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Information on EC 4.6.1.22 - Bacillus subtilis ribonuclease
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4.6.1.22 Bacillus subtilis ribonucleaseIUBMB Comments
This enzyme catalyses endonucleolytic cleavage to 2',3'-cyclic nucleotides. The cyclic products may be hydrolysed to the corresponding 3'-phosphates by 2',3'-cyclic-nucleotide 2'-phosphodiesterase (EC 3.1.4.16). The enzyme from B. subtilis is inhibited by ATP.
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Word Map
- 4.6.1.22
- exoribonuclease
-
degradosome
-
exonucleolytic
- pnpase
-
exoribonucleolytic
- pre-trna
- hfq
-
degradosome-like
- biotechnology
The enzyme appears in viruses and cellular organisms
Reaction Schemes
=
a 5'-hydroxy-ribonucleotide
+
n
nucleoside-2',3'-cyclophosphates
Synonyms
rnase y, rnase j, rnase j1, rnase j2, bacillus subtilis ribonuclease, ribonuclease p protein, endoribonuclease rnase y, ribonuclease rnase j1, bacisubin, endoribonuclease j2, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
5' end-independent RNase J1 endonuclease
Bacillus subtilis ribonuclease
Bacisubin
bifunctional 5'-3' exo/endoribonuclease
EC 3.1.27.2
-
-
formerly
-
endoribonuclease J1
endoribonuclease J2
intracellular acid ribonuclease
-
-
-
-
Proteus mirabilis RNase-2
-
-
-
-
ribonuclease J1
ribonuclease J2
ribonuclease RNase J1
ribonucleate nucleotido-2'-transferase (cyclizing)
-
-
-
-
RNase J
RNase J1
RNase J2
RNase Y
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
RNA = a 5'-hydroxy-ribonucleotide + n nucleoside-2',3'-cyclophosphates
no convertion to 3'-mononucleotides
-
RNA = a 5'-hydroxy-ribonucleotide + n nucleoside-2',3'-cyclophosphates
combined activity with the cyclic phosphodiesterase to degrade RNA
-
RNA = a 5'-hydroxy-ribonucleotide + n nucleoside-2',3'-cyclophosphates
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
[RNA] 5'-hydroxy-ribonucleotide-3'-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3'- nucleoside -2',3'-cyclophosphate-forming)
This enzyme catalyses endonucleolytic cleavage to 2',3'-cyclic nucleotides. The cyclic products may be hydrolysed to the corresponding 3'-phosphates by 2',3'-cyclic-nucleotide 2'-phosphodiesterase (EC 3.1.4.16). The enzyme from B. subtilis is inhibited by ATP.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
20 nt RNA + H2O
?
-
32pUGGUGGUGGAUCCCGGGAUC, exoribonuclease activity
-
-
?
30 nt RNA + H2O
?
-
RT-FeDEx assay of RNase J1, J2 and the RNase J1/J2 complex, 30 nt RNA labelled with a carboxyfluorescein group at its 3'-end and hybridized to a 17 nt DNA bearing a 5'-quenching group carboxymethylrhodamine, exoribonuclease activity
-
-
?
350 nt RNA + H2O
?
-
5'-triphosphate-labelled 350 nt fragment corresponding to the Bacillus subtilis thrS leader mRNA and 46 nts of coding sequence, and a 570 nt fragment corresponding to the hbs P3 transcript, endonucleolytic activity
-
-
?
DELTAermC mRNA + H2O
?
-
DELTAermC mRNA decay is RNase J1 dependent. Decay-initiating endonuclease cleavage can occur at several sites near the 3' end. Preferred RNase J1 target sites are located in the downstream half of DELTAermC mRNA, located upstream of eSL1 (ermC stem-loop 1), between eSL1 and eSL2, and between eSL2 and the 3' transcription terminator. The putative endonuclease cleavages in the body of the message are not dependent on ribosome flow. Even in the absence of these sites, stability is further increased in a strain with reduced RNase J1, suggesting alternate pathways for decay that can include exonucleolytic decay from the 5' end
-
-
?
trp:rpsO-TT RNA + H2O
?
-
endonucleolytic cleavage by ribonuclease RNase J1
-
-
?
NotI_34 RNA + H2O
?
-
artificial substrate is 5'-SSS RNA, NotI:rpsO-TT RNA, that contains the NotI site at nt 101, mutating the AU-rich sequence around nt 101 in NotI RNA reduces the enzyme activity
-
-
?
NotI_34 RNA + H2O
?
-
artificial substrate is 5'-SSS RNA, NotI:rpsO-TT RNA, that contains the NotI site at nt 101, mutating the AU-rich sequence around nt 101 in NotI RNA reduces the enzyme activity
-
-
?
RNA + H2O
2',3'-cyclic nucleotides
-
various synthetic polynucleotides
-
-
?
rpsO mRNA + H2O
?
