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5' end-labeled pre-tRNASer + H2O
?
degradation of pre-tRNASer in a processive manner, leaving a short oligonucleotide (about 3nt) product
-
-
?
A(17) + H2O
AMP + ?
-
full-length RNase R has similar activity on both poly(A) and A(17) substrates. Full-length RNase II is 20fold more active on A(17) than full-length RNase R
-
-
?
A(4) + H2O
AMP + ?
-
poor substrate, is degraded by RNase R 400fold more slowly than A(17)
-
-
?
duplex RNA + H2O
?
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
mRNA + H2O
5'-phosphomononucleotides
mRNA + H2O
?
-
purified RNase II is unable to directly catalyse A-site cleavage in vitro, RNase II-catalysed degradation of mRNA to the ribosome border is a prerequisite for A-site cleavage. Degrades ribosome-bound mRNA to positions +18 nucleotides downstream of the ribosomal A site
-
-
?
oligonucleotide + H2O
?
-
-
-
-
?
oligoribonucleotide + H2O
?
petD3 RNA + H2O
5'-phosphomononucleotides
-
-
products detected are exclusively nucleotide monophosphates
-
?
poly(A) + H2O
5'-AMP + oligo(A)
poly(A) + H2O
5'-AMP + oligonucleotide
poly(C) + H2O
5'-CMP + oligonucleotide
poly(U) + H2O
5'-UMP + oligonucleotide
polyadenosine
?
-
23 units oligonucleotide
-
-
?
polyadenosine + H2O
?
-
-
-
-
?
poly[8-3H]adenylic acid + H2O
?
precursor tRNA + H2O
mature tRNA + 5'-phosphomononucleotides
RNA
5'-phosphomononucleotides
RNA
nucleoside 5'-monophosphate
-
-
-
-
?
RNA + H2O
phosphomononucleotides
rRNA
5'-phosphomononucleotides
ss RNA + H2O
5'-phosphomononucleotides
ss RNA oligonucleotides with chain lengths less than seven + H2O
5'-phosphomononucleotides
-
at high concentrations
-
?
T4 mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
tRNA
?
-
tRNA from Escherichia coli
-
-
?
tRNAiMet + H2O
?
complete degradation of the hypomodified tRNA requires both Rrp44 and the poly(A) polymerase activity of TRAMP. The intact exosome lacking only the catalytic activity of Rrp44 fails to degrade tRNAi Met, showing this to be a specific Rrp44 substrate
-
-
?
additional information
?
-
dsRNA + H2O
?
-
-
-
-
?
dsRNA + H2O
?
Rrp44 is very efficient in degrading a duplex with a 30 overhang of 14 nucleotides and is inactive with overhangs as short as 2 or 3 nucleotides
-
-
?
m-RNA + H2O
?
-
SL9A, containing one stem-loop structure, and malE-malF operon, containing two stem-loop structures
-
-
?
m-RNA + H2O
?
-
SL9A, containing one stem-loop structure, and malE-malF operon, containing two stem-loop structures
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
Chlamydomonas sp.
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
Drosophila sp. (in: flies)
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotide
-
-
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
mRNA-degradation
-
?
mRNA + H2O
5'-phosphomononucleotides
-
synthetic mRNA substrates, either with or without a poly(A) tail, turn out to be a good choice for mimicking the actual in vivo enzyme substrates
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
synthetic mRNA substrates, either with or without a poly(A) tail, turn out to be a good choice for mimicking the actual in vivo enzyme substrates
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
mRNA-maturation
-
?
oligoribonucleotide + H2O
?
final end product of RNase II is 4-nt, whereas for RNase R it is a 2-nt fragment
-
-
?
oligoribonucleotide + H2O
?
-
final end product of Rrp44 is 4-nt
-
-
?
poly (A)
5'-AMP
-
-
-
-
?
poly (A)
5'-AMP
-
-
-
-
?
poly(A) + H2O
5'-AMP + oligo(A)
-
full-length RNase R has similar activity on both poly(A) and A(17) substrates
-
-
?
poly(A) + H2O
5'-AMP + oligo(A)
-
RNase II has a strong preference for poly(A) stretches and is highly efficient in degrading poly(A) tails. RNase II is responsible for 90% of the exonucleolytic degradation of synthetic RNA poly(A) homopolymers
-
-
?
poly(A) + H2O
5'-AMP + oligo(A)
-
RNase II has a strong preference for poly(A) stretches and is highly efficient in degrading poly(A) tails. RNase II is responsible for 90% of the exonucleolytic degradation of synthetic RNA poly(A) homopolymers
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
-
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
35-nucleotide poly(A) chain, Tyr-313 and Glu-390 are crucial for RNA specificity of RNase II, Arg-500 residue in the active site is crucial for activity but not for RNA binding. Inside the cavity the unique specific contacts for ribose established by RNase II are those with the 2nd and 4th nucleotides from the 3'-end of the RNA molecule. These contacts are necessary and sufficient for cleavage to occur, and therefore, they seem to be responsible for the RNA specificity versus DNA in RNase II
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
-
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
-
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
-
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
-
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
-
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
-
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
-
35-nucleotide poly(A) chain, RNase II final end product contains four nucleotides, while RNase R renders a two-nucleotide fragment as the final product
-
-
?
poly(A) + H2O
5'-AMP + oligonucleotide
35-nucleotide poly(A) chain, RNase R renders a two-nucleotide fragment as the final product
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
Chlamydomonas sp.
-
-
-
-
?
poly(A) + H2O
?
Drosophila sp. (in: flies)
-
-
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(A) + H2O
?
-
-
in presence of 50 nM of protein, the final product released is a 5 nt fragment.When a higher protein concentration, 250 nM, is used the protein is able to release a 4 nt end-product
-
?
poly(A) + H2O
?
-
-
-
-
?
poly(C) + H2O
5'-CMP + oligonucleotide
-
-
-
?
poly(C) + H2O
5'-CMP + oligonucleotide
-
-
-
?
poly(C) + H2O
5'-CMP + oligonucleotide
-
-
-
?
poly(U) + H2O
5'-UMP + oligonucleotide
-
-
-
?
poly(U) + H2O
5'-UMP + oligonucleotide
-
-
-
?
poly[8-3H]adenylic acid + H2O
?
-
linear substrate, activity below 325 UE·micro g-1
-
-
?
poly[8-3H]adenylic acid + H2O
?
-
linear substrate, activity below 325 UE·micro g-1
-
-
?
precursor tRNA + H2O
mature tRNA + 5'-phosphomononucleotides
-
-
-
?
precursor tRNA + H2O
mature tRNA + 5'-phosphomononucleotides
-
-
-
?
