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Synonyms
5'-3' exoribonuclease, 5'-to-3' exoribonuclease, 5'-3' exoribonuclease 2, pab-rnase j, saci-acpsf2, sso-rnase j, tk-rnase j,
more
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(A)40 + 38 H2O
adenosine + 39 AMP
5'-pC-sR47 + H2O
5'-phosphomononucleotides
5'-pppA(A)39 + H2O
ATP + 39 AMP
5'-pppA(A)41 + H2O
ATP + 41 AMP
RNA + H2O
3'-phosphomononucleotides
additional information
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(A)40 + 38 H2O
adenosine + 39 AMP
(A)40 is a 40-nt-long synthetic RNA harboring a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, SSSO-RNase J displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
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(A)40 + 38 H2O
adenosine + 39 AMP
(A)40 is a 40-nt-long synthetic RNA harboring a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, SSSO-RNase J displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
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5'-pA(A)39 + H2O
40 AMP
5'-pA(A)39 is a 40-nt-long synthetic RNA harboring a 5'-monophosphate and a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, the enzyme displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
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5'-pA(A)39 + H2O
40 AMP
5'-pA(A)39 is a 40-nt-long synthetic RNA harboring a 5'-monophosphate and a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, the enzyme displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
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5'-pC-sR47 + H2O
5'-phosphomononucleotides
sR47 RNA labeled either at its 5' end as a 5'-[32P]monophosphate. The enzyme is a highly processive 5'-to-3'-exoribonuclease.The principal product of the 5' end-labeled RNA is [32P]GMP as guanosine is the 5'-nucleotide of sR47. Single-stranded DNA is degraded by the enzyme, suggesting that the it does not discriminate between ribose and 2'-deoxyribose nucleosides. Double-stranded DNA is resistant to degradation. The enzyme requires a free 5' end to initiate degradation
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5'-pC-sR47 + H2O
5'-phosphomononucleotides
sR47 RNA labeled either at its 5' end as a 5'-[32P]monophosphate. The enzyme is a highly processive 5'-to-3'-exoribonuclease.The principal product of the 5' end-labeled RNA is [32P]GMP as guanosine is the 5'-nucleotide of sR47. Single-stranded DNA is degraded by the enzyme, suggesting that the it does not discriminate between ribose and 2'-deoxyribose nucleosides. Double-stranded DNA is resistant to degradation. The enzyme requires a free 5' end to initiate degradation
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5'-pppA(A)39 + H2O
ATP + 39 AMP
5'-pppA(A)39 is a 40-nt-long synthetic RNA harboring a 5'-triphosphate and a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, the enzyme displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
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5'-pppA(A)39 + H2O
ATP + 39 AMP
5'-pppA(A)39 is a 40-nt-long synthetic RNA harboring a 5'-triphosphate and a single radioactively labeled A nucleotide at the 5'-end. When compared with the triphosphorylated RNA, the enzyme displayes a twofold higher velocity in degrading mono-phosphorylated RNA and RNA bearing a 5'-hydroxyl group
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5'-pppA(A)41 + H2O
ATP + 41 AMP
5'-pppA(A)41 is a 42-nt-long synthetic RNA harboring a 5'-tri-phosphate and a single radioactively labeled A nucleotide at the 5'-end. Decay of 5'-PPP-40A1 RNA results in either a single nucleotide or short oligoribonucleotides, indicating an exoribonucleolytic activity. Degradation with 5' to 3' directionality in vitro
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5'-pppA(A)41 + H2O
ATP + 41 AMP
5'-pppA(A)41 is a 42-nt-long synthetic RNA harboring a 5'-tri-phosphate and a single radioactively labeled A nucleotide at the 5'-end. Decay of 5'-PPP-40A1 RNA results in either a single nucleotide or short oligoribonucleotides, indicating an exoribonucleolytic activity. Degradation with 5' to 3' directionality in vitro
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RNA + H2O
3'-phosphomononucleotides
the translation initiation factor a/eIF2(g) binds to the 5'-tri-phosphate terminus of mRNA to protect from 5'-to-3' directional decay and counteract the activity of Sso-RNase J
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RNA + H2O
3'-phosphomononucleotides
the translation initiation factor a/eIF2(g) binds to the 5'-tri-phosphate terminus of mRNA to protect from 5'-to-3' directional decay and counteract the activity of Sso-RNase J
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RNA + H2O
3'-phosphomononucleotides
the enzyme plays a major role in mRNA turnover
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RNA + H2O
3'-phosphomononucleotides
the enzyme plays a major role in mRNA turnover
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RNA + H2O
3'-phosphomononucleotides
highly processive 5'-to-3'-exoribonuclease
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additional information
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pre-tRNA(Trp) is a poor substrate
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additional information
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pre-tRNA(Trp) is a poor substrate
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additional information
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pre-tRNA(Trp) is a poor substrate
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additional information
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using synthetic RNAs as well as 5'-end-labeled natural mRNAs from Sulfolobus solfataricus, no hints for an endonucleolytic activity are obtained
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additional information
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using synthetic RNAs as well as 5'-end-labeled natural mRNAs from Sulfolobus solfataricus, no hints for an endonucleolytic activity are obtained
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additional information
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using synthetic RNAs as well as 5'-end-labeled natural mRNAs from Sulfolobus solfataricus, no hints for an endonucleolytic activity are obtained
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additional information
?
