# Patent

## Title
Protein-responsive translational regulatory system using RNA-protein interacting motif

## Abstract

An object of the present invention is to provide a translationally regulatable mRNA which has wider application and can perform specific ON-OFF regulation, an RNA-protein complex specifically bound to the mRNA, and a translational regulatory system. The present invention provides an mRNA having an RNA-protein complex interacting motif-derived nucleotide sequence 5′ to the ribosome-binding site or within the 5′ region of the open reading frame, and an mRNA having a nucleotide sequence complementary to an RNA-protein complex interacting motif-derived nucleotide sequence 5′ to the ribosome-binding site or within the 5′ region of the open reading frame.

## Background
TECHNICAL FIELD
The present invention relates to a translationally regulatable mRNA, a translational regulatory system, and a translational regulation method using RNA-protein interaction.
BACKGROUND ART
With the progress of post-genomic science, information has accumulated about the structures and functions of biomolecules such as proteins or RNAs. There has been a growing tendency of synthetic biology, which exploits such increasing information to understand the systems of life through “synthesis”, in contrast to previous reductive or analytical biology. Particularly, the artificial (re)construction of biomolecules or genetic circuits has received considerable attention in terms of not only life science research but also industrial application. Particularly, there has been a demand for the progress of translational regulatory systems which can recognize a particular protein and regulate arbitrary gene expression.
Heretofore, the conventional technique is known, in which the induction of transcription of DNA is regulated by small molecules or proteins (see Non-Patent Document 1). This technique is a method for modulating the regulation of transcription from DNAs to RNAs. However, this technique had the problem that it cannot be applied directly as a technique of regulating translation from RNAs to proteins. Moreover, there is a naturally occurring system (S15, ThrRS, etc.) in which the protein regulates a translation level upon binding to its own mRNA 5′ untranslated region (5′-UTR). However, no artificial translational repression/activation system of a target gene using such an RNP interacting motif has been constructed intracellularly or extracellularly.
Moreover, RNAs called “riboswitches”, in which mRNAs induce structural change in response to metabolites, resulting in the regulation of gene expression, have been discovered in recent years in bacteria and have received attention. However, natural riboswitches use substrates limited to small molecules such as vitamins or amino acids and therefore, cannot regulate gene expression in response to biomacromolecules such as RNAs or proteins. Furthermore, natural riboswitches are limited to systems for performing the feedback regulation of their own expressions and therefore, have not been applied so far to the development of artificial systems that regulate arbitrary gene expression. Thus, the development of artificial riboswitches having such functions has been expected.
The conventional technique is known as to translational regulation using RNA aptamers or antisense. There also exists a technique which involves introducing a small molecule theophylline-binding aptamer into an artificial RNA using yeast to prepare an “RNA switch” which performs ON/OFF regulation of gene expression in a manner dependent on the presence of theophylline (Non-Patent Document 2). However, this technique had the problem that it is a system responding to the aptamer for small molecules and therefore, cannot be applied to biomacromolecules such as proteins as substrates.

    Non-Patent Document 1: Trends Biochem Sci. 2005; 30 (6): 275-9
    Non-Patent Document 2: Nat Biotechnol. 2004 22 (7): 841-7. 2004


DISCLOSURE OF THE INVENTION
Problems to be Solved by the Invention
An object of the present invention is to provide a translationally regulatable mRNA which has wider application and can perform specific ON-OFF regulation, an mRNA-protein complex, and a translational regulatory system and a translational regulation method using the same.
Means for Solving the Problems
The present invention has been achieved for attaining the object. Specifically, according to one embodiment, the present invention provides an mRNA having an RNA-protein complex interacting motif-derived nucleotide sequence 5′ to the ribosome-binding site or within the 5′ region of the open reading frame.
According to another embodiment, the present invention provides an mRNA having a nucleotide sequence complementary to an RNA-protein complex interacting motif-derived nucleotide sequence 5′ to the ribosome-binding site or within the 5′ region of the open reading frame.
In any of the mRNAs, the interacting motif is preferably an L7Ae-derived nucleotide sequence.
In any of the mRNAs, the interacting motif is preferably a threonyl-tRNA synthetase (ThrRS)-derived nucleotide sequence.
According to an alternative embodiment, the present invention provides an RNA-protein complex comprising the mRNA and a protein specifically binding to the nucleotide sequence.
According to a further embodiment, the present invention provides a translational regulatory system comprising the mRNA and a protein specifically binding to the nucleotide sequence.
The present invention further provides a method for translational regulation of mRNA, comprising contacting the mRNA with a protein specifically binding to the protein-binding motif. In this context, the term “contacting” refers to mixing in a system in which the mRNA and the protein are movable. For example, such system may be a cell.
According to a further embodiment, the present invention provides a translational regulatory system comprising the mRNA, an RNA which specifically binds to the nucleotide sequence and is complementary to the nucleotide sequence, and a protein specifically binding to the complementary RNA. In other words, this system can be referred to as a translational regulatory system comprising (a) an mRNA having a nucleotide sequence complementary to an RNA-protein complex interacting motif-derived nucleotide sequence 5′ to the ribosome-binding site or within the 5′ region of the open reading frame, (b) an RNA having the RNA-protein complex interacting motif-derived nucleotide sequence, and (c) a protein specifically binding to the RNA (b).
According to a further embodiment, the present invention provides an artificial information conversion system which converts input information of an arbitrary substrate protein to output information of an arbitrary target protein.
According to a further embodiment, the present invention provides a simultaneous translational regulatory system which regulates the translational repression and activation of different genes using one protein, the system comprising (a) an mRNA having a nucleotide sequence complementary to an RNA-protein complex interacting motif-derived nucleotide sequence 5′ to the ribosome-binding site or within the 5′ region of the open reading frame, (b) an RNA having the RNA-protein complex interacting motif-derived nucleotide sequence, (c) a protein specifically binding to the RNA (b), and (d) an mRNA having a nucleotide sequence identical to the nucleotide sequence in the RNA (b), 5′ to the ribosome-binding site or within the 5′ region of the open reading frame, the mRNA encoding a gene different from that encoded by the mRNA (a).
According to a further embodiment, the present invention provides a plasmid vector comprising a nucleic acid sequence encoding any of the mRNAs.
According to a further embodiment, the present invention provides an intracellular translational regulatory system comprising a first plasmid vector comprising a nucleic acid sequence encoding the mRNA, and a second plasmid vector comprising a nucleic acid sequence encoding a protein specifically binding to the RNA-protein complex interacting motif-derived nucleotide sequence in the mRNA produced by the first vector.
The intracellular translational regulatory system is preferably a system for regulating protein translation in a human cancer cell.
According to a further embodiment, the present invention provides a translational regulatory system comprising a fusion protein containing L7Ae as a tag sequence and a first protein. Preferably, the translational regulatory system further comprises an mRNA having a sequence specifically binding to L7Ae and a sequence encoding a second protein.
According to a further embodiment, the present invention provides an intracellular translational regulatory system comprising a plasmid vector containing a nucleic acid sequence encoding an mRNA encoding L7Ae and a first protein. Preferably, the intracellular translational regulatory system further comprises a plasmid vector containing a nucleic acid sequence encoding an mRNA having a sequence specifically binding to L7Ae, the mRNA encoding a second protein.
Advantages of the Invention 
The present invention has the advantage that an mRNA of the present invention can regulate the translation reaction of the desired gene. Moreover, the present invention enables intracellular translational regulation and a simultaneous translational regulatory system which regulates the translational repression and activation of different genes using one protein.



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1(A) is a diagram showing an mRNA according to the first embodiment, and FIG. 1(B) is a diagram showing the state where a protein is bound to the mRNA according to the first embodiment;
FIG. 2 is a diagram showing an mRNA according to the second embodiment;
FIG. 3(A) is a diagram showing an mRNA according to the third embodiment, and FIG. 3(B) is a diagram showing the state where a complementary strand is dissociated from the mRNA according to the third embodiment;
FIG. 4 is a diagram showing EMSA on Box C/D;
FIG. 5 is a diagram showing EMSA on Box C/D mini and Box C/D minimut;
FIG. 6 is a diagram showing EMSA on ThrRS Domain 2;
FIG. 7 is a diagram showing EMSA on ThrRS Domain 234;
FIG. 8A is a diagram showing the secondary structure of EGFP UTR (SEQ ID NO:98);
FIG. 8B is a diagram showing the secondary structure of L7-UTR2 (SEQ ID NO:99);
FIG. 8C is a diagram showing the secondary structure of L7-UTR2 mut of L7Ae (SEQ ID NO:100);
FIG. 8D is a diagram showing the secondary structure of L7-UTR2 minimut (SEQ ID NO:101);
FIG. 8E is a diagram showing the secondary structure of L7-UTRS (SEQ ID NO:102);
FIG. 8F is a diagram showing the secondary structure of L7-UTR9 (SEQ ID NO:103);
FIG. 8G is a diagram showing the secondary structure of L7-UTR13 (SEQ ID NO:104);
FIG. 9 is a diagram showing the influence of the distance between the ribosome-binding site and the L7Ae-binding site;
FIG. 10 is a diagram showing comparison with translational regulation in mutants;
FIG. 11 is a diagram showing competition assay;
FIG. 12 is a diagram showing the secondary structure of ThrRS-UTRW (SEQ ID NO:105, FIG. 12A), ThrRS-UTR2 (SEQ ID NO:106, FIG. 12B) and ThrRS-UTR2 mut (SEQ ID NO:107, FIG. 12C);
FIG. 13 is a diagram showing that a complex of ThrRS-UTR and ThrRS can inhibit translation;
FIG. 14 is a diagram showing the secondary structure of L7-ORF (EGFP) (SEQ ID NO:108, FIG. 14A) and L7-ORF mut (EGFP) (SEQ ID NO:109, FIG. 14B);
FIG. 15 is a diagram showing ORF-based translational regulation;
FIG. 16 is a diagram showing results of translational regulation assay on an ON switch;
FIG. 17(a) is a schematic diagram showing the secondary structure of Box C/D-DsRed Ex (SEQ ID NO:110), FIG. 17(b) is a schematic diagram showing the secondary structure of Box C/D mut-DsRed Ex (SEQ ID NO:111), and FIG. 17(c) is a schematic diagram showing the secondary structure of DsRed Ex (SEQ ID NO:112) (used as a control) having a normal 5′-UTR sequence;
FIG. 18 is a graph showing a Relative fluorescent intensity (fluorescence intensity of the protein translated from the corresponding mRNA in the absence of L7Ae was normalized to 1.0);
FIG. 19 is a graph showing results of simultaneously regulating the translations of two mRNAs by the addition of a protein;
FIG. 20 is a vector diagram showing a pcDNA-A vector;
FIG. 21 is a vector diagram showing an L7Ae expression vector pcDNA-L7Ae, which is a plasmid vector in which the L7Ae gene was inserted downstream of the CMV promoter of a pcDNA3.1 vector (Invitrogen Corp.);
FIG. 22 is a diagram showing L7Ae expression in cultured human cells;
FIG. 23 is a diagram showing that the L7Ae expression in cultured human cells has no cytotoxicity;
FIG. 24 is a vector diagram showing a Box C/D-GFP vector;
FIG. 25 is a vector diagram showing a Box C/D mut GFP vector;
FIG. 26 is a diagram showing L7Ae expression;
FIG. 27 is diagram showing EGFP expression;
FIG. 28 is a diagram showing the quantification of L7Ae-dependent translational repression of EGFP by western blotting;
FIG. 29 is a diagram showing the FACS measurement of L7Ae-dependent translational repression of EGFP;
FIG. 30 is a diagram showing results of quantifying the translational repression of EGFP in an amount of pcDNA or pcDNA-L7Ae added of 0 to 1.6 μg;
FIG. 31 is a graph showing mRNA level comparison among samples (samples derived from Box C/D-GFP and pcDNA-L7Ae and samples derived from Box C/D-GFP and pcDNA-A) with a sample derived from only Box C/D as 1;
FIG. 32 is a graph showing mRNA level comparison among samples (samples derived from Box C/D-GFP and pcDNA-L7Ae and samples derived from Box C/D mut GFP and Box C/D-GFP) with a sample derived from only Box C/D as 1;
FIG. 33 is a fluorescence microscopic image showing the relationship of the amount of an empty vector or an L7Ae-expressing vector added with translational regulation in Box C/D-mut-GFP or Box C/D-GFP;
FIG. 34 is a fluorescence microscopic image showing that L7Ae can be used as a tag sequence for a target protein; and
FIG. 35 is a graph showing measurement of the association rate (Ka), dissociation rate (Kd), and association (KA) and dissociation (KD) constants between the Box C/D RNA and the L7Ae protein, demonstrating that in this RNA-protein complex, a motif having high affinity and a slow dissociation rate is effective for intracellular translational regulation.