RNA
5'-phosphomononucleotides
-
3' to 5'direction only
-
-
?
RNA
5'-phosphomononucleotides
-
Tyrosine aminotransferase RNA with 5'-phosphate terminus
-
-
?
RNA
5'-phosphomononucleotides
-
Tyrosine aminotransferase RNA with 5'-phosphate terminus
-
-
?
RNA
5'-phosphomononucleotides
-
synthesized using T3 RNA polimerase
-
-
?
RNA + H2O
phosphomononucleotides
RNA turnover
-
-
?
RNA + H2O
phosphomononucleotides
RNA turnover
-
-
?
rRNA
5'-phosphomononucleotides
-
-
-
-
?
rRNA
5'-phosphomononucleotides
-
-
-
-
?
rRNA + H2O
?
-
RNase R
-
-
?
rRNA + H2O
?
-
RNase R
-
-
?
siRNA + H2O
?
-
with 2-nt 3 overhangs
-
-
?
siRNA + H2O
?
-
with 2-nt 3' overhangs
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ssRNA + H2O
?
-
-
-
-
?
ssRNA + H2O
?
50fold higher affinity for ssRNA than for a corresponding ssDNA oligonucleotide
-
-
?
ssRNA + H2O
?
-
-
release of a 4 nt fragment
-
?
tRNA + H2O
?
-
poor substrate
-
-
?
tRNA + H2O
?
-
tRNA-maturation
-
-
?
tRNA + H2O
?
-
RNase BN
-
-
?
additional information
?
-
-
stem-loop structured RNA is not hydrolyzed
-
-
?
additional information
?
-
-
DNA oligomers with stem-loop structures are not hydrolyzed
-
-
?
additional information
?
-
-
helical RNA is not hydrolyzed
-
-
?
additional information
?
-
-
the enzyme is involed in processing of polycistronic tRNA transcripts. Polynucleotide phosphorylase (PNPase) and RNase II are required for the removal of the 3 Rho-dependent terminator sequences
-
-
?
additional information
?
-
-
RNase II is one of the major enzymes involved in mRNA processing. If the CSD is limiting the action of RNase II in vivo, it may play an important role working as a brake and thus preventing the massive degradation of RNA
-
-
?
additional information
?
-
-
cold-shock domains of RNase R appear to play a role in substrate recruitment, whereas the S1 domain is most likely required to position substrates for efficient catalysis. The nuclease domain alone, devoid of the cold-shock and S1 domains, is sufficient for RNase R to bind and degrade structured RNAs. RNase R binds RNA more tightly than the nuclease domain of RNase II
-
-
?
additional information
?
-
-
does not catalyze degradation of double-stranded RNA. RNase II has a CSD domain at the N-terminal end of the protein, a central RNB catalytic domain, and an S1 RNA-binding domain at the C-terminus. S1 domain is highly important for RNase II activity and its contribution to productive RNA binding is much more important than that of the CSD domain. This domain somehow prevents the rapid degradation of RNA by RNase II, which may be highly important to overall mRNA decay in Escherichia coli
-
-
?
additional information
?
-
-
RNase activity of PNPase is critical for its cold shock function, while its polymerization activity is dispensable. In vivo counterpart of PNPase that can compensate for its absence at low temperature reveals only one protein, another 3'-to-5' exonuclease, RNase II. RNase R, which is cold inducible, cannot complement the cold shock function of PNPase
-
-
?
additional information
?
-
Tyr253 and Phe358 are not essential for catalysis by RNase II. Tyr253 seems to be a critical residue in setting the smallest product generated by RNase II, thus being important for the stabilization of the 3'-end of the RNA molecule. Tyr253 is highly conserved and equivalent residues are present in many RNase II family members. Phe358 can be preventing a faster degradation of the RNA by stalling its translocation, probably due to the stacking of its aromatic ring between the bases of contiguous nucleotides. Asp201, Asp207, Asp209, and Asp210 are located in the RNase II active site. These residues are not equivalent and their functions in RNA metabolism are distinct, whereby Asp209 is the only residue essential for RNase II activity
-
-
?
additional information
?
-
-
Tyr253 and Phe358 are not essential for catalysis by RNase II. Tyr253 seems to be a critical residue in setting the smallest product generated by RNase II, thus being important for the stabilization of the 3'-end of the RNA molecule. Tyr253 is highly conserved and equivalent residues are present in many RNase II family members. Phe358 can be preventing a faster degradation of the RNA by stalling its translocation, probably due to the stacking of its aromatic ring between the bases of contiguous nucleotides. Asp201, Asp207, Asp209, and Asp210 are located in the RNase II active site. These residues are not equivalent and their functions in RNA metabolism are distinct, whereby Asp209 is the only residue essential for RNase II activity
-
-
?
additional information
?
-
RNase II is only able to cleave DNA bases when having a ribose in the 2nd or the 4th positions
-
-
?
additional information
?
-
-
RNase II is only able to cleave DNA bases when having a ribose in the 2nd or the 4th positions
-
-
?
additional information
?
-
-
RNase II degrades RNA hydrolytically in the 3' to 5' direction in a processive and sequence independent manner. RNase II activity is impaired by double-stranded RNAs
-
-
?
additional information
?
-
RNase II is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction, is sensitive to secondary structures, it is also known to stall before it reaches a double-stranded region. Although RNase II degrading activity is sequence-independent, its favourite substrate is poly(A) tails. RNase II rapidly degrades poly (A) tails, but it halts if it finds secondary structures such as the Rho-independent terminators. The degradation of polyadenylated stretches by RNase II can paradoxically protect some RNAs because the other exoribonucleases (PNPase and RNase R) need a short poly(A) tail as a toehold in order to degrade secondary structures
-
-
?
additional information
?
-
RNase II is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction, is sensitive to secondary structures, it is also known to stall before it reaches a double-stranded region. Although RNase II degrading activity is sequence-independent, its favourite substrate is poly(A) tails. RNase II rapidly degrades poly (A) tails, but it halts if it finds secondary structures such as the Rho-independent terminators. The degradation of polyadenylated stretches by RNase II can paradoxically protect some RNAs because the other exoribonucleases (PNPase and RNase R) need a short poly(A) tail as a toehold in order to degrade secondary structures
-
-
?
additional information
?
