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Method for Rapid Analysis of Mutant RNA Polymerase Activity on Templates Containing Unnatural Nucleotides

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Method for Rapid Analysis of Mutant RNA Polymerase Activity on Templates Containing Unnatural Nucleotides International Journal of Molecular Sciences Communication Method for Rapid Analysis of Mutant RNA Polymerase Activity on Templates Containing Unnatural Nucleotides Tatiana Egorova 1, Ekaterina Shuvalova 1, Sabina Mukba 1, Alexey Shuvalov 1, Peter Kolosov 2,* and Elena Alkalaeva 1,* 1 Engelhardt Institute of Molecular Biology, The Russian Academy of Sciences, 119991 Moscow, Russia; [email protected] (T.E.); [email protected] (E.S.); [email protected] (S.M.); [email protected] (A.S.) 2 Institute of Higher Nervous Activity and Neurophysiology, The Russian Academy of Sciences, 117485 Moscow, Russia * Correspondence: [email protected] (P.K.); [email protected] (E.A.); Tel.: +7-495-334-4113 (P.K.); +7-499-135-9977 (E.A.) Abstract: Pairs of unnatural nucleotides are used to expand the genetic code and create artificial DNA or RNA templates. In general, an approach is used to engineer orthogonal systems capable of reading codons comprising artificial nucleotides; however, DNA and RNA polymerases capable of recognizing unnatural nucleotides are required for amplification and transcription of templates. Under favorable conditions, in the presence of modified nucleotide triphosphates, DNA polymerases are able to synthesize unnatural DNA with high efficiency; however, the currently available RNA polymerases reveal high specificity to the natural nucleotides and may not easily recognize the unnatural nucleotides. Due to the absence of simple and rapid methods for testing the activity of mutant RNA polymerases, the development of RNA polymerase recognizing unnatural nucleotides Citation: Egorova, T.; Shuvalova, E.; is limited. To fill this gap, we developed a method for rapid analysis of mutant RNA polymerase Mukba, S.; Shuvalov, A.; Kolosov, P.; Alkalaeva, E. Method for Rapid activity on templates containing unnatural nucleotides. Herein, we optimized a coupled cell-free Analysis of Mutant RNA Polymerase translation system and tested the ability of three unnatural nucleotides to be transcribed by different Activity on Templates Containing T7 RNA polymerase mutants, by demonstrating high sensitivity and simplicity of the developed Unnatural Nucleotides. Int. J. Mol. method. This approach can be applied to various unnatural nucleotides and can be simultaneously Sci. 2021, 22, 5186. https://doi.org/ scaled up to determine the activity of numerous polymerases on different templates. Due to the 10.3390/ijms22105186 simplicity and small amounts of material required, the developed cell-free system provides a highly scalable and versatile tool to study RNA polymerase activity. Academic Editor: Kensaku Sakamoto Keywords: unnatural nucleotides; T7 RNAP; cell-free translation Received: 26 April 2021 Accepted: 10 May 2021 Published: 14 May 2021 1. Introduction Publisher’s Note: MDPI stays neutral The genetic code can be modified at different levels, namely nucleotides, codons, and with regard to jurisdictional claims in published maps and institutional affil- amino acids. At each of these levels, unnatural components can be used. Thus, unnatural iations. amino acids can be encoded by unnatural nucleotides within the three-letter codons [1–5], four-letter codons [6], or by reassignment of sense or stop codons [7–9]. The development of unnatural base pairs (UBPs) is one of the most remarkable advances in synthetic biology. UBPs, which function as a third base pair in replication, transcription, and translation, expand the genetic alphabet and can be used in various Copyright: © 2021 by the authors. applications such as site-specific fluorescence labeling, nucleic acid immobilization, and Licensee MDPI, Basel, Switzerland. DNA and RNA analysis. Originally synthesized to expand the genetic alphabet, UBPs This article is an open access article distributed under the terms and have become powerful tools for monitoring the structural changes in nucleic acids and conditions of the Creative Commons their interactions with other molecules [10–22]. Attribution (CC BY) license (https:// All UBPs obtained to date can be divided into two groups: (1) UBPs, which form hy- creativecommons.org/licenses/by/ drogen bonds between bases (hydrogen complementarity) and (2) UBPs with hydrophobic 4.0/). interactions within the pair (structural complementarity) [23–36]. The first synthesized Int. J. Mol. Sci. 2021, 22, 5186. https://doi.org/10.3390/ijms22105186 https://www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2021, 22, 5186 2 of 14 UBPs comprised hydrogen bonds. Their topology differed from that found in natural nu- cleotides, which provided specificity for enzymatic synthesis [23–31]. Later, hydrophobic UBPs were obtained [32–36]. This proved that hydrogen bonding is not the only mech- anism capable of storing and transmitting genetic information. Presently, both types of UBPs are being actively developed and improved; however, for the amplification and transcription of templates containing unnatural nucleotides, the presence of DNA and RNA polymerases capable of their recognition is required. Under favorable conditions, in presence of modified nucleotide triphosphates, DNA polymerases synthesize unnatural DNA with high efficiency [17,37–41]; then with RNA polymerases, everything is not so good. At present, the available RNA polymerases for in vitro studies are specific to natural nucleotides and do not recognize unnatural nucleotides [31,42–45]. Bacteriophage T7 RNA polymerase (T7 RNAP) is one of the widely used polymerases for incorporating UBPs into RNA. It is a one subunit protein with 883 amino acid residues (98 kDa). T7 RNAP is capable of performing a full transcription cycle without involving any additional protein factors [46]. For a better understanding of the mechanisms underlying transcription, experiments on T7 RNA polymerase mutagenesis were carried out. As a result of this mutational analysis, it was found, for example, that the Y639F mutant has an amazing ability to use both rNTP and dNTP as substrates [47]. The additional mutation S641A markedly enhanced this property; therefore, the “double” mutant Y639F/S641A was able to synthesize long mixed polynucleotides, where one, two, or three types of rNTPs were replaced by the corresponding dNTPs [48,49]. Moreover, mutant RNA polymerase is used in the development of synthetic nucleotides. For example, some mutant variants of T7 RNAP, such as Y639F, Y639F/H784A, and G542V/H772R/H784S, were obtained to increase the efficiency of incorporating pyrimidine-20-modified nucleoside triphosphates used for site-specific labeling of RNA [50]. Nevertheless, presently, no simple methods are available for determining the activity of mutant forms of RNA polymerase, synthesizing RNA on a template containing UBPs. In the present study, we proposed a new method based on a double-coupled (coupled2) cell-free transcription–translation system, in which we determined the activity of mutant T7 RNA polymerases by the luminescence of synthesized nanoluciferase (Nluc). As a result, we evaluated the transcription efficiency of unnatural templates with different mutants of T7 RNA polymerases. In our system mutant T7 RNAPs used natural ribonucleotides to transcribe DNA templates containing UBPs. Furthermore, we revealed high sensitivity and simplicity of the developed method and demonstrated the ability of the studied mutants of T7 RNA polymerase to recognize UBPs. Additionally, we demonstrated that the approach we developed for determining the activity of RNA polymerases is applicable to a wide range of UBPs. 2. Results 2.1. Overview of the Method For simple and efficient testing of the functional activity of mutant T7 RNA poly- merases, we developed a method of a coupled2 transcription–translation system. The scheme of the method is illustrated in Figure1. SP6 RNA polymerase together with a linear template for T7 RNA polymerase containing the SP6 promoter and linear template for Nluc containing the T7 promoter was added to a wheat germ extract (WGE) cell-free system for coupled transcription and translation. NanoGlo, a substrate for Nluc, was also added to the reaction. First, SP6 RNA polymerase from the SP6 promoter synthesized mRNA for translation of T7 RNA polymerase, thereby producing T7 RNAP. The newly formed T7 RNAP enzyme transcribed Nluc mRNA from the T7 promoter, and thereafter, Nluc was translated in the same lysate leading to the formation of a luminescent product. This allowed us to determine the activity of T7 RNA polymerase in one test tube, starting from the DNA encoding it, without using difficult methods to obtain and purify RNA and proteins. The addition of the Nluc DNA template containing UBPs allowed us to study Int. J. Mol. Sci. 2021, 22, x FOR PEER REVIEW 3 of 14 translated in the same lysate leading to the formation of a luminescent product. This al- lowed us to determine the activity of T7 RNA polymerase in one test tube, starting from the DNA encoding it, without using difficult methods to obtain and purify RNA and pro- Int. J. Mol. Sci. 2021, 22, 5186 teins. The addition of the Nluc DNA template containing UBPs allowed us to study3 of the 14 ability of T7 RNAP to use an unnatural template to synthesize mRNA with natural ribo- nucleotide triphosphates. the ability of T7 RNAP to use an unnatural template to synthesize mRNA with natural ribonucleotide triphosphates. (a) (b) Figure 1. 2 a 2 Figure 1. CellCell-free-free “coupled “coupled2” ”transcription transcription–translation–translation system. system. (a) Scheme ( ) Scheme of the of cell the-free cell-free “coupled “coupled2” transcription” transcription––trans-
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