1
|
Hauf S, Rotrattanadumrong R, Yokobayashi Y. Analysis of the Sequence Preference of Saporin by Deep Sequencing. ACS Chem Biol 2022; 17:2619-2630. [PMID: 35969718 PMCID: PMC9486812 DOI: 10.1021/acschembio.2c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/29/2022] [Indexed: 01/19/2023]
Abstract
Ribosome-inactivating proteins (RIPs) are RNA:adenosine glycosidases that inactivate eukaryotic ribosomes by depurinating the sarcin-ricin loop (SRL) in 28S rRNA. The GAGA sequence at the top of the SRL or at the top of a hairpin loop is assumed to be their target motif. Saporin is a RIP widely used to develop immunotoxins for research and medical applications, but its sequence specificity has not been investigated. Here, we combine the conventional aniline cleavage assay for depurinated nucleic acids with high-throughput sequencing to study sequence-specific depurination of oligonucleotides caused by saporin. Our data reveal the sequence preference of saporin for different substrates and show that the GAGA motif is not efficiently targeted by this protein, neither in RNA nor in DNA. Instead, a preference of saporin for certain hairpin DNAs was observed. The observed sequence-specific activity of saporin may be relevant to antiviral or apoptosis-inducing effects of RIPs. The developed method could also be useful for studying the sequence specificity of depurination by other RIPs or enzymes.
Collapse
Affiliation(s)
- Samuel Hauf
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Rachapun Rotrattanadumrong
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and
Engineering Unit, Okinawa Institute of Science
and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| |
Collapse
|
2
|
Sabale PM, Srivatsan SG. Responsive Fluorescent PNA Analogue as a Tool for Detecting G-quadruplex Motifs of Oncogenes and Activity of Toxic Ribosome-Inactivating Proteins. Chembiochem 2016; 17:1665-73. [PMID: 27271025 DOI: 10.1002/cbic.201600192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 12/13/2022]
Abstract
Fluorescent oligomers that are resistant to enzymatic degradation and report their binding to target oligonucleotides (ONs) by changes in fluorescence properties are highly useful in developing nucleic-acid-based diagnostic tools and therapeutic strategies. Here, we describe the synthesis and photophysical characterization of fluorescent peptide nucleic acid (PNA) building blocks made of microenvironment-sensitive 5-(benzofuran-2-yl)- and 5-(benzothiophen-2-yl)-uracil cores. The emissive monomers, when incorporated into PNA oligomers and hybridized to complementary ONs, are minimally perturbing and are highly sensitive to their neighboring base environment. In particular, benzothiophene-modified PNA reports the hybridization process with significant enhancement in fluorescence intensity, even when placed in the vicinity of guanine residues, which often quench fluorescence. This feature was used in the turn-on detection of G-quadruplex-forming promoter DNA sequences of human proto-oncogenes (c-myc and c-kit). Furthermore, the ability of benzothiophene-modified PNA oligomer to report the presence of an abasic site in RNA enabled us to develop a simple fluorescence hybridization assay to detect and estimate the depurination activity of ribosome-inactivating protein toxins. Our results demonstrate that this approach with responsive PNA probes will provide new opportunities to develop robust tools to study nucleic acids.
Collapse
Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
| |
Collapse
|
3
|
Chi BH, Kim SJ, Seo HK, Seo HH, Lee SJ, Kwon JK, Lee TJ, Chang IH. P70S6K and Elf4E dual inhibition is essential to control bladder tumor growth and progression in orthotopic mouse non-muscle invasive bladder tumor model. J Korean Med Sci 2015; 30:308-16. [PMID: 25729255 PMCID: PMC4330487 DOI: 10.3346/jkms.2015.30.3.308] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 11/10/2014] [Indexed: 11/20/2022] Open
Abstract
We investigated how the dual inhibition of the molecular mechanism of the mammalian target of the rapamycin (mTOR) downstreams, P70S6 kinase (P70S6K) and eukaryotic initiation factor 4E (eIF4E), can lead to a suppression of the proliferation and progression of urothelial carcinoma (UC) in an orthotopic mouse non-muscle invasive bladder tumor (NMIBT) model. A KU-7-luc cell intravesically instilled orthotopic mouse NMIBC model was monitored using bioluminescence imaging (BLI) in vivo by interfering with different molecular components using rapamycin and siRNA technology. We then analyzed the effects on molecular activation status, cell growth, proliferation, and progression. A high concentration of rapamycin (10 µM) blocked both P70S6K and elF4E phosphorylation and inhibited cell proliferation in the KU-7-luc cells. It also reduced cell viability and proliferation more than the transfection of siRNA against p70S6K or elF4E. The groups with dual p70S6K and elF4E siRNA, and rapamycin reduced tumor volume and lamina propria invasion more than the groups with p70S6K or elF4E siRNA instillation, although all groups reduced photon density compared to the control. These findings suggest that both the mTOR pathway downstream of eIF4E and p70S6K can be successfully inhibited by high dose rapamycin only, and p70S6K and Elf4E dual inhibition is essential to control bladder tumor growth and progression.