DESCRIPTION OF SYMBOLS


    1 mRNA
    1a mRNA
    1b mRNA
    2 RNA-protein complex interacting motif-derived nucleotide sequence
    2a RNA-protein complex interacting motif-derived nucleotide sequence
    2b nucleotide sequence complementary to RNA-protein complex interacting motif-derived nucleotide sequence
    3 ribosome-binding site
    4 open reading frame
    4a open reading frame
    4b open reading frame
    5 protein
    5b protein
    6 competitor RNA


BEST MODE FOR CARRYING OUT THE INVENTION
Hereinafter, the present invention will be described in detail with reference to the embodiments. However, the description below is not intended to limit the present invention.
With the rapid expansion of molecular biology from the late 20th century to the present, an enormous number of genes have been identified, and the functions of various biomacromolecules, particularly, proteins encoded thereby, have been elucidated. Furthermore, the detailed tertiary structures of DNAs, RNAs, and proteins have been elucidated. They have been demonstrated to function on the atomic level through intermolecular interactions and selective chemical reactions. Accordingly, if these interactions and chemical reactions could be regulated freely, novel disease therapies or methods for solving the energy problem should be developed.
Examples of approaches to achieve this include methods which involve: designing and preparing a novel molecule functioning to directly regulate the functions of a targeted molecule through the intermolecular interaction; and regulating cells or tissues using the prepared molecule. RNAs can form diverse tertiary structures. As in proteins, some RNAs have enzymatic functions, and the correlation between the functions and the structures has been revealed in detail through tertiary structure analysis. Moreover, RNAs composed by four basic units are formed based on simple construction principles. Accordingly, RNAs can be used widely in the design and construction of molecules having sophisticated tertiary structures as nano-blocks. On the other hand, proteins, which are composed of basic units as many as 20, have far more diverse and complicated tertiary structures and functions than those of RNAs. Although an enormous number of natural protein structures have been analyzed currently at high resolutions, their molecular designs and constructions are difficult and are thus limited to those having simple structures. As a result, realistically, RNAs or RNPs (RNA-protein complexes) are designed and constructed as nano-scale 3D objects having complicated functions and structures, at this time. Specifically, the combination of an “artificial RNA prepared by molecular design” and a “natural protein having a known structure” is a highly feasible approach for developing functional molecules by molecular design.
The present inventors conceived the idea that ribosome-catalyzed translation reaction is inhibited by binding a particular protein to the 5′ side of a ribosome-binding site (RBS) or the 5′ region of an open reading frame of an mRNA, and have completed the present invention.
According to the first embodiment, the present invention provides an mRNA having an RNA-protein complex interacting motif-derived protein-binding motif on the 5′ side of the ribosome-binding site. FIG. 1(A) is a diagram schematically showing the mRNA according this embodiment. In FIG. 1(A), an mRNA 1 comprises an RNA-protein complex interacting motif-derived nucleotide sequence 2, a ribosome-binding site 3, and an open reading frame 4.
[Open Reading Frame]
The mRNA 1 according to this embodiment may be an arbitrary mRNA that has the ribosome-binding site 3 and has translational functions. The sequence of the open reading frame 4 is not limited to a particular sequence. Thus, the sequence of the open reading frame 4 may have a gene that can be expressed into a desired protein, and has a start codon, though it is not limited to a particular sequence. For example, an mRNA having an open reading frame 4 having a gene encoding a fluorescent protein may be used for the purpose of confirming whether the translational functions act. Examples of the fluorescent protein include EGFP, GFP-UV, and DsRed. Their sequences are generally known.
In addition, the sequence of the open reading frame 4 may encode a protein that works as a particular pharmaceutical agent. Specifically, examples of the protein include, but not limited to, Bcl-2 family proteins regulating the apoptosis of cancer cells and antibodies specifically recognizing the surfaces of cancer cells.
[RNA-Protein Complex Interacting Motif-Derived Nucleotide Sequence]
The RNA-protein complex interacting motif-derived nucleotide sequence 2 is a site to which a particular protein specifically binds. The nucleotide sequence 2 may comprise an RNA-protein complex interacting motif-derived nucleotide sequence or a nucleotide sequence mutated from the nucleotide sequence.
In the present invention, the RNA-protein complex interacting motif-derived nucleotide sequence encompasses: a nucleotide sequence known as an RNA sequence in the RNA-protein interacting motif of a known natural RNA-protein complex; and a nucleotide sequence as an RNA sequence in an artificial RNA-protein complex interacting motif obtained by the in vitro evolution method. These RNA-protein complexes are assemblies of proteins and RNAs which are confirmed in vivo in large numbers, and are 3D objects having complicated structures.
The natural RNA-protein complex interacting motif-derived nucleotide sequence is usually composed of approximately 10 to 80 bases and known to specifically bind to a particular amino acid sequence of a particular protein in a noncovalent manner, i.e., through hydrogen bond. Such a natural RNA-protein complex interacting motif-derived nucleotide sequence can be selected from Tables 1 and 2 below. The RNA-protein interacting motif preferably used in this embodiment has such a tertiary structure as to inhibit the translational functions of the mRNA. The tertiary structure capable of inhibition refers to a structure that can compete with ribosome function, owing to its high affinity of RNA-protein interaction. Specifically, it refers to a protein-RNA interacting motif having Kd of approximately 0.1 nM to approximately 1 μM, though the Kd is not limited to this range.










TABLE 1





RNA
Protein
Kd
Reference



















5S RNA (Xenopus laevis
5R1
0.64 ± 0.10
nM
Nat Struct Biol. 1998 July; 5(7): 543-6


oocyte)


5S RNA (Xenopus laevis
5R2
0.35 ± 0.03
nM
Nat Struct Biol. 1998 July; 5(7): 543-6


oocyte)


dsRNA
B2
1.4 ± 0.13
nM
Nat Struct Mol Biol. 2005 November; 12(11): 952-7










RNA splicing motif with
Fox-1
0.49 nM at 150 mM salt
EMBO J. 2006 Jan. 11; 25(1): 163-73.


UGCAUGU element











TGE
GLD-1
9.2 ± 2
nM
J Mol Biol. 2005 Feb. 11; 346(1): 91-104.


sodB mRNA
Hfq
1.8
nM
EMBO J. 2004 Jan. 28; 23(2): 396-405.


RyhB (siRNA)
Hfq
1500
nM
Annu Rev Microbiol. 2004; 58: 303-28


mRNA
HuD
0.7 ± 0.02
nM
Nat Struct Biol. 2001 February; 8(2): 141-5


S domain of 7S RNA
human SRP19


RNA. 2005 July; 11(7): 1043-50. Epub 2005 May 31


Large subunit of SRP RNA
human SRP19
2
nM
Nat Struct Biol. 2001 June; 8(6): 515-20


23S rRNA
L1


Nat Struct Biol. 2003 February; 10(2): 104-8


23S rRNA
L11


Nat Struct Biol. 2000 October; 7(10): 834-7


5S rRNA
L18


Biochem J. 2002 May 1; 363(Pt 3): 553-61


23S rRNA
L20
13 ± 2
nM
J Biol Chem. 2003 Sep. 19; 278(38): 36522-30.


Own mRNA site1
L20
88 ± 23
nM
J Biol Chem. 2003 Sep. 19; 278(38): 36522-30.


Own mRNA site2
L20
63 ± 23
nM
Mol Microbiol. 2005 June; 56(6): 1441-56


23S rRNA
L23


J Biomol NMR. 2003 June; 26(2): 131-7


5S rRNA
L25


EMBO J. 1999 Nov. 15; 18(22): 6508-21


Own mRNA
L30


Nat Struct Biol. 1999 December; 6(12): 1081-3.


mRNA
LicT


EMBO J. 2002 Apr. 15; 21(8): 1987-97


Own mRNA
MS2 coat
39 ± 5
nM
FEBS J. 2006 April; 273(7): 1463-75


Stem-loop RNA motif
Nova-2


Cell. 2000 Feb. 4; 100(3): 323-32


SL2
Nucleocapsid
110 ± 50
nM
J Mol Biol. 2000 Aug. 11; 301(2): 491-511


Pre-rRNA
Nucleolin


EMBO J. 2000 Dec. 15; 19(24): 6870-81



p19
0.17 ± 0.02
nM
Cell. 2003 Dec. 26; 115(7): 799-811


Box C/D
L7Ae
0.9 ± 0.2
nM
RNA. 2005 August; 11(8): 1192-200.



















TABLE 2





RNA
Protein
Kd
Reference



















siRNA with the characteristic
PAZ(PiWi Argonaut


Nat Struct Biol. 2003 December; 10(12): 1026-32.


two-base 3′ overhangs
and Zwille)


dsRNA
Rnase III


Cell. 2006 Jan. 27; 124(2): 355-66


HIV-1 RRE (IIB)
RR1-38
3-8
nM
Nat Struct Biol. 1998 July; 5(7): 543-6


Own mRNA
S15
5
nM
EMBO J. 2003 Apr. 15; 22(8): 1898-908


16S rRNA
S15
6
nM
Nat Struct Biol. 2000 April; 7(4): 273-277.


Own mRNA
S15
43
nM
EMBO J. 2003 Apr. 15; 22(8): 1898-908










16S rRNA
S4
6.5 μM in 4° C.,
J Biol Chem. 1979 Mar. 25; 254(6): 1775-7




1.7 nM in 42° C.











16S rRNA
S4
18
μM
J Biol Chem. 1979 Mar. 25; 254(6): 1775-7


16S rRNA
S8
26 ± 7
nM
J Mol Biol. 2001 Aug. 10; 311(2): 311-24


mRNA
S8
200
nM
RNA. 2004 June; 10(6): 954-64


mRNA
SacY
1400
nM
EMBO J. 1997 Aug. 15; 16(16): 5019-29


SnRNA
Sm


Cold Spring Harb Symp Quant Biol. 2006; 71: 313-20.


tmRNA
SmpB
21 ± 7
nM
J Biochem (Tokyo). 2005 December; 138(6): 729-39


TD3 of tmRNA
SmpB
650
nM
J Biochem (Tokyo). 2005 December; 138(6): 729-39










U1 snRNA
snRNP U1A
0.032 ± 0.007 nM
Nat Struct Biol. 2000 October; 7(10): 834-7




(salt dependence)











S domain of 7S RNA
SRP54
500
nM
RNA. 2005 July; 11(7): 1043-50.


TAR
Tat
200-800
nM
Nucleic Acids Res. 1996 Oct. 15; 24(20): 3974-81










BIV TAR
Tat
1.3 nM or 8 nM or 60 nM
Mol Cell. 2000 November; 6(5): 1067-76




(Mg dependence)











tRNAThr
ThrRS
500
nM
Nat Struct Biol. 2002 May; 9(5): 343-7


thrS mRNA operator
ThrRS
10
nM
Trends Genet. 2003 March; 19(3): 155-61


Single stranded mRNA
TIS11d


Nat Struct Mol Biol. 2004 March; 11(3): 257-64.


PSTVd
Virp1
500
nM
Nucleic Acids Res. 2003 Oct. 1; 31(19): 5534-43


RNA hairpin; Smaug
Vts1p
30
nM
Nat Struct Mol Biol. 2006 February; 13(2): 177-8.


recognition element (SRE)


λ BoxB
λ N
90
nM
Cell. 1998 Apr. 17; 93(2): 289-99









The artificial RNA-protein complex interacting motif-derived nucleotide sequence is the nucleotide sequence of an RNA in the RNA-protein interacting motif of an artificially designed RNA-protein complex. Such a nucleotide sequence is usually composed of approximately 10 to 80 bases and designed to specifically bind to a particular amino acid sequence of a particular protein in a noncovalent manner, i.e., through hydrogen bond. Examples of such an artificial RNA-protein complex interacting motif-derived nucleotide sequence include, but not limited to, RNA aptamers specifically binding to apoptosis-inducing protein Bcl-2 family, and RNA aptamers specifically recognizing cancer cell surface antigens. Moreover, nucleotide sequences listed in Table 3 below are also known, and these can also be used as the RNA-protein complex interacting motif-derived nucleotide sequence 2 of the present invention.










TABLE 3





RNA
Protein
Kd
Reference



















Rev aptamer 5
Rev
190
nM
RNA. 2005 December; 11(12): 1848-57


Aptamer
p50
5.4 ± 2.2
nM
Proc Natl Acad Sci USA. 2003 Aug. 5;






100(16): 9268-73.