-
aspects of mRNA decay initiation in Bacillus subtilis. Endonuclease cleavage in the body of the message, rather than degradation from the native 3' end, is the rate-determining step for mRNA decay
-
-
?
rpsO mRNA + H2O
?
-
a small monocistronic mRNA, decay of rpsO mRNA in a panel of 3'-to-5' exoribonuclease mutants, overview. Endonuclease cleavage in the body of the message, rather than degradation from the native 3' end, is the rate-determining step for mRNA decay
-
-
?
trp leader RNA + H2O
?
-
endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded region. trp leader RNA is a small (140-nucleotide) RNA that results from attenuation of trp operon transcription upon binding of the regulatory TRAP complex. In the RNase J1 mutant strain, trp:rpsO-TT RNA half-life increases 2.3fold to 8.2 min
-
-
?
trp leader RNA + H2O
?
-
endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded region
-
-
?
trp leader RNA + H2O
?
-
endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded region. trp leader RNA is a small (140-nucleotide) RNA that results from attenuation of trp operon transcription upon binding of the regulatory TRAP complex. In the RNase J1 mutant strain, trp:rpsO-TT RNA half-life increases 2.3fold to 8.2 min
-
-
?
trp leader RNA + H2O
?
-
endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded region
-
-
?
additional information
?
-
-
single-turnover kinetic assays are performed using 32P-labeled pre-tRNAAsp, containing a 14-nucleotide leader sequence, as a substrate
-
-
?
additional information
?
-
-
enzyme RNase J1 possesses 5'-to-3' exoribonuclease activity, while enzymes RNase J1 and RNase J2 form a complex that also has endonuclease activity, model for the degradation of the trp leader mRNA bound to TRAP. RNase J1 is the endonuclease cleaving scRNA that is 4 nts shorter on the 3' end
-
-
?
additional information
?
-
-
RNase J is a bifunctional 5'-3' exo/endoribonuclease
-
-
?
additional information
?
-
-
RNase J1 is a dual-specificity enzyme, with both 5' exonucleolytic and endonucleolytic activities. 5'-SSS RNA is unlikely to be a good substrate for 5' exonucleolytic attack in vivo
-
-
?
additional information
?
-
-
the enzyme degrades of a large number of mRNAs as well as non coding RNAs
-
-
?
additional information
?
-
-
placement of the strongly structured stem-loop at the 5' end has no effect on RNA decay
-
-
?
additional information
?
-
-
the 5'-to-3' exoribonuclease activity of the enzyme is active on 5'-monophosphorylated or 5'-hydroxylated RNA requiring a single-stranded 5'-end, but is essentially completely inhibited by the triphosphorylated 5' ends of primary transcripts. The endonuclease activity is independent of the 5' phosphorylation status of the 5' end. The RNase J1/J2 complex has different endonucleolytic cleavage site preferences to the individual enzymes in vitro. RNase J2 has very poor 5'-to-3' exoribonuclease activity compared to RNase J1
-
-
?
additional information
?
-
-
the enzyme RNase J1 shows processive behavior on long RNAs, and behaves distributively for substrates less than 5 nucleotides in length, RNA substrate binding structure and mechansim of the enzyme, overview
-
-
?
additional information
?
-
-
the enzyme shows cleavage specificity and a preference for 5' monophosphorylated substrates
-
-
?
additional information
?
-
-
RNase J1 is a dual-specificity enzyme, with both 5' exonucleolytic and endonucleolytic activities. 5'-SSS RNA is unlikely to be a good substrate for 5' exonucleolytic attack in vivo
-
-
?
additional information
?
-
-
placement of the strongly structured stem-loop at the 5' end has no effect on RNA decay
-
-
?
additional information
?
-
ribonucleases J1 and J2 have both endoribonucleolytic and 5'-to-3' exoribonucleolytic activities. Both act on class I and class II mRNAs, overview
-
-
?
additional information
?
-
ribonucleases J1 and J2 have both endoribonucleolytic and 5'-to-3' exoribonucleolytic activities. Both act on class I and class II mRNAs, overview
-
-
?
additional information
?
-
-
ribonucleases J1 and J2 have both endoribonucleolytic and 5'-to-3' exoribonucleolytic activities. Both act on class I and class II mRNAs, overview
-
-
?
additional information
?
-
active on hasA and gyrA class I mRNAs and sagA and sda class II mRNAs
-
-
?
additional information
?
-
active on hasA and gyrA class I mRNAs and sagA and sda class II mRNAs
-
-
?
additional information
?
-
-
active on hasA and gyrA class I mRNAs and sagA and sda class II mRNAs
-
-
?
additional information
?
-
RNase J is a bifunctional 5'-3' exo/endoribonuclease, structure of enzyme bound to a 4-nucleotide RNA showing an RNA-binding channel. A second, negatively charged tunnel leads from the active site, and is ideally located to evacuate the cleaved nucleotide in 5'-3' exonucleolytic mode
-
-
?
additional information
?
