Unlike the Escherichia coli counterpart, archaeal RNase HII cannot process ribose monophosphate abasic sites and oxidized ribonucleotides embedded in DNA

Type Article
Date 2019-08
Language English
Author(s) Malfatti Matilde Clarissa1, Henneke GhislaineORCID2, Balachander Sathya3, Koh Kyung Duk4, Newnam Gary3, Uehara Ryo5, Crouch Robert J.6, Storici Francesca3, Tell Gianluca1
Affiliation(s) 1 : University of Udine, Italy
2 : Ifremer, Univ Brest, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes, France
3 : School of Biological Sciences, Georgia Institute of Technology, United States
4 : Lung Biology Center, Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
5 : Ritsumeikan Global Innovation Research Organization, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan
6 : Eunice Kennedy Shriver National Institute of Child Health and Human Developement
Source Journal Of Biological Chemistry (0021-9258) (American Society for Biochemistry & Molecular Biology (ASBMB)), 2019-08 , Vol. 294 , N. 35 , P. 13061-13072
DOI 10.1074/jbc.RA119.009493
WOS© Times Cited 4
Keyword(s) ribonuclease, bacteria, Escherichia coli (E coli), archaea, oxidative stress, abasic-ribose, oxidized-ribonucleotides, Pyrococcus abyssi, Type 2 RNase H
Abstract

The presence of ribonucleoside monophosphates (rNMPs) in nuclear DNA decreases genome stability. To ensure survival despite rNMP insertions, cells have evolved a complex network of DNA repair mechanisms, in which the ribonucleotide excision repair pathway, initiated by type 2 ribonuclease H (RNase HII/2), plays a major role. We recently demonstrated that eukaryotic RNase H2 cannot repair damaged, that is, ribose monophosphate abasic (both apurinic or apyrimidinic) site (rAP) or oxidized rNMP embedded in DNA. Currently, it remains unclear why RNase H2 is unable to repair these modified nucleic acids having either only a sugar moiety or an oxidized base. Here, we compared the endoribonuclease specificity of the RNase HII enzymes from the archaeon Pyrococcus abyssi and the bacterium Escherichia coli, examining their ability to process damaged rNMPs embedded in DNA in vitro. We found that E. coli RNase HII cleaves both rAP and oxidized rNMP sites. In contrast, like the eukaryotic RNase H2, P. abyssi RNase HII did not display any rAP or oxidized rNMP incision activities, even though it recognized them. Notably, the archaeal enzyme was also inactive on a mismatched rNMP, whereas the E. coli enzyme displayed strong preference for the mispaired rNMP over the paired rNMP in DNA. On the basis of our biochemical findings and also structural modeling analyses of RNase HII/2 proteins from organisms belonging to all three domains of life, we propose that RNases HII/2’s dual roles in RER and RNA/DNA hydrolysis result in limited acceptance of modified rNMPs embedded in DNA.

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Malfatti Matilde Clarissa, Henneke Ghislaine, Balachander Sathya, Koh Kyung Duk, Newnam Gary, Uehara Ryo, Crouch Robert J., Storici Francesca, Tell Gianluca (2019). Unlike the Escherichia coli counterpart, archaeal RNase HII cannot process ribose monophosphate abasic sites and oxidized ribonucleotides embedded in DNA. Journal Of Biological Chemistry, 294(35), 13061-13072. Publisher's official version : https://doi.org/10.1074/jbc.RA119.009493 , Open Access version : https://archimer.ifremer.fr/doc/00506/61796/