Sagittula stellata E-37
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA18971 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| AAYA01.dat.gz | Other | |||
| AAYA01.fasta.gz | Fasta.gz | |||
| AAYA01.master.dat | Other | |||
| AAYA01.dat.gz | Other |
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Project description:The hydroxycinnamates (HCAs) ferulate and p-coumarate are among the most abundant constituents of lignin, and their degradation by bacteria is an essential step in the remineralization of vascular plant material. Here, we investigate the catabolism of these two HCAs by the marine bacterium Sagittula stellata E-37, a member of the roseobacter lineage with lignolytic potential. Bacterial degradation of HCAs is often initiated by the activity of a hydroxycinnamoyl-coenzyme A (hydroxycinnamoyl-CoA) synthase. Genome analysis of S. stellata revealed the presence of two feruloyl-CoA (fcs) synthase homologs, an unusual occurrence among characterized HCA degraders. In order to elucidate the role of these homologs in HCA catabolism, fcs-1 and fcs-2 were disrupted using insertional mutagenesis, yielding both single and double fcs mutants. Growth on p-coumarate was abolished in the fcs double mutant, whereas maximum cell yield on ferulate was only 2% of that of the wild type. Interestingly, the single mutants demonstrated opposing phenotypes, where the fcs-1 mutant showed impaired growth (extended lag and ?60% of wild-type rate) on p-coumarate, and the fcs-2 mutant showed impaired growth (extended lag and ?20% of wild-type rate) on ferulate, pointing to distinct but overlapping roles of the encoded fcs homologs, with fcs-1 primarily dedicated to p-coumarate utilization and fcs-2 playing a dominant role in ferulate utilization. Finally, a tripartite ATP-independent periplasmic (TRAP) family transporter was found to be required for growth on both HCAs. These findings provide evidence for functional redundancy in the degradation of HCAs in S. stellata E-37 and offer important insight into the genetic complexity of aromatic compound degradation in bacteria.IMPORTANCE Hydroxycinnamates (HCAs) are essential components of lignin and are involved in various plant functions, including defense. In nature, microbial degradation of HCAs is influential to global carbon cycling. HCA degradation pathways are also of industrial relevance, as microbial transformation of the HCA, ferulate, can generate vanillin, a valuable flavoring compound. Yet, surprisingly little is known of the genetics underlying bacterial HCA degradation. Here, we make comparisons to previously characterized bacterial HCA degraders and use a genetic approach to characterize genes involved in catabolism and uptake of HCAs in the environmentally relevant marine bacterium Sagittula stellata We provide evidence of overlapping substrate specificity between HCA degradation pathways and uptake proteins. We conclude that S. stellata is uniquely poised to utilize HCAs found in the complex mixtures of plant-derived compounds in nature. This strategy may be common among marine bacteria residing in lignin-rich coastal waters and has potential relevance to biotechnology sectors.
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Project description:Psychrophilic marine bacterium
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Project description:To address the question of how photosynthetic bacterium Rhodopseudomonas palustris metabolize lignin derived compound p-coumarate, transcriptomics and quantitative proteomics were combined to characterize gene expression profiles at both the mRNA level and protein level in Rhodopseudomonas palustris grown with succinate, benzoate, and p-coumarate as the carbon source. Keywords: Comparison of transcriptome profiles
2008-05-07 | GSE6221 | GEO
Project description:A novel Gram-stain-negative, non-motile, halophilic bacterium designated strain M10.9XT was isolated from the inner sediment of an aluminium can collected from the Mediterranean Sea (València, Spain). Cells of strain M10.9XT were rod-shaped and occasionally formed aggregates. The strain was oxidase-negative and catalase-positive, and showed a slightly psychrophilic, neutrophilic and slightly halophilic metabolism. The phylogenetic analyses revealed that strain M10.9XT was closely related to Sagittula stellata E-37T and Sagittula marina F028-2T. The genomic G+C content of strain M10.9XT was 65.2 mol%. The average nucleotide identity and digital DNA-DNA hybridization values were 76.6 and 20.9 %, respectively, confirming its adscription to a new species within the genus Sagittula. The major cellular fatty acids were C18 : 1 ω7c/C18 : 1 ω6c and C16 : 0. The polar lipids consisted of phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid, an unidentified glycolipid, an unidentified phospholipid and an unidentified lipid. According to the resuts of a polyphasic study, strain M10.9XT represents a novel species of the genus Sagittula for which the name Sagittula salina sp. nov. (type strain M10.9XT=DSM 112301T=CECT 30307T) is proposed.
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Project description:To address the question of how photosynthetic bacterium Rhodopseudomonas palustris metabolize lignin derived compound p-coumarate, transcriptomics and quantitative proteomics were combined to characterize gene expression profiles at both the mRNA level and protein level in Rhodopseudomonas palustris grown with succinate, benzoate, and p-coumarate as the carbon source. Transcriptome profiles among Rhodopseudomonas palustris cells grown with succinate, benzoate, and p-coumarate as the carbon source were compared.
2008-05-07 | E-GEOD-6221 | biostudies-arrayexpress
Project description:Convergent microbial biocatalysis has emerged as a promising approach for the conversion of lignin side-streams into value-added chemicals in recent decades. However, the current knowledge of metabolic pathways directing the bioconversion of lignin-related aromatics is still limited to a few microbial species and unavailable for some of these compounds. Thus, the aim of this study was to identify the genes involved in the bioconversion of aromatic compounds in Xanthomonas citri subsp. citri 306 (X. citri 306), a bacterium belonging to a compelling yet untapped genus for studies on lignin-related aromatics metabolism. For this purpose, we used an integrative approach including genome data mining, RNA-seq, enzymology and gene knockout studies. The RNA-seq analysis revealed a total of 278 to 1464 differentially expressed genes (DEGs) in the aromatic-containing conditions compared to the control XVM2m-glucose, evidencing the importance of these compounds in modulating various physiological processes of X. citri 306 beyond the pathways related to their metabolism. Moreover, this work revealed the operon molRKAB, which plays a role in the first catabolic steps of the three main monolignols (p-coumaryl, coniferyl and sinapyl alcohols), besides showing all the enzymatic steps funneling them up to the tricarboxylic acid cycle. Additionally, the study uncovered aryl aldehyde reductases and efflux strategies that likely function to protect the pathogen from aromatics toxicity. Together, these findings enhance the current understanding of Xanthomonas metabolism and transcriptional responses to lignin-related aromatic compounds, shedding light on the diverse metabolic pathways available to enable the engineering of microbial chassis dedicated to lignin valorization.
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