Bacteria
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR046428.fastq.gz | Fastqsanger.gz | |||
| DRR046429_1.fastq.gz | Fastqsanger.gz | |||
| DRR046429_2.fastq.gz | Fastqsanger.gz | |||
| DRR046430_1.fastq.gz | Fastqsanger.gz |
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Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces.
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Project description:Arthrobacter chlorophenolicus A6 is a 4-chlorophenol degrading soil bacterium with high phyllosphere colonization capacity. Till now the genetic basis for the phyllosphere competency of Arthrobacter or other pollutant-degrading bacteria is uncertain. We investigated global gene expression profile of A. chlorophenolicus grown in the phyllosphere of common bean (Phaseolus vulgaris) compared to growth on agar surfaces. We designed transcriptome arrays and investigated which genes had different transcript levels in the phyllosphere of common bean (Phaseolus vulgaris) as compared to agar surfaces. Since water availability is considered an important factor in phyllosphere survival and activity, we included both high and low relative humidity treatments for the phyllosphere-grown cells. In addition, we determined the expression profile under pollutant exposure by the inclusion of two agar surface treatments, i.e. with and without 4-chlorophenol.
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Project description:Levoglucosan is produced in the pyrolysis of cellulose and starch, including from bushfires or the burning of biofuels, and is deposited from the atmosphere across the surface of the earth. We describe two levoglucosan degrading Paenarthrobacter spp. (Paenarthrobacter nitrojuajacolis LG01 and Paenarthrobacter histidinolovorans LG02) that were isolated by metabolic enrichment on levoglucosan as sole carbon source. Genome sequencing and proteomics analysis revealed expression of a series of gene clusters encoding known levoglucosan degrading enzymes, levoglucosan dehydrogenase (LGDH, LgdA), 3-keto-levoglucosan b-eliminase (LgdB1) and glucose 3-dehydrogenase (LgdC), along with an ABC transporter cassette and associated solute binding protein. However, no homologues of 3-ketoglucose dehydratase (LgdB2) were evident. The expressed gene clusters contained a range of putative sugar phosphate isomerase/xylose isomerases with weak similarity to LgdB2. Sequence similarity network analysis of genome neighbors revealed that homologues of LgdA, LgdB1 and LgdC are generally conserved in a range of bacteria in the phyla Firmicutes, Actinobacteria and Proteobacteria. One sugar phosphate isomerase/xylose isomerase cluster (LgdB3) was identified with limited distribution mutually exclusive with LgdB2. LgdB1, LgdB2 and LgdB3 adopt similar predicted 3D folds suggesting overlapping function in processing intermediates in LG metabolism. Our findings highlight the diversity within the LGDH pathway through which bacteria utilize levoglucosan as a nutrient source.
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Project description:Polylactic acid (PLA) is a promising biodegradable material used in various fields, such as mulching films and disposable packaging materials. Biological approaches for completely degrading biodegradable polymers can provide environmentally friendly solutions. However, to our knowledge, no studies have performed transcriptome profiling to analyze PLA-degrading genes of PLA-degrading bacteria. Therefore, this study reports for the first time an RNA sequence approach for tracing genes involved in PLA biodegradation in the PLA-degrading bacterium Brevibacillus brevis. In the interpretation results of the differentially expressed genes, the hydrolase genes mhqD and nap and the serine protease gene besA were up-regulated by a fold change of 7.97, 4.89, and 4.09, respectively. This result suggests that hydrolases play a key role in PLA biodegradation by B. brevis. In addition, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that genes implicated in biofilm formation were upregulated. The biodegradation of PLA starts with bacteria attaching to the surface of PLA and forming a biofilm. Therefore, it could be confirmed that the above genes were up-regulated for access to PLA and biodegradation. Our results provide transcriptome-based insights into PLA biodegradation, which pitch a better understanding of microbial biodegradation of plastics.
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Project description:This project is designed for whole transcriptome sequencing of bacteria isolated from Rhizosphere of Wheat Plant, which has its impact on overall plant growth.
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