Collapse
Affiliation(s)
- Byung Hoon Chi
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Korea
| | - Soon-Ja Kim
- Biomedical Science, Department of Medicine, Chung-Ang University Graduate School, Seoul, Korea
| | - Ho Kyung Seo
- Center for Prostate Cancer, Research Institute, National Cancer Center, Goyang, Korea
| | - Hye-Hyun Seo
- Genitourinary Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Sang-Jin Lee
- Genitourinary Cancer Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Jong Kyou Kwon
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Korea
| | - Tae-Jin Lee
- Department of Pathology, Chung-Ang University College of Medicine, Seoul, Korea
| | - In Ho Chang
- Department of Urology, Chung-Ang University College of Medicine, Seoul, Korea
| |
Collapse
|
4
|
Tanpure AA, Pawar MG, Srivatsan SG. Fluorescent Nucleoside Analogs: Probes for Investigating Nucleic Acid Structure and Function. Isr J Chem 2013. [DOI: 10.1002/ijch.201300010] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
5
|
Tanpure AA, Srivatsan SG. Synthesis and photophysical characterisation of a fluorescent nucleoside analogue that signals the presence of an abasic site in RNA. Chembiochem 2012; 13:2392-9. [PMID: 23070860 DOI: 10.1002/cbic.201200408] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Indexed: 11/07/2022]
Abstract
The synthesis and site-specific incorporation of an environment-sensitive fluorescent nucleoside analogue (2), based on a 5-(benzofuran-2-yl)pyrimidine core, into DNA oligonucleotides (ONs), and its photophysical properties within these ONs are described. Interestingly and unlike 2-aminopurine (a widely used nucleoside analogue probe), when incorporated into an ON and hybridised with a complementary ON, the emissive nucleoside 2 displays significantly higher emission intensity than the free nucleoside. Furthermore, photophysical characterisation shows that the fluorescence properties of the nucleoside analogue within ONs are significantly influenced by flanking bases, especially by guanosine. By utilising the responsiveness of the nucleoside to changes in base environment, a DNA ON reporter labelled with the emissive nucleoside 2 was constructed; this signalled the presence of an abasic site in a model depurinated sarcin/ricin RNA motif of a eukaryotic 28S rRNA.
Collapse
Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, 900, NCL Innovation Park, Dr. Homi Bhabha Road, Pune 411008, India
| | | |
Collapse
|
6
|
Tanpure AA, Patheja P, Srivatsan SG. Label-free fluorescence detection of the depurination activity of ribosome inactivating protein toxins. Chem Commun (Camb) 2012; 48:501-3. [DOI: 10.1039/c1cc16667k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
7
|
Sturm MB, Tyler PC, Evans GB, Schramm VL. Transition state analogues rescue ribosomes from saporin-L1 ribosome inactivating protein. Biochemistry 2009; 48:9941-8. [PMID: 19764816 DOI: 10.1021/bi901425h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribosome inactivating proteins (RIPs) catalyze the hydrolytic depurination of one or more adenosine residues from eukaryotic ribosomes. Depurination of the ribosomal sarcin-ricin tetraloop (GAGA) causes inhibition of protein synthesis and cellular death. We characterized the catalytic properties of saporin-L1 from Saponaria officinalis (soapwort) leaves, and it demonstrated robust activity against defined nucleic acid substrates and mammalian ribosomes. Transition state analogue mimics of small oligonucleotide substrates of saporin-L1 are powerful, slow-onset inhibitors when adenosine is replaced with the transition state mimic 9-deazaadenine-9-methylene-N-hydroxypyrrolidine (DADMeA). Linear, cyclic, and stem-loop oligonucleotide inhibitors containing DADMeA and based on the GAGA sarcin-ricin tetraloop gave slow-onset tight-binding inhibition constants (K(i)*) of 2.3-8.7 nM under physiological conditions and bind up to 40000-fold tighter than RNA substrates. Saporin-L1 inhibition of rabbit reticulocyte translation was protected by these inhibitors. Transition state analogues of saporin-L1 have potential in cancer therapy that employs saporin-L1-linked immunotoxins.