-
the enzyme RNase J1 shows processive behavior on long RNAs, and behaves distributively for substrates less than 5 nucleotides in length, RNA substrate binding structure and mechansim of the enzyme, overview
-
-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
rpsO mRNA + H2O
?
-
aspects of mRNA decay initiation in Bacillus subtilis. Endonuclease cleavage in the body of the message, rather than degradation from the native 3' end, is the rate-determining step for mRNA decay
-
-
?
trp leader RNA + H2O
?
-
endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded region. trp leader RNA is a small (140-nucleotide) RNA that results from attenuation of trp operon transcription upon binding of the regulatory TRAP complex. In the RNase J1 mutant strain, trp:rpsO-TT RNA half-life increases 2.3fold to 8.2 min
-
-
?
trp leader RNA + H2O
?
-
endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded region. trp leader RNA is a small (140-nucleotide) RNA that results from attenuation of trp operon transcription upon binding of the regulatory TRAP complex. In the RNase J1 mutant strain, trp:rpsO-TT RNA half-life increases 2.3fold to 8.2 min
-
-
?
additional information
?
-
-
enzyme RNase J1 possesses 5'-to-3' exoribonuclease activity, while enzymes RNase J1 and RNase J2 form a complex that also has endonuclease activity, model for the degradation of the trp leader mRNA bound to TRAP. RNase J1 is the endonuclease cleaving scRNA that is 4 nts shorter on the 3' end
-
-
?
additional information
?
-
-
RNase J is a bifunctional 5'-3' exo/endoribonuclease
-
-
?
additional information
?
-
-
RNase J1 is a dual-specificity enzyme, with both 5' exonucleolytic and endonucleolytic activities. 5'-SSS RNA is unlikely to be a good substrate for 5' exonucleolytic attack in vivo
-
-
?
additional information
?
-
-
the enzyme degrades of a large number of mRNAs as well as non coding RNAs
-
-
?
additional information
?
-
-
RNase J1 is a dual-specificity enzyme, with both 5' exonucleolytic and endonucleolytic activities. 5'-SSS RNA is unlikely to be a good substrate for 5' exonucleolytic attack in vivo
-
-
?
additional information
?
-
ribonucleases J1 and J2 have both endoribonucleolytic and 5'-to-3' exoribonucleolytic activities. Both act on class I and class II mRNAs, overview
-
-
?
additional information
?
-
ribonucleases J1 and J2 have both endoribonucleolytic and 5'-to-3' exoribonucleolytic activities. Both act on class I and class II mRNAs, overview
-
-
?
additional information
?
-
-
ribonucleases J1 and J2 have both endoribonucleolytic and 5'-to-3' exoribonucleolytic activities. Both act on class I and class II mRNAs, overview
-
-
?
additional information
?
-
RNase J is a bifunctional 5'-3' exo/endoribonuclease, structure of enzyme bound to a 4-nucleotide RNA showing an RNA-binding channel. A second, negatively charged tunnel leads from the active site, and is ideally located to evacuate the cleaved nucleotide in 5'-3' exonucleolytic mode
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Zn2+
Zn2+
binding structure in the beta-lactamase domain of the enzyme, overview
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
GDP
-
less effective than ATP, competitive inhibitor, inhibition influenced by pH, enhanced inhibition at pH 7.0
GTP
-
less effective than ATP, competitive inhibitor, inhibition influenced by pH, enhanced inhibition at pH 7.0
additional information
-
the 5'-to-3' exoribonuclease activity of the enzyme is active on 5'-monophosphorylated or 5'-hydroxylated RNA, but is essentially completely inhibited by the triphosphorylated 5' ends of primary transcripts
-
ADP
-
inhibition influenced by pH, enhanced inhibition at pH 7.5; less effective than ATP but more potent in the crude ribonuclease preparation
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Anemia, Hypochromic
Chloroplast RNase J compensates for inefficient transcription termination by removal of antisense RNA.
bacillus subtilis ribonuclease deficiency
RNase J participates in a pentatricopeptide repeat protein-mediated 5' end maturation of chloroplast mRNAs.
Infections
Evolution of Listeria monocytogenes During a Persistent Human Prosthetic Hip Joint Infection.
