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Information on EC 3.6.4.13 - RNA helicase and Organism(s) Arabidopsis thaliana and UniProt Accession B9DFG3
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3.6.4.13 RNA helicaseIUBMB Comments
RNA helicases utilize the energy from ATP hydrolysis to unwind RNA. Some of them unwind RNA with a 3' to 5' polarity , other show 5' to 3' polarity . Some helicases unwind DNA as well as RNA [7,8]. May be identical with EC 3.6.4.12 (DNA helicase).
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Word Map
- 3.6.4.13
-
single-stranded
- strand
- viruses
- duplex
- fork
-
retinoic
- nucleic
- chromatin
-
acid-inducible
- mda5
- dsrnas
- ssdna
-
rna-binding
-
stall
-
werner
-
nonstructural
-
bloom
- polyproteins
-
dna-dependent
- primase
-
exonuclease
- replisome
-
spliceosome
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hexameric
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minichromosome
-
differentiation-associated
- dengue
-
g-quadruplexes
- eif4g
-
single-molecule
-
unwound
-
replicase
-
restart
-
ifn-stimulated
-
nonsense-mediated
- rpa
- rad51
-
holliday
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polyi:c
- flavivirus
- tfiih
- exoribonuclease
-
ifn-beta
-
d-loops
- pigmentosum
-
cap-dependent
- xeroderma
-
positive-stranded
- pre-rrnas
-
overhang
- pharmacology
- medicine
- drug development
The taxonomic range for the selected organisms is: Arabidopsis thaliana
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
Synonyms
helicase, rig-i, rna helicase, eif4a, ddx3x, dead-box rna helicase, ns3 helicase, dead-box helicase, ddx21, rna helicase a, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
SYSTEMATIC NAME
IUBMB Comments
ATP phosphohydrolase (RNA helix unwinding)
RNA helicases utilize the energy from ATP hydrolysis to unwind RNA. Some of them unwind RNA with a 3' to 5' polarity [3], other show 5' to 3' polarity [8]. Some helicases unwind DNA as well as RNA [7,8]. May be identical with EC 3.6.4.12 (DNA helicase).
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
additional information
?
-
ISE2 associates with numerous chloroplast RNA species, chloroplast rRNAs are potential ISE2 substrates. ISE2 associates with transcripts containing C-to-U editing sites
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additional information
?
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ISE2 associates with numerous chloroplast RNA species, chloroplast rRNAs are potential ISE2 substrates. ISE2 associates with transcripts containing C-to-U editing sites
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additional information
?
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using yeast two-hybrid and pull-down assays it is shown that RH22 interacts with the 50S ribosomal protein RPL24
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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
additional information
?
-
ISE2 associates with numerous chloroplast RNA species, chloroplast rRNAs are potential ISE2 substrates. ISE2 associates with transcripts containing C-to-U editing sites
-
-
-
additional information
?
-
-
ISE2 associates with numerous chloroplast RNA species, chloroplast rRNAs are potential ISE2 substrates. ISE2 associates with transcripts containing C-to-U editing sites
-
-
-
additional information
?
-
-
using yeast two-hybrid and pull-down assays it is shown that RH22 interacts with the 50S ribosomal protein RPL24
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
AtRH3 is predominantly expressed in young leaves, peaking in 2-week-old seedlings and decreasing to very low levels in older leaf tissue
additional information
enzyme RH3 accumulates in stroma and nucleoids of green tissues, with peak accumulation during chloroplast biogenesis. No enzyme activity in stems or roots of seedlings
additional information
expression pattern of ATRH7 in different tissues, overview. Enzyme AtRH7 is expressed ubiquitously and its levels of the expression are higher in rapidly growing tissues, including the young rosette leaves, the lateral roots, and the root tips, while comparatively weaker activity is also detected in other parts of the plants
additional information
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expression pattern of ATRH7 in different tissues, overview. Enzyme AtRH7 is expressed ubiquitously and its levels of the expression are higher in rapidly growing tissues, including the young rosette leaves, the lateral roots, and the root tips, while comparatively weaker activity is also detected in other parts of the plants
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
additional information
additional information
enzyme RH3 accumulates in stroma and nucleoids of green tissues, with peak accumulation during chloroplast biogenesis
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additional information
AtRH7localizes mainly to the nucleolus and to a minor degree to the nucleoplasm. AtRH7 forms a complex with AtCSP3 mainly in the nucleolus, with a smaller portion in the nucleoplasm
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additional information
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AtRH7localizes mainly to the nucleolus and to a minor degree to the nucleoplasm. AtRH7 forms a complex with AtCSP3 mainly in the nucleolus, with a smaller portion in the nucleoplasm
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
