Structural characterization of NrnC identifies unifying features of dinucleotidases
- Cornell University, United States
- University of Maryland, United States
- Centre for Structural Systems Biology (CSSB), Germany
Abstract
RNA degradation is fundamental for cellular homeostasis. The process is carried out by various classes of endolytic and exolytic enzymes that together degrade an RNA polymer to mono-ribonucleotides. Within the exoribonucleases, nano-RNases play a unique role as they act on the smallest breakdown products and hence catalyze the final steps in the process. We recently showed that oligoribonuclease (Orn) acts as a dedicated diribonucleotidase, defining the ultimate step in RNA degradation that is crucial for cellular fitness (Kim et al., 2019). Whether such a specific activity exists in organisms that lack Orn-type exoribonucleases remained unclear. Through quantitative structure-function analyses we show here that NrnC-type RNases share this narrow substrate length preference with Orn. Although NrnC employs similar structural features that distinguish these two classes as dinucleotidases from other exonucleases, the key determinants for dinucleotidase activity are realized through distinct structural scaffolds. The structures together with comparative genomic analyses of the phylogeny of DEDD-type exoribonucleases indicates convergent evolution as the mechanism of how dinucleotidase activity emerged repeatedly in various organisms. The evolutionary pressure to maintain dinucleotidase activity further underlines the important role these analogous proteins play for cell growth.
Data availability
The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.rcsb.org (PDB ID codes 7MPL, 7MPM, 7MPN, 7MPO, 7MPP, 7MPQ, 7MPR, 7MPS, 7MPT, 7MPU, 7MQB/EMD-23941, 7MQD/EMD-23943, 7MQF/EMD-23945, 7MQH/EMD-23947, 7MQC/EMD-23942, 7MQE/EMD-23944, 7MQG/EMD-23946, 7MQI/EMD-23948).
Article and author information
Author details
J Christopher Fromme
Funding
National Institutes of Health (R01AI142400)
- Vincent T Lee
National Institutes of Health (R01GM123609)
- Holger Sondermann
National Institutes of Health (R35GM136258)
- J Christopher Fromme
The funding sources were not involved in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Lormand 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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Structural characterization of NrnC identifies unifying features of dinucleotidases
eLife 10:e70146.
https://doi.org/10.7554/eLife.70146
Further reading
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- Microbiology and Infectious Disease
Chlamydia trachomatis is an obligate intracellular bacterial pathogen with a unique developmental cycle. It differentiates between two functional and morphological forms: the elementary body (EB) and the reticulate body (RB). The signals that trigger differentiation from one form to the other are unknown. EBs and RBs have distinctive characteristics that distinguish them, including their size, infectivity, proteome, and transcriptome. Intriguingly, they also differ in their overall redox status as EBs are oxidized and RBs are reduced. We hypothesize that alterations in redox may serve as a trigger for secondary differentiation. To test this, we examined the function of the primary antioxidant enzyme alkyl hydroperoxide reductase subunit C (AhpC), a well-known member of the peroxiredoxins family, in chlamydial growth and development. Based on our hypothesis, we predicted that altering the expression of ahpC would modulate chlamydial redox status and trigger earlier or delayed secondary differentiation. Therefore, we created ahpC overexpression and knockdown strains. During ahpC knockdown, ROS levels were elevated, and the bacteria were sensitive to a broad set of peroxide stresses. Interestingly, we observed increased expression of EB-associated genes and concurrent higher production of EBs at an earlier time in the developmental cycle, indicating earlier secondary differentiation occurs under elevated oxidation conditions. In contrast, overexpression of AhpC created a resistant phenotype against oxidizing agents and delayed secondary differentiation. Together, these results indicate that redox potential is a critical factor in developmental cycle progression. For the first time, our study provides a mechanism of chlamydial secondary differentiation dependent on redox status.