Infections
Functional studies of E. faecalis RNase J2 and its role in virulence and fitness.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
additional information
-
apparent dissociation constants (Kapp) for TRAP binding to various trp leader RNA derivatives
-
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.024
pre-tRNAAsp
-
R60C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.1
pre-tRNAAsp
-
R65C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.11
pre-tRNAAsp
-
R7C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.15
pre-tRNAAsp
-
D15C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.2
pre-tRNAAsp
-
N61C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.22
pre-tRNAAsp
-
R68C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.23
pre-tRNAAsp
-
K64C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.23
pre-tRNAAsp
-
wild-type, single turnover cleavage rate constant kobs
-
0.24
pre-tRNAAsp
-
H3C mutant, single turnover cleavage rate constant kobs
-
0.26
pre-tRNAAsp
-
D42C mutant, single turnover cleavage rate constant kobs
-
0.26
pre-tRNAAsp
-
R62C mutant, single turnover cleavage rate constant kobs
-
0.27
pre-tRNAAsp
-
E40C mutant, single turnover cleavage rate constant kobs
-
0.27
pre-tRNAAsp
-
R45C mutant, single turnover cleavage rate constant kobs
-
0.27
pre-tRNAAsp
-
R45C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.27
pre-tRNAAsp
-
R60C mutant, single turnover cleavage rate constant kobs
-
0.27
pre-tRNAAsp
-
R7C mutant, single turnover cleavage rate constant kobs
-
0.28
pre-tRNAAsp
-
D15C mutant, single turnover cleavage rate constant kobs
-
0.28
pre-tRNAAsp
-
R65C mutant, single turnover cleavage rate constant kobs
-
0.28
pre-tRNAAsp
-
V46C mutant, single turnover cleavage rate constant kobs
-
0.29
pre-tRNAAsp
-
K64C mutant, single turnover cleavage rate constant kobs
-
0.3
pre-tRNAAsp
-
E40C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.3
pre-tRNAAsp
-
H3C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.3
pre-tRNAAsp
-
N61C mutant, single turnover cleavage rate constant kobs
-
0.31
pre-tRNAAsp
-
Q38C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.32
pre-tRNAAsp
-
V46C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.33
pre-tRNAAsp
-
Q38C mutant, single turnover cleavage rate constant kobs
-
0.34
pre-tRNAAsp
-
R62C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.37
pre-tRNAAsp
-
D42C mutant, single turnover cleavage rate constant kobs, protein contains an AOP modification at the cysteine residue
-
0.37
pre-tRNAAsp
-
R68C mutant, single turnover cleavage rate constant kobs
-
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene rnjA encoding RNase J1, anf gene rnjB encoding RNase J2
-
-
brenda
gene rny encoding RNase Y under control of the inducible Pspac promoter
-
-
brenda
-
134516, 134517, 134518, 134520, 682841, 683898, 683963, 710551, 729206, 729973, 730720, 730932, 730975
-
-
brenda
gene rny encoding RNase Y under control of the inducible Pspac promoter
-
-
brenda
RNase J1; serotype M3, i.e. group A streptococcus or GAS, gene rnjA encodes RNase J1
UniProt
brenda
RNase J2; serotype M3, i.e. group A streptococcus or GAS, gene rnjB encodes RNase J2
UniProt
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
additional information
decay of class I and class II messages are affected differently by RNases J1 and J2 in exponential phase, both RNases increase the decay rate for class I messages which are degraded rapidly in exponential phase, but show a delay phase before decay of class II messages is initiated, overview
brenda
additional information
decay of class I and class II messages are affected differently by RNases J1 and J2 in exponential phase, both RNases increase the decay rate for class I messages which are degraded rapidly in exponential phase, but show a delay phase before decay of class II messages is initiated, overview
brenda
additional information
-
decay of class I and class II messages are affected differently by RNases J1 and J2 in exponential phase, both RNases increase the decay rate for class I messages which are degraded rapidly in exponential phase, but show a delay phase before decay of class II messages is initiated, overview
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
-
Bacillus subtilis endonucleases Bs-RNase III, RNase M5, RNase P, RNase Z, EndoA, and Mini-III are not involved in rpsO mRNA decay, the upstream products are degraded by polynucleotide phosphorylase (PNPase), and the downstream products were degraded by the 5' exonuclease activity of RNase J1
physiological function
additional information
evolution
-
RNase J is a key member of the beta-CASP family of metallo-beta-lactamases
evolution
RNase J is a key member of the beta-CASP family of metallo-beta-lactamases
evolution
the enzyme belongs to the beta-CASP subfamily of metallo-beta-lactamases
malfunction
-
DELTAermC mRNA shows increased stability in a RNase J1 mutant strain, that contains reduced level of RNase J1. Insertion of a strong stem-loop structure at +65 results in increased stability. Weakening this stem-loop structure results in reversion to wild-type stability. RNA fragments containing the 3' end are detected in a strain with reduced RNase J1 expression, but are undetectable in the wild-type. The 5' ends of these fragments map to the upstream side of predicted stem-loop structures, consistent with an impediment to RNase J1 5' exonuclease processivity. RNase J1 is involved even in decay of the RNA encoded by a 129-nt deletion construct, perhaps by a 59-to-39 exonucleolytic pathway or by cleavage at sites in the upstream half of the RNA. Deletion of the three target sites results in increased mRNA half-life (ca. 15 min)
