7, 2019

Complete genome sequence of Clostridium pasteurianum NRRL B-598, a non-type strain producing butanol.

The strain Clostridium pasteurianum NRRL B-598 is non-type, oxygen tolerant, spore-forming, mesophilic and heterofermentative strain with high hydrogen production and ability of acetone-butanol fermentation (ethanol production being negligible). Here, we present the annotated complete genome sequence of this bacterium, replacing the previous draft genome assembly. The genome consisting of a single circular 6,186,879bp chromosome with no plasmid was determined using PacBio RSII and Roche 454 sequencing. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Photorhabdus temperata subsp. thracensis 39-8(T), an entomopathogenic bacterium for the improved commercial bioinsecticide.

Photorhabdus temperata subsp. thracensis 39-8(T), a symbiotic bacterium from an entomopathogenic nematode Heterorhabditis bacteriophora, is a novel bacterium harboring insect pathogenicity. Herein, we present the complete genome sequence of strain 39-8(T), which consists of one circular chromosome of 5,147,098bp with a GC content of 44.10%. This genetic information will provide insights into biotechnological applications of the genus Photorhabdus producing insecticidal toxins, leading to the enhanced commercial bioinsecticide in agricultural pest control. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence, metabolic model construction and phenotypic characterization of Geobacillus LC300, an extremely thermophilic, fast growing, xylose-utilizing bacterium.

We have isolated a new extremely thermophilic fast-growing Geobacillus strain that can efficiently utilize xylose, glucose, mannose and galactose for cell growth. When grown aerobically at 72°C, Geobacillus LC300 has a growth rate of 2.15h(-1) on glucose and 1.52h(-1) on xylose (doubling time less than 30min). The corresponding specific glucose and xylose utilization rates are 5.55g/g/h and 5.24g/g/h, respectively. As such, Geobacillus LC300 grows 3-times faster than E. coli on glucose and xylose, and has a specific xylose utilization rate that is 3-times higher than the best metabolically engineered organism to date. To gain more insight into the metabolism of Geobacillus LC300 its genome was sequenced using PacBio?s RS II single-molecule real-time (SMRT) sequencing platform and annotated using the RAST server. Based on the genome annotation and the measured biomass composition a core metabolic network model was constructed. To further demonstrate the biotechnological potential of this organism, Geobacillus LC300 was grown to high cell-densities in a fed-batch culture, where cells maintained a high xylose utilization rate under low dissolved oxygen concentrations. All of these characteristics make Geobacillus LC300 an attractive host for future metabolic engineering and biotechnology applications. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

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July 7, 2019

Complete genome sequence of Serratia fonticola DSM 4576(T), a potential plant growth promoting bacterium.

Here, we present the first complete genome sequence of Serratia fonticola DSM 4576(T), a potential plant growth promoting (PGP) bacterium which confers solubilization of inorganic phosphate, indole-3-acetic acid production, hydrogen cyanideproduction, siderophore production and assimilation of ammonia through the glutamate synthase (GS/GOGAT) pathway. This genome sequence is valuable for functional genomics and ecological studies which are related to PGP and biocontrol activities. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome of Pandoraea pnomenusa RB-38, an oxalotrophic bacterium isolated from municipal solid waste landfill site.

Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Streptomyces ambofaciens ATCC 23877, the spiramycin producer.

Streptomyces ambofaciens ATCC23877 is a soil bacterium industrially exploited for the production of the macrolide spiramycin which is used in human medicine as an antibacterial and anti-toxoplasmosis chemical. Its genome consists of a 8.3Mbp linear chromosome and a 89kb circular plasmid. The complete genome sequence reported here will enable us to investigate Streptomyces genome evolution and to discover new secondary metabolites with potential applications notably in human medicine. Copyright © 2015 Elsevier B.V. All rights reserved.

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July 7, 2019

Complete genome sequence of Arthrobacter sp. ERGS1:01, a putative novel bacterium with prospective cold active industrial enzymes, isolated from East Rathong glacier in India.

We report the complete genome sequence of Arthrobacter sp. ERGS1:01, a novel bacterium which produces industrial enzymes at low temperature. East Rathong glacier in Sikkim Himalayas is untouched and unexplored for microbial diversity though it has a rich source of glaciers, alpine and meadows. Genome sequence has provided the basis for understanding its adaptation under harsh condition of Himalayan glacier, its ability to produce cold active industrial enzymes and has unlocked opportunities for microbial bioprospection from East Rathong glacier. Copyright © 2015. Published by Elsevier B.V.

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July 7, 2019

The complete genome sequence of a high pristinamycin-producing strain Streptomyces pristinaespiralis HCCB10218.

Streptomyces pristinaespiralis produces the streptogramin-like antibiotic pristinamycin, which is a mixture of two structurally different components: pristinamycin I (PI) and pristinamycin II (PII). Herein, we report the complete genome sequence of a high pristinamycin-producing strain HCCB10218 (8.5Mb) obtained by using PacBio RSII combined with Illumina HiSeq 2500 sequencing system. The genome sequence presented here provides clues for the mechanism underlying the higher pristinamycin production of HCCB10218. Copyright © 2015 Elsevier B.V. All rights reserved.

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