-
-
RNase II is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction, is sensitive to secondary structures, it is also known to stall before it reaches a double-stranded region. Although RNase II degrading activity is sequence-independent, its favourite substrate is poly(A) tails. RNase II rapidly degrades poly (A) tails, but it halts if it finds secondary structures such as the Rho-independent terminators. The degradation of polyadenylated stretches by RNase II can paradoxically protect some RNAs because the other exoribonucleases (PNPase and RNase R) need a short poly(A) tail as a toehold in order to degrade secondary structures
-
-
?
additional information
?
-
RNase R is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction. RNase R can easily degrade highly structured RNAs, but requires a single stranded region in order to be able to bind to the substrates. It was shown to be a key enzyme involved in the degradation of polyadenylated RNA
-
-
?
additional information
?
-
RNase R is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction. RNase R can easily degrade highly structured RNAs, but requires a single stranded region in order to be able to bind to the substrates. It was shown to be a key enzyme involved in the degradation of polyadenylated RNA
-
-
?
additional information
?
-
-
RNase R is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction. RNase R can easily degrade highly structured RNAs, but requires a single stranded region in order to be able to bind to the substrates. It was shown to be a key enzyme involved in the degradation of polyadenylated RNA
-
-
?
additional information
?
-
the enzyme substrate is a 30mer oligoribonucleotide (5' CCCGACACCAACCACUAAAAAAAAAAAAAA-3') labeled at 5'-end with [c-32P]ATP through T4 polynucleotide kinase
-
-
?
additional information
?
-
-
RNase activity of PNPase is critical for its cold shock function, while its polymerization activity is dispensable. In vivo counterpart of PNPase that can compensate for its absence at low temperature reveals only one protein, another 3'-to-5' exonuclease, RNase II. RNase R, which is cold inducible, cannot complement the cold shock function of PNPase
-
-
?
additional information
?
-
-
RNase II is one of the major enzymes involved in mRNA processing. If the CSD is limiting the action of RNase II in vivo, it may play an important role working as a brake and thus preventing the massive degradation of RNA
-
-
?
additional information
?
-
-
does not catalyze degradation of double-stranded RNA. RNase II has a CSD domain at the N-terminal end of the protein, a central RNB catalytic domain, and an S1 RNA-binding domain at the C-terminus. S1 domain is highly important for RNase II activity and its contribution to productive RNA binding is much more important than that of the CSD domain. This domain somehow prevents the rapid degradation of RNA by RNase II, which may be highly important to overall mRNA decay in Escherichia coli
-
-
?
additional information
?
-
the enzyme substrate is a 30mer oligoribonucleotide (5' CCCGACACCAACCACUAAAAAAAAAAAAAA-3') labeled at 5'-end with [c-32P]ATP through T4 polynucleotide kinase
-
-
?
additional information
?
-
-
ds RNA is not hydrolyzed
-
-
?
additional information
?
-
-
ds DNA is not hydrolyzed
-
-
?
additional information
?
-
-
3'-phosphorylated RNA is not hydrolyzed
-
-
?
additional information
?
-
interactions between NKRF, 5'->3' exoribonuclease 2 (XRN2) and the negative elongation factor (NELF)-E in HeLa cells
-
-
?
additional information
?
-
-
at optimal (37°C) or elevated (42°C) growth temperatures, the loss of RNase R in the RNase R mutant has no major consequence on bacterial growth and has a moderate impact on normal gene regulation. At lower temperatures (25°C or 30°C), the loss of RNase R has a significant impact on bacterial growth and results in the accumulation of structured RNA degradation products. Concurrently, gene regulation is affected and specifically results in an increased expression of the competence regulon. Loss of the exoribonuclease activity of RNase R is sufficient to induce competence development, a genetically programmed process normally triggered as a response to environmental stimuli. The temperature-dependent expression of competence genes in the rnr mutant is independent of previously identified competence regulators. The rnr mutant is competent for genetic transformation. RNase R is dispensable for the intracellular multiplication of Legionella pneumophila in both human and protozoan hosts. A physiological role of RNase R is to eliminate structured RNA molecules that are stabilized by low temperature, which in turn may affect regulatory networks, compromising adaptation to cold and thus resulting in decreased viability
-
-
?
additional information
?
-
-
at optimal (37°C) or elevated (42°C) growth temperatures, the loss of RNase R in the RNase R mutant has no major consequence on bacterial growth and has a moderate impact on normal gene regulation. At lower temperatures (25°C or 30°C), the loss of RNase R has a significant impact on bacterial growth and results in the accumulation of structured RNA degradation products. Concurrently, gene regulation is affected and specifically results in an increased expression of the competence regulon. Loss of the exoribonuclease activity of RNase R is sufficient to induce competence development, a genetically programmed process normally triggered as a response to environmental stimuli. The temperature-dependent expression of competence genes in the rnr mutant is independent of previously identified competence regulators. The rnr mutant is competent for genetic transformation. RNase R is dispensable for the intracellular multiplication of Legionella pneumophila in both human and protozoan hosts. A physiological role of RNase R is to eliminate structured RNA molecules that are stabilized by low temperature, which in turn may affect regulatory networks, compromising adaptation to cold and thus resulting in decreased viability
-
-
?
additional information
?
-
the base preference for RNase 2 is UpG
-
-
?
additional information
?
-
-
the base preference for RNase 2 is UpG
-
-
?
additional information
?
-
-
3'-phosphorylated RNA is not hydrolyzed
-
-
?
additional information
?
-
mRNA is a direct substrate for RNase R
-
-
?
additional information
?
-
-
mRNA is a direct substrate for RNase R
-
-
?
additional information
?
-
RNase R is a 3'-5'-exoribonuclease that is very processive and can efficiently digest RNAs having extensive secondary structures, such as rRNA, RNAs containing repetitive extragenic palindromic (REP) sequences, or the transfer-messenger RNA required for trans-translation.
-
-
?
additional information
?
-
-
RNase R is a 3'-5'-exoribonuclease that is very processive and can efficiently digest RNAs having extensive secondary structures, such as rRNA, RNAs containing repetitive extragenic palindromic (REP) sequences, or the transfer-messenger RNA required for trans-translation.
-
-
?
additional information
?
-
RNase R is also involved in the processing of 16S and 5S rRNA
-
-
?
additional information
?
-
-
RNase R is also involved in the processing of 16S and 5S rRNA
-
-
?
additional information
?
-
The absence of RNase R leads to moderate increases in the mRNA levels of some RNases and RNA helicases, but other RNases and RNA helicases are not affected.
-
-
?
additional information
?
-
-
The absence of RNase R leads to moderate increases in the mRNA levels of some RNases and RNA helicases, but other RNases and RNA helicases are not affected.
-
-
?
additional information
?
