Sulfitobacter sp. NAS-14.1
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA13591 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Dimethylsufoniopropionate (DMSP) is an important and abundant organic sulfur compound and an important substrate for marine bacterioplankton. The Roseobacter clade of marine alpha-proteobacteria, including Silicibacter pomeroyi strain DSS3, are known to be a key phylogenetic group involved in DMSP degradaton. The fate of DMSP has important implications for the global sulfur cycle, but the genes involved in this process and their regulation are largely unknown. S. pomeroyi is capable of performing two major pathways of DMSP degradation, making it an interesting model organism. Based on the full genome sequence of this strain we designed an oligonucleotide-based microarray for the detection of transcripts of nearly all genes. The array was used to study the transcriptional response of S. pomeroyi cultures to additions of DMSP or Acetate in a time series experiment. We identified a number of DMSP-upregulated genes that could be assigned to potential roles in the metabolization of DMSP. DMSP also affected the transcription of other groups of genes, including genes for transport and metabolization of peptides, amino-acids and polyamines. High DMSP concentrations may be a chemical signal indicating phytoplankton abundance and elicit a regulatory response aimed at making maximum use of the available nutrients under these conditions. Keywords: Microarray, marine bacterium, messenger RNA, transcription, sulfur metabolism
2007-12-09 | GSE5480 | GEO
Project description:Dimethylsufoniopropionate (DMSP) is an important and abundant organic sulfur compound and an important substrate for marine bacterioplankton. The Roseobacter clade of marine alpha-proteobacteria, including Silicibacter pomeroyi strain DSS3, are known to be a key phylogenetic group involved in DMSP degradaton. The fate of DMSP has important implications for the global sulfur cycle, but the genes involved in this process and their regulation are largely unknown. S. pomeroyi is capable of performing two major pathways of DMSP degradation, making it an interesting model organism. Based on the full genome sequence of this strain we designed an oligonucleotide-based microarray for the detection of transcripts of nearly all genes. The array was used to study the transcriptional response of S. pomeroyi cultures to additions of DMSP or Acetate in a time series experiment. We identified a number of DMSP-upregulated genes that could be assigned to potential roles in the metabolization of DMSP. DMSP also affected the transcription of other groups of genes, including genes for transport and metabolization of peptides, amino-acids and polyamines. High DMSP concentrations may be a chemical signal indicating phytoplankton abundance and elicit a regulatory response aimed at making maximum use of the available nutrients under these conditions. Keywords: Microarray, marine bacterium, messenger RNA, transcription, sulfur metabolism The array design is based on the complete genome sequence of S. pomeroyi strain DSS 3 and available from Genbank (Accession numbers CP000031 and CP000032). Probes for all identified potential genes were designed by Combimatrix using proprietary software. A total of 4161 genes out of the 4348 identified potential genes on the S. pomeroyi genome are represented on the array. When possible, two probes per gene were designed.
2007-12-09 | E-GEOD-5480 | biostudies-arrayexpress
Project description:Kentrophoros ciliates are found worldwide in coastal marine sediment, and have an obligate symbiosis with sulfur-oxidizing Gammaproteobacteria called Candidatus Kentron. The genomes of different Kentron species suggest that they are chemolithoheterotrophs, producing new biomass from organic carbon substrates. We investigated the metaproteome of Kentrophoros sp. H and its symbiont (from two sites in the Mediterranean), to verify that hypothesized pathways of carbon and energy metabolism are indeed expressed, and to estimate the stable isotope fractionation in biomass, which can be a signature of the carbon sources used by the organism.
2019-05-31 | PXD011616 | Pride
Project description:Sulfoquinovose (SQ) and sulfoquinovosyl glycerol (SQGro), derived from abundant membrane sulfolipids termed sulfoquinovosyl diacylglycerols (SQDG) produced by photosynthetic organisms, serve as sources of carbon and sulfur for bacteria. The conversion processes of these sulfoquinovosyl compounds (SQ, SQGro, and SQDG) within marine ecosystems, and their quantitative contributions to the marine organic matter pool, are poorly understood. We have identified Alteromonas macleodii, a cosmopolitan marine bacterium, as a novel organism capable of metabolizing SQ and SQGro. A. macleodii possesses a sulfoquinovosidase that converts SQGro to SQ, and is a member of a distinct clade within glycoside hydrolase family 31 distinct from other sulfoqinovosidases. The ubiquitous presence of sulfoquinovosidases and their transcripts throughout marine environments suggests active metabolism of sulfoquinovose glycosides, particularly in the sunlit surface ocean. Complementing these observations, we demonstrate that marine algae and cyanobacteria produce significant quantities of SQGro, and field samples from coastal and open ocean environments enabled estimation of the annual turnover of SQGro in the teragram range. Together with SQDG and SQ, these sulfoquinovosyl compounds constitute a substantial portion of the marine organic sulfur, estimated at around 1.5 petagrams of carbon turnover per annum. These findings reveal a vast, previously unappreciated pool of organosulfonates within the microbial food web that contributes significantly to the marine carbon and sulfur cycles.