malfunction
conditional mutants for both RNases J1 and J2 require induction for growth
malfunction
-
depletion of RNase J1 in a strain also lacking RNase J2 leads to a modest increase in global mRNA stability. transcriptome analysis shows a relatively minor effect of depleting cells for RNase J1 alone or inactivating RNase J2. The double mutant has altered levels for over 600 transcripts with about equal numbers of transcripts showing increased and decreased levels, significant increase in half-life for four specific transcripts cspC, spoVG, tagDccand yweA. Depletion of RNase J1 leads to an accumulation of 3' fragments of RNA
malfunction
-
lowering RNase Y concentration may affect RNA decay indirectly via an effect on RNase J1, which is thought to exist with RNase Y in a degradosome complex
malfunction
-
mRNAs are upregulated following enzyme depletion, transcript profile of total RNA preparations from duplicate cultures of the depletion strain SSB447, overview
malfunction
-
rpsO mRNA half-life is unchanged in a strain that has decreased RNase J1 activity and no RNase J2 activity, but it is 2.3fold higher in a strain with decreased activity of RNase Y
malfunction
-
lowering RNase Y concentration may affect RNA decay indirectly via an effect on RNase J1, which is thought to exist with RNase Y in a degradosome complex
-
physiological function
-
RNase J1 is essential, while its paralogue RNase J2 is not. RNases J1 and J2 form a complex that is likely to be the predominant form of these enzymes in wild-type cells: RNase J2 co-purifies with His-tagged RNase J1 from Escherichia coli or with Flag-tagged RNase J1 from Bacillus subtilis and RNases J1 and J2 interact in vivo in a yeast two-hybrid assay. While both RNase J1 and the RNase J1/J2 complex have robust 5'-to-3' exoribonuclease activity in vitro, RNase J2 has at least two orders of magnitude weaker exonuclease activity. Association of the two proteins also has an effect on the endoribonucleolytic properties of RNases J1 and J2. While the individual enzymes have similar endonucleolytic cleavage activities and specificities, as a complex they behave synergistically to alter cleavage site preference and to increase cleavage efficiency at specific sites
physiological function
-
endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded regionis critical for initiation of trp leader RNA decay, the enzyme accesses its internal target site on trp leader RNA in a 5' end-independent manner. The mechanism of trp leader RNA decay is not dependent on TRAP binding
physiological function
-
enzyme RNase J has been shown to play an extensive role in mRNA turnover. The bifunctional 5'-3' exo/endoribonuclease RNase J is involved in the maturation and turnover of RNAs in prokaryotes
physiological function
enzyme RNase J has been shown to play an extensive role in mRNA turnover. The bifunctional 5'-3' exo/endoribonuclease RNase J is involved in the maturation and turnover of RNAs in prokaryotes
physiological function
-
in Bacillus subtilis, the dual activity 5' exo- and endoribonucleases J1 and J2 are important players in mRNA and stable RNA maturation and degradation. The two nucleases in the cell primarily act as a heterodimer in vivo
physiological function
ribonucleases J1 and J2 participate in degradation and regulatory processing of mRNA. mRNA decay is important in regulation of virulence factors of Streptococcus pyogenes, both of these RNases are essential for growth of the organism. RNases J1 and J2 affect the rate of decay of class I messages and the length of the first phase in decay of class II messages, overview
physiological function
-
RNase Y is a key endoribonuclease affecting global mRNA stability in Bacillus subtilis, in which endonucleolytic cleavage plays a major role in the mRNA metabolism, it plays a key role in initiating the decay of a large number of mRNAs as well as non coding RNAs
physiological function
-
RNase Y is an endoribonuclease affecting global mRNA metabolism, it affects the expression of the Bacillus subtilis infCrpmI-rplT operon, encoding translation initiation factor IF3 and the ribosomal proteins L35 and L20, which is an operon autoregulated by a complex L20-dependent transcription attenuation mechanism. The readthrough transcript of a second promoter P1, upstream of the promoter P2, is stabilized in a strain depleted for RNase Y, while the readthrough transcript of P2 is not. Under these conditions infC biosynthesis is repressed threefold, regulatory model for the control of the Bacillus subtilis infC operon, overview
physiological function
-
RNase Y mediates the initiation of rpsO mRNA decay, the stability of the specific mRNA is determined by RNase Y
physiological function
-
role of enzymes RNase J1 and RNase J2 in both general and specific mRNA turnover, the enzymes RNase J1 and RNase J2 form a complex with 5'-to-3' exoribonuclease and endonucleolytic activity that plays a key role in the turnover and maturation of many RNAs in Bacillus subtilis. The 5'-to-3 exoribonuclease activity may be the more important of the complex's two modes of action. In addition to interacting with each other, RNase J1 and J2 might be part of a Bacillus subtilis degradosome complex containing two other ribonucleases, RNase Y and PNPase, phosphofructokinase and enolase
