DNA watermarks in non-coding regulatory sequences
© Barnekow et al; licensee BioMed Central Ltd. 2009
Received: 04 February 2009
Accepted: 07 July 2009
Published: 07 July 2009
DNA watermarks can be applied to identify the unauthorized use of genetically modified organisms. It has been shown that coding regions can be used to encrypt information into living organisms by using the DNA-Crypt algorithm. Yet, if the sequence of interest presents a non-coding DNA sequence, either the function of a resulting functional RNA molecule or a regulatory sequence, such as a promoter, could be affected. For our studies we used the small cytoplasmic RNA 1 in yeast and the lac promoter region of Escherichia coli.
The lac promoter was deactivated by the integrated watermark. In addition, the RNA molecules displayed altered configurations after introducing a watermark, but surprisingly were functionally intact, which has been verified by analyzing the growth characteristics of both wild type and watermarked scR1 transformed yeast cells. In a third approach we introduced a second overlapping watermark into the lac promoter, which did not affect the promoter activity.
Even though the watermarked RNA and one of the watermarked promoters did not show any significant differences compared to the wild type RNA and wild type promoter region, respectively, it cannot be generalized that other RNA molecules or regulatory sequences behave accordingly. Therefore, we do not recommend integrating watermark sequences into regulatory regions.
DNA watermarks can be used for authenticating genetically modified organisms or in future for labeling animals in breeding [1, 2]. It has already been shown in silico and in vivo that these watermarks do not affect the translation of proteins [1–4]. These assumptions only apply to coding regions, thus the insertion of watermarks into regulatory sequences like promoter regions or regulatory RNA molecules, had to be examined. In our studies we integrated watermark sequences into a widely known promoter region of bacteria. Watermarks integrated into regulatory regions like promoter or enhancer sequences can affect their functionality. We integrated watermark sequences into the lac promoter of Escherichia coli to examine, whether the watermarks affect the promoter activity. The lac operon of Escherichia coli consists of a promoter, three operators and three genes (lacY, lacZ and lacA), coding for the β-galactoside permease, β-galactosidase and β-galactoside transacetylase, which are required for the lactose metabolism in Escherichia coli . The β-galactosidase cleaves the lactose into glucose and galactose . The promoter sequence of the lac operon consists of two highly conserved regions called the -35 (TTTACA) and -10 (TATGTT) regions, upstream from the transcription start. It has already been shown that single point mutations within conserved regions can affect or even stop promoter activity of different promoters (Additional file 1) [6–10].
In a second approach we integrated a watermark sequence into a regulatory RNA molecule called small cytoplasmic RNA 1 (scR1) from yeast (scR1 gene on chromosome V of Saccharomyces cerevisiae, http://www.yeastgenome.org/). The scR1 consists of 519 nucleotides and represents the homologous RNA molecule in Saccharomyces cerevisiae to the mammalian 7SL RNA, which is part of the signal recognition particle (SRP), necessary for the targeting of proteins into the endoplasmic reticulum (ER) [11–13]. The SRP complex is a ribonucleoprotein consisting of six polypeptides and the 7SL RNA. In Saccharomyces cerevisiae the six polypeptides are SRP14, SRP19, SRP21, SRP54, SRP68 and SRP72 . The SRP displays a GTPase activity . The 7SL molecule is a conserved functional RNA constituting the backbone of the SRP complex and has been shown to be essential for all organisms tested, except Saccharomyces cerevisiae cells. Saccharomyces cerevisiae cells are viable without scR1, but have a reduced reproduction rate [11, 12, 14, 16–21].
Results and discussion
The analyses of the watermarked DNA sequences of both, the scR1 and the lac promoter sequence with the DNA-Crypt fuzzy controller, reveal that the use of any correction code is not recommended.
Qualitative β-galactosidase assays
qualitative β-galactosidase assay
Our results show that the integration of watermarks is not suitable for regulatory regions like promoter or regulatory RNA molecules. We have shown that these watermarks can deactivate promoter regions and further affect the secondary structure of regulatory RNA molecules. Although the watermarked scR1 was not deactivated by the integration of a watermark sequence, the secondary structure prediction displayed an altered structure. These results cannot be generalized for other RNA molecules.