-
mRNA is a direct substrate for RNase R
-
-
?
additional information
?
-
RNase R is a 3'-5'-exoribonuclease that is very processive and can efficiently digest RNAs having extensive secondary structures, such as rRNA, RNAs containing repetitive extragenic palindromic (REP) sequences, or the transfer-messenger RNA required for trans-translation.
-
-
?
additional information
?
-
RNase R is also involved in the processing of 16S and 5S rRNA
-
-
?
additional information
?
-
The absence of RNase R leads to moderate increases in the mRNA levels of some RNases and RNA helicases, but other RNases and RNA helicases are not affected.
-
-
?
additional information
?
-
-
3'-phosphorylated RNA is not hydrolyzed
-
-
?
additional information
?
-
-
poly(G) is not hydrolyzed
-
-
?
additional information
?
-
-
capped mRNA is not hydrolyzed
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additional information
?
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Dis3 is responsible for exosome core activity
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?
additional information
?
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except for the more loosely associated Rtf1, the remaining components Paf1, Ctr9, Cdc73, and Leo1 of the Paf1 complex stay stably associated with one another in an RNase-resistant complex after dissociation from Pol II and chromatin
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?
additional information
?
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-
except for the more loosely associated Rtf1, the remaining components Paf1, Ctr9, Cdc73, and Leo1 of the Paf1 complex stay stably associated with one another in an RNase-resistant complex after dissociation from Pol II and chromatin
-
-
?
additional information
?
-
RNase activity of Dis3 is required for proper kinetochore formation and establishment of kinetochore-microtubule interactions. Dis3 is suggested to contribute to kinetochore formation through an involvement in heterochromatic silencing at both outer centromeric repeats and within the central core region
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?
additional information
?
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RNase activity of Dis3 is required for proper kinetochore formation and establishment of kinetochore-microtubule interactions. Dis3 is suggested to contribute to kinetochore formation through an involvement in heterochromatic silencing at both outer centromeric repeats and within the central core region
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-
?
additional information
?
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enzyme has no preference for poly(A) or randomized sequenced RNA
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?
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mRNA + H2O
5'-phosphomononucleotides
precursor tRNA + H2O
mature tRNA + 5'-phosphomononucleotides
RNA
5'-phosphomononucleotides
-
3' to 5'direction only
-
-
?
RNA
nucleoside 5'-monophosphate
-
-
-
-
?
RNA + H2O
phosphomononucleotides
ss RNA + H2O
5'-phosphomononucleotides
tRNAiMet + H2O
?
complete degradation of the hypomodified tRNA requires both Rrp44 and the poly(A) polymerase activity of TRAMP. The intact exosome lacking only the catalytic activity of Rrp44 fails to degrade tRNAi Met, showing this to be a specific Rrp44 substrate
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?
additional information
?
-
mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
mRNA + H2O
5'-phosphomononucleotides
-
-
-
?
precursor tRNA + H2O
mature tRNA + 5'-phosphomononucleotides
-
-
-
?
precursor tRNA + H2O
mature tRNA + 5'-phosphomononucleotides
-
-
-
?
RNA + H2O
phosphomononucleotides
RNA turnover
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-
?
RNA + H2O
phosphomononucleotides
RNA turnover
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-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
ss RNA + H2O
5'-phosphomononucleotides
-
-
-
?
additional information
?
-
-
the enzyme is involed in processing of polycistronic tRNA transcripts. Polynucleotide phosphorylase (PNPase) and RNase II are required for the removal of the 3 Rho-dependent terminator sequences
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?
additional information
?
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-
RNase II is one of the major enzymes involved in mRNA processing. If the CSD is limiting the action of RNase II in vivo, it may play an important role working as a brake and thus preventing the massive degradation of RNA
-
-
?
additional information
?
-
-
RNase II degrades RNA hydrolytically in the 3' to 5' direction in a processive and sequence independent manner. RNase II activity is impaired by double-stranded RNAs
-
-
?
additional information
?
-
RNase II is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction, is sensitive to secondary structures, it is also known to stall before it reaches a double-stranded region. Although RNase II degrading activity is sequence-independent, its favourite substrate is poly(A) tails. RNase II rapidly degrades poly (A) tails, but it halts if it finds secondary structures such as the Rho-independent terminators. The degradation of polyadenylated stretches by RNase II can paradoxically protect some RNAs because the other exoribonucleases (PNPase and RNase R) need a short poly(A) tail as a toehold in order to degrade secondary structures
-
-
?
additional information
?
-
RNase II is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction, is sensitive to secondary structures, it is also known to stall before it reaches a double-stranded region. Although RNase II degrading activity is sequence-independent, its favourite substrate is poly(A) tails. RNase II rapidly degrades poly (A) tails, but it halts if it finds secondary structures such as the Rho-independent terminators. The degradation of polyadenylated stretches by RNase II can paradoxically protect some RNAs because the other exoribonucleases (PNPase and RNase R) need a short poly(A) tail as a toehold in order to degrade secondary structures
-
-
?
additional information
?
-
-
RNase II is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction, is sensitive to secondary structures, it is also known to stall before it reaches a double-stranded region. Although RNase II degrading activity is sequence-independent, its favourite substrate is poly(A) tails. RNase II rapidly degrades poly (A) tails, but it halts if it finds secondary structures such as the Rho-independent terminators. The degradation of polyadenylated stretches by RNase II can paradoxically protect some RNAs because the other exoribonucleases (PNPase and RNase R) need a short poly(A) tail as a toehold in order to degrade secondary structures
-
-
?
additional information
?
-
RNase R is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction. RNase R can easily degrade highly structured RNAs, but requires a single stranded region in order to be able to bind to the substrates. It was shown to be a key enzyme involved in the degradation of polyadenylated RNA
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-
?
additional information
?
-
RNase R is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction. RNase R can easily degrade highly structured RNAs, but requires a single stranded region in order to be able to bind to the substrates. It was shown to be a key enzyme involved in the degradation of polyadenylated RNA
-
-
?
additional information
?
-
-
RNase R is a hydrolytic exoribonuclease that processively degrades RNA in the 3'-5' direction. RNase R can easily degrade highly structured RNAs, but requires a single stranded region in order to be able to bind to the substrates. It was shown to be a key enzyme involved in the degradation of polyadenylated RNA
-
-
?
additional information
?
-
-
RNase II is one of the major enzymes involved in mRNA processing. If the CSD is limiting the action of RNase II in vivo, it may play an important role working as a brake and thus preventing the massive degradation of RNA
-
-
?
additional information
?