physiological function
-
endonucleolytic cleavage by ribonuclease RNase J1 in a 3'-proximal, single-stranded regionis critical for initiation of trp leader RNA decay, the enzyme accesses its internal target site on trp leader RNA in a 5' end-independent manner. The mechanism of trp leader RNA decay is not dependent on TRAP binding
-
physiological function
-
RNase Y is an endoribonuclease affecting global mRNA metabolism, it affects the expression of the Bacillus subtilis infCrpmI-rplT operon, encoding translation initiation factor IF3 and the ribosomal proteins L35 and L20, which is an operon autoregulated by a complex L20-dependent transcription attenuation mechanism. The readthrough transcript of a second promoter P1, upstream of the promoter P2, is stabilized in a strain depleted for RNase Y, while the readthrough transcript of P2 is not. Under these conditions infC biosynthesis is repressed threefold, regulatory model for the control of the Bacillus subtilis infC operon, overview
-
physiological function
-
in Bacillus subtilis, the dual activity 5' exo- and endoribonucleases J1 and J2 are important players in mRNA and stable RNA maturation and degradation. The two nucleases in the cell primarily act as a heterodimer in vivo
-
additional information
-
modeling of the enzyme reaction involving the binding of the RNA to the surface of the beta-CASP domain to explain the enzyme's processive action, enzyme residues involved in RNA recognition, overview. RNA-binding channel and proposed nucleotide exit tunnel of RNase J, model of Bacillus subtilis RNase J1/J2 heterodimer bound to RNA, overview
additional information
modeling of the enzyme reaction involving the binding of the RNA to the surface of the beta-CASP domain to explain the enzyme's processive action, enzyme residues involved in RNA recognition, RNA-binding channel and proposed nucleotide Exit tunnel of RNase J, modeling, overview
additional information
-
the enzyme is conformationally heterogeneous and folds with multiphasic kinetics, indicating the presence of an equilibrium and kinetic intermediate in its folding mechanism, NMR spectroscopy analysis, overview. RNase P protein is the protein subunit in the RNase P ribonucleoholoenzyme, it is an intrinsically disordered protein. Without the binding partners, P protein is predominantly unfolded but can be induced to fold in the presence of different small anions, e.g. sulfate. The N-terminal and C-terminal helical regions are mostly unfolded in the intermediate. The protonation of His22 may play a major role in the energetics of the equilibria between the unfolded, intermediate, and folded state ensembles of P protein, possible role for the intermediate in the enzyme holoenzyme assembly process. HSQC spectrum of folded P protein and unfolded P protein, overview
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). CS12A_ACISB
Acidaminococcus sp. (strain BV3L6)
1307
0
151207
Swiss-Prot
-
CS12A_FRATN
Francisella tularensis subsp. novicida (strain U112)
1300
0
151915
Swiss-Prot
-
A0A8F8DEV7_9ESCH
116
0
12492
TrEMBL
-
RNJ_THET2
Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)
573
0
64031
Swiss-Prot
-
RNJ1_STRP3
Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)
560
0
61111
Swiss-Prot
-
RNJ2_STRP3
Streptococcus pyogenes serotype M3 (strain ATCC BAA-595 / MGAS315)
553
0
61179
Swiss-Prot
-
CS12A_FRATN
Francisella tularensis subsp. novicida (strain U112)
1300
0
151915
Swiss-Prot
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
RNase J1 exists primarily in a heterotetrameric complex with RNase J2
additional information
-
RNase J1 exists primarily in a heterotetrameric complex with RNase J2
-
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POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ribonucleoprotein
-
RNase P protein is the protein subunit in the RNase P holoenzyme and is an intrinsically disordered protein
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
enzyme with bound 4 nt RNA with sequence CUGG or a 16 nt RNA, using catalytically inactive mutant H77A and a 2'-O-methylated, 3'-fluorescein-labeled RNAs, X-ray diffraction crystal structure determination and analysis at 2.5-3.1 A resolution, molecular replacement
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
F107W
-
site-directed mutagenesis, pH titration experiments and comparison to the wild-type enzyme
H105K
-
site-directed mutagenesis, pH titration experiments and comparison to the wild-type enzyme
H22K
-
site-directed mutagenesis, pH titration experiments and comparison to the wild-type enzyme
H3K
-
site-directed mutagenesis, pH titration experiments and comparison to the wild-type enzyme
additional information
additional information
-
construction of a deletion mutant od gene rny encoding RNas Y
additional information
-
depletion of RNase J1 is achieved by growing the cells without inducer until a decrease in growth rate becomes perceptible
additional information
-
turnover of trp:rpsO-TT RNA 3 end-containing decay intermediates in the wild-type and RNase J1 mutant strains in the presence or absence of TRAP: in the case of trp leader RNA, such decay intermediates accumulate in the RNase J1 mutant strain. The results show about a 2fold greater abundance of 3' end-containing fragments in the RNase J1 mutant strain compared with the wild-type strain, with no significant difference between the presence or absence of TRAP
additional information