Collapse
Affiliation(s)
- Matthew B Sturm
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | | | | |
Collapse
|
8
|
Srivatsan S, Greco N, Tor Y. A Highly Emissive Fluorescent Nucleoside that Signals the Activity of Toxic Ribosome-Inactivating Proteins. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200802199] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
9
|
Srivatsan SG, Greco NJ, Tor Y. A highly emissive fluorescent nucleoside that signals the activity of toxic ribosome-inactivating proteins. Angew Chem Int Ed Engl 2008; 47:6661-5. [PMID: 18683267 PMCID: PMC2633406 DOI: 10.1002/anie.200802199] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Seergazhi G. Srivatsan
- Dr. S. G. Srivatsan, Dr. N. J. Greco, Prof. Y. Tor, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0358 (USA), Fax: (+1)858-534-0202, E-mail:
| | - Nicholas J. Greco
- Dr. S. G. Srivatsan, Dr. N. J. Greco, Prof. Y. Tor, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0358 (USA), Fax: (+1)858-534-0202, E-mail:
| | - Yitzhak Tor
- Dr. S. G. Srivatsan, Dr. N. J. Greco, Prof. Y. Tor, Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093-0358 (USA), Fax: (+1)858-534-0202, E-mail:
| |
Collapse
|
10
|
Wrzesiński J, Szczepanik W, Ciesiołka J, Jezowska-Bojczuk M. tRNAPhe cleavage by aminoglycosides is triggered off by formation of an abasic site. Biochem Biophys Res Commun 2005; 331:267-71. [PMID: 15845388 DOI: 10.1016/j.bbrc.2005.03.161] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Indexed: 11/19/2022]
Abstract
This communication reports the characteristics of the mechanism of highly specific tRNA(Phe) cleavage, which occurs in the anticodon loop in the presence of aminoglycoside antibiotic-neomycin B. The data prove that the cleavage requires previous depurination of the polynucleotide chain at position 37, which is occupied by a hypermodified guanine base-wybutine. The results suggest that the phenomenon, previously considered as selective with respect to the presence of tRNA hypermodification, may concern far more RNA molecules, namely the ones carrying abasic sites.
Collapse
Affiliation(s)
- Jan Wrzesiński
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | | | | | | |
Collapse
|
11
|
Liu RS, Huang H, Yang Q, Liu WY. Purification of alpha-sarcin and an antifungal protein from mold (Aspergillus giganteus) by chitin affinity chromatography. Protein Expr Purif 2002; 25:50-8. [PMID: 12071698 DOI: 10.1006/prep.2001.1608] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A simple method for preparation of alpha-sarcin and an antifungal protein (AFP) from mold (Aspergillus giganteus MDH 18894) has been developed. alpha-Sarcin and AFP were purified simultaneously by chitin affinity column chromatography and gel filtration. By this method, 4.5 mg of pure alpha-sarcin and 6.9 mg of pure AFP were obtained from 2 liters of culture medium. Compared with other purification methods such as ion-exchange column chromatography, this procedure was very simple and specific. The purified alpha-sarcin and AFP were homogeneous as characterized by SDS-polyacrylamide gel electrophoresis. Both alpha-sarcin and AFP exhibited the binding activity to generated chitin. Soluble glycochitin decreased the intensity of fluorescence of alpha-sarcin and made the lambda(em)m shift from 340 to 347 nm. Titration of alpha-sarcin with N-bromosuccinimide under native conditions revealed that two tryptophans (Trps) were all located in the core part of alpha-sarcin molecule. This indicated that Trps were not involved in the binding of alpha-sarcin to chitin. Glycochitin in the culture medium increased the expression of alpha-sarcin, while it had no effect on the expression of AFP. Unlike other ligands such as Cibacron blue for the affinity purification of alpha-sarcin and AFP, glycochitin increased the nuclease activity of alpha-sarcin.
Collapse
Affiliation(s)
- Ren-shui Liu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, 320 Yue-Yang Road, Shanghai 200031, China
| | | | | | | |
Collapse
|
12
|
He WJ, Tang S, Liu WY, Stirpe F. Nonspecific deadenylation on sarcin/ricin domain RNA catalyzed by gelonin under acidic conditions. Arch Biochem Biophys 2002; 399:181-7. [PMID: 11888204 DOI: 10.1006/abbi.2001.2748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Gelonin is a single-chain ribosome-inactivating protein that can hydrolyze the glycosidic bond of a highly conserved adenosine residue in the sarcin/ricin domain (SRD) of the largest RNA in ribosome and thus irreversibly inhibit protein synthesis. Recently, the specificity in substrate recognition was challenged by the fact that gelonin could remove adenines from some other oligoribonucleotide substrates. However, the site specificity of gelonin to deadenylate various substrates were unknown. Hereby, the effect of pH values upon site specificity of the deadenylation activity of gelonin was studied using the synthetic oligoribonucleotide (named SRD RNA) that mimicked the ribosomal SRD. Interestingly, gelonin gradually acquired the ability to nonspecifically remove adenines from SRD RNA when pH values changed from neutral to acidic conditions. Another two SRD RNA mutants, either with the conserved adenosine deleted or with the tetraloop converted, showed very similar cleavage style to wild-type SRD RNA, underscoring the important role of pH value in site specificity of recognition by gelonin. Furthermore, the RNA N-glycosidase activity of gelonin was also enhanced with the decreasing of pH values. In addition, no obvious change was observed in the molecular conformation of gelonin at various pH values. Taken together, our data implied that the protonation of adenosines in SRD RNA was potentially an important factor for the nonspecific deadenlyation by gelonin.
Collapse
Affiliation(s)
- Wen-Jun He
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, 320 Yue-yang Road, Shanghai 200031, China
| | | | | | | |
Collapse
|