ISE2 is a non-canonical Ski2-like RNA helicase that represents a separate sub-clade unique to green photosynthetic organisms. ISE2's evolutionary conservation may be explained by its numerous roles in regulating chloroplast gene expression
malfunction
chloroplasts in leaves with reduced ISE2 expression show reduced thylakoid contents and increased stromal volume, indicative of defective development. Embryonic-lethal phenotype of Arabidopsis ise2 mutants. Changes observed in RNA editing in tissues with decreased ISE2 levels (ISE2-SUP leaves) are due to the specific effects of ISE2 and not due to general chlorosis, RNA editing is also measured in chlorotic leaves resulting from disruption of other genes
physiological function
increased size exclusion limit2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Enzyme ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana. ISE2 is required for the splicing of group II introns from chloroplast transcripts. ISE2 is required for site-specific chloroplast C-to-U RNA editing. ISE2 is required for chloroplast rRNA processing and splicing of group II introns. And ISE2 is required for accumulation of 30S and 50S ribosomal RNAs and chloroplast-encoded proteins
evolution
DEAD-box proteins comprise the largest family of RNA helicases in plants, and exist in most organisms. They possess 12 conserved motifs that are involved in ATPase, helicase, and RNA binding activities, and participate in a variety of RNA-associated events from transcription to RNA decay. Some DEAD-box proteins are involved in the regulation of plant growth and development through ribosome biogenesis. Phylogenetic analysis, and evolutionary and functional relationships of AtRH7. AtRH7 belongs to a family whose members are involved in rRNA and mRNA processing. AtRH7 shares a conserved function with Escherichia coli enzyme CsdA under cold conditions
malfunction
physiological function
additional information
domain organization of RH3 protein. RH3 and ClpR2 interact genetically, but RH3 is unlikely to be a substrate for the Clp protease
malfunction
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by using wild-type, helps mutant and overexpression lines of Arabidopsis, it is shown that, in the low-K+ condition, AtHELPS inhibits Arabidopsis seed germination via decreased K+ influx into roots. Expression of AKT1, CBL1, CBL9 and CIPK23 is regulated by AtHELPS under low-K+ stress
malfunction
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knockdown of RH22 expression results in virescent seedlings with clear defects in chloroplast ribosomal RNA accumulation. The precursors of 23S and 4.5S, but not 16S, rRNA accumulate in rh22 mutants
malfunction
AtRH3 null mutants are embryo lethal, whereas a weak allele results in pale-green seedlings with defects in splicing of several group II introns and rRNA maturation as well as reduced levels of assembled ribosomes,phenotype overview
malfunction
knockout mutant lines display several morphological alterations such as disturbed vein pattern, pointed first true leaves, and short roots, which resemble ribosome-related mutants of Arabidopsis thaliana. In addition, aberrant floral development as also observed in rh7 mutants. When the mutants are germinated at low temperature (12°C), both radicle and first leaf emergence are severely delayed, after exposure of seedlings to a long period of cold, the mutants develop aberrant, fewer, and smaller leaves. RNA blots and circular RT-PCR reveal that 35S and 18S rRNA precursors accumulate to higher levels in the mutants than in wild-type under both normal and cold conditions, suggesting the mutants are partially impaired in pre-rRNA processing
physiological function
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RH22 may function in the assembly of 50S ribosomal subunits in chloroplasts
physiological function
the enzyme is under strong developmental control. Cross talk between the chloroplast and the nucleus is used to regulate RH3 levels. Enzyme RH3 functions in the splicing of group II introns and possibly also contributes to the assembly of the 50S ribosomal particle
physiological function
the cold-inducible DEAD-Box RNA helicase AtRH7 regulates plant growth and development under low temperature in Arabidopsis thaliana. AtRH7 affects rRNA biogenesis and is an interactor of Arabidopsis cold shock domain protein 3 (AtCSP3), which is an RNA chaperone involved in cold adaptation. The enzyme can complement the Escherichia coli DELTAcsdA mutant, which is deficient in growth at low temperatures
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). ISE2_ARATH
1171
0
132437
Swiss-Prot
Chloroplast (Reliability: 2)
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
proteolytic modification
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enzyme contains a 58-amino acid transit peptide that is predicted to be targeted to the chloroplast
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
virus-induced ISE2 gene silencing, TRV constructs are introduced into Agrobacterium strain GV3101 for plant infiltrations. Loss of ISE2 compromises C-to-U RNA editing at specific sites. Total RNA is isolated from leaves of the same age as the ISE2-SUP leaves analyzed, and RNA editing at the six candidate ISE2-specific sites and several unaffected sites is measured. The clpP1-559 site exhibited reduced RNA editing efficiency in both the ISE2-SUP and the var2-2 leaves, but the extent of RNA editing in ISE2-SUP leaves (25%) is less than half of that in var2-2 leaves (59%). Thus, depletion of ISE2 has a more drastic effect on the RNA editing efficiency at the clpP1-559 site than depletion of FTSH2. Similarly, while the var2-2 mutant displays decreased RNA editing at petL-5 and rpoA-200, the decrease at those sites is more drastic in ISE2-SUP leaves than in var2-2 leaves. Accumulation of chloroplast mRNAs is altered in the absence of ISE2
