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DNA Synthesis from Aberrant Substrates by KlenTaq DNA Polymerase : A Functional and Structural Analysis

DNA Synthesis from Aberrant Substrates by KlenTaq DNA Polymerase : A Functional and Structural Analysis

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BLATTER, Nina, 2013. DNA Synthesis from Aberrant Substrates by KlenTaq DNA Polymerase : A Functional and Structural Analysis [Dissertation]. Konstanz: University of Konstanz

@phdthesis{Blatter2013Synth-28876, title={DNA Synthesis from Aberrant Substrates by KlenTaq DNA Polymerase : A Functional and Structural Analysis}, year={2013}, author={Blatter, Nina}, address={Konstanz}, school={Universität Konstanz} }

Blatter, Nina 2014-09-01T09:08:54Z 2014-09-01T09:08:54Z Blatter, Nina eng 2013 DNA Synthesis from Aberrant Substrates by KlenTaq DNA Polymerase : A Functional and Structural Analysis terms-of-use The high substrate specificity of replicative DNA polymerases is essential in order to maintain the stability of a cell’s genome.[160] But furthermore, it is fundamental to understand how a DNA polymerase can adapt to or discriminate between aberrant or non-cognate substrates present in various biological processes. The evolution of DNA polymerases towards an enhanced acceptance of non-cognate substrates is also a paramount goal of directed enzyme evolution, as these enzymes pave the way for various biotechnological applications. In this study, the focus is on KlenTaq DNA polymerase adapting to abasic sites present in DNA and on the processing of RNA as a non-cognate substrate.<br /><br /><br />In the first part of this work, the enzyme’s incorporation mechanism opposite an abasic site was investigated. Abasic sites are the result of a spontaneous or enzymatic loss of the nucleobase and are the most common damage in DNA observed under physiological conditions.[76] Although they are non-instructive, DNA polymerases from family A and B preferentially incorporate dAMP opposite the lesion, a phenomenon termed ‘A-rule’.[78, 83, 84, 97-100, 102] This preference results in transversion mutations often found in human cancers.[112] Thus, it is vital to understand how DNA polymerases process these lesions and why dAMP is preferred. Superior desolvation and stacking interactions of adenine were always thought to be the major determinants for the ‘A-rule’.[108, 109] However, Dr. Samra Obeid was able to obtain crystal structures of KlenTaq in complex with an abasic site analogue containing template, which suggested a possible bypass mechanism as well as the mechanistic origin for the purine selectivity of this DNA polymerase.[72] A highly conserved amino acid side chain (Tyr671) was suggested to replace the missing nucleobase in the template strand and mimic a six membered pyrimidine nucleobase in shape and size, thus directing for purine incorporation in order to maintain an optimal geometric fit at the active site. But, crystal structure analysis only provides a static view of nucleotide incorporation. For further evidence that an ‘amino acid templating’ mechanism is facilitating the incorporation of purines, functional studies were required and performed in this work. By mutating the tyrosine at position 671 via site-directed mutagenesis, variants were generated and subsequently analysed in primer extension experiments as well as kinetic studies to further corroborate the important role of this side chain in abasic site bypass.<br />Analysis of a Y671A variant demonstrated the significance of the aromatic moiety at this position in general, whereas a Y671F mutant highlighted the importance of hydrogen bond formation between the cognate tyrosine’s hydroxyl group and the N3 of the incoming adenine. Incorporation studies of a modified nucleotide, namely 3-deaza-2’-deoxyadenosine-5’-triphosphate (d3DATP), opposite an abasic site, as well as primer extension experiments with a variant containing 2,3,5-fluorotyrosine at position 671, further confirmed the stabilizing effect of the hydrogen bond formed.<br /><br /><br />Analysis of a Y671W mutant provided the most compelling evidence that indeed an ‘amino acid templating’ mechanism is at work with an optimal geometric fit at the active site as the major determinant. In detail, primer extension experiments and kinetic analysis of Y671W revealed that the purine selectivity could be switched to preferential pyrimidine incorporation. It is assumed that the bicyclic indole, consisting of a six‐membered ring fused to a five‐membered ring, mimics the approximate size and shape of a purine and in consequence directs for pyrimidine incorporation to conserve the geometric fit at the active site. Thus, the functional studies corroborated the lesion bypass mechanism derived from the crystal structure analysis.