BMV Gag aptamer
BMV Gag
20
nM
RNA. 2005 December; 11(12): 1848-57


BMV Gag aptamer
CCMV Gag
260
nM
RNA. 2005 December; 11(12): 1848-57


CCMV Gag aptamer
CCMV Gag
280
nM
RNA. 2005 December; 11(12): 1848-57


CCMV Gag aptamer
BMV Gag
480
nM
RNA. 2005 December; 11(12): 1848-57









The artificial RNA-protein complex can be prepared by using the molecular design and in vitro evolution methods in combination. The in vitro evolution method can produce aptamers or ribozymes by screening functional RNAs from a molecular library having various sequence diversities and repeating the amplification and transcription reactions of the genes (DNAs). Thus, an RNA-protein interacting motif adapted to an RNP having functions and structures of interest based on molecular design in advance can be extracted from natural RNP molecules or can be prepared artificially by the in vitro evolution method.
In this embodiment, for the RNA-protein complex interacting motif-derived nucleotide sequence 2, the RNA-protein complex serving as an origin of the nucleotide sequence preferably has a dissociation constant Kd of approximately 0.1 nM to approximately 1 μM. This is because affinity sufficient for competing with ribosome-mRNA interaction is necessary.
Specific examples of the RNA-protein complex interacting motif-derived nucleotide sequence 2 include, but not limited to, nucleotide sequences such as a nucleotide sequence 5′-GGGCGUGAUGCGAAAGCUGACCC-3′ (SEQ ID NO:9) which can bind to L7Ae (Moore T et al., Structure Vol. 12, pp. 807-818 (2004)) known to participate in RNA modification such as RNA methylation or pseudouridylation, and a nucleotide sequence 5′-GGCGUAUGUGAUCUUUCGUGUGGGUCACCACUGCGCC-3′ (SEQ ID NO:19) which can bind to threonyl-tRNA synthetase (Cell (Cambridge, Mass.) v97, pp. 371-381 (1999)), an aminoacylating enzyme, known to have feedback inhibition which inhibits translation upon binding to its own mRNA.
Moreover, a moiety that interacts with a Bcl-xL aptamer protein specifically binding to a cancer cell-specific endogenous protein Bcl-xL may be used as the RNA-protein complex interacting motif-derived nucleotide sequence 2. Such a Bcl-2 family CED-9-derived nucleotide sequence used as the RNA-protein complex interacting motif-derived nucleotide sequence 2 is R9-2; 5′-GGGUGCUUCGAGCGUAGGAAGAAAGCCGGGGGCUGCAGAUAAUGUAUAGC-3′ (SEQ ID NO:113), which is described in detail in Yang C, et al., J Biol Chem. 2006; 281 (14): 9137-44. In addition, a nucleotide sequence derived from an RNA aptamer sequence binding to NF-kappa B can be used as the RNA-protein complex interacting motif-derived nucleotide sequence 2.
The RNA-protein complex interacting motif-derived nucleotide sequence 2 is incorporated to 5′ to the ribosome-binding site 3 in the mRNA 1. The term “5′ to the ribosome-binding site” in the mRNA refers to a position 2 to 10 bases (inclusive) distant from the ribosome-binding site toward the 5′ end. In FIG. 1(A), a nucleotide sequence that may be located between the RNA-protein complex interacting motif-derived nucleotide sequence 2 and the ribosome-binding site 3 is indicated in line. In this embodiment, the nucleotide sequence that may be located between the RNA-protein complex interacting motif-derived nucleotide sequence 2 and the ribosome-binding site 3 is not limited to a particular nucleotide sequence.
Moreover, the mRNA 1 according to this embodiment may have a 5′-terminal sequence forming a stem-loop structure (not shown), which is located 5′ to the RNA-protein complex interacting motif-derived nucleotide sequence 2. This is because the transcriptional efficiency of the mRNA 1 may be enhanced. Examples of the sequence forming a stem-loop structure include usually known structures. Those skilled in the art can introduce an arbitrary stem structure for enhancing transcriptional efficiency into the 5′ end using the standard method.
Next, the mechanism of translational regulation according to the first embodiment will be described specifically.
[ON-to-OFF Translational Regulation]
When a protein specifically binding to the RNA-protein complex interacting motif-derived nucleotide sequence 2 is absent in the state shown in FIG. 1(A), a ribosome, if any, can freely bind to the ribosome-binding site 3 under conditions involving approximately 33 to 41° C. and pH 6.0 to 8.0. Accordingly, the translation of the mRNA is performed as normal. Here, a protein 5 specifically binding to the RNA-protein complex interacting motif-derived nucleotide sequence 2 is added thereto. FIG. 1(B) shows the relationship of the mRNA 1 and the protein 5 in the presence of the protein. In FIG. 1(B), the protein 5 is specifically bound to the RNA-protein complex interacting motif-derived nucleotide sequence 2. Further, the protein 5 blocks the ribosome-binding site 3 through its steric hindrance. Therefore, a ribosome, if any, cannot bind to the ribosome-binding site 3. Accordingly, the translation reaction of the mRNA 1 fails to function. In this way, the translation reaction of the mRNA 1 can be regulated in an ON-to-OFF manner by adding the particular protein 5 to the protein-free system of the mRNA 1 (state of FIG. 1(A)).
Moreover, similar ON-to-OFF translational regulation can be achieved not only by adding the particular protein to the system but also by responding to, for example, a protein endogenously expressed in vivo. Specifically, for example, an mRNA 1 that has an aptamer against proteins (e.g., Bcl-xL) specifically expressed in certain cancer cells, as the RNA-protein complex interacting motif-derived nucleotide sequence 2 and has a fluorescent protein-encoding sequence as an open reading sequence may be introduced in cells in vivo. In such a case, fluorescent protein expression is regulated in an ON-to-OFF manner only in cells that have expressed the proteins specifically expressed in certain cancer cells. Therefore, cells that do not emit fluorescence, i.e., cancer-bearing cells, can be detected specifically.
Thus, such an mRNA and a protein can be used as a translational regulatory system. Moreover, in light of the above-mentioned mechanism, a translational regulation method can be provided by contacting the mRNA with the protein. Furthermore, a complex of the mRNA and the protein may be used in such a translational system or translational regulation method. Moreover, the use of them enables construction of an artificial information conversion system which converts input information of an arbitrary substrate protein to output information of an arbitrary target protein.
The mRNA according to the first embodiment of the present invention allows regulation of translation reaction as described above. Moreover, in the applicative aspect of use of the mRNA according to the first embodiment, the RNA-protein complex interacting motif-derived nucleotide sequence 2 is designed to specifically bind to a protein formed due to a particular disease. Further, the open reading frame is designed to incorporate therein a gene encoding a protein that relieves or treats the disease. The resulting mRNA can be used as a drug for the particular disease.
The second embodiment of the present invention provides an mRNA having an RNA-protein complex interacting motif-derived nucleotide sequence within the open reading frame. FIG. 2 is a diagram schematically showing the mRNA according to this embodiment. In FIG. 2, an mRNA 1a according to this embodiment comprises an open reading frame 4a and an RNA-protein complex interacting motif-derived nucleotide sequence 2a located therewithin.
This embodiment is not only used preferably in the translational regulation of the mRNA free from a ribosome-binding site, specifically, an mRNA derived from an origin other than bacteria (e.g., E. coli), but also used in an mRNA containing a ribosome-binding site. In FIG. 2, the description of the ribosome-binding site is omitted. However, this embodiment is not intended to exclude the presence of the ribosome-binding site.
In this embodiment, the RNA-protein complex interacting motif-derived nucleotide sequence 2a is located within the open reading frame 4a. The position of the RNA-protein complex interacting motif-derived nucleotide sequence 2a may be set to an arbitrary position within the open reading frame 4a. The RNA-protein complex interacting motif-derived nucleotide sequence 2a can be placed, for example, immediately 3′ to the start codon AUG. Moreover, the RNA-protein complex interacting motif-derived nucleotide sequence 2a may be placed via approximately 1 to 20 bases 3′ to the start codon AUG. Particularly, it may be placed via approximately 1 to 10 bases 3′ to the start codon AUG. In this context, when the RNA-protein complex interacting motif-derived nucleotide sequence 2a is inserted within the open reading frame 4a, the motif-derived nucleotide sequence 2a can be supplemented, if necessary, with 1 base or 2 bases such that the base number of the inserted nucleotide sequence is an multiple of 3 to prevent frameshift.
When a protein specifically binding to the RNA-protein complex interacting motif-derived nucleotide sequence 2a is absent in the state shown in FIG. 2, a ribosome, if any, initiates the translation of the mRNA 1a under conditions involving approximately 36 to 42° C. and pH 6 to 7.6. However, in the presence of the protein, the protein specifically binds to the RNA-protein complex interacting motif-derived nucleotide sequence 2a and sterically blocks the adjacent open reading frame 4a. Therefore, the ribosome-catalyzed translation is repressed.
According to the second embodiment, the mRNA translation can be regulated by sterically blocking the open reading frame 4a. In this context, the use of the mRNA according to this embodiment can also achieve, as in the first embodiment, a translational regulatory system comprising the mRNA and the protein, a complex of the mRNA and the protein, and a translational regulation method.
According to the third embodiment, the present invention provides an mRNA having a nucleotide sequence complementary to an RNA-protein complex interacting motif-derived nucleotide sequence 5′ to the ribosome-binding site or within the 5′ region of the open reading frame. FIG. 3(A) is a diagram schematically showing the mRNA according to this embodiment. In FIG. 3(A), an mRNA 1b according to this embodiment comprises an open reading frame 4b and a nucleotide sequence 2b complementary to an RNA-protein complex interacting motif-derived nucleotide sequence, located therewithin. In this case as well, the complementary nucleotide sequence 2b can be supplemented, if necessary, with 1 base or 2 bases such that the base number of the inserted nucleotide sequence is a multiple of 3.
The mRNA 1b according to this embodiment differs from the mRNA of the second embodiment in that the RNA-protein complex interacting motif-derived nucleotide sequence according to the second embodiment is changed to the nucleotide sequence 2b complementary to an RNA-protein complex interacting motif-derived nucleotide sequence. In this context, the nucleotide sequence 2b complementary to an RNA-protein complex interacting motif-derived nucleotide sequence may comprise not only a completely complementary sequence but also a sequence mutated therefrom.
[OFF-to-ON Translational Regulation]
Next, the OFF-to-ON translational regulation of the mRNA will be described using the mRNA 1b according to this embodiment. In the state shown in FIG. 3(A), the nucleotide sequence 2b complementary to an RNA-protein complex interacting motif-derived nucleotide sequence, in the mRNA 1b, is bound in advance to a competitor RNA 6 having the RNA-protein complex interacting motif-derived nucleotide sequence of the mRNA 1b. When a protein 5b shown in FIG. 3(B) is intracellularly absent, the competitor RNA 6 is bound to the sequence 2b in the mRNA 1b. This state is the state shown in FIG. 3(A). This competitor RNA 6 does not have to be completely identical to the RNA-protein complex interacting motif-derived nucleotide sequence and may contain a mutation. In this state, translation does not start even in the presence of a ribosome. This is because the competitor RNA 6 blocks ribosome binding to the mRNA 1b. 
To this system, a protein 5b specifically binding to the competitor RNA 6 having the RNA-protein complex interacting motif-derived nucleotide sequence is added. The added state is shown in FIG. 3(B). The state shown here in FIG. 3(B) is brought about by the intracellular expression of the protein 5b. Here, the addition of the protein 5b can inhibit the specific binding between the competitor RNA 6 having the protein-binding motif-derived sequence and the mRNA 1b. The ribosome-catalyzed translation reaction of the open reading frame 4b starts upon inhibition of the binding between the RNA 6 and the mRNA 1b through the reaction with the particular protein 5b. In this way, the translation reaction of the mRNA 1b can be regulated in an OFF-to-ON manner by adding the protein 5b to the system in which the particular competitor RNA 6 is bound to the mRNA 1b (state of FIG. 3(A)).
In FIG. 3, the embodiment is shown, in which the nucleotide sequence 2b complementary to an RNA-protein complex interacting motif-derived nucleotide sequence is located within the open reading frame 4b. However, in a modification of this embodiment, the nucleotide sequence complementary to an RNA-protein complex interacting motif-derived nucleotide sequence may be located 5′ to the ribosome-binding site. The aspect may be the same as that of the first embodiment in which the RNA-protein complex interacting motif-derived nucleotide sequence is located 5′ to the ribosome-binding site. In this case as well, OFF-to-ON translational regulation can be performed by the same action as in the third embodiment. Moreover, the use of the mRNA according to this embodiment can also achieve a translational regulatory system comprising the mRNA and the protein, a complex of the mRNA and the protein, and a translational regulation method.
According to the fourth embodiment, the present invention provides a modification of the third embodiment and relates to a simultaneous OFF-to-ON/ON-to-OFF translational regulatory system.
The simultaneous translational regulatory system according to the fourth embodiment of the present invention comprises an mRNA 1b, a competitor RNA 6, and a protein 5b specifically binding to the competitor RNA 6 shown in FIG. 3(A) described in the third embodiment and further comprises a second mRNA. The second mRNA has a sequence identical to the competitor RNA 6, 5′ to the ribosome-binding site or within the 5′ region of the open reading frame, and encodes a gene different from that encoded by the mRNA 1b. Since the second mRNA has a sequence identical to the competitor RNA 6, and it specifically binds to the protein 5b. Specifically, the second mRNA is of type whose translation is inhibited in a manner dependent on the presence of the protein 5b. In the description below, the mRNA 1b shown in FIG. 3(A) is referred to as a first mRNA.
[Simultaneous OFF-to-ON/ON-to-OFF Translational Regulation]
In this context, the addition of the protein 5b to the system containing the first mRNA 1b and the competitor RNA 6 achieves OFF-to-ON translational regulation as described in the third embodiment. Furthermore, when the second mRNA is present in this system in the presence of an excess of the protein 5b, this protein 5b specifically binds to the second mRNA and hinders its translation. Therefore, the translation of the second mRNA is regulated to achieve ON-to-OFF translational regulation. In this way, the fourth embodiment enables simultaneous OFF-to-ON/ON-to-OFF translational regulation.
For example, the first mRNA 1b and the second mRNA may have fluorescent protein genes differing in type as their ORFs. In such a case, OFF-to-ON translational regulation is performed in one of them, while ON-to-OFF translational regulation is performed in the other mRNA. They can be observed easily using a fluorescence microscope or the like by applying EGFP (green) to one of the fluorescent protein genes and DsRed (red) to the other gene. Thus, this system would be useful.
According to the fifth embodiment, the present invention provides an intracellular translational regulatory system comprising a vector containing a nucleic acid encoding any of the RNAs and/or any of the proteins used in the first to fourth embodiments.
Translational regulation can be performed preferably, particularly in cancer cells. Both the repression and promotion of protein expression can be performed according to the procedures of the ON-to-OFF translational regulation and the OFF-to-ON translational regulation, respectively. Moreover, the presence or absence of such regulation can be confirmed based on the expression of a marker protein. In this case, the mRNA and a protein-encoding gene can be introduced into cells using plasmid vectors.
A technique of preparing plasmid vectors expressing the desired RNA or protein is already known by those skilled in the art. These vectors can be prepared by conventional methods. For example, L7Ae-expressing vectors can be constructed by inserting the L7Ae-encoding gene downstream of a CMV promoter within vectors conventionally used in intracellular protein expression for humans. On the other hand, vectors expressing an mRNA in which Box C/D known as a sequence to which L7Ae specifically binds, or its mutant Box C/D mut is inserted within the 5′ region of the EGFP open reading frame, can also be prepared by amplifying the corresponding genes by PCR and inserting them within vectors routinely used in intracellular protein expression for humans. Furthermore, when L7Ae is desired to be intracellularly expressed at the intended timing, vectors capable of expressing L7Ae by addition to a tetracycline (Tet) medium may be prepared. Such vectors capable of expressing L7Ae by the addition to a tetracycline medium contain an L7Ae-encoding gene downstream of a Tet operator sequence and comprise, as a component, a vector or cell constitutively expressing a Tet repressor.