-
turnover of trp:rpsO-TT RNA 3 end-containing decay intermediates in the wild-type and RNase J1 mutant strains in the presence or absence of TRAP: in the case of trp leader RNA, such decay intermediates accumulate in the RNase J1 mutant strain. The results show about a 2fold greater abundance of 3' end-containing fragments in the RNase J1 mutant strain compared with the wild-type strain, with no significant difference between the presence or absence of TRAP
-
additional information
-
depletion of RNase J1 is achieved by growing the cells without inducer until a decrease in growth rate becomes perceptible
-
additional information
-
construction of a deletion mutant od gene rny encoding RNas Y
-
additional information
construction of a tetracycline-inducible mutant for RNase J1 from strain MGAS315, conditional mutant JRS7316, the enzyme-deficient strain shows growth defects, phenotype overview
additional information
construction of a tetracycline-inducible mutant for RNase J1 from strain MGAS315, conditional mutant JRS7316, the enzyme-deficient strain shows growth defects, phenotype overview
additional information
-
construction of a tetracycline-inducible mutant for RNase J1 from strain MGAS315, conditional mutant JRS7316, the enzyme-deficient strain shows growth defects, phenotype overview
additional information
construction of a tetracycline-inducible mutant for RNase J2 from strain MGAS315, the enzyme-deficient strain shows growth defects, phenotype overview
additional information
construction of a tetracycline-inducible mutant for RNase J2 from strain MGAS315, the enzyme-deficient strain shows growth defects, phenotype overview
additional information
-
construction of a tetracycline-inducible mutant for RNase J2 from strain MGAS315, the enzyme-deficient strain shows growth defects, phenotype overview
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant protein P proteins from Escherichia coli strain BL21 (DE3) pLysS
-
RNases J1, J2 and the RNase J1/J2 complex purified on cobalt column and by gel filtration
-
the protein is purified from Bacillus subtilis cultures, using a DEAE-Sepharose Fast Flow column, a Phenyl Sepharose 6 Fast Flow column and a hydroxyapatite column
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
chromosomal DNA from the RNase J1 conditional mutant strain used to transform Bacillus subtilis host BG1 to erythromycin resistance. The RNase J1 conditional strain also contains plasmid pMAP65, which carries extra copies of the lacI gene. Preparation and transformation of Bacillus subtilis competent cell cultures. RNase J1 transcription under control of an IPTG-inducible promoter in the RNase J1 conditional mutant strain
-
cloning of rnjB gene, encoding RNase J2, and/or rnjA gene expressing RNase J1 in the pET28a vector together or alone. Overexpression of C-terminal His-tagged RNase J1 and/or C-terminal His-tagged RNase J2 simultaneously or alone in Escherichia coli strain BL21 CodonPlus
-
gene rnjA, DNA and amino acid sequence determination and analysis, sequence comparison to Bacillus subtilis enzyme, phylogenetic analysis
gene rnjB is transcribed constitutively from a sigma A promoter. Gene rnjA is transcribed as a bicistronic transcript from a single promoter, optimal expression of RNase J1 from gene rnjA requires cotranscription and cotranslation with the upstream ykzG gene, sequence and regulatory elements upstream of the rnjA open reading frame, overview. In the absence of coupled translation, RNase J1 expression is decreased more than 5fold, transcription of the ykzG operon initiates at a sigma A promoter with a noncanonical35 box that is required for optimal transcription. In Bacillus subtilis strain SSB356, the rnjA gene is under the control of the xylose-inducible Pxyl promoter
-
gene rnjB, DNA and amino acid sequence determination and analysis, sequence comparison to Bacillus subtilis enzyme, phylogenetic analysis
gene rny, encoding RNase Y under control of the inducible Pspac promoter, DNA and amino acid sequence determination and analysis
-
into the pET28b vector for expression in Escherichia coli BL21DE3pLysS cells
-
overexpression of wild-type and mutant protein P proteins in Escherichia coli strain BL21 (DE3) pLysS
-
the wild-type ykqC gene is cloned into the pET28 vector for expression in Escherichia coli BL21 CodonPlus cells, the plasmids pMUTIN-4M, pBS-Spc and pSWEET are used for the construction of different Bacillus subtilis strains
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
biosynthesis of enzyme RNase J1 is autocontrolled within a small range (1.4fold) and also slightly stimulated (1.4fold) in the absence of enzyme RNase J2
biosynthesis of enzyme RNase J1 is autocontrolled within a small range (1.4fold) and also slightly stimulated (1.4fold) in the absence of enzyme RNase J2
-
biosynthesis of enzyme RNase J1 is autocontrolled within a small range (1.4fold) and also slightly stimulated (1.4fold) in the absence of enzyme RNase J2
-
-
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RENATURED/Commentary
ORGANISM
UNIPROT
LITERATURE
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
biotechnology
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Nishimura, S.; Maruo, B.
Intracellular ribonuclease from Bacillus subtilis
Biochim. Biophys. Acta
40
355-357
1960
Bacillus subtilis
brenda
Yamasaki, M.; Arima, K.
Intracellular ribonuclease of Bacillus subtilis; specific inhibition by ATP and dATP
Biochem. Biophys. Res. Commun.
