The nucleic acid data:
IRESite Id: 242 Version: 6
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2009-08-30 13:34:34
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  hopefully_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  PV
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
61252
The mRNA/+RNA description: 
Human poliovirus 1 Mahoney, complete genome.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The organism containing this mRNA with IRES segment in its genome:
Human poliovirus 1 Mahoney
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
The total number of notable open-reading frames (ORFs):
  1
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
polyprotein
The description of the protein encoded in this ORF:
polyprotein
The translational frameshift (ribosome slippage) involved:
  0
The ribosome read-through involved:
  no
The alternative forms of this protein occur by the alternative initiation of translation:
  not tested
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  743-7372
Remarks:
The 5'-UTR viral sequence matches the IRES segment used experimentally, for example included in the pSBC-1
(GI:58272) vector from Dirks et al., 1993 who obtained the sequence of the poliovirus type 1 Mahoney strain
from P. Sarnow extending from nt 1 to 628.

Pelletier et al. (1988) reported the IRES activity in the region 320-631.
Citations:
Dirks W., Wirth M., Hauser H. (1993) Dicistronic transcription units for gene expression in mammalian cells. Gene. 128(2):247-249
IRESs:
IRES:
Version: 6 Last change: 2009-08-30 13:34:34
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  PV_type1_Mahoney
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  320-631
Conclusion:
  strongly_supported_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Dirks W., Wirth M., Hauser H. (1993) Dicistronic transcription units for gene expression in mammalian cells. Gene. 128(2):247-249
Pelletier J, Kaplan G, Racaniello VR, Sonenberg N (1988) Cap-independent translation of poliovirus mRNA is conferred by sequence elements within the 5' noncoding region. Mol. Cell. Biol. 8(3):1103-1112
Trono D, Pelletier J, Sonenberg N, Baltimore D (1988) Translation in mammalian cells of a gene linked to the poliovirus 5' noncoding region. Science. 241(4864):445-448
IRES trans-acting factor (ITAFS):
IRES trans-acting factor (ITAF):
Version: 2 Last change: 2009-08-30 03:13:28
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
PTB
ITAF fullname:
polypyrimidine-tract binding protein (unspecified isoform)
ITAF description (long):
polypyrimidine-tract binding protein
3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_and_must_be_supplemented
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vivo
The organism where action of this ITAF was studied:
Homo sapiens
Remarks:
Transfected BS-C-1 cells transcripts co-expressing PTB produced 12-fold more reporter protein but only 2.4x
more in HeLa cells which contain more of endogenous PTB (Gosert et al., 2000).
Citations:
Hunt S. L., Hsuan J. J., Totty N., Jackson R. J. (1999) unr, a cellular cytoplasmic RNA-binding protein with five cold-shock domains, is required for internal initiation of translation of human rhinovirus RNA. Genes. Dev. 13(4):437-448
Gosert R, Chang KH, Rijnbrand R, Yi M, Sangar DV, Lemon SM (2000) Transient expression of cellular polypyrimidine-tract binding protein stimulates cap-independent translation directed by both picornaviral and flaviviral internal ribosome entry sites In vivo. Mol. Cell. Biol. 20(5):1583-1595
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
ITAF abbreviated name:
Unr
ITAF fullname:
upstream of N-ras
ITAF description (long):
Unr protein is known to bind to gaagaaguaa
3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vivo
The organism where action of this ITAF was studied:
Mus musculus ES
Citations:
Boussadia O., Niepmann M., Creancier L., Prats A. C., Dautry F., Jacquemin-Sablon H. (2003) Unr is required in vivo for efficient initiation of translation from the internal ribosome entry sites of both rhinovirus and poliovirus. J. Virol. 77(6):3353-3359
IRES trans-acting factor (ITAF):
Version: 5 Last change: 2009-08-30 14:01:31
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
OPTIONAL: The interacting RNA base range (if any):
1-95,230-430
ITAF protein characteristics:
Version: 3 Last change: 2009-08-30 14:16:52
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
PCBP-2
ITAF fullname:
poly(rC)-binding protein 2 (39 kDa)
ITAF description (long):
Required for poliovirus IRES activity (Blyn et al. 1996 and 1997) and replication (Toyoda et al., 2007). Its amount is not limiting in rabbit reticulocyte lysates (RRL) (Hunt and Jackson 1999).
