Marine metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA263191 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. Bioinformatic analysis identified genes encoding polyamine transporters in 74 of 109 marine bacterial genomes surveyed, a surprising frequency for a class of organic nitrogen compounds not generally recognized as an important source of carbon and nitrogen for marine bacterioplankton. The genome sequence of marine model bacterium Silicibacter pomeroyi DSS-3 contains a number of genes putatively involved in polyamine use, including six four-gene ATP-binding cassette transport systems. In the present study, polyamine uptake and metabolism by S. pomeroyi was examined to confirm the role of putative polyamine-related genes, and to investigate how well current gene annotations reflect function. A comparative whole-genome microarray approach (Bürgmann et al., 2007) allowed us to identify key genes for transport and metabolism of spermidine in this bacterium, and specify candidate genes for in situ monitoring of polyamine transformations in marine bacterioplankton communities.
2008-12-31 | GSE13781 | GEO
Project description:Polyamines, such as putrescine and spermidine, are aliphatic organic compounds with multiple amino groups. They are found ubiquitously in marine systems. However, compared with the extensive studies on the concentration and fate of other dissolved organic nitrogen compounds in seawater, such as dissolved free amino acids (DFAA), investigations of bacterially-mediated polyamine transformations have been rare. Bioinformatic analysis identified genes encoding polyamine transporters in 74 of 109 marine bacterial genomes surveyed, a surprising frequency for a class of organic nitrogen compounds not generally recognized as an important source of carbon and nitrogen for marine bacterioplankton. The genome sequence of marine model bacterium Silicibacter pomeroyi DSS-3 contains a number of genes putatively involved in polyamine use, including six four-gene ATP-binding cassette transport systems. In the present study, polyamine uptake and metabolism by S. pomeroyi was examined to confirm the role of putative polyamine-related genes, and to investigate how well current gene annotations reflect function. A comparative whole-genome microarray approach (Bürgmann et al., 2007) allowed us to identify key genes for transport and metabolism of spermidine in this bacterium, and specify candidate genes for in situ monitoring of polyamine transformations in marine bacterioplankton communities. Silicibacter pomeroyi DSS-3 cells were grown in chemostat in a modified marine basal medium (MBM) containing spermidine as sole carbon and nitrogen source. Serine was used as a substrate to provide comparative data for an amino acid. After reach stable condition, total RNA were extracted, mRNA were purified and aa-aRNA were amplified and fluoresently labled before hybridize on array chips. The array design is described in Burgmann et al., 2007
2010-05-14 | E-GEOD-13781 | biostudies-arrayexpress
Project description:Temporal dynamics of the particle-attached and free-living microbial communities from coastal seawater
| PRJNA308497 | ENA
Project description:We investigated the ascomycete truffle Tuber melanosporum exploits DNA methylation and transcription to cope with the more than 45,000 repeated elements that are present in its genome. Whole-genome bisulfite sequencing and RNA-sequencing, were performed on different developmental stages of this symbiotic hypogeous fungus -fruitbody (FB), free-living mycelium (FLM), and ectomycorrhiza. Examination of DNA methylation and transcription of truffle in its free living mycelium (FLM), fruit body (FB), and ectomycorrhizal root tips (ECM)
2014-01-01 | E-GEOD-49700 | biostudies-arrayexpress
Project description:Polyamine-transforming bacterioplankton in seawater
| PRJNA263185 | ENA
Project description:Free-living bacteria communities in water
| PRJDB3069 | ENA