-
interactions between NKRF, 5'->3' exoribonuclease 2 (XRN2) and the negative elongation factor (NELF)-E in HeLa cells
-
-
?
additional information
?
-
-
at optimal (37°C) or elevated (42°C) growth temperatures, the loss of RNase R in the RNase R mutant has no major consequence on bacterial growth and has a moderate impact on normal gene regulation. At lower temperatures (25°C or 30°C), the loss of RNase R has a significant impact on bacterial growth and results in the accumulation of structured RNA degradation products. Concurrently, gene regulation is affected and specifically results in an increased expression of the competence regulon. Loss of the exoribonuclease activity of RNase R is sufficient to induce competence development, a genetically programmed process normally triggered as a response to environmental stimuli. The temperature-dependent expression of competence genes in the rnr mutant is independent of previously identified competence regulators. The rnr mutant is competent for genetic transformation. RNase R is dispensable for the intracellular multiplication of Legionella pneumophila in both human and protozoan hosts. A physiological role of RNase R is to eliminate structured RNA molecules that are stabilized by low temperature, which in turn may affect regulatory networks, compromising adaptation to cold and thus resulting in decreased viability
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-
?
additional information
?
-
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at optimal (37°C) or elevated (42°C) growth temperatures, the loss of RNase R in the RNase R mutant has no major consequence on bacterial growth and has a moderate impact on normal gene regulation. At lower temperatures (25°C or 30°C), the loss of RNase R has a significant impact on bacterial growth and results in the accumulation of structured RNA degradation products. Concurrently, gene regulation is affected and specifically results in an increased expression of the competence regulon. Loss of the exoribonuclease activity of RNase R is sufficient to induce competence development, a genetically programmed process normally triggered as a response to environmental stimuli. The temperature-dependent expression of competence genes in the rnr mutant is independent of previously identified competence regulators. The rnr mutant is competent for genetic transformation. RNase R is dispensable for the intracellular multiplication of Legionella pneumophila in both human and protozoan hosts. A physiological role of RNase R is to eliminate structured RNA molecules that are stabilized by low temperature, which in turn may affect regulatory networks, compromising adaptation to cold and thus resulting in decreased viability
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?
additional information
?
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the base preference for RNase 2 is UpG
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?
additional information
?
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the base preference for RNase 2 is UpG
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?
additional information
?
-
mRNA is a direct substrate for RNase R
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-
?
additional information
?
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-
mRNA is a direct substrate for RNase R
-
-
?
additional information
?
-
RNase R is a 3'-5'-exoribonuclease that is very processive and can efficiently digest RNAs having extensive secondary structures, such as rRNA, RNAs containing repetitive extragenic palindromic (REP) sequences, or the transfer-messenger RNA required for trans-translation.
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-
?
additional information
?
-
-
RNase R is a 3'-5'-exoribonuclease that is very processive and can efficiently digest RNAs having extensive secondary structures, such as rRNA, RNAs containing repetitive extragenic palindromic (REP) sequences, or the transfer-messenger RNA required for trans-translation.
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?
additional information
?
-
RNase R is also involved in the processing of 16S and 5S rRNA
-
-
?
additional information
?
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-
RNase R is also involved in the processing of 16S and 5S rRNA
-
-
?
additional information
?
-
The absence of RNase R leads to moderate increases in the mRNA levels of some RNases and RNA helicases, but other RNases and RNA helicases are not affected.
-
-
?
additional information
?
-
-
The absence of RNase R leads to moderate increases in the mRNA levels of some RNases and RNA helicases, but other RNases and RNA helicases are not affected.
-
-
?
additional information
?
-
mRNA is a direct substrate for RNase R
-
-
?
additional information
?
-
RNase R is a 3'-5'-exoribonuclease that is very processive and can efficiently digest RNAs having extensive secondary structures, such as rRNA, RNAs containing repetitive extragenic palindromic (REP) sequences, or the transfer-messenger RNA required for trans-translation.
-
-
?
additional information
?
-
RNase R is also involved in the processing of 16S and 5S rRNA
-
-
?
additional information
?
-
The absence of RNase R leads to moderate increases in the mRNA levels of some RNases and RNA helicases, but other RNases and RNA helicases are not affected.
-
-
?
additional information
?
-
-
Dis3 is responsible for exosome core activity
-
-
?
additional information
?
-
RNase activity of Dis3 is required for proper kinetochore formation and establishment of kinetochore-microtubule interactions. Dis3 is suggested to contribute to kinetochore formation through an involvement in heterochromatic silencing at both outer centromeric repeats and within the central core region
-
-
?
additional information
?
-
-
RNase activity of Dis3 is required for proper kinetochore formation and establishment of kinetochore-microtubule interactions. Dis3 is suggested to contribute to kinetochore formation through an involvement in heterochromatic silencing at both outer centromeric repeats and within the central core region
-
-
?
