Ribonuclease H

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ribonuclease H
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retroviral ribonuclease H
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NCBIproteins

Ribonuclease H (abbreviated RNase H or RNH) is a family of non-

mechanism. Members of the RNase H family can be found in nearly all organisms, from bacteria to archaea to eukaryotes
.

The family is divided into evolutionarily related groups with slightly different

domains of life.[4] Additionally, RNase H1-like retroviral ribonuclease H domains occur in multidomain reverse transcriptase proteins, which are encoded by retroviruses such as HIV and are required for viral replication.[5][6]

In eukaryotes, ribonuclease H1 is involved in

mitochondrial genome. Both H1 and H2 are involved in genome maintenance tasks such as processing of R-loop structures.[2][7]

Classification and nomenclature

Ribonuclease H is a family of

Holliday junction resolvases, Piwi and Argonaute proteins, various exonucleases, and the spliceosomal protein Prp8.[8][9]

RNases H can be broadly divided into two subtypes, H1 and H2, which for historical reasons are given Arabic numeral designations in

Homo sapiens RNase H1.[2][7] In E. coli and many other prokaryotes, the rnhA gene encodes HI and the rnhB gene encodes HII. A third related class, called HIII, occurs in a few bacteria and archaea; it is closely related to prokaryotic HII enzymes.[4]

Structure

H. sapiens, PDB: 3P56
​.

The

glutamate residues, often referred to as the DEDD motif. These residues interact with catalytically required magnesium ions.[7][5]

RNases H2 are larger than H1 and usually have additional helices. The

TATA box binding domain.[7] Retroviral RNase H domains occurring in multidomain reverse transcriptase proteins have structures closely resembling the H1 group.[5]

RNases H1 have been extensively studied to explore the relationships between structure and enzymatic activity. They are also used, especially the

basic substrate-binding surface. The C-helix has a scattered taxonomic distribution; it is present in the E. coli and human RNase H1 homologs and absent in the HIV RNase H domain, but examples of retroviral domains with C-helices do exist.[15][16]

Function

Ribonuclease H enzymes cleave the

5' phosphate group on either end of the cut site with a two-metal-ion catalysis mechanism, in which two divalent cations, such as Mg2+ and Mn2+, directly participate in the catalytic function.[17] Depending on the differences in their amino acid sequences, these RNases H are classified into type 1 and type 2 RNases H.[7][18] Type 1 RNases H have prokaryotic and eukaryotic RNases H1 and retroviral RNase H. Type 2 RNases H have prokaryotic and eukaryotic RNases H2 and bacterial RNase H3. These RNases H exist in a monomeric form, except for eukaryotic RNases H2, which exist in a heterotrimeric form.[19][20] RNase H1 and H2 have distinct substrate preferences and distinct but overlapping functions in the cell. In prokaryotes and lower eukaryotes, neither enzyme is essential, whereas both are believed to be essential in higher eukaryotes.[2] The combined activity of both H1 and H2 enzymes is associated with maintenance of genome stability due to the enzymes' degradation of the RNA component of R-loops.[21][22]

Ribonuclease H1

Identifiers
SymbolRNase H
PfamPF00075
Pfam clanCL0219
InterProIPR002156
PROSITEPS50879
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

Ribonuclease H1 enzymes require at least four

S. cerevisiae, they produce defects in stress response.[23]

In many eukaryotes, including

embryogenesis due to defects in replicating mitochondrial DNA.[2][24][25] The defects in mitochondrial DNA replication induced by loss of RNase H1 are likely due to defects in R-loop processing.[22]

Ribonuclease H2

Identifiers
SymbolRNase HII
PfamPF01351
Pfam clanCL0219
InterProIPR024567
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

In prokaryotes, RNase H2 is enzymatically active as a monomeric protein. In eukaryotes, it is an obligate heterotrimer composed of a catalytic subunit A and structural subunits B and C. While the A subunit is closely homologous to the prokaryotic RNase H2, the B and C subunits have no apparent homologs in prokaryotes and are poorly conserved at the

PCNA, which localizes H2 to replication foci.[28]

Both prokaryotic and eukaryotic H2 enzymes can cleave single ribonucleotides in a strand.

5' deoxyribonucleotide, while eukaryotic enzymes are more processive and hydrolyze both types of substrate with similar efficiency.[2][27] The substrate specificity of RNase H2 gives it a role in ribonucleotide excision repair, removing misincorporated ribonucleotides from DNA, in addition to R-loop processing.[29][30][28] Although both H1 and H2 are present in the mammalian cell nucleus, H2 is the dominant source of RNase H activity there and is important for maintaining genome stability.[28]

Some prokaryotes possess an additional H2-type gene designated RNase HIII in the Roman-numeral nomenclature used for the prokaryotic genes. HIII proteins are more closely related to the H2 group by

sequence identity and structural similarity, but have substrate preferences that more closely resemble H1.[7][31] Unlike HI and HII, which are both widely distributed among prokaryotes, HIII is found in only a few organisms with a scattered taxonomic distribution; it is somewhat more common in archaea and is rarely or never found in the same prokaryotic genome as HI.[32]

Mechanism

HIV-1
RNase H domain

The active site of nearly all RNases H contains four negatively charged amino acid residues, known as the DEDD motif; often a histidine e.g. in HIV-1, human or E. coli is also present.[2][7]

The charged residues bind two metal ions that are required for catalysis; under physiological conditions these are magnesium ions, but manganese also usually supports enzymatic activity,[2][7] while calcium or high concentration of Mg2+ inhibits activity.[11][33][34]

Based on experimental evidence and computer simulations the enzyme activates a water molecule bound to one of the metal ions with the conserved histidine.

pKa
and is likely to be protonated. The mechanism is similar to
RNase T and the RuvC subunit in the Cas9
enzyme which both also use a histidine and a two-metal ion mechanism.

