Recombinant Desulfovibrio vulgaris Ribonuclease Y (rny), partial
Description
Role of Ribonuclease Y in Bacteria
Ribonuclease Y (RNase Y) is a crucial enzyme involved in RNA metabolism, particularly in the degradation of messenger RNA (mRNA) in bacteria. It is well-studied in Bacillus subtilis, where it plays a key role in initiating mRNA decay and regulating riboswitch turnover . RNase Y is known to interact with other enzymes like RNase J1 and polynucleotide phosphorylase to facilitate RNA degradation .
General Features of RNase Y
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Function: RNase Y acts as an endoribonuclease, cleaving RNA molecules internally. This activity is essential for the turnover of structured RNAs, such as those formed by riboswitches .
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Localization: In Bacillus subtilis, RNase Y is associated with the cell membrane and interacts with cytoplasmic proteins .
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Regulation: RNase Y can autoregulate its synthesis by affecting the stability of its own mRNA .
Potential Applications and Research Directions
While specific data on recombinant Desulfovibrio vulgaris Ribonuclease Y is scarce, studying this enzyme could provide insights into RNA metabolism in sulfate-reducing bacteria. These bacteria are significant in geochemical cycles and biotechnological applications, but their genetic regulatory mechanisms are not well understood .
Research Challenges and Future Directions
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Limited Information: There is a lack of detailed research on the recombinant version of RNase Y from Desulfovibrio vulgaris.
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Potential for Biotechnology: Understanding RNase Y in Desulfovibrio vulgaris could offer new avenues for manipulating RNA stability and gene expression in biotechnologically relevant bacteria.
Data Table: Comparison of RNase Y in Different Bacteria
| Feature | Bacillus subtilis RNase Y | Potential in Desulfovibrio vulgaris |
|---|---|---|
| Function | Endoribonuclease | Presumed similar role |
| Localization | Membrane-associated | Unknown |
| Regulation | Autoregulates synthesis | Potential for similar regulation |
| Interactions | RNase J1, PNP, others | Unknown |
| Biotechnological Potential | Gene expression control | Potential for RNA stability manipulation |
References:
Product Specs
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Target Background
Endoribonuclease initiating mRNA decay.
KEGG: dvu:DVU2671
STRING: 882.DVU2671
Q&A
Basic Research Questions
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What is Ribonuclease Y and what is its role in bacterial RNA metabolism?
Ribonuclease Y (RNase Y) represents one of the three major families of bacterial RNA decay systems, alongside RNase E and RNase J. It is ubiquitous in the Firmicute phylum and scattered across most other bacterial phyla, with notable exceptions in Cyanobacteria and Alpha-, Beta-, and Gamma-proteobacteria . In bacteria like Desulfovibrio vulgaris, RNase Y likely plays a crucial role in RNA turnover, which is essential for proper gene regulation.
RNase Y functions as an endoribonuclease that cleaves RNA at specific sites rather than digesting from the ends. This targeted cleavage allows for precise control of transcript abundance and can generate specific RNA fragments with distinct biological functions. The enzyme's activity directly impacts mRNA half-lives, thereby affecting protein synthesis rates and cellular adaptation to changing environmental conditions.
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Why is studying RNase Y in Desulfovibrio vulgaris important for understanding bacterial adaptation?
D. vulgaris Hildenborough is a model sulfate-reducing bacterium that plays essential roles in global carbon and sulfur cycling . These bacteria can be found in diverse environments, from anaerobic sediments to the human gut, and can adapt to various stressors .
Studying RNase Y in D. vulgaris provides insights into:
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RNA metabolism in anaerobic bacteria, which may differ from well-studied aerobes
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Post-transcriptional regulation during environmental stress responses
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Gene expression control during metabolic shifts between sulfate reduction and alternative growth modes
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Potential regulatory mechanisms affecting bioremediation capabilities, as D. vulgaris can reduce toxic metals like uranium and chromium
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What is known about the structural domains of bacterial RNase Y proteins?
Based on studies in other bacteria, RNase Y typically contains several distinct domains with specific functions :
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N-terminal membrane anchoring alpha-helix: Tethers the protein to the cell membrane
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Disordered coiled-coil domain: Likely involved in protein-protein interactions
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RNA binding KH domain: Responsible for substrate recognition and binding
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HD domain: Contains the catalytic active site for RNA cleavage
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C-terminal region: Function remains unknown
While the specific structure of D. vulgaris RNase Y has not been fully characterized in the provided literature, these domains are likely conserved based on the high similarity observed between RNase Y proteins from different bacterial species .
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How does RNase Y target selection differ from other endoribonucleases?
RNase Y demonstrates specific targeting mechanisms that distinguish it from other bacterial ribonucleases:
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Unlike many ribonucleases, RNase Y doesn't cleave RNAs at random positions but consistently cuts at specific sites
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Cleavage efficiency appears to be driven by the primary nucleotide sequence immediately downstream of the cleavage site
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Base-pairing in secondary structures located a few nucleotides downstream of the cleavage site is important for recognition
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The positioning of cleavage is roughly localized by downstream secondary structure and fine-tuned by the nucleotide immediately upstream of the cleavage site
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There is often a strong preference for a purine (especially G over A) immediately upstream of the cleaved phosphodiester bond
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