A dedicated diribonucleotidase resolves a key bottleneck as the terminal step of RNA degradation
- University of Maryland, United States
- Cornell University, United States
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.
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Vibrio cholerae Oligoribonuclease bound to pGGProtein Data Bank, 6N6A.
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Vibrio cholerae Oligoribonuclease bound to pAAProtein Data Bank, 6N6C.
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Vibrio cholerae Oligoribonuclease bound to pAGProtein Data Bank, 6N6D.
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Vibrio cholerae Oligoribonuclease bound to pGAProtein Data Bank, 6N6E.
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Vibrio cholerae Oligoribonuclease bound to pGCProtein Data Bank, 6N6F.
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Vibrio cholerae Oligoribonuclease bound to pCGProtein Data Bank, 6N6G.
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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.
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A dedicated diribonucleotidase resolves a key bottleneck as the terminal step of RNA degradation
eLife 8:e46313.
https://doi.org/10.7554/eLife.46313
Further reading
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- Immunology and Inflammation
- Microbiology and Infectious Disease
Pseudomonas aeruginosa (PA) is an opportunistic, frequently multidrug-resistant pathogen that can cause severe infections in hospitalized patients. Antibodies against the PA virulence factor, PcrV, protect from death and disease in a variety of animal models. However, clinical trials of PcrV-binding antibody-based products have thus far failed to demonstrate benefit. Prior candidates were derivations of antibodies identified using protein-immunized animal systems and required extensive engineering to optimize binding and/or reduce immunogenicity. Of note, PA infections are common in people with cystic fibrosis (pwCF), who are generally believed to mount normal adaptive immune responses. Here, we utilized a tetramer reagent to detect and isolate PcrV-specific B cells in pwCF and, via single-cell sorting and paired-chain sequencing, identified the B cell receptor (BCR) variable region sequences that confer PcrV-specificity. We derived multiple high affinity anti-PcrV monoclonal antibodies (mAbs) from PcrV-specific B cells across three donors, including mAbs that exhibit potent anti-PA activity in a murine pneumonia model. This robust strategy for mAb discovery expands what is known about PA-specific B cells in pwCF and yields novel mAbs with potential for future clinical use.