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evolution
RC-RNase 2, a cytotoxic ribonuclease isolated from oocytes of bullfrog Rana catesbeiana, consists of 105 residues linked with 4 disulfide bridges and belongs to the bovine pancreatic ribonuclease (RNase A) superfamily. Among the RC-RNases, the base preference for RNase 2 is UpG but CpG for RCRNase 4, while RC-RNase possesses the base specificity of both UpG and CpG. RC-RNase 2 or 4 has much lower catalytic activity but only 3fold less cytotoxicity than RC-RNase. The differences of side-chain conformations of subsite residues among RNase A, RC-RNase, RC-RNase 4 and rRNase 2 are related to their distinct catalytic activities and base preferences. Chemical shift perturbations of three RC-RNases with various substrate analogues, overview
evolution
RNase II is another 3'-5' hydrolytic exoribonuclease from the RNase II family of exoribonucleases
evolution
RNase R is another 3'-5' hydrolytic exoribonuclease from the RNase II family of exoribonucleases
malfunction
-
instead of A-site cleavage, translational pausing in DELTARNase II cells produces transcripts that are truncated +12 and +28 nucleotides downstream of the A-site codon. Deletion of RNase R has little effect on A-site cleavage. Polynucleotide phosphorylase overexpression restores A-site cleavage activity to DELTARNase II cells
malfunction
-
a specific subclass of var genes called upsA are strongly up-regulated in parasites that expressed a defective PfRNase II (C-terminally tagged with the FKBP destabilization domain) compared to wild-type parasites. Different combinations of up to 3 distinct upsA var genes, together with an upsC var gene, were upregulated simultaneously in single parasite clones
malfunction
RNase II thermolability of the rnb500 phenotype is due to the Cys284Tyr mutation within the RNB domain, which abolishes activity by increasing protein kinetic instability at the nonpermissive temperature. In vivo and in vitro investigation of RNase II mutation(s) that confer the rnb500 phenotype
malfunction
RNase R mutants form more biofilms than wild-type cells
malfunction
-
RNase II thermolability of the rnb500 phenotype is due to the Cys284Tyr mutation within the RNB domain, which abolishes activity by increasing protein kinetic instability at the nonpermissive temperature. In vivo and in vitro investigation of RNase II mutation(s) that confer the rnb500 phenotype
-
metabolism
-
exoribonuclease-mediated gene silencing, mechanism and a more general regulatory role of ribonucleases in dynamic gene expression in Plasmodium falciparum, overview
metabolism
NF-kappaB-repressing factor phosphorylation regulates transcription elongation via its interactions with 5'->3' exoribonuclease 2 and negative elongation factor. Interleukin-1 has a more drastic effect on NELF-E or XRN2 binding to NKRF than the M1 mutation
metabolism
role for RNase II Lys501 acetylation in modulating cell growth during stress conditions
metabolism
the enzyme is involved in cell motility and biofilm formation
physiological function
-
plays an important role in RelE-independent A-site cleavage
physiological function
major hydrolytic exoribonuclease RNase II is associated with the degradosome components endoribonuclease E, RNA helicase B, polynucleotide phosphorylase and enolase. Formation of the RNase II-degradosome complex requires the degradosomal proteins RNA helicase B and polynucleotide phosphorylase as well as a C-terminal domain of endoribonuclease E that contains binding sites for the other degradosomal proteins
physiological function
mutants lacking both ribonuclease RNR1 and polynucleotide phosphorylase exhibit embryo lethality. Combination of a RNR1 null mutation with weak polynucleotide phosphorylase mutant alleles leads to chlorotic plants which display a global reduction in RNA abundance. The enzymes catalyze a two-step maturation of mRNA 3' ends, with RNR1 polishing 3' termini created by polynucleotide phosphorylase. The bulky quaternary structure of polynucleotide phosphorylase compared with RNR1 may explain this activity split between the two enzymes. The RNR1 single mutant overaccumulates most mRNA species when compared with the wild type. The excess mRNAs in RNR1 are often present in non-polysomal fractions, and mostly show a substantial increase in stability
physiological function
-
RNase II protein is essential for vialbilty
physiological function
RNase II self-interaction and the ability of the protein to assemble into organized cellular structures requires the membrane binding domain. The ability of RNase II to maintain cell viability in the absence of exoribonuclease polynucleotide phosphorylase is markedly diminished when the RNase II cellular structures are lost due to changes in the amphipathicity of the amino-terminal helix
physiological function
-
although genes represent monocistronic units that are expressed in a life cycle stage-specific manner, posttranscriptional regulation via translational repression of mRNA has been observed in parasite stages that transition from the vertebrate host to the Anopheles vector. In Plasmodium falciparum stages that infect human erythrocytes, a subgroup of genes that have been thought to be transcriptionally silent are actually transcribed but degraded immediately by an RNase II that is recruited to these gene loci. This cryptic RNA is not detectable in steady-state RNA but has been detected using nuclear run-on techniques and in mutant RNase II parasites. Nascent RNA degradation controls virulence genes expressed in a monoallelic fashion and noncoding RNAs (ncRNAs), but also a number of housekeeping-like of genes. PfRNase II is recruited to certain gene loci and accelerates the decay of mRNAs and ncRNA. PfRNase II is highly enriched at the promoters and introns of silenced upsA gene loci, and transcription analysis revealed that any nascent transcripts from these genes are only short-lived, cryptic mRNAs. Exoribonuclease-mediated gene silencing, mechanism, overview
physiological function
cytotoxic ribonucleases with antitumor activity are found in the oocytes and early embryos of frogs
physiological function
interactions between NKRF, 5'->3' exoribonuclease 2 (XRN2) and the negative elongation factor (NELF)-E in HeLa cells. Interleukin IL-1 stimulation leads to decrease in NKRF amino acids 421-429 phosphorylation and dissociation of NELF-E and XRN2 by concomitant resumption of transcription elongation of a synthetic reporter or the endogenous NKRF target gene, interleukin IL-8. 5'->3' exoribonuclease 2 (XRN2) is implicated in inhibition of transcription elongation via the termination of initiated transcripts in many RNA Pol II-dependent promoters
physiological function
RNase II is a 3' to 5' processive exoribonuclease and is the major hydrolytic enzyme in Escherichia coli accounting for about 90% of the total activity. Acetylation of residue Lys501 in RNase II, reversibly controlled by the acetyltransferase Pka and the deacetylase CobB, affects binding of the substrate and decreases the catalytic activity of RNase II. As a consequence, the steady-state level of target RNAs of RNase II may be altered in the cells. Under conditions of slowed growth, the acetylation level of RNase II is elevated and the activity of RNase II decreases, emphasizing the importance of this regulatory process
physiological function
the RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene expression. In Escherichia coli there are three main exoribonucleases (RNase II, RNase R and PNPase) involved in RNA degradation. RNase II, RNase R and PNPase significantly impair the motility of the cells
physiological function
the RNA steady-state levels in the cell are a balance between synthesis and degradation rates. Although transcription is important, RNA processing and turnover are also key factors in the regulation of gene expression. In Escherichia coli there are three main exoribonucleases (RNase II, RNase R and PNPase) involved in RNA degradation. RNase R is a critical enzyme involved in RNA and protein quality control, namely in the degradation of defective tRNAs and rRNAs and is involved in RNA degradation during trans-translation. RNase R is involved in virulence, it affects virulence by altering the motility of the pathogens. RNase II, RNase R and PNPase significantly impair the motility of the cells
