Ribonuclease H: properties, substrate specificity and roles in retroviral reverse transcription
Open accessAbstract
Retroviral reverse transcriptases possess both a DNA polymerase and an RNase H activity. The linkage with the DNA polymerase activity endows the retroviral RNases H with unique properties not found in the cellular counterparts. In addition to the typical endonuclease activity on a DNA/RNA hybrid, cleavage by the retroviral enzymes is also directed by both DNA 3′ recessed and RNA 5′ recessed ends, and by certain nucleotide sequence preferences in the vicinity of the cleavage site. This spectrum of specificities enables retroviral RNases H to carry out a series of cleavage reactions during reverse transcription that degrade the viral RNA genome after minus‐strand synthesis, precisely generate the primer for the initiation of plus strands, facilitate the initiation of plus‐strand synthesis and remove both plus‐ and minus‐strand primers after they have been extended.
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The polymerase-dependent ribonuclease H cleavage mode occurs during pauses in DNA synthesis and leaves nicks in the RNA as reverse transcriptase slides along it.
“This mode is polymerase-dependent and occurs during pauses in DNA synthesis, leaving nicks in the RNA as RT slides along it [27,28].”
From Retroviral RNase H: structure, mechanism, and inhibition (2021) · cites this paper as [28]
The DNA 3′ end-directed cleavage section reports RNase H cleavage at pause sites during polymerization, and STEP 1 says this mode cleaves the RNA concomitantly with DNA synthesis, presumably at pause sites. These passages support intermittent RNA cleavage, but the paper hedges the timing and does not describe RT sliding along the RNA. (LLM, conf=0.86)
Experimental — accuracy not yet measured5'-end RNA-directed cleavage is determined by the position of 5'-recessed RNA in the DNA polymerase active site and removes longer RNA fragments still base-paired to the minus DNA.
“The 5'-end RNA-directed cleavage is determined by the position of the 5’-recessed RNA (from nicks) in the DNA polymerase active site and removes longer RNA fragments that remain base-paired to the minus DNA [26-28,52-54].”
From Retroviral RNase H: structure, mechanism, and inhibition (2021) · cites this paper as [28]
The “RNA 5' end-directed cleavage” section says reverse transcriptase binds a hybrid with a recessed RNA 5' end and cleaves the RNA about 13–19 nucleotides from that end; it proposes an interaction near the polymerase active site. But the same section explicitly says an RNA 5' end at a nick is not recognized for this cleavage mode by HIV-1 and M-MLV RNases H; a 2–3-nucleotide upstream gap permits it. The cited passages do not establish that this mode removes the longer fragments remaining paired to minus DNA. (LLM, conf=0.87)
Experimental — accuracy not yet measuredRNase H enzymes are found across all three domains of life and in retroviruses such as HIV.
“RNase H enzymes are found across all three domains of life, and they are present in other systems, including retroviruses (i.e. HIV)”
From Ribonucleotide errors, RNase HII, and ribonucleotide excision repair (2026) · cites this paper as Champoux and Schultz 2009
The Introduction identifies HIV-1 as a focus of the review, and Structure-function considerations discusses RNases H from bacteria and humans. These passages support the retroviral, bacterial, and eukaryotic examples, but the paper does not establish their presence across all three domains of life; the archaeal domain is not addressed. (LLM, conf=0.88)
Experimental — accuracy not yet measuredThe two-metal-binding mechanism has been widely accepted based on structural and functional experiments.
“Based on these structural and functional experiments, the two metal-binding mechanism has been widely accepted [27,28,30,31,63,64].”
From Retroviral RNase H: structure, mechanism, and inhibition (2021) · cites this paper as [28]
Experimental — accuracy not yet measuredRetroviral reverse transcriptases have three modes of RNA hydrolysis by ribonuclease H: 3'-end DNA-directed cleavage, 5'-end RNA-directed cleavage, and non-directed or internal cleavage.
“Retroviral RTs, including HIV-1 RT and avian myeloblastosis virus (AMV) RT, which function as heterodimers, as well as M-MLV RT, which functions as a monomer, have three modes of RNA hydrolysis by RNH: 3'-end DNA directed cleavage, 5'-end RNA directed cleavage, and non-directed or internal cleavage [26-28,31,52-54].”
From Retroviral RNase H: structure, mechanism, and inhibition (2021) · cites this paper as [28]
Non-directed or internal cleavages occur within larger RNA/DNA duplex segments and may depend in part on the RNA sequence.
“Non-directed or internal cleavages take place within larger segments of RNA/DNA duplex and might depend, in part, on the sequence of the RNA [28,52,55].”
From Retroviral RNase H: structure, mechanism, and inhibition (2021) · cites this paper as [28]
The ribonuclease H activity of reverse transcriptase hydrolyzes RNA in RNA/DNA hybrids during DNA synthesis and is critical for virus replication.
“The RNH activity of RT is responsible for hydrolysis of RNA of RNA/DNA hybrids during synthesis and, thus, is critical for virus replication [3,25-28].”
From Retroviral RNase H: structure, mechanism, and inhibition (2021) · cites this paper as [28]
During DNA polymerization, the 3'-end of the elongating DNA in the polymerase active site orients the RNA strand in the ribonuclease H active site, allowing cleavage 15-20 nucleotides from the 3'-DNA terminus.
“During DNA polymerization from the RNA template, the 3'-end of the elongating DNA is positioned in the polymerase active site and orients the RNA strand in the RNH active site, which allows RNH to cleave the RNA at a position 15-20 nucleotides away from the 3’-DNA terminus [27,28,55,56].”
From Retroviral RNase H: structure, mechanism, and inhibition (2021) · cites this paper as [28]
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“RNase H enzymes are found across all three domains of life, and they are present in other systems, including retroviruses (i.e. HIV) (Doolittle et al. 1989; Crouch 1990; Kohlstaedt et al. 1992; Champoux and Schultz 2009; Tadokoro and Kanaya 2009).”
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- Authors
- Champoux, J. J., & Schultz, S. J.
- Affiliations
- University of Washington (US)
- Venue
- The FEBS Journal
- Publisher
- Wiley
- Published
- 2009-02-25
- Volume
- 276
- Issue
- 6
- Pages
- 1506-1516
- ISSN
- 1742-464X (ISSN-L)
- 1742-4658
- PMC
- PMC2742777
- OpenAlex
- W1610099020
- Semantic Scholar
- fd9c879ef2a58643a006e57265918cbd987703c1
- Cited by
- 77
- References
- 104
- Citations by year
- 2026: 3 · 2024: 1 · 2023: 3 · 2022: 3 · 2021: 5 · 2020: 4 · 2019: 4 · 2018: 8 · 2017: 4 · 2016: 4 · 2015: 5 · 2014: 1 · 2013: 8 · 2012: 9
- FWCI
- 0.93
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- FEBS Journal (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- National Cancer Institute (CA51605, R01CA051605, R37CA051605)
- Topics
- Health Sciences › Medicine › Infectious Diseases › HIV/AIDS drug development and treatment
- Life Sciences › Immunology and Microbiology › Virology › HIV Research and Treatment
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and Retrovirus Studies
- Keywords
- RNase H, reverse transcriptase, substrate specificity, primer removal, viral RNA degradation
- MeSH terms
- Models, Molecular, Protein Conformation, Retroviridae, Structure-Activity Relationship, Substrate Specificity, Transcription, Genetic, Ribonuclease H, Biocatalysis
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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