additional information
-
virus-induced ISE2 gene silencing, TRV constructs are introduced into Agrobacterium strain GV3101 for plant infiltrations. Loss of ISE2 compromises C-to-U RNA editing at specific sites. Total RNA is isolated from leaves of the same age as the ISE2-SUP leaves analyzed, and RNA editing at the six candidate ISE2-specific sites and several unaffected sites is measured. The clpP1-559 site exhibited reduced RNA editing efficiency in both the ISE2-SUP and the var2-2 leaves, but the extent of RNA editing in ISE2-SUP leaves (25%) is less than half of that in var2-2 leaves (59%). Thus, depletion of ISE2 has a more drastic effect on the RNA editing efficiency at the clpP1-559 site than depletion of FTSH2. Similarly, while the var2-2 mutant displays decreased RNA editing at petL-5 and rpoA-200, the decrease at those sites is more drastic in ISE2-SUP leaves than in var2-2 leaves. Accumulation of chloroplast mRNAs is altered in the absence of ISE2
additional information
construction of double knockdown mutant rh3-4/clpr2-1, chloroplast rps12-int1 splicing defects in mutant rh3-4
additional information
generation of RH7 knockout mutant lines, several morphological alterations such as disturbed vein pattern, pointed first true leaves, and short roots, which resemble ribosome-related mutants of Arabidopsis thaliana, phenotype analysis of rh7-5 and rh7-8 mutants under 22°C, overview. Knockout mutants of AtRH7 display several morphological alterations during vegetative and reproductive growth. In addition, the mutants exhibit severe defects in germination and leaf development under long-term low temperature conditions. Accumulation of rRNA precursors in rh7 mutant plants corroborate the hypothesis that AtRH7 affects ribosome biogenesis. AtRH7 mutations affect ribosomal RNA biogenesis in the nucleolus
additional information
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generation of RH7 knockout mutant lines, several morphological alterations such as disturbed vein pattern, pointed first true leaves, and short roots, which resemble ribosome-related mutants of Arabidopsis thaliana, phenotype analysis of rh7-5 and rh7-8 mutants under 22°C, overview. Knockout mutants of AtRH7 display several morphological alterations during vegetative and reproductive growth. In addition, the mutants exhibit severe defects in germination and leaf development under long-term low temperature conditions. Accumulation of rRNA precursors in rh7 mutant plants corroborate the hypothesis that AtRH7 affects ribosome biogenesis. AtRH7 mutations affect ribosomal RNA biogenesis in the nucleolus
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene RH7, phylogenetic analysis, promoter:GUS transgenic plants AtRH7 quantitative real-time PCR expression analysis. AtRH7 is fused to the C-terminus of YFP and expressed in opnion cells revealing that AtRH7 localizes mainly to the nucleolus and to a minor degree to the nucleoplasm. The enzyme can complement the Escherichia coli DELTAcsdA mutant, which is deficient in growth at low temperatures
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
5 to 10fold upregulation of enzyme AtRH3 in plastid caseinolytic protease mutants. AtRH3 up-regulation is not a direct consequence of reduced proteolysis but constitutes a compensatory response at both RH3 transcript and protein levels to impaired chloroplast biogenesis. RH3 up-regulation is nt specific for ClpPR core protease mutants but is a general result of defects in chloroplast biogenesis
expression of AtHELPS is induced by low-K+, zeatin and cold treatments
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Xu, R.R.; Qi, S.D.; Lu, L.T.; Chen, C.T.; Wu, C.A.; Zheng, C.C.
A DExD/H box RNA helicase is important for K+ deprivation responses and tolerance in Arabidopsis thaliana
FEBS J.
278
2296-2306
2011
Arabidopsis thaliana
Chi, W.; He, B.; Mao, J.; Li, Q.; Ma, J.; Ji, D.; Zou, M.; Zhang, L.
The function of RH22, a DEAD RNA helicase, in the biogenesis of the 50S ribosomal subunits of Arabidopsis chloroplasts
Plant Physiol.
158
693-707
2012
Arabidopsis thaliana
Asakura, Y.; Galarneau, E.; Watkins, K.P.; Barkan, A.; van Wijk, K.J.
Chloroplast RH3 DEAD box RNA helicases in maize and Arabidopsis function in splicing of specific group II introns and affect chloroplast ribosome biogenesis
Plant Physiol.
159
961-974
2012
Zea mays (A0A1D6GDY8), Zea mays, Arabidopsis thaliana (Q8L7S8)
Bobik, K.; McCray, T.N.; Ernest, B.; Fernandez, J.C.; Howell, K.A.; Lane, T.; Staton, M.; Burch-Smith, T.M.
The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana
Plant J.
91
114-131
2017
Arabidopsis thaliana (B9DFG3), Arabidopsis thaliana, Arabidopsis thaliana Col-0 (B9DFG3)
EXTERNAL LINKS (specific for EC-Number 3.6.4.13)
Transporter Classification Database (TCDB): 1.I.1.1.3, 1.G.3.1.7, 3.A.18.1.1, 1.A.53.1.5, 1.A.85.1.6, 1.A.53.1.7, 1.G.3.1.2, 1.G.3.1.1, 3.A.22.1.1, 1.A.53.1.11, 1.A.53.1.6
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