additional information
-
stability of RNAse II-RNA interactions and effects on the enzyme reaction mechanism processing and degrading RNA molecules, analysis by surface plasmon resonance and electrophoretic mobility shift Assay, overview
additional information
-
RNase II of Plasmodium falciparum is a non-canonical exoribonuclease that contains a putative RNase II domain (termed PfRNase II). Loss of PfRNase II affects the strict gene counting mechanism that controls monoallelic var gene expression
additional information
solution structure of recombinant RC-RNase 2 by heteronuclear NMR technique, overview. The substrate-related residues in the base specificity among native RC-RNases are derived using the chemical shift perturbation on ligand binding
additional information
-
solution structure of recombinant RC-RNase 2 by heteronuclear NMR technique, overview. The substrate-related residues in the base specificity among native RC-RNases are derived using the chemical shift perturbation on ligand binding
additional information
transcriptomic analysis
additional information
transcriptomic analysis
additional information
-
transcriptomic analysis
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C284Y
RNase II thermolability of the rnb500 phenotype is due to the Cys284Tyr mutation within the RNB domain, which abolishes activity by increasing protein kinetic instability at the nonpermissive temperature. Expression of RNase II C284Y and the double mutant (D126N and C284Y) does not allow growth at the nonpermissive temperature of 44°C. Structural mapping and partial multiple sequence alignment of RNase II thermosensitive phenotype mutations, overview
D126N
site-directed mutagenesis, the RNase II mutant exhibits a slightly decreased growth at 44°C suggesting some thermosensitivity which does not account for a major phenotype. This individual mutation is not detrimental for the function of RNase II in vivo. the RNase II D126N variant exhibits substantial catalytic activity
D126N/C284Y
site-directed mutagenesis, expression of RNase II C284Y and the double mutant (D126N and C284Y) does not allow growth at the nonpermissive temperature of 44°C
D155M
-
truncated RNase II protein pETIIDELTACSD1DELTAS1 consisting of the nuclease domain alone, but lacking any part of CSD2. Removal of the RNA-binding domains does allow RNase II to proceed further
D278N
-
mutation at the catalytic center of RNase R, is inactive on A(4), but retains 4% activity of wild-type RNase R on poly(A) and A(17)
K501Q
site-directed mutagenesis, mutation of Lys501 results in up to 80% reduction in acetylation of RNase II
K501R
site-directed mutagenesis, mutation of Lys501 results in up to 80% reduction in acetylation of RNase II
R500K
shows less than 0.1% of the specific activity present in the wild-type
D209N
-
has less than 1% of the wild-type RNase activity, has similar affinities for the RNA substrate as the wild-type enzyme
-
C284Y
-
RNase II thermolability of the rnb500 phenotype is due to the Cys284Tyr mutation within the RNB domain, which abolishes activity by increasing protein kinetic instability at the nonpermissive temperature. Expression of RNase II C284Y and the double mutant (D126N and C284Y) does not allow growth at the nonpermissive temperature of 44°C. Structural mapping and partial multiple sequence alignment of RNase II thermosensitive phenotype mutations, overview
-
D126N
-
site-directed mutagenesis, the RNase II mutant exhibits a slightly decreased growth at 44°C suggesting some thermosensitivity which does not account for a major phenotype. This individual mutation is not detrimental for the function of RNase II in vivo. the RNase II D126N variant exhibits substantial catalytic activity
-
D126N/C284Y
-
site-directed mutagenesis, expression of RNase II C284Y and the double mutant (D126N and C284Y) does not allow growth at the nonpermissive temperature of 44°C
-
C425A
-
cannot be classified as polymorphic in the Japanese population. In the Korean, Mongolian, Ovambo, Turkish, and German DNA no genotype other than homozygotic 425C allele in RNASE2 at each single nucleotide polymorphism site is found
D275A
-
is stable and produced in amounts similar to those seen for the wild-type enzyme, but it cannot repress competence
D283R
-
is stable and produced in amounts similar to those seen for the wild-type enzyme, but it cannot repress competence
D275A
-
is stable and produced in amounts similar to those seen for the wild-type enzyme, but it cannot repress competence
-
D283R
-
is stable and produced in amounts similar to those seen for the wild-type enzyme, but it cannot repress competence
-
A815F
degrades RNA duplexes with 7 or 14 nucleotides of ssRNA overhang significantly slower (about 4fold) than the wild-type enzyme
A815W
degrades RNA duplexes with 7 or 14 nucleotides of ssRNA overhang significantly slower (about 3fold) than the wild-type enzyme
D201N
significant loss of activity in degradation of poly(A) (0.2% of that of the wild-type enzyme). Generates a 10-11-nt fragment as a major degradation product, although longer reaction times result in the usual 4-nt fragment as a secondary product
D201N
activity is highly impaired, 0.2% of the specific activity of wild-type enzyme
D201N
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
D201N/E390A
very similar specific specific activity to the wild-type
D201N/E390A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
D201N/Y313F
shows less than 0.1% of the specific activity present in the wild-type
D201N/Y313F
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
D201N/Y313F/E390A
shows less than 0.1% of the specific activity present in the wild-type
D201N/Y313F/E390A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
D207N
still retains 12% activity
D207N
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
D209N
-
has less than 1% of the wild-type RNase activity, has similar affinities for the RNA substrate as the wild-type enzyme
D209N
-
catalytically inactive, is unable to complement RNase II deletion
D209N
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
D210N
significant loss of activity in degradation of poly(A) (0.3% of that of the wild-type enzyme). Generates a 10-11-nt fragment as a major degradation product, although longer reaction times result in the usual 4-nt fragment as a secondary product
D210N
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
E390A
specific activity is very similar to that of the wild-type
E390A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
E542A
extraordinary catalysis and binding abilities that turns RNase II into a super-enzyme. More than a 100fold increase in the specific exoribonucleolytic activity, significantly increases affinity for the poly(A) substrate
E542A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
F358A
the protein is 2fold more active than the wild-type
F358A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
R500A
shows more than a 40000fold reduction in specific activity when compared with the wild-type
R500A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
Y253A
26% of the activity of the enzyme persists, significantly impairs RNA binding
Y253A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
Y253A/F358A
12% of the activity of the enzyme persists, whereas RNA binding affinity is not significantly affected
Y253A/F358A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
Y313A
100fold reduction of specific activity
Y313A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
Y313F
specific activity is very similar to that of the wild-type
Y313F
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
Y313F/E390A
specific activity is not affected
Y313F/E390A
-
site-directed mutagenesis, kinetic constants for enzyme-RNA interaction compared to the wild-type enzyme
D551N
mutation in Rrp44-cat abolishes the exonucleolytic activity of Rrp44 without affecting its ability to bind RNA
D551N
abolishes the exonucleolytic activity
additional information
-