The mechanism of the release of the cleaved product is still unresolved. Experimental evidence from time-resolved crystallography and similar nucleases points to a role of a third ion in the reaction recruited to the active site. [36][37]

In human biology

The human genome contains four genes encoding RNase H:

  • RNASEH1, an example of the H1 (monomeric) subtype
  • RNASEH2A, the catalytic subunit of the trimeric H2 complex
  • RNASEH2B, a structural subunit of the trimeric H2 complex
  • RNASEH2C, a structural subunit of the trimeric H2 complex

In addition, genetic material of

human endogenous retroviruses. Such integration events result in the presence of genes encoding retroviral reverse transcriptase, which includes an RNase H domain. An example is ERVK6.[38] Long terminal repeat (LTR) and non-long terminal repeat (non-LTR) retrotransposons are also common in the genome and often include their own RNase H domains, with a complex evolutionary history.[39][40][41]

Role in disease

protein-protein interactions with other proteins in the cell.[42]

In small studies, mutations in human RNase H1 have been associated with chronic progressive external ophthalmoplegia, a common feature of mitochondrial disease.[25]

Mutations in any of the three RNase H2 subunits are well-established as causes of a

type I interferon. AGS can also be caused by mutations in other genes: TREX1, SAMHD1, ADAR, and MDA5/IFIH1, all of which are involved in nucleic acid processing.[44] Characterization of mutational distribution in an AGS patient population found 5% of all AGS mutations in RNASEH2A, 36% in 2B, and 12% in 2C.[45] Mutations in 2B have been associated with somewhat milder neurological impairment[46] and with an absence of interferon-induced gene upregulation that can be detected in patients with other AGS-associated genotypes.[44]

In viruses

See also: Retroviral ribonuclease H
The crystal structure of the HIV reverse transcriptase heterodimer (yellow and green), with the RNase H domain shown in blue (active site in magenta spheres). The orange nucleic acid strand is RNA, the red strand is DNA.[47]

Two groups of

human immunodeficiency virus and hepatitis B virus, respectively. Both encode large multifunctional reverse transcriptase (RT) proteins containing RNase H domains.[48][49]

Retroviral RT proteins from

DNA-dependent DNA polymerase activity synthesizes plus-strand DNA, generating double-stranded DNA as the final product. The second step of this process is carried out by an RNase H domain located at the C-terminus of the RT protein.[5][6][52][53]

RNase H performs three types of cleaving actions: non-specific degradation of the plus-strand RNA genome, specific removal of the minus-strand

tRNA primer, and removal of the plus-strand purine-rich polypurine tract (PPT) primer.[54] RNase H plays a role in the priming of the plus-strand, but not in the conventional method of synthesizing a new primer sequence. Rather RNase H creates a "primer" from the PPT that is resistant to RNase H cleavage. By removing all bases but the PPT, the PPT is used as a marker for the end of the U3 region of its long terminal repeat.[53]

Because RNase H activity is required for viral proliferation, this domain has been considered a

Reverse-transcriptase inhibitors that specifically inhibit the polymerase function of RT are in widespread clinical use, but not inhibitors of the RNase H function; it is the only enzymatic function encoded by HIV that is not yet targeted by drugs in clinical use.[52][56]

Evolution

RNases H are widely distributed and occur in all

phylogenetic relationships, suggesting that horizontal gene transfer may have played a role in establishing the distribution of these enzymes. RNase HI and HIII rarely or never appear in the same prokaryotic genome. When an organism's genome contains more than one RNase H gene, they sometimes have significant differences in activity level. These observations have been suggested to reflect an evolutionary pattern that minimizes functional redundancy among RNase H genes.[7][32] RNase HIII, which is unique to prokaryotes, has a scattered taxonomic distribution and is found in both bacteria and archaea;[32] it is believed to have diverged from HII fairly early.[58]

The evolutionary trajectory of RNase H2 in eukaryotes, especially the mechanism by which eukaryotic homologs became obligate heterotrimers, is unclear; the B and C subunits have no apparent homologs in prokaryotes.[2][27]

Applications

Because RNase H specifically degrades only the RNA in double-stranded RNA:DNA hybrids, it is commonly used as a

archaeon Pyrococcus abyssi.[62] Of note, the ribonuclease inhibitor protein commonly used as a reagent is not effective at inhibiting the activity of either HI or HII.[59]

History

Ribonucleases H were first discovered in the laboratory of

reverse transcription.[66][67] It later became clear that calf thymus extract contained more than one protein with RNase H activity[68] and that E. coli contained two RNase H genes.[69][70] Originally, the enzyme now known as RNase H2 in eukaryotes was designated H1 and vice versa, but the names of the eukaryotic enzymes were switched to match those in E. coli to facilitate comparative analysis, yielding the modern nomenclature in which the prokaryotic enzymes are designated with Roman numerals and the eukaryotic enzymes with Arabic numerals.[2][26][31][71] The prokaryotic RNase HIII, reported in 1999, was the last RNase H subtype to be identified.[31]

Characterizing eukaryotic RNase H2 was historically a challenge, in part due to its low abundance.

sequence identity to their homologs in other organisms, and the corresponding human proteins were conclusively identified only after mutations in all three were found to cause Aicardi–Goutières syndrome.[2][3]

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External links
Retrieved from "https://en.wikipedia.org/w/index.php?title=Ribonuclease_H&oldid=1173711602"