2025-08-25 | PXD058686 | Pride
Project description:Sulfoquinovose (SQ) and sulfoquinovosyl glycerol (SQGro), derived from abundant membrane sulfolipids termed sulfoquinovosyl diacylglycerols (SQDG) produced by photosynthetic organisms, serve as sources of carbon and sulfur for bacteria. The conversion processes of these sulfoquinovosyl compounds (SQ, SQGro, and SQDG) within marine ecosystems, and their quantitative contributions to the marine organic matter pool, are poorly understood. We have identified Alteromonas macleodii, a cosmopolitan marine bacterium, as a novel organism capable of metabolizing SQ and SQGro. A. macleodii possesses a sulfoquinovosidase that converts SQGro to SQ, and is a member of a distinct clade within glycoside hydrolase family 31 distinct from other sulfoqinovosidases. The ubiquitous presence of sulfoquinovosidases and their transcripts throughout marine environments suggests active metabolism of sulfoquinovose glycosides, particularly in the sunlit surface ocean. Complementing these observations, we demonstrate that marine algae and cyanobacteria produce significant quantities of SQGro, and field samples from coastal and open ocean environments enabled estimation of the annual turnover of SQGro in the teragram range. Together with SQDG and SQ, these sulfoquinovosyl compounds constitute a substantial portion of the marine organic sulfur, estimated at around 1.5 petagrams of carbon turnover per annum. These findings reveal a vast, previously unappreciated pool of organosulfonates within the microbial food web that contributes significantly to the marine carbon and sulfur cycles.
2025-08-25 | PXD058710 | Pride
Project description:Dimethylsulfoniopropionate degrading marine bacterium
| PRJNA13560 | ENA
Project description:Chemoautotrophic bacteria belonging to the genus Sulfurimonas in the class Campylobacteria (formerly classified as Epsilonproteobacteria) play a key role in the sulfur cycle in a variety of oxygen-deficient or –limited and sulfide-rich marine and terrestrial environments. Previously, they were identified as key players in the turnover of zero-valence sulfur, a central intermediate in the marine sulfur cycle, and S. denitrificans was further shown to be able to oxidize cyclooctasulfur. However, at present the mechanism involved in the activation and metabolism of cyclooctasulfur is not known. To this end, we assessed the transcriptome and proteome of S. denitrificans grown with either thiosulfate or cyclooctasulfur as the electron donor. While the overall profiles under the two growth conditions were rather similar, distinct differences were observed that could be attributed to the utilization of cyclooctasulfur. This included a higher abundance of expressed genes and proteins related to attachment in the presence of cyclooctasulfur and the differential expression of the sulfur-oxidation multienzyme complex (SOX). S. denitrificans uses the SOX system for the oxidation of reduced sulfur compounds, including two copies of the sulfur-binding SoxYZ proteins, encoded in two gene clusters: soxABXYZ1 and soxCDYZ2. While the proteins of both operons of the SOX system were detected in the presence of thiosulfate, only proteins of the soxCDYZ2 operon were detected when grown with cylcooctasulfur. Based on these findings a model for the oxidation of cylcooctasulfur is being proposed that might also apply to other Campylobacteria that share the same arrangement of the SOX system. Our results have implications for interpreting metatranscriptomic and -proteomic data and for the observed high level of diversification of soxYZ2 among sulfur-oxidizing Campylobacteria.
2019-07-22 | PXD009127 | Pride
Project description:The unicellular cyanobacterium Synechocystis sp. PCC 6803 is a model system for studying biochemistry, genetics and molecular biology of photobiological processes. Despite its importance in basic and applied research, the genome-wide picture of transcriptional regulation in this bacterium is limited. Characteristic transcriptional responses to changes in the growth environment are expected to provide a scaffold for describing the Synechocystis transcriptional regulatory network as well as efficient means for functional annotation of genes in the genome. We designed, validated and used Synechocystis genome-wide oligonucleotide (70-mer) microarray (representing 96.7% of all chromosomal ORFs) to study transcriptional activity of the cyanobacterial genome in response to S deprivation. The microarray data were verified by quantitative RT-PCR. We made five main observations: 1) Transcriptional changes upon sulfate withdrawal were relatively moderate, but significant and consistent with growth kinetics; 2) S acquisition genes encoding for a high-affinity sulfate transporter were significantly induced, while decreased transcription of genes for phycobilisome, photosystems I and II, cytochrome b6/f, and ATP synthase indicated reduced light-harvesting and photosynthetic activity; 3) S deprivation elicited transcriptional responses associated with general growth arrest and stress; 4) A large number of genes regulated by S availability encode hypothetical proteins or proteins of unknown function; 5) Hydrogenase structural and maturation accessory genes were not identified as differentially expressed, even though increased hydrogen evolution was observed. The expression profiles recorded by using this oligonucleotide-based microarray platform revealed that during transition from the condition of plentiful sulfur to no sulfur, Synechocystis undergoes coordinated transcriptional changes, including genes whose products are involved in sensing nutrient limitations and tuning bacterial metabolism. The transcriptional profile of the nutrient limitation was dominated by decrease in abundances of many transcripts. However, these changes were unlikely due to the across-the-board, non-specific shut down of transcription in a condition of growth arrest. Down-regulation of transcripts encoding proteins whose function depends on a cellular sulfur status indicated that the observed repression has a specific regulatory component. The repression of certain sulfur-related genes was paralleled by activation of genes involved in internal and external S scavenging. Keywords: stress response, time course
2008-07-24 | GSE11970 | GEO
Project description:We announce the complete genome sequence of a lytic podovirus, ΦCB2047-B, which infects the bacterium Sulfitobacter sp. strain 2047, a member of the Roseobacter clade. Genome analysis revealed ΦCB2047-B to be an N4-like phage, with its genome having high nucleotide similarity to other N4-like roseophage genomes.
| S-EPMC3894267 | biostudies-literature