37
430-436
1969
Bacillus subtilis
brenda
Yamasaki, M.; Arima, K.
Regulation of intracellular ribonuclease of Bacillus subtilis by ATP and ADP
Biochim. Biophys. Acta
139
202-204
1967
Bacillus subtilis
brenda
Center, M.S.; Behal, F.J.
Studies on the ribonuclease activity of Proteus mirabilis
Biochim. Biophys. Acta
151
698-699
1968
Proteus mirabilis
brenda
Yamasaki, M.; Arima, K.
ATP-inhibited ribonuclease of Bacillus subtilis. II. Effect of adenosine triphosphate and other compounds
Biochim. Biophys. Acta
209
475-483
1970
Bacillus subtilis
brenda
Niranjanakumari, S.; Day-Storms, J.J.; Ahmed, M.; Hsieh, J.; Zahler, N.H.; Venters, R.A.; Fierke, C.A.
Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage
RNA
13
521-535
2007
Bacillus subtilis
brenda
Britton, R.A.; Wen, T.; Schaefer, L.; Pellegrini, O.; Uicker, W.C.; Mathy, N.; Tobin, C.; Daou, R.; Szyk, J.; Condon, C.
Maturation of the 5 end of Bacillus subtilis 16S rRNA by the essential ribonuclease YkqC/RNase J1
Mol. Microbiol.
63
127-138
2007
Bacillus subtilis
brenda
Liu, Y.; Chen, Z.; Ng, T.B.; Zhang, J.; Zhou, M.; Song, F.; Lu, F.; Liu, Y.
Bacisubin, an antifungal protein with ribonuclease and hemagglutinating activities from Bacillus subtilis strain B-916
Peptides
28
553-559
2007
Bacillus subtilis, Bacillus subtilis B-916
brenda
Mathy, N.; Hebert, A.; Mervelet, P.; Benard, L.; Dorleans, A.; Li De La Sierra-Gallay, I.; Noirot, P.; Putzer, H.; Condon, C.
Bacillus subtilis ribonucleases J1 and J2 form a complex with altered enzyme behaviour
Mol. Microbiol.
75
489-498
2010
Bacillus subtilis
brenda
Yao, S.; Sharp, J.S.; Bechhofer, D.H.
Bacillus subtilis RNase J1 endonuclease and 5 exonuclease activities in the turnover of DeltaermC mRNA
RNA
15
2331-2339
2009
Bacillus subtilis
brenda
Chang, Y.C.; Franch, W.R.; Oas, T.G.
Probing the folding intermediate of Bacillus subtilis RNase P protein by nuclear magnetic resonance
Biochemistry
49
9428-9437
2010
Bacillus subtilis
brenda
Yao, S.; Bechhofer, D.H.
Initiation of decay of Bacillus subtilis rpsO mRNA by endoribonuclease RNase Y
J. Bacteriol.
192
3279-3286
2010
Bacillus subtilis
brenda
Jamalli, A.; Hebert, A.; Zig, L.; Putzer, H.
Control of expression of the RNases J1 and J2 in Bacillus subtilis
J. Bacteriol.
196
318-324
2014
Bacillus subtilis, Bacillus subtilis SSB1002
brenda
Deikus, G.; Bechhofer, D.H.
5' End-independent RNase J1 endonuclease cleavage of Bacillus subtilis model RNA
J. Biol. Chem.
286
34932-34940
2011
Bacillus subtilis, Bacillus subtilis BG626
brenda
Bugrysheva, J.; Scott, J.
The ribonucleases J1 and J2 are essential for growth and have independent roles in mRNA decay in Streptococcus pyogenes
Mol. Microbiol.
75
731-743
2010
Streptococcus pyogenes (Q8K5W8), Streptococcus pyogenes (Q8K7S6), Streptococcus pyogenes
brenda
Bruscella, P.; Shahbabian, K.; Laalami, S.; Putzer, H.
RNase Y is responsible for uncoupling the expression of translation factor IF3 from that of the ribosomal proteins L35 and L20 in Bacillus subtilis
Mol. Microbiol.
81
1526-1541
2011
Bacillus subtilis, Bacillus subtilis SSB447
brenda
Laalami, S.; Bessieres, P.; Rocca, A.; Zig, L.; Nicolas, P.; Putzer, H.
Bacillus subtilis RNase Y activity in vivo analysed by tiling microarrays
PLoS ONE
8
e54062
2013
Bacillus subtilis
brenda
Condon, C.
What is the role of RNase J in mRNA turnover?
RNA Biol.
7
316-321
2010
Bacillus subtilis
brenda
Dorleans, A.; Li de la Sierra-Gallay, I.; Piton, J.; Zig, L.; Gilet, L.; Putzer, H.; Condon, C.
Molecular basis for the recognition and cleavage of RNA by the bifunctional 5'-3' exo/endoribonuclease RNase J
Structure
19
1252-1261
2011
Bacillus subtilis, Thermus thermophilus (Q72JJ7)
brenda
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