The fifth embodiment of the present invention enables intracellular translational regulation. Translational regulation in cells, particularly, cancer cells, is highly possibly applicable therapeutically and can therefore serve as very useful means.
According to the sixth embodiment, the present invention provides a translational regulatory system comprising a fusion protein containing L7Ae as a tag sequence and a first protein.
This fusion protein is specifically a fusion protein comprising L7Ae and a first protein as another arbitrary protein. Hereinafter, such a fusion protein is also referred to as a tag sequence-fused protein. Examples of the first protein as an arbitrary protein include, but not limited to, fluorescent proteins, apoptosis-inducing proteins, apoptosis-repressing proteins, and organellar localized proteins. Theoretically, the desired protein can be used.
The translational regulatory system according to this embodiment further comprises an mRNA having a sequence specifically binding to L7Ae and a sequence encoding a second protein. Specifically, the fusion protein is preferably used together with the mRNA. In the mRNA, the sequence specifically binding to L7Ae is preferably a Box C/D sequence. Alternatively, a sequence mutated from the Box C/D sequence with the Kink-turn motif structure maintained may be used. On the other hand, the second protein encoded by this mRNA is preferably a protein different from the fusion protein. Theoretically, the second protein may be an arbitrary protein and can be determined based on its combination with the first protein constituting the fusion protein. The second protein encoded by the mRNA is preferably a green fluorescent protein for a red fluorescent protein used as the first protein or is preferably an apoptosis-repressing protein for an apoptosis-inducing protein used as the first protein. In addition, some combinations such as some intracellular signaling proteins may be used, in which the translation of the second protein is preferably repressed by the expression of the first protein.
Such a tag sequence-fused protein and an mRNA can be prepared according to the known method as long as genes encoding the desired first and second proteins are known. Moreover, when the protein and the mRNA are used in an intracellular translational regulatory system, plasmid vectors expressing them can be prepared and introduced into cells. These plasmid vectors can be prepared in the same way as in the description of the fifth embodiment by inserting the desired gene thereinto.
Next, the action of the translational regulatory system achieved by such a tag sequence-fused protein and an mRNA will be described. Here, the case will be described, in which the tag sequence-fused protein is a fusion protein of L7Ae and a red fluorescent protein and the mRNA has a Box C/D sequence and encodes a green fluorescent protein, though the present invention is not limited thereto. Plasmid vectors expressing this mRNA are introduced into cells. As a result, the mRNA is translated in the absence of the tag sequence-fused protein to express the green fluorescent protein. To introduce the tag sequence-fused protein into these cells, plasmid vectors having a nucleic acid sequence encoding the tag sequence-fused protein are introduced into the cells. This results in the intracellular expression of the tag sequence-fused protein. Then, the expressed tag sequence-fused protein binds to the mRNA. More specifically, L7Ae constituting the tag sequence-fused protein specifically binds to the Box C/D sequence on the mRNA. Upon this binding, the mRNA translation is repressed to prevent the production of the green fluorescent protein. On the other hand, since the tag sequence-fused protein is continuously produced, the red fluorescent protein constituting the tag-fused protein increases in number. This is observed under a fluorescence microscope such that the green color and the red color become lighter and darker, respectively, with a lapse of time. In this way, the combined use of the tag sequence-fused protein and the mRNA can achieve a translational regulatory system that performs the translation of a target gene in response to the expression of a predetermined gene.
According to the sixth embodiment, a system that represses the translation of a target gene, for example, green fluorescent protein translation, in response to the expression of an arbitrary gene, for example, red fluorescent protein expression, can be constructed intracellularly by adding L7Ae as a tag sequence to the protein. Furthermore, the protein to be fused to the L7Ae tag sequence may be set to, for example, an apoptosis-repressing protein, and the target gene to be regulated may be set to a gene encoding an apoptosis-inducing protein. In such a case, a signaling circuit can be rewired such that it can effectively induce the apoptosis of cells overexpressing apoptosis-repressing proteins, such as cancer cells. Such a translational regulatory system that performs the translation of a target gene in response to the expression of a predetermined gene is a promising tool constituting artificial genetic circuits.
EXAMPLES
A protein-responsive translational regulatory system using a protein-RNA interacting motif (RNP motif) according to the present invention is a technique of using a naturally extracted or artificially prepared RNP motif to regulate translation reaction in an ON-to-OFF or OFF-to-ON manner. Specifically, the ON-to-OFF regulation is established by inserting an RNA-protein complex interacting motif-derived nucleotide sequence into an mRNA. In this regulation, in the presence of a target protein, the protein competes with ribosome binding or entry through its binding to the mRNA to cause translational inhibition. The OFF-to-ON regulation is established by first inserting an antisense sequence of an RNA-protein complex interacting motif-derived nucleotide sequence, 5′ region of the open reading frame of an mRNA. Next, an RNA comprising the RNA-protein complex interacting motif-derived nucleotide sequence is added to the reaction solution to form a complementary strand with the antisense strand inserted in the mRNA, resulting in translational inhibition. The addition of a substrate protein thereto inhibits the binding of the RNA comprising the protein-binding motif to the mRNA to activate translation. In Examples below, proteins generally called L7Ae and ThrRS are used. However, proteins that can be used in the reactions are not limited to only L7Ae or ThrRS. Hereinafter, specific examples of experiments or assays will be described.
Example 1
[Preparation of RNA-Protein Complex Interacting Motifs (RNAs and Proteins) Used in Translational Regulation]
[Preparation of L7Ae-Binding RNA Box C/D]
L7Ae-binding RNA Box C/D (SEQ ID NO: 5) was prepared by preparing a DNA template containing a T7 promoter, followed by transcription reaction using T7 RNA polymerase. The details will be shown below. First, 100 μL of reaction solution was prepared for preparing DNA. The reaction solution contained a mixture of 1 ng of Box C/D template (5′-CTAATACGACTCACTATAGGCCAGAGTGGGCGTGATGCATGTCTAGGAAACTAGA CATGCTGACCCACTCTGGCC-3′) (SEQ ID NO: 1), 5 μL each of 10 μM Box C/D Fwd (5′-CTAATACGACTCACTATAGGCCAG-3′) (SEQ ID NO: 2) and Box C/D Rev (5′-GGCCAGAGTGGGTCAGCAT-3′) (SEQ ID NO: 3), 8 μL of 2.5 mM dNTP (TAKARA BIO INC.), 10 μL of Ex taq 10× buffer (TAKARA BIO INC.), and 0.5 μL of Ex taq DNA polymerase (TAKARA BIO INC.). 25 cycles each involving 94° C. for 30 seconds, 53° C. for 30 seconds, and 72° C. for 1 minute were performed for extension (SEQ ID NO: 4) using Gradient Master Cycler (Eppendorf). After the reaction, the extension product was subjected to phenol treatment, diethyl ether treatment, and ethanol precipitation and dissolved in 10 μL of ultrapure water. The solution was used as a template for transcription. Transcription reaction was performed under conditions involving, for 32P radiolabeling, 40 mM Tris-Cl (pH 7.5), 5 mM DTT, 1 mM spermidine, 5 mM MgCl2, 1.25 mM ATP, 1.25 mM CTP, 1.25 mM UTP, 0.25 mM GTP, [32P-α]GTP (PerkinElmer Inc.), 20 U RNase inhibitor (TOYOBO CO., LTD.), and 35 ng/μL T7 RNA polymerase. In 100 μL of the system, 5 μL of the template was used and reacted at 37° C. for 3 hours to overnight. For non-labeling, transcription reaction was performed using MEGAshortscript (trademark) (Ambion, Inc.). The transcription reaction using MEGAshortscript was performed as follows. 1 μg of template DNA dissolved in ultrapure water, 2 μL of T7 10× Reaction Buffer, 2 μL of T7 ATP Solution (75 mM) (the same recipe for CTP, GTP, and UTP), and 2 μL of T7 Enzyme Mix were mixed and adjusted with ultrapure water to the whole amount of 20 μL. This reaction solution was reacted at 37° C. for 4 hours to overnight. Both the solutions, after the reaction, were supplemented with 1 μL of TURBO DNase (MEGAshortscript (trademark), Ambion, Inc.) and incubated at 37° C. for 15 minutes to decompose the template DNA. Then, each transcript was subjected to phenol treatment and ethanol precipitation for purification. After the precipitation, the resulting product was dissolved in 20 μL of denaturing dye (80% formamide, 0.17% XC, 0.27% BPB) and electrophoresed on a 12% polyacrylamide (29:1) denaturing gel. A gel having the size of interest was excised, and elution was performed overnight at 37° C. by the addition of 500 μL of elution buffer (0.3 M sodium acetate (pH 7.0)). The eluted RNA was subjected again to phenol extraction, diethyl ether extraction, and ethanol precipitation for purification.
[Preparation of Box C/D Mini and Box C/D Minimut]
L7Ae-binding RNA Box C/D mini (SEQ ID NO: 9) and Box C/D minimut (SEQ ID NO: 10) were separately prepared through transcription reaction using Box C/D mini primer (5′-GGGTCAGCTTTCGCATCACGCCCTATAGTGAGTCGTATTAGC-3′) (SEQ ID NO: 7) or Box C/D minimut primer (5′-GGGGCAGCTTTCGCATGACGCCCTATAGTGAGTCGTATTAGC-3′) (SEQ ID NO: 8) as a template and T7 RNA polymerase. Reaction was performed under conditions involving, for 32P radiolabeling, 0.75 μM T7 primer (5′-GCTAATACGACTCACTATA-3′) (SEQ ID NO: 6), 0.75 μM template, 40 mM Tris-Cl (pH 7.5), 5 mM DTT, 1 mM spermidine, 5 mM MgCl2, 1.25 mM ATP, 1.25 mM CTP, 1.25 mM UTP, 0.25 mM GTP, [32P-α]GTP (PerkinElmer Inc.), 20 U RNase inhibitor (TOYOBO CO., LTD.), and 35 ng/μL T7 RNA polymerase. In 100 μL of the system, the template was reacted at 37° C. for 3 hours to overnight. For non-labeling, transcription reaction was performed using MEGAshortscript (trademark) (Ambion, Inc.). The transcription reaction using MEGAshortscript was performed as follows. 0.75 μL of 100 μM T7 primer dissolved in ultrapure water, 0.75 μL of 100 μM Box C/D mini, 2 μL of T7 10× Reaction Buffer, 2 μL of T7 ATP Solution (75 mM) (the same recipe for CTP, GTP, and UTP), and 2 μL of T7 Enzyme Mix were mixed and adjusted with ultrapure water to the whole amount of 20 μL. This reaction solution was reacted at 37° C. for 4 hours to overnight. After the reaction, the resulting product was purified in the same way as above using electrophoresis on a 15% polyacrylamide (29:1) denaturing gel.
[Preparation of ThrRS-Binding RNA Domain 234 and Domain 2]
ThrRS-binding RNA Domain 234 (SEQ ID NO: 15) and Domain 2 (SEQ ID NO: 19) were separately prepared in the same way as in Box C/D by preparing a DNA template containing a T7 promoter, followed by transcription reaction using T7 RNA polymerase. First, 100 μL of reaction solution was prepared for preparing DNA. The reaction solution for Domain 234 contained a mixture of 1 μL of 10 ng/μL ThrRS Domain 234 template (5′-GATTGCGAACCAATTTAGCATTTGTTGGCTAAATGGTTTCGCAATGAACTGTTAAT AAACAAATTTTTCTTTGTATGTGATCTTTCGTGTGGGTCACCA-3′) (SEQ ID NO: 11), 5 μL each of 10 μM ThrRS Domain 234 Fwd (5′-CTAATACGACTCACTATAGGATTGCGAACCAATTTAGCATTTGTTGG-3′) (SEQ ID NO: 12) and ThrRS Domain 234 Rev (5′-TTTGCAGTGGTGACCCACACGAAAGATCAC-3′) (SEQ ID NO: 13), 8 μL of 2.5 mM dNTP (TAKARA BIO INC.), 10 μL of Ex taq 10× buffer (TAKARA BIO INC.), and 0.5 μL of Ex taq DNA polymerase (TAKARA BIO INC.). 25 cycles each involving 94° C. for 30 seconds, 55° C. for 30 seconds, and 72° C. for 1 minute were performed for extension (SEQ ID NO: 14) using Gradient Master Cycler (Eppendorf). The reaction solution for Domain 2 contained a mixture of 5 μL each of 10 μM ThrRS Domain 2 Fwd (5′-CTAATACGACTCACTATAGGCGTATGTGATCTTTCGTGTGGGTCAC-3′) (SEQ ID NO: 16) and ThrRS Domain 2 Rev (5′-GGCGCAGTGGTGACCCACACGAAAGATCAC-3′) (SEQ ID NO: 17), 8 μL of 2.5 mM dNTP (TAKARA BIO INC.), 10 μL of Ex taq 10× buffer (TAKARA BIO INC.), and 0.5 μL of Ex taq DNA polymerase (TAKARA BIO INC.). 10 cycles each involving 94° C. for 30 seconds, 52° C. for 30 seconds, and 72° C. for 1 minute were performed for extension (SEQ ID NO: 18) using Gradient Master Cycler (Eppendorf). After the reaction, each extension product was subjected to phenol treatment, diethyl ether treatment, and ethanol precipitation and dissolved in 10 μL of ultrapure water. The solution was used as a template for transcription. Transcription reaction and purification were performed in the same way as in Box C/D using a 12% polyacrylamide (29:1) denaturing gel for Domain 234 and a 15% polyacrylamide (29:1) denaturing gel for Domain 2.
[Preparation of L7Ae]
The protein L7Ae used in the RNA-protein complex interacting motif was expressed (SEQ ID NO: 66) using plasmids kindly provided by Dr. Alexander Huttenhofer. The plasmids were prepared by amplifying an insert from A. fulgidus using primers L7Ae Fwd (5′-CTGACATATGTACGTGAGATTTGAGGTTC 3′) (SEQ ID NO: 64) and L7Ae Rev (5′-CTGACTCGAGTTACTTCTGAAGGCCTTTAATC-3′) (SEQ ID NO: 65) and incorporating the insert into a pET-28b+ vector (Novagen) cleaved with restriction enzymes NdeI and XhoI. Expression and purification methods will be shown below.
First, E. coli BL21(DE3)pLysS was transformed with the plasmids. The obtained colonies were inoculated to 5 mL of LB medium containing 25 μg/mL kanamycin and 100 μg/mL chloramphenicol and shake-cultured overnight at 37° C. Subsequently, the whole amount of the culture solution was subcultured in 500 mL of LB medium containing 25 μg/mL kanamycin and 100 μg/mL chloramphenicol. The solution was shake-cultured at 37° C. until O.D.600 of 0.6 to 0.7 and then shake-cultured overnight at 30° C. after addition of 500 μL of 1 M IPTG (final concentration: 1 mM) for expression induction. The bacterial cells were collected by centrifugation (4° C., 6000 rpm, 20 min) and sonicated by the addition of 5 mL of a sonication buffer (50 mM Na phosphate, 0.3 M NaCl, pH 8.0) to disrupt the bacterial cells. The sonication was performed by repeating 6 times the procedure of cooling on ice, followed by ultrasonic application for 15 seconds. Then, impure proteins were denatured at 80° C. for 15 minutes. The supernatant was collected by centrifugation (4° C., 6000 rpm, 20 min). Histidine-tagged proteins were purified by the batch method using an Ni-NTA column (QIAGEN GmbH). Specifically, the supernatant and 1 mL of Ni-NTA were first mixed and stirred at 4° C. for 1 hour. Then, the mixture was charged into a column and washed twice with 4 mL of wash buffer (50 mM Na phosphate, 0.3 M NaCl, 20 mM imidazole, pH 8.0). Stepwise elution was performed using two runs of 1 mL each of 50 mM, 100 mM, 200 mM, and 300 mM imidazole elution buffers (prepared by adding imidazole to 50 mM Na phosphate, 0.3 M NaCl (pH 8.0)). 17% SDS-PAGE was used for confirmation. Subsequently, proteins were concentrated using Microcon YM-3 (Millipore Corp.), and the concentrate was replaced by a dialysis buffer (20 mM Hepes-KOH, 1.5 mM MgCl2, 150 mM KCl, 5% glycerol (pH 7.5)). Moreover, the protein concentration was determined by the Bradford method using Protein Assay (BIO-RAD LABORATORIES INC.).
[Preparation of ThrRS]
The protein ThrRS used in the RNA-protein complex interacting motif was expressed (SEQ ID NO: 67) using plasmids kindly provided by Dr. Yoshihiro Shimizu. The plasmids were prepared by extracting ThrRS from E. coli and incorporating it into pQE-30 vectors (QIAGEN GmbH). Expression and purification methods will be shown below.
First, E. coli M15(pREP4) was transformed with the plasmids. The obtained colonies were inoculated to 3 mL of LB medium containing 50 μg/mL ampicillin and shake-cultured overnight at 37° C. Subsequently, the whole amount of the culture solution was subcultured in 50 mL of LB medium containing 50 μg/mL ampicillin. The solution was shake-cultured at 37° C. until O.D.600 of 0.4 to 0.6 and then shake-cultured overnight at 37° C. after addition of 25 μL of 1 M IPTG (final concentration: 0.5 mM) for expression induction. The bacterial cells were collected by centrifugation (4° C., 6000 rpm, 20 min) and sonicated by the addition of 5 mL of a sonication buffer (50 mM Na phosphate, 0.3 M NaCl, pH 8.0) to disrupt the bacterial cells. The sonication was performed by repeating 6 times the procedure of cooling on ice, followed by ultrasonic application for 15 seconds. Then, impure proteins were denatured at 80° C. for 15 minutes. The supernatant was collected by centrifugation (4° C., 6000 rpm, 20 min). Histidine-tagged proteins were purified by the same batch method as above using an Ni-NTA column (QIAGEN GmbH). 8% SDS-PAGE was used for confirmation. Subsequently, proteins were concentrated using Microcon YM-30 (Millipore Corp.), and the concentrate was replaced by a dialysis buffer (25 mM Hepes-KOH, 5 mM MgCl2, 50 mM KCl, 1 mM DTT, 5% glycerol (pH 7.5)). Moreover, the protein concentration was determined by the Bradford method using Protein Assay (BIO-RAD LABORATORIES INC.).