<br /><br /><br />In a second aspect of this work, template-independent addition of nucleotides at blunt-ended DNA was investigated.[107] The high preference for dAMP incorporation at blunt-ended DNA resembles the incorporation opposite an abasic site. Crystal structure analysis performed by Dr. Samra Obeid revealed the same arrangement in the active site of the enzyme with Tyr671 directing for preferential purine incorporation. Functional studies performed in this work with the tryptophane mutant Y671W corroborated these findings in primer extension and kinetic studies.<br /><br /><br /><br />In the second project of this work, the acceptance of another non-cognate substrate of KlenTaq DNA polymerase was investigated. In general, the substrate selection of a DNA polymerase is a very stringent process;[160] the acceptance of non-cognate substrates, however, facilitates new applications in biotechnology, molecular biology and diagnostics. This part of my work focused on the ability of the DNA-dependent DNA polymerase KlenTaq to accept or exclude the non-cognate template RNA regarding two different aspects. First, the idea was to develop a KlenTaq variant which is able to accept DNA and RNA as the templating nucleic acid, thus facilitating the enzyme’s application in reverse transcription PCR (RT-PCR), resulting in it being a valuable tool in transcriptome analysis, in pathogen detection as well as in disease-specific marker recognition.[14] Second, we wanted to obtain insights into the fundamental biological question of how a DNA-dependent DNA polymerase can discriminate between DNA and RNA as a templating nucleic acid.<br /><br /><br />The detection and quantification of RNA in RT-PCR is generally mediated by two enzymes: a reverse transcriptase and a PCR-competent DNA polymerase. However, several drawbacks arise from the heat-instability of retroviral reverse transcriptases.[143] Thus, the use of one enzyme, a thermostable DNA-dependent DNA polymerase capable of reverse transcription, would offer the possibility to perform one step RT-PCR at high temperatures minimizing secondary structure formation of RNA,[142] enhance specificity[142] and, in general, supersede the use of two enzymes, thereby eliminating problems such as inhibitory effects between a reverse transcriptase and a DNA polymerase.[152-154] An additional reverse transcription step, necessary for the reverse transcriptase, could be omitted, further providing a work and time reduction.<br /><br /><br />For this purpose, two KlenTaq mutants, M1 (L322M, L459M, S515R, I638F, S739G, E773G) and M747K, exhibiting some reverse transcriptase[148] and lesion bypass activity,[159] were recombined by DNA shuffling. Screening of the generated library for PCR and reverse transcriptase activity yielded enzyme mutants with properties by far exceeding the parental enzymes. Sequencing and functional characterization of the most promising variants indicated that four mutations (L459M, S515R, I638F and M747K) are important for the observed increase in reverse transcriptase activity. One mutant which featured one mutation less showed an overall loss in enzyme activity, whereas variants with more mutations resulted in no gain in reverse transcriptase activity.<br /><br /><br />In summary, we gained a new generation of KlenTaq variants which exhibit an up to 20-fold gain in reverse transcriptase activity compared to the parental variant KTq M1, and a more than 100-fold increase compared to KTq M747K. The results suggest a surprising synergistic effect of the mutations. Further RT-PCR experiments with the purified enzymes confirmed the superior reverse transcriptase activity of the identified variants. RT-KTq 2, which possesses the most promising mutations L459M, S515R, I638F and M747K, was selected for in depth-analysis. The enzyme was successfully applied in real-time multiplex RT-PCR, facilitating rapid detection of influenza viruses A and B. Thus, it provides a valuable tool for rapid RT-PCR, crucial e.g. in important fields of clinical diagnostics such as point of care testing, as a reverse transcription step can be omitted and preceding reaction condition optimizations for a reverse transcriptase and a DNA polymerase are redundant. The thermostable enzyme further offers the possibility to perform RT-PCR at high temperatures, preventing unspecific priming and secondary structure formation of mRNA. The full-length enzyme of the variant showed further promising properties which facilitates its future application in TaqMan based RT-PCR.