The affect of integrated watermarks in non-coding regulatory regions cannot be generalized and has to be tested in every single case. Therefore, we propose not to integrate watermark sequences into regulatory sequences.
We wanted to integrate a watermark into the lac promoter containing the answer to life, the universe, and everything . Further we wanted to encrypt the watermark 'TB' into the scR1 gene and 'WWU' into the lac promoter sequence, respectively. To demonstrate the flexibility of our algorithm we used different translation codes. The first one only used the binary representation. The second translation code used for the scR1 experiments just slightly differs from the standard one used in DNA-Crypt . The third one imitates the official international Morse code. But identical binary encoding tables described in Heider and Barnekow 2007 were used . The inserted DNA watermark sequences are
42 → 1010102 → CCC
TB → 10011000012 → CGCTG
WWU → .--.--..- → 01101100112 → GCATA
We created artificial reading frames within the scR1 gene and the lac promoter sequence that do not exist in non-coding regions, to apply the DNA-Crypt algorithm. Because of cost-benefit equation, we scanned manually for the best location within the DNA sequences of the scR1 gene and the lac promoter for integrating authenticating watermarks. The two watermark sequences in the lac promoter region overlap.
DNA-Crypt fuzzy controller
The watermark sequences were analyzed with the DNA-Crypt fuzzy controller with standard settings. The life time was set at 1000 cycles . Based on the three input dimensions, the length of the watermark sequence, individual mutation rate and life time, the DNA-Crypt fuzzy controller recommends, based on the rule base, whether to use a specific mutation correction code or not .
Secondary structure prediction
The secondary structure predictions of the RNA molecules were performed using the ViennaRNA-1.5 web interface with rescaled energy parameters to 30°C . The three dimensional structure predictions were created with Blender.
The site-directed mutagenesis was used to integrate the watermark sequences into the wild type DNA. We used a modified QuikChange(R) Site-Directed Mutagenesis Kit protocol from Stratagene (Stratagene, Amsterdam, The Netherlands) described in Heider and Barnekow 2008 . For the scR1 studies we used the Yep352-SCR1 plasmid carrying the wild type sequence of the scR1 gene (a kind gift of Giorgio Dieci, Universita di Parma, Italy) . For our lac promoter studies we used the pBluescriptII KS+ plasmid (Stratagene, Amsterdam, The Netherlands). The site-directed mutagenesis was performed with the following primer sequences:
scR1 – forward primer:
5'-GCACATTGTGGCC GTG CCC TCT GGG ATGGAGTGTGTC-3'
scR1 – reverse primer:
lac – forward primer:
lac – reverse primer:
5'-TGTAAA GCC TGGGG TCCCAAATGAGTGAGCTAAC-3'
lac2 – forward primer:
5'-CTCACTCATTAGGCC CCC CAGGCC TTACACTTTATGC-3'
lac2 – reverse primer:
The bold letters represent the watermark sequences. The mutagenesis was confirmed by sequencing with the M13 primer 5'-GTAAAACGACGGCCAGT-3' and the lac-SEQ primer 5'-CCGCCTCTCCCCGCG-3', respectively.
Transformation of bacteria
For our lac promoter studies we used the Escherichia coli DH5α strain. 20 ml 2YT were inoculated with 200 μ l overnight culture of DH5α bacteria and incubated at 37°C to an OD600 of 0.3 to 0.5. The cells were centrifuged for 10 minutes at 2000 × g and mixed with 10 ml ice-cold sterile 0.1 M CaCl2. After incubation for 30 minutes on ice, the cells were centrifuged for 10 minutes at 4°C 2000 × g and resuspended in 2 ml ice-cold 0.1 M CaCl2. 200 μ l of the cells were mixed up with 50 ng DNA. After incubation for 30 minutes on ice, the cells were incubated for 45 seconds at 42°C and cooled down for 2 minutes on ice. After mixing with 500 μ l 2YT the cells were incubated for 45 minutes at 37°C and 220 rpm. Finally 200 μ l of the cell suspension were plated and grown overnight on 2YT plates containing ampicillin.