Example 2
[Confirmation of RNP Complex Formation by EMSA (Electrophoretic Mobility Shift Assay)]
[EMSA on Box C/D, Box C/D Mini, and Box C/D Minimut]
The reaction of L7Ae with Box C/D, Box C/D mini, or Box C/D minimut was performed at a final concentration of 10 nM, 25 nM, or 25 nM RNA, respectively. The reaction was performed as follows under conditions involving 10 nM or 25 nM RNA, 20 mM Hepes-KOH, 150 mM KCl, 1.5 mM MgCl2, 2 mM DTT, 0.001 U/mL tRNA, 3% glycerol, and 0 to 500 nM protein. First, 1 μL of 32P-labeled RNA was denatured at 80° C. for 5 minutes and then supplemented with 4 μL of 5× binding buffer (100 mM Hepes-KOH (pH 7.5), 750 mM KCl, 7.5 mM MgCl2, 10 mM DTT, 0.005 U/ρL tRNA, 15% glycerol) and ultrapure water. Then, the solution was mixed with the protein to adjust the whole amount to 20 μL. The reaction solution was left on ice for 60 minutes. 2 μL of dye (0.25% BPB, 0.25% XC, 30% glycerol) was added thereto, and the mixture was electrophoresed on a 8% nondenaturing polyacrylamide gel at 4° C. for 3 to 4 hours. Then, the gel was dried for 1 hour using a gel drier and analyzed for its radiation dose intensity using Bio-Imaging Analyzer (BAS2500; FUJIFILM) (FIGS. 4 and 5).
As a result, both Box C/D and Box C/D mini were confirmed to increase the band in an L7Ae protein concentration-dependent manner. This indicates that Box C/D or Box C/D mini binds to L7Ae. On the contrary, no such increase in band was seen in the mutant Box C/D minimut, demonstrating that it does not bind to L7Ae at these protein concentrations.
[EMSA on Domain 234 and Domain 2]
The reaction of ThrRS with Domain 234 or Domain 2 was performed as follows under conditions involving final concentrations of 20 nM RNA, 25 mM Hepes-KOH, 50 mM KCl, 5 mM MgCl2, 1 mM DTT, 5% glycerol, and 0 to 40 μM protein. First, 4 μL of 200 nM 32P-labeled RNA was denatured at 80° C. for 5 minutes and then supplemented with 4 μL of 5× binding buffer (75 mM Hepes-KOH, 250 mM KCl, 25 mM MgCl2, 5 mM DTT, 25% glycerol) and ultrapure water. Then, the solution was mixed with the protein to adjust the whole amount to 20 μL. The reaction solution was left on ice for 60 minutes. 2 μL of dye (0.25% BPB, 0.25% XC, 30% glycerol) was added thereto, and the mixture was electrophoresed on a 12% nondenaturing polyacrylamide gel at 4° C. for 3 to 4 hours. Then, the gel was dried for 1 hour using a gel drier and analyzed for its radiation dose intensity using Bio-Imaging Analyzer (BAS2500; FUJIFILM) (FIGS. 6 and 7).
As a result, both ThrRS Domain 234 and ThrRS Domain 2 were confirmed to increase the band in a ThrRS protein concentration-dependent manner. This indicates that ThrRS Domain 234 or Domain 2 binds to ThrRS. Particularly, a supershifted band was seen in the ThrRS Domain 2. This suggests that ThrRS bound to Domain 2 was dimerized. As is also evident from the degree of band smear, Domain 234 has stronger binding than only Domain 2.
Example 3
[Preparation of Original EGFP and Protein-Responsive Artificial RNA Switches]
Original EGFP and protein-responsive artificial RNAs were prepared by performing PCR twice or three times using pEGFP (Clontech).
[Preparation of Original EGFP]
pEGFP was used as a template to perform 1st PCR using EGFP 1st Fwd (5′-AAGGAGATATACCAATGGTGAGCAAGGGCGAG-3′) (SEQ ID NO: 20) and EGFP Rev (5′-TATTCATTACCCGGCGGCGGTCACGAA-3′) (SEQ ID NO: 22) as primers. 50 μL of reaction solution contained a mixture of 1 ng of template, 1.5 μL of 10 μM each DNA primers, 5 μL of 2 mM dNTPs, 5 μL of 10×KOD-PLUS-buffer ver. 2, 2 μL of 25 mM MgSO4, and 1 μL of KOD-PLUS-DNA polymerase. Reaction was performed by initially performing incubation at 94° C. for 2 minutes and then 20 cycles each involving 94° C. for 15 seconds, 50° C. for 30 seconds, and 68° C. for 1 minute.
In the description below, only a template and primers will be shown because PCR was performed under the same conditions as above.
After the reaction, the reaction solution was subjected to phenol treatment and ethanol precipitation and dissolved in a nondenaturing dye (30% glycerin, 0.075% xylene cyanol, 0.075% bromophenol blue, 69.85% ultrapure water). The band of interest was separated and excised using low melting point agarose SEAPLAQUE GTG AGAROSE (FMC Corp.). The excised agarose fragment was supplemented with 200 μL of TE, then incubated at 65° C. for 30 minutes, and then subjected to 3 phenol treatments, diethyl ether treatment, and ethanol precipitation for DNA purification.
Next, the product was used as a template to perform 2nd PCR using Universal primer (5′-GAAATTAATACGACTCACTATAGGGAGACCACAACGGTTTCCCTCTAGAAATAAT TTTGTTTAACTTTAAGAAGGAGATATACCA-3′) (SEQ ID NO: 21) and EGFP Rev as primers. After the reaction, separation and purification were performed in the same way as above, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 23). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). The transcription reaction using MEGAscript was performed in the same way as in MEGAshortscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 24) obtained through the transcription reaction was purified using RNeasy MinElute (trademark) Cleanup Kit (QIAGEN GmbH). The purification using RNeasy MinElute (trademark) Cleanup Kit was performed as follows.
The transcription reaction solution was adjusted to 100 μL by the addition of 80 μL of ultrapure water, further supplemented with 350 μL of Buffer RLT, and sufficiently mixed. 250 μL of ethanol was added thereto and completely mixed by pipetting. The sample was applied to RNeasy MinElute Spin Column loaded in a 2-mL collection tube and centrifuged at 10,000 rpm for 15 seconds using a high-speed refrigerated microcentrifuge MX-100 (TOMY SEIKO CO., LTD.), and the flow-through fraction was discarded. The spin column was transferred to a new 2-mL collection tube, and 500 μL of Buffer RPE was added onto the spin column using a pipette. The sample was centrifuged at 10,000 rpm for 15 seconds, and the flow-through fraction was discarded. After addition of 500 μL of 80% ethanol to the RNeasy MinElute Spin Column, the sample was centrifuged at 10,000 rpm for 2 minutes, and the flow-through fraction was discarded. The RNeasy MinElute Spin Column was transferred to a new 2-mL collection tube. The sample was centrifuged at 14,000 rpm for 5 minutes with the spin column cap opened, and the flow-through fraction was discarded. The spin column was transferred to a new 1.5-mL collection tube, and 20 μL of ultrapure water was added to the center of the silica gel membrane. The sample was centrifuged at 14,000 rpm for 5 minutes for elution. This eluate was used in concentration measurement using DU640 SPECTROPHOTOMETER.
[Preparation of L7-UTR2]
The EGFP 1st PCR product was used as a template to perform 2nd PCR using L7-UTR2 2nd Fwd (5′-GGAGACCACAACGGTTTCCCTCGGGCGTGATGCGAAAGCTGACCCAGAAGGAGA TATACCAATGGTGAGC-3′) (SEQ ID NO: 25) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using stem-loop primer (5′-GAAATTAATACGACTCACTATAGGGAGACCACAACGGTTTCC-3′) (SEQ ID NO: 26) and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 27). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 28) obtained through the transcription reaction was purified using RNeasy MinElute (trademark) Cleanup Kit (QIAGEN GmbH), followed by concentration measurement.
[Preparation of L7-UTR5]
The EGFP 1st PCR product was used as a template to perform 2nd PCR using L7-UTR5 2nd Fwd (5′-GGAGACCACAACGGTTTCCCTCGGGCGTGATGCGAAAGCTGACCCTTAAGAAGG AGATATACCAATGGTGAGC-3′) (SEQ ID NO: 29) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using stem-loop primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 30). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 31) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of L7-UTR9]
The EGFP 1st PCR product was used as a template to perform 2nd PCR using L7-UTR9 2nd Fwd (5′-GGAGACCACAACGGTTTCCCTCGGGCGTGATGCGAAAGCTGACCCAACTTTAAGA AGGAGATATACCAATGGTGAGC-3′) (SEQ ID NO: 32) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using stem-loop primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 33). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 34) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of L7-UTR13]
The EGFP 1st PCR product was used as a template to perform 2nd PCR using L7-UTR13 2nd Fwd (5′-GGAGACCACAACGGTTTCCCTCGGGCGTGATGCGAAAGCTGACCCGTTTAACTTT AAGAAGGAGATATACCAATGGTGAGC-3′) (SEQ ID NO: 35) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using stem-loop primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 36). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 37) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of L7-UTR2 Mut]
The EGFP 1st PCR product was used as a template to perform 2nd PCR using L7-UTR2 mut 2nd Fwd (5′-GGAGACCACAACGGTTTCCCTCGGGCGTCATGCGAAAGCTGCCCCAGAAGGAGA TATACCAATGGTGAGC-3′) (SEQ ID NO: 38) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using stem-loop primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 39). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 40) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of L7-UTR2 Minimut]
The EGFP 1st PCR product was used as a template to perform 2nd PCR using L7-UTR2 minimut 2nd Fwd (5′-GGAGACCACAACGGTTTCCCTCGGGGAAACCCAGAAGGAGATATACCAATGGTG AGC-3′) (SEQ ID NO: 41) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using stem-loop primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 42). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 43) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of L7-ORF (Box C/D GFP)]
pEGFP was used as a template to perform 1st PCR using L7-ORF 1st Fwd (5′-AAGGAGATATACCAATGGGGCGTGATGCGAAAGCTGACCCTGTGAGCAAGGGCG AGGAG-3′) (SEQ ID NO: 44) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 2nd PCR using Universal primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 45). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 46) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of L7-ORF Mut (Box C/D Mut GFP)]
pEGFP was used as a template to perform 1st PCR using L7-ORF mut 1st Fwd (5′-AAGGAGATATACCAATGAGGGGAAACCCAGTGAGCAAGGGCGAGGAG-3′) (SEQ ID NO: 47) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 2nd PCR using Universal primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 48). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 49) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of ThrRS-UTRW]
pEGFP was used as a template to perform 1st PCR using ThrRS-UTRW 1st Fwd (5′-GTGATCTTTCGTGTGGGTCACCACTGCAAATAAGGATATAAAATGGTGAGCAAGG GCGAG-3′) (SEQ ID NO: 50) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 2nd PCR using ThrRS Domain 234 template and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using ThrRS Domain 234 Fwd and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 51). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 52) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of ThrRS-UTR2]
The EGFP 1st PCR product was used as a template to perform 2nd PCR using ThrRS-UTR2 2nd Fwd (5′-GGAGACCACAACGGTTTCCCTCGGCGTATGTGATCTTTCGTGTGGGTCACCACTG CGCCAGAAGGAGATATACCAATGGTG-3′) (SEQ ID NO: 53) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using stem-loop primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 54). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 55) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of ThrRS-UTR2 Mut]
The EGFP 1st PCR product was used as a template to perform 2nd PCR using ThrRS-UTR2 mut 2nd Fwd (5′-GGAGACCACAACGGTTTCCCTCGGCGTATGTGATCTTTCATGTGGGTCACCACTG CGCCAGAAGGAGATATACCAATGGTG-3′) (SEQ ID NO: 56) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 3rd PCR using stem-loop primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 57). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 58) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of ON Switch]
pEGFP was used as a template to perform 1st PCR using ON switch 1st Fwd (5′-AAGGAGATATACCAATGCAGCTTTCGCATCACGTGAGCAAGGGCGAGGAG-3′) (SEQ ID NO: 59) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 2nd PCR using Universal primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 60). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 61) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement. This RNA had, in the open reading frame (ORF), an insert of a sequence to be hybridized with antisence shown below.
[Preparation of Antisence]
Antisence was prepared using T7 primer and antisence primer (5′-GGTGGGTCAGCTTTCGCATCACGCCCACCTATAGTGAGTCGTATTAGC-3′) (SEQ ID NO: 62), and MEGAshortscript (trademark) (Ambion, Inc.). This antisence contains therein an L7Ae-binding site (Box C/D mini). After the reaction, the reaction product was purified (SEQ ID NO: 63) by electrophoresis on a 15% polyacrylamide (29:1) denaturing gel in the same way as in Box C/D mini.
Example 4
[Translational Regulation Assay on L7-UTR]
Translational regulation assay on L7-UTR was conducted using PURE system (Post Genome Institute Co., Ltd.). All ON-to-OFF translational regulations were assayed as follows. First, 5 μL of Solution A, 1 μL of 3.75 μM RNA, and the protein were mixed and adjusted with ultrapure water to the whole amount of 8 μL. The solution was left at 4° C. for 1 hour. Then, 2 μL of Solution B was added thereto and reacted at 37° C. for 75 minutes. After the reaction, the solution was adjusted with ultrapure water to 200 μL and measured at an excitation wavelength of 485 nm and an absorption wavelength of 535 nm using infinite F200 (TECAN Trading AG). The secondary structure of EGFP UTR used as a control is shown in FIG. 8A. The secondary structure of L7-UTR2 is shown in FIG. 8B; the secondary structure of L7-UTR5 is shown in FIG. 8E; the secondary structure of L7-UTR9 is shown in FIG. 8F; and the secondary structure of L7-UTR13 is shown in FIG. 8G. In these diagrams, reference numeral 4 depicts an open reading frame; reference numeral 3 depicts a ribosome-binding site; reference numeral 2 depicts an RNA-protein complex interacting motif-derived nucleotide sequence; and reference numeral 7 depicts an enhancer. All the RNAs had an L7Ae-binding motif (Box C/D) nucleotide sequence inserted in EGFP 5′-UTR and were designed to have a distance of 2 bases, 5 bases, 9 bases, or 13 bases between the RBS and the motif.
As is evident from the assay results, the incorporation of the L7Ae motif inhibits translation in response to increase in protein concentration. As is also evident, translational inhibitory effect decreases depending on the distance between the motif and the RBS (FIG. 9). The secondary structure of L7-UTR2 mut of L7Ae is shown in FIG. 8C, and the secondary structure of L7-UTR2 minimut is shown in FIG. 8D. These had a mutation in the L7Ae-binding site of L7-UTR2. Although slight translational inhibition was also observed in these mutants, this translational inhibitory effect was shown to be smaller than that in L7-UTR2 (FIG. 10).
Competition assay using L7-UTR2 was conducted using Box C/D as a competitor. Specifically, 5 μL of Solution A, 1 μL of 3.75 μM RNA, 1 μL of 10 to 100 μM competitor, and 1 μL of 50 μM protein were mixed and adjusted with ultrapure water to the whole amount of 8 μL. The solution was left at 4° C. for 1 hour. Then, 2 μL of Solution B was added thereto and reacted at 37° C. for 75 minutes. After the reaction, measurement was performed in the same way as above. As is evident from the results, the efficiency of translation decreased due to the addition of the protein shows recovery by the addition of the competitor Box C/D. This result suggests that this translational inhibition is influenced by L7Ae and the L7Ae-binding site (FIG. 11). These assay results indicated that ribosome binding to the mRNA can be regulated by the steric hindrance of the protein as designed.
[Translational Regulation Assay on ThrRS-UTR]
The same assay as in L7-UTR was conducted on ThrRS-UTR. Assay conditions were the same as in L7-UTR. The secondary structures of ThrRS-UTRW, ThrRS-UTR2, and ThrRS-UTR2 mut are shown in FIG. 12. In these diagram, reference numeral 4 depicts an open reading frame; reference numeral 3 depicts a ribosome-binding site; and reference numeral 2 depicts an RNA-protein complex interacting motif-derived nucleotide sequence. As in L7-UTR, each protein-binding RNA was inserted in 5′-UTR: in ThrRS-UTRW (FIG. 12A), Domain 234 was inserted in 5′-UTR; and in ThrRS-UTR2 (FIG. 12B), Domain 2 was inserted in 5′-UTR. ThrRS-UTR2 mut (FIG. 12C) had a mutation in the ThrRS-binding site (Domain 2) of ThrRS-UTR2 and was used as a mutant.
As is evident from the results, translation is inhibited depending on the concentration of the ThrRS protein. ThrRS-UTRW had larger inhibitory effect than that of ThrRS-UTR2, owing to difference in binding affinity. Moreover, as in L7-UTR, smaller translational inhibitory effect was observed in the mutant (FIG. 13). These results indicated that for ON-to-OFF translational regulation, the input protein can be selected arbitrarily by exchanging the protein-binding motif on the mRNA.
[Translational Regulation Assay on L7-ORF (Box C/D GFP)]
