A dedicated diribonucleotidase resolves a key bottleneck as the terminal step of RNA degradation
Abstract
Degradation of RNA polymers, an ubiquitous process in all cells, is catalyzed by specific subsets of endo- and exoribonucleases that together recycle RNA fragments into nucleotide monophosphate. In γ-proteobacteria, 3-'5' exoribonucleases comprise up to eight distinct enzymes. Among them, Oligoribonuclease (Orn) is unique as its activity is required for clearing short RNA fragments, which is important for cellular fitness. However, the molecular basis of Orn's unique cellular function remained unclear. Here we show that Orn exhibits exquisite substrate preference for diribonucleotides. Crystal structures of substrate-bound Orn reveal an active site optimized for diribonucleotides. While other cellular RNases process oligoribonucleotides down to diribonucleotide entities, Orn is the one and only diribonucleotidase that completes the terminal step of RNA degradation. Together, our studies indicate RNA degradation as a step-wise process with a dedicated enzyme for the clearance of a specific intermediate pool, diribonucleotides, that affects cellular physiology and viability.
Data availability
The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID codes 6N6A, 6N6C, 6N6D, 6N6E, 6N6F, 6N6G, 6N6H, 6N6I, 6N6J, and 6N6K). Source data files have been provided for Figures.
-
Vibrio cholerae Oligoribonuclease bound to pGGProtein Data Bank, 6N6A.
-
Vibrio cholerae Oligoribonuclease bound to pAAProtein Data Bank, 6N6C.
-
Vibrio cholerae Oligoribonuclease bound to pAGProtein Data Bank, 6N6D.
-
Vibrio cholerae Oligoribonuclease bound to pGAProtein Data Bank, 6N6E.
-
Vibrio cholerae Oligoribonuclease bound to pGCProtein Data Bank, 6N6F.
-
Vibrio cholerae Oligoribonuclease bound to pCGProtein Data Bank, 6N6G.
-
Vibrio cholerae Oligoribonuclease bound to pCpUProtein Data Bank, 6N6H.
Article and author information
Author details
Funding
National Institute of Allergy and Infectious Diseases (R01AI110740)
- Vincent T Lee
National Institute of General Medical Sciences (R01GM123609)
- Holger Sondermann
National Science Foundation (MCB1051440)
- Wade C Winkler
Cystic Fibrosis Foundation (LEE16G0)
- Vincent T Lee
National Institute of Diabetes and Digestive and Kidney Diseases (R01AI110740)
- Vincent T Lee
National Institute of General Medical Sciences (T32-GM080201)
- Cordelia A Weiss
National Institute of Allergy and Infectious Diseases (R01AI142400)
- Wade C Winkler
- Holger Sondermann
- Vincent T Lee
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2019, Kim et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,109
- views
-
- 270
- downloads
-
- 27
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Further reading
-
- Microbiology and Infectious Disease
Saprolegnia parasitica is one of the most virulent oomycete species in freshwater aquatic environments, causing severe saprolegniasis and leading to significant economic losses in the aquaculture industry. Thus far, the prevention and control of saprolegniasis face a shortage of medications. Linalool, a natural antibiotic alternative found in various essential oils, exhibits promising antimicrobial activity against a wide range of pathogens. In this study, the specific role of linalool in protecting S. parasitica infection at both in vitro and in vivo levels was investigated. Linalool showed multifaceted anti-oomycetes potential by both of antimicrobial efficacy and immunomodulatory efficacy. For in vitro test, linalool exhibited strong anti-oomycetes activity and mode of action included: (1) Linalool disrupted the cell membrane of the mycelium, causing the intracellular components leak out; (2) Linalool prohibited ribosome function, thereby inhibiting protein synthesis and ultimately affecting mycelium growth. Surprisingly, meanwhile we found the potential immune protective mechanism of linalool in the in vivo test: (1) Linalool enhanced the complement and coagulation system which in turn activated host immune defense and lysate S. parasitica cells; (2) Linalool promoted wound healing, tissue repair, and phagocytosis to cope with S. parasitica infection; (3) Linalool positively modulated the immune response by increasing the abundance of beneficial Actinobacteriota; (4) Linalool stimulated the production of inflammatory cytokines and chemokines to lyse S. parasitica cells. In all, our findings showed that linalool possessed multifaceted anti-oomycetes potential which would be a promising natural antibiotic alternative to cope with S. parasitica infection in the aquaculture industry.