Transformation of yeast
We used the YRA130 ΔscR1::His3 yeast strain for our scR1 experiments that has a reduced reproduction rate (a kind gift of Peter Walter, University of California, San Francisco, USA). The yeast strain YRA130 was transformed using the lithium acetate method and grown on SD-ura plates .
The activity of the lac promoter was verified by qualitative and quantitative β-galactosidase assays, using 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (X-Gal, Carl Roth GmbH, Karlsruhe, Germany) and ONPG (Carl Roth GmbH, Karlsruhe, Germany), respectively. For the qualitative β-galactosidase assay we pipetted 40 μ l 100 mM IPTG (Carl Roth GmbH, Karlsruhe, Germany) and 40 μ l X-Gal (20 mg/ml) onto a 2YT agar plate containing ampicillin. After drying the plates for one hour, 20 μ l of overnight cultures were plated and incubated overnight at 37°C. The quantitative analyses we performed using the method established by Miller in 1972, except some modifications published by Zhang and Bremer and some additional modifications [25, 26]. We used 100 μ l of IPTG induced overnight culture for our assays and froze them for 30 minutes at 20°C before adding the permealization buffer. In addition we used a substrate buffer containing 3 mg/ml instead of 1 mg/ml ONPG to guarantee saturation for the β-galactosidase.
The growth characteristics of YRA130, and the Yep352-SCR1 and Yep352-SCR1-TB transformed YRA130 cells were analyzed by measuring optical densities at 600 nm every 60 minutes for nine hours (Pharmacia LKB Novaspec II).
The authors want to thank Peter Walter (University of California, San Francisco, USA) for the YRA130 strain, Giorgio Dieci (Universita di Parma, Italy) for the Yep352-SCR1 plasmid and Sarah-Jane Barnard for critically reading the manuscript. This work is part of the PhD thesis of D.H.
- Heider D, Barnekow A: DNA-based watermarks using the DNA-Crypt algorithm. BMC Bioinformatics. 2007, 8: 176-PubMed CentralView ArticlePubMedGoogle Scholar
- Heider D, Kessler D, Barnekow A: Watermarking sexually reproducing diploid organisms. Bioinformatics. 2008, 24: 1961-1962.View ArticlePubMedGoogle Scholar
- Heider D, Barnekow A: DNA watermarks and sexual transmission. Europ J Cell Biol. 2008, 87S1: 58-Google Scholar
- Heider D, Barnekow A: DNA watermarks: A proof of concept. BMC Molecular Biology. 2008, 9: 40-PubMed CentralView ArticlePubMedGoogle Scholar
- Beckwith JR: Regulation of the lac operon. Recent studies on the regulation of lactose metabolism in Escherichia coli support the operon model. Science. 1967, 156 (3775): 597-604.View ArticlePubMedGoogle Scholar
- Rothmel RK, LeClerc JE: Mutational analysis of the lac regulatory region: second-site changes that activate mutant promoters. Nucleic Acids Research. 1989, 17 (10): 3909-3925.PubMed CentralView ArticlePubMedGoogle Scholar
- Depto AS, Stenberg RM: Regulated Expression of the Human Cytomegalovirus pp65 Gene: Octamer Sequence in the Promoter Is Required for Activation by Viral Gene Products. Journal of Virology. 1989, 63 (3): 1232-1238.PubMed CentralPubMedGoogle Scholar
- Bentley K, Deacon N, Sonza S, Zeichner S, Churchill M: Mutational analysis of the HIV-1 LTR as a promoter of negative sense transcription. Arch Virol. 2004, 149: 2277-2294.View ArticlePubMedGoogle Scholar
- Romano G, Suon S, Jin H, Donaldson AE, Iacovitti L: Characterization of Five Evolutionary Conserved Regions of the Human Tyrosine Hydroxylase (TH) Promoter: Implications for the Engineering of a Human TH Minimal Promoter Assembled in a Self-Inactivating Lentiviral Vector System. J Cell Physiol. 2005, 204 (2): 666-677.PubMed CentralView ArticlePubMedGoogle Scholar