The same assay as above was conducted on L7-ORF (Box C/D GFP). Assay conditions were the same as in L7-UTR. The secondary structures of L7-ORF (Box C/D GFP) and L7-ORF mut (Box C/D mut GFP) are shown in FIG. 14. In these diagram, reference numeral 4 depicts an open reading frame; reference numeral 3 depicts a ribosome-binding site; reference numeral 2 depicts an RNA-protein complex interacting motif-derived nucleotide sequence; and reference numeral 7 depicts an enhancer. Unlike L7-UTR, each protein-binding RNA motif was inserted in ORF: in L7-ORF (Box C/D GFP) (FIG. 14A), the L7Ae-binding site (Box C/D) was inserted in ORF immediately after the start codon; and in L7-ORF mut (Box C/D mut GFP) (FIG. 14B) used as a mutant, Stem-Loop was inserted in this site. As a result, translation is inhibited with increase in the concentration of the L7Ae protein. Moreover, as in L7-UTR and ThrRS-UTR, smaller translational inhibitory effect was shown in the mutant. These results indicated that the L7Ae protein bound to the mRNA open reading frame inhibits ribosome entry (FIG. 15).
[Translational Regulation Assay on ON Switch]
To assay OFF-to-ON translational regulation, 5 μL of Solution A, 1 μL of 500 nM RNA, 1 μL of 10 μM antisence RNA, and the protein were mixed and adjusted with ultrapure water to the whole amount of 8 μL. The solution was heat-treated at 60° C. for 3 minutes and immediately cooled on ice. After the 15-minute cooling on ice, 2 μL of Solution B was added thereto and reacted at 37° C. for 75 minutes. After the reaction, measurement was performed in the same way as above. As a result, the translation inhibited due to the addition of antisence RNA showed a recovery by the addition of the protein (FIG. 16). This is probably because L7Ae binding to antisence RNA represses the translational inhibition.
Example 5
Next, to demonstrate that the output gene is arbitrarily changed, Example is shown, in which translational regulation was performed with a red fluorescent protein DsRed-Express (DsRed-Ex) as a target, while the translational regulation/activation of two different genes was simultaneously promoted.
[Preparation of Control DsRed-Ex and Protein-Responsive Artificial RNA Switch]
Control DsRed-Ex and a protein-responsive artificial RNA were prepared by performing twice PCR using pDsRed-Ex vectors (Clontech).
[Preparation of Control DsRed-Ex]
pDsRed Ex was used as a template to perform 1st PCR using DsRed Ex 1st Fwd (5′-AAGGAGATATACCAATGGCCTCCTCCGAGGAC-3′) (SEQ ID NO: 68) and DsRed Ex Rev (5′-TATTCATTACTACAGGAACAGGTGGTGGC-3′) (SEQ ID NO: 69) as primers. 50 μL of reaction solution contained a mixture of 1 ng of template, 1.5 μL of 10 μM each DNA primers, 5 μL of 2 mM dNTPs, 5 μL of 10×KOD-PLUS-buffer ver. 2, 2 μL of 25 mM MgSO4, and 1 μL of KOD-PLUS-DNA polymerase. Reaction was performed by initially performing incubation at 94° C. for 2 minutes and then 20 cycles each involving 94° C. for 15 seconds, 50° C. for 30 seconds, and 68° C. for 1 minute.
In the description below, only a template and primers will be shown because PCR was performed under the same conditions as above. After the reaction, the reaction solution was subjected to phenol treatment and ethanol precipitation and dissolved in a nondenaturing dye (30% glycerin, 0.075% xylene cyanol, 0.075% bromophenol blue, 69.85% ultrapure water). The band of interest was separated and excised using low melting point agarose SEAPLAQUE GTG AGAROSE (FMC Corp.). The excised agarose fragment was supplemented with 200 μL of TE, then incubated at 65° C. for 30 minutes, and then subjected to 3 phenol treatments, diethyl ether treatment, and ethanol precipitation for DNA purification.
Next, the product was used as a template to perform 2nd PCR using Universal primer (5′-GAAATTAATACGACTCACTATAGGGAGACCACAACGGTTTCCCTCTAGAAATAAT TTTGTTTAACTTTAAGAAGGAGATATACCA-3′) (SEQ ID NO: 21) and DsRed Ex Rev as primers. After the reaction, separation and purification were performed in the same way as above, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 70). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). The transcription reaction using MEGAscript was performed in the same way as in MEGAshortscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 71) obtained through the transcription reaction was purified using RNeasy MinElute (trademark) Cleanup Kit (QIAGEN GmbH). The purification using RNeasy MinElute (trademark) Cleanup Kit was performed as follows.
The transcription reaction solution was adjusted to 100 μl by the addition of 80 μL of ultrapure water, further supplemented with 350 μL of Buffer RLT, and sufficiently mixed. 250 μL of ethanol was added thereto and completely mixed by pipetting. The sample was applied to RNeasy MinElute Spin Column loaded in a 2-mL collection tube and centrifuged at 10,000 rpm for 15 seconds using a high-speed refrigerated microcentrifuge MX-100 (TOMY SEIKO CO., LTD.), and the flow-through fraction was discarded. The spin column was transferred to a new 2-mL collection tube, and 500 μL of Buffer RPE was added onto the spin column using a pipette. The sample was centrifuged at 10,000 rpm for 15 seconds, and the flow-through fraction was discarded. After addition of 500 μL of 80% ethanol to the RNeasy MinElute Spin Column, the sample was centrifuged at 10,000 rpm for 2 minutes, and the flow-through fraction was discarded. The RNeasy MinElute Spin Column was transferred to a new 2-mL collection tube. The sample was centrifuged at 14,000 rpm for 5 minutes with the spin column cap opened, and the flow-through fraction was discarded. The spin column was transferred to a new 1.5-mL collection tube, and 20 μL of ultrapure water was added to the center of the silica gel membrane. The sample was centrifuged at 14,000 rpm for 5 minutes for elution. This eluate was used in concentration measurement using DU640 SPECTROPHOTOMETER.
[Preparation of Box C/D-DsRed-Ex]
pDsRed Ex was used as a template to perform 1st PCR using Box C/D-DsRed-Ex 1st Fwd (5′-AAGGAGATATACCAATGGGGCGTGATGCGAAAGCTGACCCTGCCTCCTCCGAGG ACGTC-3′) (SEQ ID NO: 72) and DsRed Ex Rev as primers. Next, the resulting product was used as a template to perform 2nd PCR using Universal primer and DsRed Ex Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 73). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 74) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of Box C/D Mutant-DsRed-Ex]
pDsRed Ex was used as a template to perform 1st PCR using Box C/D mutant 1st Fwd (5′-AAGGAGATATACCAATGAGGGGAAACCCAGCCTCCTCCGAGGACGTC-3′) (SEQ ID NO: 75) and DsRed Ex Rev as primers. Next, the resulting product was used as a template to perform 2nd PCR using Universal primer and DsRed Ex Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 76). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 77) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement.
[Preparation of ON Switch]
pEGFP was used as a template to perform 1st PCR using ON switch 1st Fwd (5′-AAGGAGATATACCAATGCAGCTTTCGCATCACGTGAGCAAGGGCGAGGAG-3′) (SEQ ID NO: 59) and EGFP Rev as primers. Next, the resulting product was used as a template to perform 2nd PCR using Universal primer and EGFP Rev as primers. After the reaction, separation and purification were performed, and the purification product was dissolved in ultrapure water. The solution was used as a template for transcription reaction (SEQ ID NO: 60). Transcription reaction was performed using MEGAscript (trademark) (Ambion, Inc.). RNA (SEQ ID NO: 61) obtained through the transcription reaction was purified in the same way as above, followed by concentration measurement. This RNA had, in the open reading frame (ORF), an insert of a sequence to be hybridized with antisence shown below.
[Preparation of Antisence 25 Mer]
Antisence 25 mer was prepared using T7 primer and antisence 25 mer primer (5′-GGGGTCAGCTTTCGCATCACGCCCCTATAGTGAGTCGTATTAGC-3′) (SEQ ID NO: 78), and MEGAshortscript (trademark) (Ambion, Inc.). This antisence contains therein an L7Ae-binding site (Box C/D mini). After the reaction, the reaction product was purified by electrophoresis on a 15% polyacrylamide (29:1) denaturing gel in the same way as in Box C/D mini.
[Translational Regulation Assay on Box C/D-DsRed-Ex]
Translational regulation assay on Box C/D-DsRed-Ex was conducted using PURE system (Post Genome Institute Co., Ltd.). All ON-to-OFF translational regulations were assayed as follows. First, 5 μL of Solution A, 1 μL of 3.75 μM RNA, and the protein were mixed and adjusted with ultrapure water to the whole amount of 8 μL. The solution was left at 4° C. for 1 hour. Then, 2 μL of Solution B was added thereto and reacted at 37° C. for 75 minutes. After the reaction, the solution was adjusted with ultrapure water to 200 μL and measured at an excitation wavelength of 535 nm and an absorption wavelength of 595 nm using infinite F200 (TECAN Trading AG). The secondary structure of Box C/D-DsRed-Ex is shown in FIG. 17(a). Moreover, the secondary structure of DsRed-Ex used as a control is shown in FIG. 17(c). In these diagram, reference numeral 3 depicts a ribosome-binding site, and reference numeral 2 depicts an RNA-protein complex interacting motif-derived nucleotide sequence.
As is evident from the assay results, the incorporation of the L7Ae-binding Box C/D motif within the 5′ region of mRNA ORF inhibits translation in response to increase in protein concentration. The secondary structure of Box C/D mut-DsRed-Ex is shown in FIG. 17(b). This had a mutation in the L7Ae-binding site (Box C/D motif) of Box C/D-DsRed-Ex. FIG. 18 shows an added L7Ae concentration-dependent fluorescence intensity ratio to 0 μM L7Ae-derived fluorescence intensity defined as 1. Although slight translational inhibition was observed in the controls DsRed-Ex and Box C/D mut-DsRed-Ex using the high concentrations of L7Ae (5 to 10 μM), this translational inhibitory effect was shown to be significantly smaller than that in Box C/D-DsRed-Ex.
[Simultaneous Translational Regulation Assay on ON Switch and Box C/D-DsRed-Ex]
To assay the EGFP gene-targeting simultaneous translational regulation of ON switch and Box C/D-DsRed-Ex, 5 μL of Solution A, 0.5 μL of 1 μM ON switch RNA (SEQ ID NO: 61), 1 μL of 3.75 μM Box C/D-DsRed-Ex RNA (SEQ ID NO: 74), 0.5 μL of 20 μM antisence 25 mer (SEQ ID NO: 63), and the L7Ae protein (SEQ ID NO: 66) were mixed and adjusted with ultrapure water to the whole amount of 8 μL. The solution was heat-treated at 70° C. for 3 minutes and immediately cooled on ice. After the 15-minute cooling on ice, 2 μL of Solution B was added thereto and reacted at 37° C. for 75 minutes. After the reaction, the solution was adjusted with ultrapure water to 200 μL and measured at an excitation wavelength of 485 nm and an absorption wavelength of 535 nm using infinite F200 (TECAN Trading AG). Further, the solution was measured at an excitation wavelength of 535 nm and an absorption wavelength of 595 nm using infinite F200 (TECAN Trading AG). The results are shown in FIG. 19. As a result, the translation of ON switch RNA inhibited due to the addition of antisence RNA (this inhibition was confirmed based on EGFP expression) showed a recovery by the addition of the L7Ae protein, whereas the translation of Box C/D-DsRed-Ex was repressed by the addition of the L7Ae protein. This indicates that the addition of the protein of one kind could simultaneously regulate the translations of two different mRNAs in opposite directions (translational repression/activation).
[Preparation of pcDNA-L7Ae by Restriction Enzyme Treatment]
pL7Ae was used as a template to perform PCR using Fwd (5′-CACCAAGCTTATGTACGTGAGATTTGAGGTTCC-3′) (SEQ ID NO: 79) and Rev (5′-CCGCTCGAGCTTCTGAAGGCCTTTAATTCTTC-3′) (SEQ ID NO: 80) as primers. 50 μL of reaction solution contained a mixture of 5 ng of template, 1.5 μL of 10 μM each DNA primers, 4 μL of 2.5 mM dNTPs, 5 μL of 10×KOD-PLUS-buffer ver. 2, 1.6 μL of 25 mM MgSO4, and 1 μL of KOD-PLUS-DNA polymerase. Reaction was performed by initially performing incubation at 94° C. for 2 minutes and then 25 cycles each involving 94° C. for 15 seconds, 52° C. for 30 seconds, and 68° C. for 1 minute. The reaction product was subjected to phenol treatment, diethyl ether treatment, and ethanol precipitation for DNA purification. This purification product was dissolved in 15 μL of ultrapure water. The solution was used as a template for restriction enzyme treatment. A total of 20 μL of system involving 5 μL of template, 2 μL of buffer, 1 μL of HindIII, 1 μL of XhoI, 2 μL of 10×BSA, and 9 μL of ultrapure water was incubated at 37° C. for 2 h. The band of interest was separated and excised using low melting point agarose SEAPLAQUE GTG AGAROSE (FMC Corp.). The excised agarose fragment was supplemented with 200 μL of TE, then incubated at 65° C. for 30 minutes, and then subjected to 2 phenol treatments, diethyl ether treatment, and ethanol precipitation for DNA purification. The same restriction enzyme treatment as above was also performed on pcDNA vectors (Invitrogen Corp.). A total of 20 μL of system involving 2 ng of template, 2 μL of buffer, 1 μL of HindIII, 1 μL of XhoI, 2 μL of 10×BSA, and 13 μL of ultrapure water was incubated at 37° C. for 2 h. The band of interest was separated and excised using low melting point agarose SEAPLAQUE GTG AGAROSE (FMC Corp.). The excised agarose fragment was supplemented with 200 μL of TE, then incubated at 65° C. for 30 minutes, and then subjected to phenol treatment, diethyl ether treatment, and ethanol precipitation for DNA purification. This purification product was dissolved in 10 μL of ultrapure water and used in BAP treatment. A total of 50 μL of system involving 10 μL of template, 33 μL of ultrapure water, 2 μL of BAP, and 5 μL of buffer was incubated at 37° C. for 2 h. The band of interest was separated and excised using low melting point agarose SEAPLAQUE GTG AGAROSE (FMC Corp.). The excised agarose fragment was supplemented with 200 μL of TE, then incubated at 65° C. for 30 minutes, and then subjected to 2 phenol treatments, diethyl ether treatment, and ethanol precipitation for DNA purification.
A total of 4 μL involving 1 μL of insert, 1 μL of vector, and 2 μL of Ligation High was incubated at 16° C. for 2 h, and JM109 was transformed with the ligation product. pcDNA-L7Ae was purified by miniprep.
[Preparation of Box C/D-GFP by Site-Directed Mutagenesis]
Full-length pEGFP-N1 (Clontech) plasmids were amplified as a template using phosphorylated primers and a high-fidelity PCR enzyme KOD-PLUS- (TOYOBO CO., LTD.). The PCR product was self-ligated using Ligation High (TOYOBO CO., LTD.) to prepare Box C/D-GFP. Fwd Box C/D-EGFP primer (5′-GGGCGTGATGCGAAAGCTGACCCTGTGAGCAAGGGCGAGGAGCTG-3′) (SEQ ID NO: 81) and Rev Box C/D-EGFP primer (5′-CATGGTGGCGACCGGTGGATC-3′) (SEQ ID NO: 82) were used. 50 μL of reaction solution contained a mixture of 5 ng of template, 1.5 μL of 10 μM each DNA primers, 4 μL of 2.5 mM dNTPs, 5 μL of 10×KOD-PLUS- buffer, and 1 μL of KOD-PLUS-DNA polymerase. Reaction was performed by initially performing incubation at 94° C. for 2 minutes and then 25 cycles each involving 98° C. for 10 seconds and 68° C. for 4 minutes. Next, the template plasmid was digested by the action of a restriction enzyme DpnI specifically decomposing methylated DNA. Further, the PCR product was self-circularized by self-ligation.
[Preparation of Box C/D Mut GFP by Site-Directed Mutagenesis]
Fwd Box C/D mut EGFP primer (5′-AGGGGAAACCCAGTGAGCAAGGGCGAGGAGCTG-3′) (SEQ ID NO: 83) was prepared and used in gene amplification with pEGFP-N1 (Clontech) plasmids as a template. The other procedures were performed in the same way as above to prepare Box C/D mut GFP.
Example 6
Western blotting was conducted for confirming L7Ae expression in cultured human cancer cells.
On the day before transfection, cervical cancer-derived HeLa cells were seeded at a concentration of 0.5×106 cells/well to a 6-well plate and cultured in a 37° C. CO2 incubator. Next day, the cells were transfected using Lipofectamine 2000 (trademark) (Invitrogen Corp.). The amount of pcDNA-A (FIG. 20) (SEQ ID NO: 84) or L7Ae expression vector pcDNA-L7Ae (SEQ ID NO: 85) (FIG. 21) added was set to 1 μg, 2 μg, and 4 μg. According to this amount, the amount of Lipofectamine 2000 was set to 2.5 μl, 5 μl, and 10 μl. These DNA-lipid complexes were incubated at room temperature for 20 minutes and added dropwise to the cells. In this context, the L7Ae expression vector pcDNA-L7Ae is a plasmid vector in which the L7Ae gene is inserted downstream of the CMV promoter of a pcDNA3.1 vector (Invitrogen Corp.). After 4 hours, medium replacement was performed.
29 hours after the transfection, the wells were washed twice with PBS and then supplemented with 300 μl of RIPA buffer (1×PBS, 1% NP40, 0.5% Sodium deoxycholate, 0.1% SDS), and the cells were dissociated from the wells using a cell scraper. The lysates were disrupted using a syringe equipped with 21G needle. After addition of 10 μl of 10 mg/ml PMSF, the mixture was left standing on ice for 30 minutes, and supernatants were collected by centrifugation (4° C., 15000 g, 20 min) Likewise, 53 hours after the transfection, proteins were collected. The protein concentration was determined by the Lowry method using DC-Protein Assay (BIO-RAD LABORATORIES INC.).
L7Ae was detected by western blotting. The proteins extracted from the cells were deployed by SDS-PAGE and subjected to western blotting. A primary antibody Anti-c-Myc (Ab-1) (Calbiochem) (1/500) and a secondary antibody Goat Anti-Mouse IgG (H+L)-HRP conjugate (BIO-RAD LABORATORIES INC.) (1/2000) were used. A color was developed using ECL Plus (trademark) (GE Healthcare) and detected using LAS3000 (FUJIFILM). From these results, L7Ae expression caused by pcDNA-L7Ae introduction could be confirmed in the HeLa cells. Protein extraction from cells and L7Ae detection shown below were performed in the same way as above. FIG. 22 is a diagram showing intracellular L7Ae expression. In the diagram, the lane 1 was supplemented with 4 μg of pcDNA-A:10 μl of Lipofectamine; the lane 2 was supplemented with 2 μg of pcDNA-A:5 μl of Lipofectamine; the lane 3 was supplemented with 1 μg of pcDNA-A:2.5 μl of Lipofectamine; the lane 4 was supplemented with 4 μg of pcDNA-L7Ae:10 μl of Lipofectamine; the lane 5 was supplemented with 2 μg of pcDNA-L7Ae:5 μl of Lipofectamine; and the lane 6 was supplemented with 1 μg of pcDNA-L7Ae:2.5 μl of Lipofectamine. This diagram demonstrated that L7Ae is expressed within human cancer cells 29 hours after the transfection. Even 53 hours after the transfection, its expression was confirmed, though the expression level was decreased.
