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The complete alk sequences of Rhodococcus erythropolis from Lake Baikal.

ABSTRACT: BACKGROUND:Rhodococci are bacteria able to degrade a wide range of hydrocarbons, including the alkanes present in crude oil, due to alk genes in their genomes. FINDINGS:Genome sequencing of DNA from Rhodococcus erythropolis strain 4 (obtained from a deep-water bitumen mound) revealed four alk genes, and the predicted amino acid sequences coded by these genes were highly conserved, having sections up to 11 amino acid residues. CONCLUSIONS:Obtained four genes from Rhodococcus erythropolis were similar to corresponding genes from other bacteria collected from other environments, including marine sources. This indicated a large-scale horizontal alk gene transfer between bacteria from different subgenera.

SUBMITTER: Likhoshvay A

PROVIDER: S-EPMC4227987 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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The complete alk sequences of Rhodococcus erythropolis from Lake Baikal.

Likhoshvay Alexander A Lomakina Anna A Grachev Mihail M

SpringerPlus 20141021

<h4>Background</h4>Rhodococci are bacteria able to degrade a wide range of hydrocarbons, including the alkanes present in crude oil, due to alk genes in their genomes.<h4>Findings</h4>Genome sequencing of DNA from Rhodococcus erythropolis strain 4 (obtained from a deep-water bitumen mound) revealed four alk genes, and the predicted amino acid sequences coded by these genes were highly conserved, having sections up to 11 amino acid residues.<h4>Conclusions</h4>Obtained four genes from Rhodococcus ...[more]

PMID: 25392791

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Project description:BackgroundBelonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process.ResultsBy five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host's regulatory mechanisms to create an environment conducive for virion production.ConclusionsThe Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control.

Dataset Information

The complete alk sequences of Rhodococcus erythropolis from Lake Baikal.

Publications

The complete alk sequences of Rhodococcus erythropolis from Lake Baikal.

Similar Datasets

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