Chemistry-based RNA technologies: demonstration of usefulness of libraries of ribozymes and short hairpin RNAs (shRNAs)

Mechanism of action of hammerhead ribozymes has been investigated and their intracellular activities have been improved. Based on the improved ribozymes and more recently discovered natural RNAi, we have created libraries of both ribozymes and short hairpin RNAs (shRNAs). The introduction of a library of active ribozymes or shRNAs into cells, and the subsequent screening for phenotypic changes, allows the rapid identification of gene function.

Loss-of-function screening by randomized intracellular antibodies: identification of hnRNP-K as a potential target for metastasis

We have developed a loss-of-function screening system on the basis of intracellular expression of single domain antibodies. We demonstrate its use in identification of potential targets of metastasis of human cancerous cells. Randomized intracellular antibodies were expressed in highly metastatic cells, and a derivative pool of cells with loss of migration phenotype in chemotaxis assay was isolated. Isolation of antibodies from cells with loss of migration phenotype and identification of their target proteins revealed the involvement of the heterogeneous nuclear ribonucleoprotein K (hnRNP-K), a multifunctional signaling protein, in metastasis. Furthermore, we found that the cytoplasmic accumulation of hnRNP-K is crucial for its role in metastasis. The results demonstrate (i) the advantages of our functional interference screening over the gene-knockouts and gene-silencing, (ii) hnRNP-K as a potential target of metastasis, and (iii) a potential anti-metastasis peptide validated in in vitro cell migration assays.

Molecular design and delivery of siRNA

Double stranded short interfering RNAs (siRNAs) mediate gene silencing in a sequence specific manner. By virtue of their specific gene silencing activity and owing to the recent discoveries on their plasmid and virus driven expression, siRNAs are being widely adopted in research and therapeutics. Efforts were made to optimize the siRNA expression system for the application in therapy. One major obstacle in developing RNA interference (RNAi) therapy is the delivery of siRNAs to the target cells. Combination of novel molecular targeting technologies, such as recombinant protein technology and ribosome display technology, will enable to deliver gene silencing agents to target cells specifically and efficiently.

Specific N-terminal biotinylation of a protein in vitro by a chemically modified tRNA(fmet) can support the native activity of the translated protein

Biotinylation of a protein generally involves chemical modification of a translated protein. Using this methodology, however, biotinylation at a specific position remains difficult. We investigated whether it would be possible to use an Escherichia coli initiator tRNA(fmet) aminoacylated with methionine biotinylated at the alpha-amino group to introduce a biotin tag specifically at the N terminus. We report here that a biotin tag could be incorporated into the green fluorescent protein (GFP) at the N-terminal site, in the presence of an E. coli initiator tRNA(fmet) aminoacylated with methionine biotinylated at the alpha-amino group. The biotinylated GFP was purified by simple monomeric streptavidin-agarose affinity column chromatography. Based on the total amount of GFP molecules, the purification yield and the biotin labelling efficiency of this system were approximately 7% and 10-20%, respectively, according to the densitometric analysis of Western blots. Judging from the results of a fluorescence imaging experiment, almost all the purified GFP molecules retained the native fluorescence activity. Importantly, the present results support the hypothesis that the E. coli initiator tRNA(fmet) aminoacylated with a relatively large substituent can be recognized by an E. coli ribosome and adequately placed at the P site to initiate translation.

Modified peptide selection in vitro by introduction of a protein-RNA interaction

The ribosome display system is a very effective and powerful tool for in vitro screening of transcribed mRNAs that encode proteins (or peptides) with specific (known or unknown) functions. The system depends on the stability of ribosome-mRNA complexes that have been formed as a result of the removal of a stop codon. To assess the general applicability of the system, we examined the stability of ribosome-mRNA complexes in the presence and absence of a stop codon, as well as in the presence and the absence of an additional interaction between the translated peptide and its mRNA within the ribosome-mRNA complex. The additional interaction that we exploited was the interaction between a tandemly fused MS2 coat-protein (MSp) dimer and the RNA sequence of the corresponding specific binding motif, C-variant (Cv). The MSp dimer and Cv were placed, respectively, at the N-terminal end of a nascent protein, translated in vitro, and at the 5' end of the protein's mRNA, and consequently further stabilize the ribosome-mRNA complex. To our surprise, we were able to select proteins even in the presence of a stop codon. Moreover, as we had anticipated, the interaction between the MSp dimer and Cv enhanced the stability of the ribosome-mRNA complex, suggesting that this kind of interaction might be useful in the design of an efficient ribosome display selection strategy. Indeed, the yield of the mRNAs of interest after selection was increased upon the introduction of the interaction between the MSp dimer and Cv.