To evaluate the influence of L7Ae expression on cytotoxicity, WST1 assay was conducted. On the day before transfection, HeLa cells were seeded at a concentration of 1.0×104 cells/well to a 96-well plate and cultured in a 37° C. CO2 incubator. Next day, the cells were transfected using Lipofectamine 2000 (trademark) (Invitrogen Corp.). The amount of pcDNA-A or pcDNA-L7Ae added was set to 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, and 0.40 μg, and 0.25 μl of Lipofectamine 2000 was added to each sample. These DNA-lipid complexes were incubated at room temperature for 20 minutes and added dropwise to the cells. After 4 hours, medium replacement was performed. 24 hours after the transfection, the number of live cells was measured by WST1 assay using Cell Proliferation Reagent WST-1 (trademark) (Roche Diagnostics Corp.). It was shown that L7Ae expression has no cytotoxicity within this time. FIG. 23 is a diagram showing that L7Ae expression has no cytotoxicity 24 hours after the transfection.
The L7Ae-dependent repression of Box C/D-GFP protein expression was measured by western blotting.
On the day before transfection, HeLa cells were seeded at a concentration of 0.5×106 cells/well to a 6-well plate and cultured in a 37° C. CO2 incubator. Next day, the cells were transfected using Lipofectamine 2000 (trademark) (Invitrogen Corp.). 0, 0.5, 1.0, 1.5, or 2.0 μg of pcDNA-L7Ae was added to 1.0 μg of Box C/D-GFP (FIG. 24) (SEQ ID NO: 86) or Box C/D mut GFP (FIG. 25) (SEQ ID NO: 87), and 5 μl of Lipofectamine 2000 was added to each sample. These DNA-lipid complexes were incubated at room temperature for 20 minutes and added dropwise to the cells. After 4 hours, medium replacement was performed. 24 hours after the transfection, proteins were extracted in the same way as above, and L7Ae (FIG. 26) and EGFP (FIG. 27) were detected by western blotting. A primary antibody GFP (B-2) SC9996 (Santa Cruz Biotechnology, Inc.) (1/200) and a secondary antibody Goat Anti-Mouse IgG (H+L)-HRP conjugate (BIO-RAD LABORATORIES INC.) (1/2000) were used for EGFP. The L7Ae expression-dependent repression of EGFP expression specific for Box C/D-GFP could be confirmed. FIG. 26 is a diagram showing L7Ae expression. From this diagram, the coexpression of L7Ae with Box C/D-GFP or Box C/D mut GFP could be confirmed by western blotting to exhibit no difference in L7Ae expression level therebetween. FIG. 27 is a diagram showing L7Ae-dependent translational repression of EGFP. As is evident from this diagram, the expression of pcDNA-L7Ae significantly represses Box C/D-GFP expression. On the other hand, these results demonstrated that expression repressive effect on Box C/D mut GFP is smaller than that on Box C/D-GFP.
Moreover, the bands obtained by western blotting were analyzed using LAS3000 (FUJIFILM) and Multi Gauge Ver 3.0 (FUJIFILM). The value of 1.0 μg of Box C/D-GFP or Box C/D mut GFP supplemented with 0.5 μg of pcDNA-L7Ae (+) was calculated with that free from pcDNA-L7Ae (−) defined as 1. The results of this quantification by western blotting are shown in FIG. 28.
The L7Ae-dependent repression of protein expression was measured by FACS.
On the day before transfection, HeLa cells were seeded at a concentration of 0.5×105 cells/well to a 24-well plate and cultured in a 37° C. CO2 incubator. Next day, the cells were transfected using Lipofectamine 2000 (trademark) (Invitrogen Corp.). 0, 0.05, 0.10, 0.15, 0.20, 0.40, 0.80, or 1.60 μg of pcDNA-A or pcDNA-L7Ae was added to 0.2 μg of Box C/D-GFP or Box C/D mut GFP, and 1 μl of Lipofectamine 2000 was added to each sample. These DNA-lipid complexes were incubated at room temperature for 20 minutes and added dropwise to the cells. After 4 hours, medium replacement was performed.
24 hours after the transfection, the medium was discarded, and the cells were dissociated from the wells using 200 μl of Trypsin EDTA and supplemented with 200 μl of DMEM/F12. The mixture was transferred to a FACS tube and analyzed using FACS Aria (BD). In this context, FACS is a method which involves irradiating free cells passing through a thin tube with laser beam and analyzing cell fractionation based on the intensity of fluorescence generated from the cells. Here, live cells were gated, and 10000 cells were measured by FITC. The results demonstrated that the repression of EGFP expression occurs in a manner specific for the cells transfected with pcDNA-L7Ae and Box C/D-GFP. More detailed analysis was achieved by comparison with the western blotting results. FIG. 29 is a graph showing the measurement results. In the diagram, Mock represents those transfected with only Lipofectamine 2000 (trademark) (Invitrogen Corp.) without the addition of DNA; and 0, 0.10, 0.20, or 0.80 μg of pcDNA-A (shown in the left columns) or pcDNA-L7Ae (shown in the right columns) was added to Box C/D-GFP (solid line) and Box C/D mut GFP (dotted line) fixed to 0.2 μg. FIG. 30 shows results of quantifying L7Ae expression-dependent repression specific for Box C/D-GFP translation by analysis based on the FACS data of FIG. 29.
Next, change in mRNA level during the L7Ae-dependent repression of protein expression was measured by real-time PCR.
On the day before transfection, HeLa cells were seeded at a concentration of 0.5×106 cells/well to a 6-well plate and cultured in a 37° C. CO2 incubator. 0, 0.5, 1.0, or 2.0 μg of pcDNA-L7Ae was added to 1.0 μg of Box C/D-GFP or Box C/D mut GFP, and 5 μl of Lipofectamine 2000 was added to each sample. Moreover, 0, 0.5, 1.0, or 2.0 μg of pcDNA-L7Ae or pcDNA-A was added to 1.0 μg of Box C/D-GFP, and 5 μl of Lipofectamine 2000 was added to each sample. These DNA-lipid complexes were incubated at room temperature for 20 minutes and added dropwise to the cells. After 4 hours, medium replacement was performed. 24 hours after the transfection, RNA extraction and DNA removal were performed using RNAqueous 4PCR Kit (trademark) (Ambion, Inc.).
1.5 μg (or 0.5 μg) of the extracted RNA was used as a template to synthesize cDNA using High-Capacity cDNA Reverse Transcription Kits (trademark) (Applied Biosystems Inc.), random primers, and reverse transcriptase. Real-time PCR was performed by the intercalation method using 1/20000 diluted cDNA as a template and LightCycler 480 SYBR Green I Master (trademark) (Roche Diagnostics Corp.). PCR reaction and real-time fluorescence detection were performed using LightCycler 480 (trademark) (Roche Diagnostics Corp.). Reaction conditions involved an initial denaturation step set to 95° C. for 5 minutes and an amplification step set to 95° C. for 10 seconds in denaturation, 60° C. for 10 seconds in annealing, and 72° C. for 3 seconds in extension, and this cycle was performed 45 times. Melting curve analysis was conducted at 95° C. for 5 seconds in denaturation, 65° C. for 15 seconds in annealing, and target temperature set to 98° C., and finally, the reaction solution was cooled at 50° C. for 10 seconds to terminate the measurement. The Ct value was determined by the Second Derivative Maximum method. The target EGFP gene was amplified using 481P Fwd (5′-CAAGGAGGACGGCAACA-3′) (SEQ ID NO: 88) and Rev (5′-CCTTGATGCCGTTCTTCTGC-3′) (SEQ ID NO: 89). A reference gene GAPDH was amplified using GAPDH Fwd (5′-AGCCACATCGCTCAGACAC-3′) (SEQ ID NO: 90) and Rev (5′-GCCCAATACGACCAAATCC-3′) (SEQ ID NO: 91). The amplification product was confirmed to be a single target product by melting curve analysis and electrophoresis. The results were evaluated by relative quantification. The amount of EGFP was normalized with GAPDH, and the normalized value was used in comparison among samples with a sample supplemented only with Box C/D-GFP (or Box C/D mut GFP) defined as 1. It was shown that the difference in expression level among the samples is within 2 times. From these results, no change in the mRNA level of L7Ae-specific Box C/D-GFP was confirmed, demonstrating that L7Ae does not regulate the transcription level of Box C/D-GFP mRNA.
FIG. 31 is a graph showing Box C/D-GFP mRNA level comparison among samples (samples derived from Box C/D-GFP and pcDNA-L7Ae and samples derived from Box C/D-GFP and pcDNA-A) with a sample derived from only Box C/D-GFP as 1. 0, 0.5, 1.0, or 2.0 μg of pcDNA-L7Ae or pcDNA-A was added to Box C/D-GFP fixed to 1.0 μg. The left bars represent the results from pcDNA-L7Ae added to Box C/D-GFP, and the right bars represent the results from pcDNA-A added to Box C/D-GFP. The ordinate represents the expression levels of samples with the Box C/D-GFP mRNA level of a sample supplemented with 1.0 μg of Box C/D-GFP as 1. The abscissa represents the amounts of pcDNA-L7Ae and pcDNA-A added. FIG. 32 is a graph showing mRNA level comparison among samples (samples derived from Box C/D-GFP and pcDNA-L7Ae and samples derived from Box C/D mut GFP and pcDNA-L7Ae) with a sample derived from only Box C/D as 1. (FIG. 8)
0, 0.5, 1.0, or 2.0 μg of pcDNA-L7Ae was added to Box C/D-GFP or Box C/D mut GFP fixed to 1.0 μg. The left bars represent the results from pcDNA-L7Ae added to Box C/D-GFP, and the right bars represent the results from pcDNA-L7Ae added to Box C/D mut GFP. The ordinate represents the expression levels of samples with the Box C/D-GFP or Box C/D mut GFP mRNA level of a sample supplemented with 1.0 μg of Box C/D-GFP or Box C/D mut GFP as 1. The abscissa represents the amount of pcDNA-L7Ae added.
The L7Ae expression-dependent repression of Box C/D-GFP expression was observed using fluorescence microscopic photographs.
On the day before transfection, HeLa cells were seeded at a concentration of 0.5×105 cells/well to a 24-well plate and cultured in a 37° C. CO2 incubator. Next day, the cells were transfected using Lipofectamine 2000 (trademark) (Invitrogen Corp.). 0, 0.05, 0.10, 0.15, or 0.20 μg of pcDNA-A or pcDNA-L7Ae was added to 0.2 μg of Box C/D-GFP or Box C/D mut GFP, and 1 μl of Lipofectamine 2000 was added to each sample. These DNA-lipid complexes were incubated at room temperature for 20 minutes and added dropwise to the cells. After 4 hours, medium replacement was performed. 24 hours after the transfection, photographs were taken under a fluorescence microscope. FIG. 33 is a fluorescence microscopic photograph showing the expression repressive effect of L7Ae on Box C/D-GFP. This drawing revealed that the fluorescence intensity of Box C/D-GFP is significantly reduced in the boxed region. This demonstrated that L7Ae expression specifically represses Box C/D-GFP translation.
Next, an experiment will be described which demonstrated that L7Ae can be used as a tag sequence for a target protein. pcDNA-L7Ae could be replaced by pcDNA3.1-L7Ae DsRed.
On the day before transfection, HeLa cells were seeded at a concentration of 0.5×105 cells/well to a 24-well plate and cultured in a 37° C. CO2 incubator. Next day, the cells were transfected using Lipofectamine 2000 (trademark) (Invitrogen Corp.). 0, 0.2, 0.4, 0.8, or 1.6 μg of pcDNA3.1-DsRed or pcDNA3.1-L7Ae DsRed was added to 0.2 μg of Box C/D-GFP or Box C/D mut GFP, and 1 μl of Lipofectamine 2000 was added to each sample. These DNA-lipid complexes were incubated at room temperature for 20 minutes and added dropwise to the cells. After 4 hours, medium replacement was performed. 24 hours after the transfection, photographs were taken under a fluorescence microscope. FIG. 34 is a fluorescence microscopic photograph. This drawing revealed that the fluorescence intensity of Box C/D-GFP is significantly reduced along with the expression of pcDNA3.1-L7Ae-DsRed in the boxed region. As the red fluorescent proteins are expressed by the cells, the expression of the green fluorescent proteins is repressed. This demonstrated that a system that represses the translation of a target gene, for example, green fluorescent protein translation, in response to the expression of an arbitrary gene, for example, red fluorescent protein expression, can be constructed intracellularly by adding L7Ae as a tag sequence to the protein.
Example 7 
To examine the binding property of L7Ae to the RNA complexes used in Examples above, reaction rate constants were calculated using inter-biomolecular interaction analyzer “BIACORE3000”.
[Preparation of L7Ae-Binding RNA Box C/D Mini Bia and Box C/D Mini Mutant Bia]
L7Ae-binding RNAs used in BIACORE were prepared by preparing a DNA template containing, at the 3′ end of Box C/D mini or Box C/D mini mutant, a complementary strand of a DNA sequence (5′-CCGGGGATCCTCTAGAGTC-3′) (SEQ ID NO: 92) immobilized on the BIACORE sensor chip, and a T7 promoter, followed by transcription reaction using T7 RNA polymerase. A reaction solution contained a mixture of 0.1 μM Box C/D mini bia template (5′-CCGGGGATCCTCTAGAGTCGGGTCAGCTTTCGCATCACGCCCTATAGTGAGTCGT ATTAGC-3′) (SEQ ID NO: 93), 5 μL each of 10 μM T7 promoter (5′-GCTAATACGACTCACTATAGG-3′) (SEQ ID NO: 94) and 10 μM Biacore Rev (5′-CCGGGGATCCTCTAGAGT-3′) (SEQ ID NO: 95), 8 μl of 2.5 mM dNTP (TAKARA BIO INC.), 10 μL of Ex Taq 10× buffer (TAKARA BIO INC.), and 0.5 μL of Ex Taq DNA polymerase (TAKARA BIO INC.). 25 cycles each involving 94° C. for 30 seconds, 60° C. for 30 seconds, and 72° C. for 30 seconds were performed for extension using DNA Engine PCT-200 (BIO-RAD LABORATORIES INC.). After the reaction, the extension product was subjected to phenol treatment, diethyl ether treatment, and ethanol precipitation and dissolved in 10 μL of ultrapure water. The solution was used as a template for transcription. For Box C/D mini mutant bia, the same procedures as above were performed using 0.1 μM Box C/D minimut template (5′-CCGGGGATCCTCTAGAGTCGGGGCAGCTTTCGCATGACGCCCTATAGTGAGTCGT ATTAGC-3′) (SEQ ID NO: 96) as a template in a reaction solution.
For transcription reaction, 10 μL of template DNA, 70 μL of 10× T7 RNA polymerase buffer (400 mM Tris-HCl (pH 7.5), 50 mM DTT, 10 mM Spermidine, 150 mM MgCl2), 70 μL of 10× rNTPs (12.5 mM rATP, 12.5 mM rCTP, 12.5 mM rUTP, 12.5 mM rGTP), and 14 μL of T7 RNA polymerase were mixed and reacted at 37° C. for 3 hours. The reaction solution was supplemented with 5 μL of TURBO DNase (Ambion, Inc.) and incubated at 37° C. for 1 hour to decompose the template DNA. Then, the transcript was subjected to phenol treatment and ethanol precipitation for purification. After the precipitation, the resulting product was dissolved in 20 μL of denaturing dye (80% formamide, 0.17% XC, 0.27% BPB) and electrophoresed on a 12% polyacrylamide (29:1) denaturing gel. A gel having the size of interest was excised, and elution was performed overnight at 37° C. by the addition of 500 μL of elution buffer (0.3 M sodium acetate (pH 7.0), 0.1% SDS). The eluted RNA was subjected again to phenol extraction, diethyl ether extraction, and ethanol precipitation for purification.
[Immobilization of Ligand (Biotin DNA) onto BIACORE Sensor Chip]
Onto a streptavidin-immobilized sensor chip (SA chip) (GE Healthcare), 80 μL of 1 μM N-terminally biotinylated DNAs (5′-CCGGGGATCCTCTAGAGTC-3′) (SEQ ID NO: 97) was added at a flow rate of 10 μL/min and immobilized using Amine Coupling Kit (GE Healthcare).
[Immobilization of Ligand RNA onto SA Chip]
RNAs were adjusted to 1 μM with HBS-EP buffer (10 mM HEPES (pH 7.4), 150 mM NaCl, 3 mM EDTA, 0.005% Surfactant P20) (GE Healthcare), then refolded through reaction at 80° C. for 10 min and at room temperature for 10 min, and then diluted 1/100 with 1 M KCl. 300 μL of the dilution was added to the chip at a flow rate of 10 μL/min to immobilize the RNAs corresponding to 52 RU (resonance unit) through the hybridization to the DNAs immobilized on the SA chip.
[L7Ae Association and Dissociation]
L7Ae was adjusted to 0 nM, 2.5 nM, 5 nM, 7.5 nM, 10 nM, 15 nM, 20 nM, and 25 nM with a running buffer (10 mM Tris-HCl (pH 8.0), 150 mM NaCl, 5% glycerol, 125 μg/ml tRNA, 62.5 μg/ml BSA, 1 mM DTT, 0.05% Tween 20). Each 50 μL aliquot was added at a flow rate of 50 μL/min for association with the RNA. Dissociation was performed for 5 minutes at the same flow rate as above. After association and dissociation measurements, the addition of 10 μL of 2 M KCl was repeated several times at a flow rate of 20 μL/min to forcedly dissociate, from the RNA, L7Ae undissociated for the 5 minutes. Three measurements were performed for each concentration.
[Calculation of Reaction Rate Constants]
The sensorgram of the flow cell bound with the Box C/D mini mutant bia RNA was subtracted from that of the flow cell bound with the Box C/D mini bia RNA. Based thereon, reaction rate constants (association rate constant (ka), dissociation rate constant (kd), association constant (KD), and dissociation constant (KA)) were calculated by Global fitting using the 1:1 (Langmuir) binding model of BIAevaluation analysis software. The results are shown in Table 4 and FIG. 35. This diagram demonstrated that the RNP motif that can be used in intracellular translational regulation has strong binding affinity (KD=up to 1 nM) and has a slow dissociation rate (Kd=up to 1×10−4), i.e., has the feature that the RNA and the protein hardly dissociates from each other once forming an RNP complex.