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nuclear yeast Rat1 catalyzes exonucleolytic cleavage of RNA in the 5'- to 3'-direction to yield nucleoside 5'-phosphates, it forms a complex with Rai1 that stabilizes Rat1 and helps target 5x02 monophosphate RNA by its diphosphohydrolase activity. The efficiency of termination increases as the RNA transcript undergoing degradation by Rat1 gets longer, which suggests that Rat1 may generate a driving force for dissociating RNAPII from the template while degrading the nascent transcripts to catch up to the polymerase. Rat1/Rai1 itself is not sufficient to terminate RNAPII in vitro. Yeast Rat1/Rai1 does not terminate Escherichia coli RNAP, implying that a specific interaction between Rat1/Rai1 and RNAPII may be required for termination. Rat1/Rai1 do not show ATPase activity, ATP hydrolysis may be crucial to promote RNAPII termination but is not driven by Rat1/Rai1. The 5'-3' exoribonuclease activity of Rat1 is essential for RNAPII termination, quantification of the remaining RNAs after Rat1/Rai1 treatment without or with ATP
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additional information
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nuclear yeast Rat1 catalyzes exonucleolytic cleavage of RNA in the 5'- to 3'-direction to yield nucleoside 5'-phosphates, it forms a complex with Rai1 that stabilizes Rat1 and helps target 5x02 monophosphate RNA by its diphosphohydrolase activity. The efficiency of termination increases as the RNA transcript undergoing degradation by Rat1 gets longer, which suggests that Rat1 may generate a driving force for dissociating RNAPII from the template while degrading the nascent transcripts to catch up to the polymerase. Rat1/Rai1 itself is not sufficient to terminate RNAPII in vitro. Yeast Rat1/Rai1 does not terminate Escherichia coli RNAP, implying that a specific interaction between Rat1/Rai1 and RNAPII may be required for termination. Rat1/Rai1 do not show ATPase activity, ATP hydrolysis may be crucial to promote RNAPII termination but is not driven by Rat1/Rai1. The 5'-3' exoribonuclease activity of Rat1 is essential for RNAPII termination, quantification of the remaining RNAs after Rat1/Rai1 treatment without or with ATP
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RNA + H2O
3'-phosphomononucleotides
RNA + H2O
3'-phosphomononucleotides
the translation initiation factor a/eIF2(g) binds to the 5'-tri-phosphate terminus of mRNA to protect from 5'-to-3' directional decay and counteract the activity of Sso-RNase J
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-
?
RNA + H2O
3'-phosphomononucleotides
the translation initiation factor a/eIF2(g) binds to the 5'-tri-phosphate terminus of mRNA to protect from 5'-to-3' directional decay and counteract the activity of Sso-RNase J
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RNA + H2O
3'-phosphomononucleotides
the enzyme plays a major role in mRNA turnover
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RNA + H2O
3'-phosphomononucleotides
the enzyme plays a major role in mRNA turnover
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?
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ATP
ATP significantly enhances Rat1/Rai1-mediated RNAPII termination. The ATP-dependent effect seems to be unique to Rat1/Rai1. ATP addition does not stimulate the processivity of Rat1. Rather, it slightly reduces the exonuclease activity because 1 mM of ATP is sufficient to chelate the Mg2+ ion necessary for the nuclease activity of Rat1, suggesting that ATP affects Rat1-mediated termination in a somewhat different manner
additional information
NTP misincorporation induces RNAPII pausing and enhances termination by Rat1/Rai1. When ATP misincorporates into RNA transcripts, the elongation of RNAPII is significantly blocked, presumably due to the disruption and/or rearrangement of the RNAPII active center, RNAPII with a disrupted active center might be more effectively terminated by Rat1/Rai1
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additional information
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NTP misincorporation induces RNAPII pausing and enhances termination by Rat1/Rai1. When ATP misincorporates into RNA transcripts, the elongation of RNAPII is significantly blocked, presumably due to the disruption and/or rearrangement of the RNAPII active center, RNAPII with a disrupted active center might be more effectively terminated by Rat1/Rai1
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Amyotrophic Lateral Sclerosis
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Apraxias
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Ataxia
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Choriocarcinoma
Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection.
Dengue
Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection.
Frontotemporal Dementia
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Hepatitis C
XRN1 Stalling in the 5' UTR of Hepatitis C Virus and Bovine Viral Diarrhea Virus Is Associated with Dysregulated Host mRNA Stability.
Infections
Expression of the Arabidopsis Xrn4p 5'-3' exoribonuclease facilitates degradation of tombusvirus RNA and promotes rapid emergence of viral variants in plants.