A system based on specific protein-RNA interactions for analysis of target protein-protein interactions in vitro: successful selection of membrane-bound Bak-Bcl-xL proteins in vitro

Ribosome display systems are very effective and powerful tools for in vitro screening of transcribed mRNAs that encode proteins (or peptides) with specific (known or unknown) functions. We have modified such a system by exploiting the interaction between a tandemly fused MS2 coat-protein (MSp) dimer and the RNA sequence of the corresponding specific binding motif, C-variant (or Cv). We placed the MSp dimer at the N-terminus of a nascent protein and the Cv binding motif was attached to the 5' end of the protein's mRNA. This configuration enhanced the stability of the ribosome-mRNA complex. We demonstrate here that this improved ribosome display system provides an effective method for identifying the gene for a protein that binds to a protein of interest. We visualized the formation of polysome complexes in this advanced polysome display by atomic force microscopy (AFM) and found that the AFM images of polysomes in our system were different from those observed in the case of conventional ribosome display systems. Our results suggest that our technology might usefully complement yeast two-hybrid assays.

Preparation of a whole genome phage library using fragmented Escherichia coli genome and its characterization of protein binding properties by surface plasmon resonance

A novel phage library has been prepared using the Escherichia coli genome digested with three restriction enzymes. The resulting DNA fragments were ligated to the expression vector pCANTAB5 to obtain the library of recombinant M13 phages displaying relatively long exogenous peptides. The library was screened to isolate recombinant phages with high affinity to alkaline phosphatase (AP) from calf intestine. After four rounds of panning three phages (AP1, AP2 and AP3) were shown to have specific binding properties toward AP by enzyme-linked immunosorbent assay. The phages were further characterized by surface plasmon resonance (SPR). Among the three phages AP3 bound the AP-immobilized sensor chip most and caused the highest resonant angle shift. The sensor response decreased with the decrease of the concentration of AP3 added. Furthermore, displacement of AP3 from the AP-immobilized sensor chip was observed upon injection of AP solution to the SPR system, whereas injection of bovine serum albumin solution led to the great increase of the sensor response. This result indicates the specific binding of AP3 to AP.

A novel approach to selection of functional proteins

We present here a novel approach to connect phenotype and genotype in vitro by exploiting a strong interaction between RNA and protein. This strong interaction was used for the selection of functional proteins, such as dihydrofolate reductase (DHFR) and streptavidin, which were chosen as examples. The noncovalent but strong interaction should be useful as a novel tool for the future selection of functional proteins.

Development of an advanced polysome display system dependent on a specific protein-RNA motif interaction

The ribosome display system is a very powerful too for in vitro screening of mRNAs that encode proteins (or peptides) with specific (known and unknown) functions. The ribosome display system depends on the stability of ribosome-mRNA complexes that have been achieved by the removal of a stop codon. An additional interaction we employed was between tandem fused MS2 coat protein (MSp) dimer and the RNA of its specific motif called a "C-variant" (or "Cv"). The MSp dimer and the Cv were placed at the N-terminal end of a nascent protein translated in vitro and the 5'-end of its mRNA, that might circularize the polysome complex and, as a result, further stabilize the ribosome-mRNA complex. The selectivity of mRNAs after selection was increased 2-fold by the introduction of the interaction between the MSp dimer and Cv.

A novel immobilization method of an active protein via in vitro N-terminal specific incorporation system of nonnatural amino acids

Recently, we succeeded in incorporating a biotin tag into an active protein, but only at the N-terminal site, in the presence of an Escherichia coli initiator tRNA(fMet) aminoacylated with methionine biotinylated at the alpha-amino group. The biotinylated protein was immobilized on a streptavidin-matrix. We have tried to increase the biotin labeling efficiency (immobilization efficiency) by decreasing concentrations of non-biotinylated tRNA(fMet)s in the translation system.

Novel approach for linking genotype to phenotype in vitro by exploiting an extremely strong interaction between RNA and protein

We recently isolated an aptamer that binds to the Tat protein of HIV-1 with extremely high affinity and specificity (Yamamoto, R.; et al. Genes Cells 2000, 5, 371.). In the present study, we exploited this strong binding to develop a novel coupling method that links genotype with phenotype. To strengthen the original RNA-protein interaction still further, we connected three units of the aptamer in tandem and three units of a peptide derived from Tat that interacted with the aptamer. The binding of the resultant RNA, which consisted of three units of the aptamer, to the resultant peptide, which consisted of three units of the peptide, was extremely strong. In fact, the RNA-protein interaction was one of the strongest ever reported, with an apparent K(d) below 16 pM. This strong interaction was attempted for the selection of functional proteins, namely, dihydrofolate reductase (DHFR) or streptavidin, which we chose as an example, and we succeeded in the expected selection, although to a limited extent, of the target protein. The noncovalent but strong interaction described above should be useful as a novel tool for the future selection of functional proteins from pools of random sequences of amino acids.