TABLE 4







ka (1/Ms)
kd (1/s)
KA (1/M)
KD (M)









1.46E+05
1.02E−04
1.43E+09
7.01E−10










In Examples above, two expressions GFP and EGFP are used in gene and RNA nomenclatures and both mean a gene and an RNA, respectively, derived from the EGFP (Enhanced Green Fluorescent Protein) gene.
INDUSTRIAL APPLICABILITY
In in vitro applications, the present invention can function as biosensors or artificial genetic circuits that respond to downstream signal proteins (e.g., fluorescent or luminescent proteins) in response to the expression of an arbitrary protein. Alternatively, by intracellular introduction, the present invention can function as systems that detect cells expressing a particular gene without destroying the cells, or as devices for artificial genetic circuits, which convert the expression of an arbitrary protein in an ON-to-OFF or OFF-to-ON manner in response to the expression of an arbitrary protein. Thus, the present invention can be developed into techniques of regulating the fate of cells.

## Claims

1. An isolated non-naturally occurring mRNA encoding a protein comprising an RNA-protein complex interacting motif nucleotide sequence incorporated 5′ to a ribosome-binding site in a position 2 to 10 bases distant from the ribosome-binding site or within the 5′ region of an open reading frame, wherein the interacting motif comprises nucleic acid sequence SEQ ID NO:9, wherein an RNA-protein complex of the interacting motif and L7Ae protein has a dissociation constant Kd of approximately 0.1 nM to approximately 1 μM between the motif and L7Ae and the interacting motif interacts with L7Ae protein.

2. An RNA-protein complex comprising an mRNA according to claim 1 and a protein specifically binding to the nucleotide sequence.

3. A translational regulatory kit comprising an mRNA according to claim 1 and a protein specifically binding to the nucleotide sequence.

4. A method for translational regulation of mRNA, comprising contacting the mRNA according to claim 1 with a protein specifically binding to the RNA-protein complex interacting motif nucleotide sequence.

5. An artificial information conversion method which converts input information of an arbitrary substrate protein to output information of an arbitrary target protein using an mRNA according to claim 1, comprising steps of
preparing the mRNA of claim 1 having an open reading frame encoding the arbitrary target protein; and
contacting the mRNA with the substrate protein that specifically binds to the RNA-protein complex interacting motif nucleotide sequence.

6. A plasmid vector comprising a nucleic acid sequence encoding an mRNA according to claim 1.

7. An intracellular translational regulatory kit comprising
a first plasmid vector comprising a nucleic acid sequence encoding an mRNA according to claim 1, and
a second plasmid vector comprising a nucleic acid sequence encoding a protein specifically binding to the RNA-protein complex interacting motif nucleotide sequence.

8. The kit according to claim 7, for regulating protein translation in a human cancer cell.