3.3.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate
Remarks:
Cytosines in regions 93-95 and 98-100 are required for viral replication while not translation although they
are present in the cloverleaf structure in region 1-89 (Toyoda et al., 2007).

PCBP2 also binds to domain IV of PV IRES and is required for ts activity (Blyn et al., 1996, 1997; Gamarnik et
al., 1997; Walter et al., 2002). Blyn et al. (1997) reported that PCBP1 cannot functionally replace PCBP2 in
HeLa cells in respect to translation initiation. This is in agreement with Walter et al. (2002) who reported
that PCBP1 can replace PCBP2 only in respect to replication.
Citations:
Hunt S. L., Jackson R. J. (1999) Polypyrimidine-tract binding protein (PTB) is necessary, but not sufficient, for efficient internal initiation of translation of human rhinovirus-2 RNA. RNA. 5(3):344-359
Toyoda H, Franco D, Fujita K, Paul AV, Wimmer E (2007) Replication of poliovirus requires binding of the poly(rC) binding protein to the cloverleaf as well as to the adjacent C-rich spacer sequence between the cloverleaf and the internal ribosomal entry site. J. Virol. 81(18):10017-10028
Blyn LB, Swiderek KM, Richards O, Stahl DC, Semler BL, Ehrenfeld E (1996) Poly(rC) binding protein 2 binds to stem-loop IV of the poliovirus RNA 5' noncoding region: identification by automated liquid chromatography-tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 93(20):11115-11120
Blyn LB, Towner JS, Semler BL, Ehrenfeld E (1997) Requirement of poly(rC) binding protein 2 for translation of poliovirus RNA. J. Virol. 71(8):6243-6246
Gamarnik AV, Andino R (1997) Two functional complexes formed by KH domain containing proteins with the 5' noncoding region of poliovirus RNA. RNA. 3(8):882-892
Walter BL, Parsley TB, Ehrenfeld E, Semler BL (2002) Distinct poly(rC) binding protein KH domain determinants for poliovirus translation initiation and viral RNA replication. J. Virol. 76(23):12008-12022
IRES trans-acting factor (ITAF):
Version: 1 Last change: 2009-08-29 12:27:35
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 2 Last change: 2009-08-29 12:19:15
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
La
ITAF fullname:
La autoantigen
ITAF description (long):
La autoantigen (p52), 52 kDa RNA binding protein, predominantly localized to nucleus, unwinds the dsRNA in ATP-dependent manner, forms a dimer
3.4.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally_although_in_limiting_concentration
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate
Citations:
Craig AW, Svitkin YV, Lee HS, Belsham GJ, Sonenberg N (1997) The La autoantigen contains a dimerization domain that is essential for enhancing translation. Mol. Cell. Biol. 1(17):163-169
Meerovitch K, Svitkin YV, Lee HS, Lejbkowicz F, Kenan DJ, Chan EK, Agol VI, Keene JD, Sonenberg N (1993) La autoantigen enhances and corrects aberrant translation of poliovirus RNA in reticulocyte lysate. J. Virol. 7(67):3798-3807
Svitkin YV, Meerovitch K, Lee HS, Dholakia JN, Kenan DJ, Agol VI, Sonenberg N (1994) Internal translation initiation on poliovirus RNA: further characterization of La function in poliovirus translation in vitro. J. Virol. 3(68):1544-1550
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 37
Version: 1 Last change: 2009-08-30 03:08:45
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
IRES
The 2D structure causes frameshift:
no
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
178-224
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
For the structure probing authors used alpha sarcin or RNase T1 at 30 oC and DMS.
Citations:
Najita L, Sarnow P (1990) Oxidation-reduction sensitive interaction of a cellular 50-kDa protein with an RNA hairpin in the 5' noncoding region of the poliovirus genome. Proc. Natl. Acad. Sci. U.S.A. 15(87):5846-5850
Last change to the database: 2015-04-16 16:45:23 GMT+1