<br />Few thermostable enzymes capable of both reverse transcription and PCR are commercially available,[147, 151] probably also due to the lack of knowledge regarding the mechanism of how DNA-dependent DNA polymerases discriminate between the templating nucleic acids DNA and RNA. Therefore, it is difficult to rationally design such DNA polymerases. The lack of knowledge is due to the fact that structural data of DNA-dependent DNA polymerases, whose wild-type parental ancestors show no significant reverse transcriptase activity, processing RNA is not available. Thus, we set out to crystallize KlenTaq DNA polymerase in complex with RNA as substrate to get insights into the fundamental question how DNA-dependent DNA polymerases discriminate between the templating nucleic acids DNA and RNA.<br />Although crystallization trials of KlenTaq wild-type in complex with a DNA/RNA hybrid failed, we were able to obtain crystals of the RT-KTq 2 variant in complex with an all DNA as well as a DNA/RNA hybrid duplex and could solve the structures. For the first time, we received insights into how a DNA-dependent DNA polymerase processes RNA. Together with Dipl.-Biol. Konrad Bergen, we identified the crucial role of the mutations present in the enzyme variant which enabled the mutant to accommodate the distinct geometry of the hybrid duplex, allowing an efficient processing of RNA as template. Consequently, we also gained insights into the restraints present in the wild-type enzyme which prevent efficient RNA processing.<br />The L459M mutation contributes to prevent the clash of the thumb domain with the hybrid duplex and facilitates the nucleotide binding motif in the thumb domain to maintain its interactions with the nucleic acid duplex. Furthermore, the S515R mutation stabilizes this motif by interacting with surrounding amino acid residues. Whereas the role of I638F is difficult to predict, we suggest that the M747K mutation increases the positively charged surface potential in the proximity of the negatively charged substrate backbone and thus enhances the acceptance of non-cognate substrates by electrostatic interactions.<br /><br /><br />A last aspect of this work focused on the increased substrate spectra of the new KlenTaq variants. With these enzymes in hand, many applications come to mind. The increased lesion bypass activity makes them valuable tools for paleontological, archaeological or forensic studies in which damaged DNA has to be processed in PCR reactions.[217] The high error-rate combined with the ability to perform PCR would allow the generation of mutated genes that are useful e.g., for directed enzyme evolution.[122]<br /><br /><br /><br />This work consisted of two major studies which both investigated DNA synthesis by KlenTaq DNA polymerase from two aberrant substrates, abasic site containing templates and RNA. Both studies give insights into the nature of template processing by DNA polymerases: In general, one can conclude that these enzymes possess a certain flexibility to adapt to non-cognate substrates. This flexibility can be altered or enhanced by directed enzyme evolution. In detail, an amino acid residue assumes the role of the templating nucleobase in abasic site bypass and directs for preferential purine incorporation. However, mutation of this residue still allowed the enzyme to bypass the lesion, but altered the enzyme’s bypass behaviour towards preferential pyrimidine incorporation. Additionally, the poor processing of RNA as template by KlenTaq DNA polymerase was enhanced by introducing specific mutations into the enzyme. Thus, the intrinsic poor binding and processing of the non-cognate substrate RNA was efficiently increased by directed enzyme evolution and resulted in the enzyme’s high reverse transcriptase activity.<br />In this work, directed enzyme evolution also facilitated the investigation of biological processes and mechanisms. Mutating the tyrosine residue 671 to tryptophane approved a proposed model for the ‘A-rule’. Furthermore, evolution of KlenTaq DNA polymerase wild-type towards a mutant capable of processing RNA allowed insights into the restrictions present in the wild-type enzyme, which might be responsible for discriminating between the two templates DNA and RNA. Thus, by directed enzyme evolution, insights were gained into fundamental principles of DNA synthesis.

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