- Almeida AM, Murakami Y, Layton DM, Hillmen P, Sellick GS, Maeda Y, Richards S, Patterson S, Kotsianidis I, Crawford LMDH, Baker A, Ferguson M, Roberts I, Houlston R, Kinoshita T, Karadimitris A: Hypomorphic promoter mutation in PIGM causes inherited glycosylphosphatidylinositol deficiency. Nature Medicine. 2006, 12: 846-851.View ArticlePubMedGoogle Scholar
- Felici F, Cesareni G G, Hughes JM: The Most Abundant Small Cytoplasmic RNA of Saccharomyces cerevisiae Has an Important Function Required for Normal Cell Growth. Mol Cell Biol. 1989, 9 (8): 3260-3268.PubMed CentralView ArticlePubMedGoogle Scholar
- Dieci G, Giuliodori S, Catellani M, Percudani R, Ottonello S: Intragenic Promoter Adaptation and Facili-tated RNA Polymerase III Recycling in the Transcription of SCR1, the 7SL RNA Gene of Saccharomyces cerevisiae. J Biol Chem. 2001, 277: 6903-6914.View ArticlePubMedGoogle Scholar
- Wild K, Weichenrieder O, Strub K, Sinning I, Cusack S: Towards the structure of the mammalian signal recognition particle. Curr Opin Struct Biol. 2002, 12: 72-81.View ArticlePubMedGoogle Scholar
- Rosenblad AM, Gorodkin J, Knudsen B, Zwieb C, Samuelsson T: SRPDB (Signal Recognition Particle Database). Nucleic Acids Res. 2003, 31: 363-364.PubMed CentralView ArticlePubMedGoogle Scholar
- Borschbach M, Hauke S, Pyka M, Heider D: Opportunities and limitations of a principle component analysis optimized machine learning approach for the identification and classification of cancer involved proteins. Communications of the SIWN. 2009, 6: 85-89.Google Scholar
- Hann BC, Walter P: The signal sequence recognition particle in S.cerevisiae. Cell. 1991, 67: 131-144.View ArticlePubMedGoogle Scholar
- Stirling CJ, Hewitt EW: The S. cerevisiae SEC65 gene encodes a component of yeast signal recognition particle with homology to human SRP19. Nature. 1992, 356: 534-537.View ArticlePubMedGoogle Scholar
- Ogg SC, Poritz MA, Walter P: Signal sequence recognition particle receptor is important for cell growth and protein secretion in Saccharomyces cerevisiae. Mol Biol Cell. 1992, 3: 895-911.PubMed CentralView ArticlePubMedGoogle Scholar
- Brown J, Hann BC, Medzihradszky KF, Niwa M, Burlingame AL, Walter P: Subunits of the Saccharomyces cerevisiae signal recognition particle required for itsfunctional expression. EMBO J. 1994, 13: 4390-4400.PubMed CentralPubMedGoogle Scholar
- Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22: 4673-4680.PubMed CentralView ArticlePubMedGoogle Scholar
- Kin T, et al: fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences. Nucleic Acids Res. 2007, 35 (Database issue): D145-D148.PubMed CentralView ArticlePubMedGoogle Scholar
- Vienna RNA Secondary Structure Prediction, A web interface to the RNAfold programm version 1.5. [http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi]
- Adams D: The Hitchhiker's Guide to the Galaxy. 1979, Ballantine BooksGoogle Scholar
- Kail M, Barnekow A: Identification and characterization of interacting partners of Rab GTPases by yeast two-hybrid analyses. Methods Mol Biol. 2008, 440: 111-125.View ArticlePubMedGoogle Scholar
- Miller JH: J.H. Miller Experiments in Molecular Genetics. Cold Spring Harbor Laboratory 1972 chap. J.H. Miller Assay of β-Galactosidase, 352-355.
- Zhang X, Bremer H: Control of the Escherichia coli rrnB P1 Promoter Strength by ppGpp. J Biol Chem. 1995, 270 (19): 11181-11189.View ArticlePubMedGoogle Scholar
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