Structural characterization of NrnC identifies unifying features of dinucleotidases

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 pro...

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Autores principales:	Justin D Lormand, Soo-Kyoung Kim, George A Walters-Marrah, Bryce A Brownfield, J Christopher Fromme, Wade C Winkler, Jonathan R Goodson, Vincent T Lee, Holger Sondermann
Formato:	article
Lenguaje:	EN
Publicado:	eLife Sciences Publications Ltd 2021
Materias:	RNases enzyme mechanism dinucleotides Bartonella henselae Brucella melitensis Pseudomonas aeruginosa Medicine R Science Q Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/faff46fbe60f46f196b3edd0f5ca5dc5
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spelling	oai:doaj.org-article:faff46fbe60f46f196b3edd0f5ca5dc52021-11-30T11:44:51ZStructural characterization of NrnC identifies unifying features of dinucleotidases10.7554/eLife.701462050-084Xe70146https://doaj.org/article/faff46fbe60f46f196b3edd0f5ca5dc52021-09-01T00:00:00Zhttps://elifesciences.org/articles/70146https://doaj.org/toc/2050-084XRNA 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 and Orn employ similar structural features that distinguish these two classes of 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, indicate 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.Justin D LormandSoo-Kyoung KimGeorge A Walters-MarrahBryce A BrownfieldJ Christopher FrommeWade C WinklerJonathan R GoodsonVincent T LeeHolger SondermanneLife Sciences Publications LtdarticleRNasesenzyme mechanismdinucleotidesBartonella henselaeBrucella melitensisPseudomonas aeruginosaMedicineRScienceQBiology (General)QH301-705.5ENeLife, Vol 10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	RNases enzyme mechanism dinucleotides Bartonella henselae Brucella melitensis Pseudomonas aeruginosa Medicine R Science Q Biology (General) QH301-705.5
spellingShingle	RNases enzyme mechanism dinucleotides Bartonella henselae Brucella melitensis Pseudomonas aeruginosa Medicine R Science Q Biology (General) QH301-705.5 Justin D Lormand Soo-Kyoung Kim George A Walters-Marrah Bryce A Brownfield J Christopher Fromme Wade C Winkler Jonathan R Goodson Vincent T Lee Holger Sondermann Structural characterization of NrnC identifies unifying features of dinucleotidases
description	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 and Orn employ similar structural features that distinguish these two classes of 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, indicate 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.
format	article
author	Justin D Lormand Soo-Kyoung Kim George A Walters-Marrah Bryce A Brownfield J Christopher Fromme Wade C Winkler Jonathan R Goodson Vincent T Lee Holger Sondermann
author_facet	Justin D Lormand Soo-Kyoung Kim George A Walters-Marrah Bryce A Brownfield J Christopher Fromme Wade C Winkler Jonathan R Goodson Vincent T Lee Holger Sondermann
author_sort	Justin D Lormand
title	Structural characterization of NrnC identifies unifying features of dinucleotidases
title_short	Structural characterization of NrnC identifies unifying features of dinucleotidases
title_full	Structural characterization of NrnC identifies unifying features of dinucleotidases
title_fullStr	Structural characterization of NrnC identifies unifying features of dinucleotidases
title_full_unstemmed	Structural characterization of NrnC identifies unifying features of dinucleotidases
title_sort	structural characterization of nrnc identifies unifying features of dinucleotidases
publisher	eLife Sciences Publications Ltd
publishDate	2021
url	https://doaj.org/article/faff46fbe60f46f196b3edd0f5ca5dc5
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Structural characterization of NrnC identifies unifying features of dinucleotidases

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