Muscular Atrophy, Spinal
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Neoplasms
Upregulation of XRN2 acts as an oncogene in oral squamous cell carcinoma and correlates with poor prognosis.
Spinocerebellar Ataxias
SETX (senataxin), the helicase mutated in AOA2 and ALS4, functions in autophagy regulation.
Virus Diseases
Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection.
Zika Virus Infection
Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection.
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evolution
yeast Rat1 is evolutionarily well conserved from yeast to human (Xrn2 in human)
physiological function
the enzyme plays a major role in mRNA turnover
physiological function
yeast Rat1 is an essential nuclear protein. Within a complex with Rai1, the 5'-3' exoribonuclease Rat1 promotes termination of RNA polymerase II (RNAPII) on protein-coding genes. The 5'-3' exoribonuclease activity of Rat1 is essential for RNAPII termination. Rat1 forms a complex with Rai1 that stabilizes Rat1 and helps target 5' monophosphate RNA by its diphosphohydrolase activity. Within a complex with Rai1, the 5'-3' exoribonuclease Rat1 promotes termination of RNAPII on protein-coding genes, overview. RNAPII is prone to more effective termination by Rat1/Rai1 when its catalytic site is disrupted due to NTP misincorporation, implying that paused RNAPII, which is often found in vivo near termination sites, can adopt a similar configuration to Rat1/Rai1 and trigger termination. Rat1/Rai1 itself is not sufficient to terminate RNAPII in vitro. Multiple-mechanistic features contribute to Rat1-mediated termination of RNAPII. NTP misincorporation induces RNAPII pausing and enhances termination by Rat1/Rai1, Rat1/Rai1 more effectively terminates RNAPII when a non-cognate NTP (ATP, CTP or UTP), rather than cognate GTP. Exoribonuclease activity is required for Rat1 not only to approach RNAPII but also to accumulate a sufficient driving force to dislodge the polymerase from the DNA template
physiological function
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the enzyme plays a major role in mRNA turnover
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E209A
significantly reduced activity compared with the wild type protein
H388A
significantly reduced activity compared with the wild type protein
H410A
mutant enzyme has full activity
H86A
significantly reduced activity compared with the wild type protein
E209A
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significantly reduced activity compared with the wild type protein
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H388A
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significantly reduced activity compared with the wild type protein
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H410A
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mutant enzyme has full activity
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H86A
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significantly reduced activity compared with the wild type protein
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E203A/D233A/D235A
site-directed mutagenesis, mutation of three active site residues, mutant rat1EDD does not show 5'-3' exoribonuclease activity, and rat1EDD/Rai1 complex does not degrade RNAs or decrease RNAPII elongation, demonstrating that RNA degradation by exonuclease activity is critical to RNAPII termination
H410V
significant loss of activity
additional information
to address the biological significance of Saci-aCPSF2, a deletion mutant is constructed, and the influence of SaciaCPSF2 on the transcriptome profile is assessed employing high throughput RNA sequencing
additional information
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to address the biological significance of Saci-aCPSF2, a deletion mutant is constructed, and the influence of SaciaCPSF2 on the transcriptome profile is assessed employing high throughput RNA sequencing
additional information
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to address the biological significance of Saci-aCPSF2, a deletion mutant is constructed, and the influence of SaciaCPSF2 on the transcriptome profile is assessed employing high throughput RNA sequencing
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Clouet-d'Orval, B.; Rinaldi, D.; Quentin, Y.; Carpousis, A.J.
Euryarchaeal beta-CASP proteins with homology to bacterial RNase J Have 5'- to 3'-exoribonuclease activity
J. Biol. Chem.
285
17574-17583
2010
Thermococcus kodakarensis (Q5JH57), Pyrococcus abyssi (Q9V076), Pyrococcus abyssi, Pyrococcus abyssi GE5 / CNCM I-1302 / DSM 25543 (Q9V076)
brenda
Märtens, B.; Amman, F.; Manoharadas, S.; Zeichen, L.; Orell, A.; Albers, S.V.; Hofacker, I.; Bläsi, U.
Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2
PLoS One
8
e76569
2013
Sulfolobus acidocaldarius (Q4J6E1), Sulfolobus acidocaldarius, Sulfolobus acidocaldarius DSM 639 (Q4J6E1)
brenda
Hasenöhrl, D.; Konrat, R.; Bläsi, U.
Identification of an RNase J ortholog in Sulfolobus solfataricus: implications for 5'-to-3' directional decay and 5'-end protection of mRNA in crenarchaeota
RNA
17
99-107
2011
Saccharolobus solfataricus (Q980D0), Saccharolobus solfataricus, Saccharolobus solfataricus P2 (Q980D0)
brenda
Park, J.; Kang, M.; Kim, M.
Unraveling the mechanistic features of RNA polymerase II termination by the 5'-3' exoribonuclease Rat1
Nucleic Acids Res.
43
2625-2637
2015
Saccharomyces cerevisiae (Q02792), Saccharomyces cerevisiae
brenda