construction of a large set of RNase II truncated proteins and comparison of them to the wild-type regarding their exoribonucleolytic activity and RNA-binding ability. The dissociation constants are determined using different single- or double-stranded substrates. The results obtained reveal that S1 is the most important domain in the establishment of stable RNAprotein complexes, and its elimination results in a drastic reduction on RNA-binding ability. The N-terminal CSD plays a very specific role in RNase II, preventing a tight binding of the enzyme to single-stranded poly(A) chains. The biochemical results obtained with a mutant that lacks both putative RNA-binding domains, reveals the presence of an additional region involved in RNA binding. Such region, is identified by sequence analysis and secondary structure prediction as a third putative RNA-binding domain located at the N-terminal part of RNB catalytic domain
additional information
hybrid proteins are constructed by replacing the S1 domain of RNase II for the S1 from RNase R and PNPase, and their exonucleolytic activity and RNA-binding ability are examined. Both the S1 domains of RNase R and PNPase are able to partially reverse the drop of RNA-binding ability and exonucleolytic activity resulting from removal of the S1 domain of RNase II. The S1 domains investigated are not equivalent
additional information
-
hybrid proteins are constructed by replacing the S1 domain of RNase II for the S1 from RNase R and PNPase, and their exonucleolytic activity and RNA-binding ability are examined. Both the S1 domains of RNase R and PNPase are able to partially reverse the drop of RNA-binding ability and exonucleolytic activity resulting from removal of the S1 domain of RNase II. The S1 domains investigated are not equivalent
additional information
-
DELTACSDb and DELTAS1b mutants, are more than 90% soluble. Similarly, the solubility of the RNB derivative, which lacks both putative RNA-binding domains, is also greater than 90%. The DELTACSDa mutant is only 60% soluble. Elimination of the whole CSD domain (DELTACSDb) or part of it (DELTACSDa) does not affect the exonucleolytic activity of RNase II, and even improves its activity significantly
additional information
-
RNase RDELTACSDs is missing the first 221 amino acids of RNase R, which include CSD1 and CSD2. RNase RDELTABasic lacks the 83 amino acids from the C terminus, which comprise the low complexity, highly basic region. RNase RDELTAS1 is truncated 170 amino acids from the C-terminus to remove both the S1 domain and the low complexity, highly basic region. RNase RDELTACSDsDELTAS1 consists of the nuclease domain alone, and, therefore, lacks all of the putative RNA-binding domains. Decrease in affinity upon deletion of either the CSDs or the S1 domain. RNase RDELTABasic displays 2fold higher activity than full-length wild-type RNase R. RNase RDELTACSDs looses 30% of the activity of full-length RNase R on poly(A) 90% on the shorter A(17) substrate. The RNase RDELTACSDsDELTAS1 truncated protein retains only 0.5% activity of the full-length protein on poly(A), and only 0.02% activity on A(17). All of the RNase R-truncated proteins have comparable activity on A(4)
additional information
construction of deletion mutant DELTArnb. Comparison of the mutant transcriptome with the wild-type, to determine the global effects of the deletion of the exoribonucleases in exponential phase, reveals that the deletion of RNase II significantly affects 187 transcripts. Many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The exoribonuclease also affects some stable RNAs. The RNase II mutant is shown to produce more biofilm than the wild-type control. Differential expression analysis of the transcriptome of exoribonucleases mutants and phenotypes, overview. For example, nirB (Nitrite reductase [NAD(P)H] large subunit) is down-regulated in DELTArnb with a fold-change of 0.36 while in the DELTArnr mutant nirB is up-regulated with a fold-change of 9.11
additional information
construction of deletion mutant DELTArnb. Comparison of the mutant transcriptome with the wild-type, to determine the global effects of the deletion of the exoribonucleases in exponential phase, reveals that the deletion of RNase II significantly affects 187 transcripts. Many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The exoribonuclease also affects some stable RNAs. The RNase II mutant is shown to produce more biofilm than the wild-type control. Differential expression analysis of the transcriptome of exoribonucleases mutants and phenotypes, overview. For example, nirB (Nitrite reductase [NAD(P)H] large subunit) is down-regulated in DELTArnb with a fold-change of 0.36 while in the DELTArnr mutant nirB is up-regulated with a fold-change of 9.11
additional information
-
construction of deletion mutant DELTArnb. Comparison of the mutant transcriptome with the wild-type, to determine the global effects of the deletion of the exoribonucleases in exponential phase, reveals that the deletion of RNase II significantly affects 187 transcripts. Many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The exoribonuclease also affects some stable RNAs. The RNase II mutant is shown to produce more biofilm than the wild-type control. Differential expression analysis of the transcriptome of exoribonucleases mutants and phenotypes, overview. For example, nirB (Nitrite reductase [NAD(P)H] large subunit) is down-regulated in DELTArnb with a fold-change of 0.36 while in the DELTArnr mutant nirB is up-regulated with a fold-change of 9.11
additional information
construction of deletion mutant DELTArnb. Comparison of the mutant transcriptome with the wild-type, to determine the global effects of the deletion of the exoribonucleases in exponential phase, reveals that the deletion of RNase R significantly affects 202 transcripts. Many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The exoribonuclease also affects some stable RNAs. The RNase R mutant is shown to produce more biofilm than the wild-type control. Differential expression analysis of the transcriptome of exoribonucleases mutants and phenotypes, overview
additional information
construction of deletion mutant DELTArnb. Comparison of the mutant transcriptome with the wild-type, to determine the global effects of the deletion of the exoribonucleases in exponential phase, reveals that the deletion of RNase R significantly affects 202 transcripts. Many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The exoribonuclease also affects some stable RNAs. The RNase R mutant is shown to produce more biofilm than the wild-type control. Differential expression analysis of the transcriptome of exoribonucleases mutants and phenotypes, overview
additional information
-
construction of deletion mutant DELTArnb. Comparison of the mutant transcriptome with the wild-type, to determine the global effects of the deletion of the exoribonucleases in exponential phase, reveals that the deletion of RNase R significantly affects 202 transcripts. Many of the transcripts are actually down-regulated in the exoribonuclease mutants when compared to the wild-type control. The exoribonuclease also affects some stable RNAs. The RNase R mutant is shown to produce more biofilm than the wild-type control. Differential expression analysis of the transcriptome of exoribonucleases mutants and phenotypes, overview
additional information
-
DELTACSDb and DELTAS1b mutants, are more than 90% soluble. Similarly, the solubility of the RNB derivative, which lacks both putative RNA-binding domains, is also greater than 90%. The DELTACSDa mutant is only 60% soluble. Elimination of the whole CSD domain (DELTACSDb) or part of it (DELTACSDa) does not affect the exonucleolytic activity of RNase II, and even improves its activity significantly
-
additional information
Rrp44 242-1001 (Rrp44DELTAN) lacks the predicted N-terminal PIN domain, shows no detectable difference in activity toward ssRNA substrates as compared to recombinant Rrp44
additional information
-
Rrp44 242-1001 (Rrp44DELTAN) lacks the predicted N-terminal PIN domain, shows no detectable difference in activity toward ssRNA substrates as compared to recombinant Rrp44
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