| 1. |
- Fijolek, Artur, 1974-
(author)
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Salvage and de novo synthesis of nucleotides in Trypanosoma brucei and mammalian cells
- 2008
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Doctoral thesis (other academic/artistic)abstract
- All living cells are dependent on nucleic acids for their survival. The genetic information stored in DNA is translated into functional proteins via a messenger molecule, the ribonucleic acid (RNA). Since DNA and RNA can be considered as polymers of nucleotides (NTPs), balanced pools of NTPs are crucial to nucleic acid synthesis and repair. The de novo reduction of ribonucleoside diphosphates (NDPs) to deoxyribonucleoside diphosphates (dNDPs), the precursors for DNA synthesis, is catalyzed by the enzyme ribonucleotide reductase (RNR). In cycling cells the dominant form of mammalian RNR consists of two proteins called R1 and R2. A proteasome-mediated degradation completely deprives postmitotic cells of R2 protein. The nonproliferating cells use instead a p53 inducible small RNR subunit, called p53R2 to synthesize dNTPs for mitochondrial DNA replication and DNA repair. To address the ongoing controversy regarding the localization and subsequently function and regulation of RNR subunits, the subcellular localization of all the mammalian RNR subunits during the cell cycle and after DNA damage was followed as a part of this thesis. Irrespective of the employed methodology, only a cytosolic localization could be observed leading to a conclusion that the dNTPs are synthesized in the cytosol and transported into the nucleus or mitochondria for DNA synthesis and repair. Thus, our data do not support the suggestion that nuclear translocation is a new additional mechanism regulating ribonucleotide reduction in mammalian cells. In an attempt to find a cure for African sleeping sickness, a lethal disease caused by a human pathogen, Trypanosoma brucei, nucleotide metabolism of the parasite was studied. The trypanosomes exhibit strikingly low CTP pools compared with mammalian cells and they also lack salvage of cytidine/cytosine making the parasite CTP synthetase a potential target for treatment of the disease. Following expression, purification and kinetic studies of the recombinant T. brucei CTP synthetase it was found that the enzyme has a higher Km value for UTP than the mammalian CTP synthetase. In combination with a lower UTP pool the high Km may account for the low CTP pool in trypanosomes. The activity of the trypanosome CTP synthetase was irreversibly inhibited by the glutamine analog acivicin, a drug extensively tested as an antitumor agent. Daily injections of acivicin to trypanosome-infected mice were sufficient to suppress the parasite infections. The drug was shown to be trypanocidal when added to cultured bloodstream T. brucei for four days at 1 uM concentration. Therefore, acivicin may qualify as a drug with “desirable” properties, i.e. cure within 7 days, according to the current Target Product Profiles of WHO and DNDi. Trypanosomes lack de novo purine biosynthesis and are therefore dependent on exogenous purines such as adenosine that is taken up from the blood by high-affinity transporters. We found that besides the cleavage-dependent pathway, where adenosine is converted to adenine by inosine-adenosine-guanosine-nucleoside hydrolase, T. brucei can also salvage adenosine by adenosine kinase (AK). The efficient adenosine transport combined with a high-affinity AK yields a strong salvage system in T. brucei, but on the other hand makes the parasites highly sensitive to adenosine analogs such as adenine arabinoside (Ara-A). The cleavage-resistant Ara-A was shown to be readily taken up by the parasites and phosphorylated by the TbAK-dependent pathway, inhibiting trypanosome proliferation and survival by incorporation into nucleic acids and by affecting nucleotide levels in the parasite.
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| 2. |
- Jonna, Venkateswara Rao, 1980-
(author)
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Class I Ribonucleotide Reductases : overall activity regulation, oligomerization, and drug targeting
- 2017
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Doctoral thesis (other academic/artistic)abstract
- Ribonucleotide reductase (RNR) is a key enzyme in the de novo biosynthesis and homeostatic maintenance of all four DNA building blocks by being able to make deoxyribonucleotides from the corresponding ribonucleotides. It is important for the cell to control the production of a balanced supply of the dNTPs to minimize misincorporations in DNA. Because RNR is the rate-limiting enzyme in DNA synthesis, it is an important target for antimicrobial and antiproliferative molecules. The enzyme RNR has one of the most sophisticated allosteric regulations known in Nature with four allosteric effectors (ATP, dATP, dGTP, and dTTP) and two allosteric sites. One of the sites (s-site) controls the substrate specificity of the enzyme, whereas the other one (a-site) regulates the overall activity. The a-site binds either dATP, which inhibits the enzyme or ATP that activates the enzyme. In eukaryotes, ATP activation is directly through the a-site and in E. coli it is a cross-talk effect between the a and s-sites. It is important to study and get more knowledge about the overall activity regulation of RNR, both because it has an important physiological function, but also because it may provide important clues to the design of antibacterial and antiproliferative drugs, which can target RNR.Previous studies of class I RNRs, the class found in nearly all eukaryotes and many prokaryotes have revealed that the overall activity regulation is dependent on the formation of oligomeric complexes. The class I RNR consists of two subunits, a large α subunit, and a small β subunit. The oligomeric complexes vary between different species with the mammalian and yeast enzymes cycle between structurally different active and inactive α6β2 complexes, and the E. coli enzyme cycles between active α2β2 and inactive α4β4 complexes. Because RNR equilibrates between many different oligomeric forms that are not resolved by most conventional methods, we have used a technique termed gas-phase electrophoretic macromolecule analysis (GEMMA). In the present studies, our focus is on characterizing both prokaryotic and mammalian class I RNRs. In one of our projects, we have studied the class I RNR from Pseudomonas aeruginosa and found that it represents a novel mechanism of overall activity allosteric regulation, which is different from the two known overall activity allosteric regulation found in E. coli and eukaryotic RNRs, respectively. The structural differences between the bacterial and the eukaryote class I RNRs are interesting from a drug developmental viewpoint because they open up the possibility of finding inhibitors that selectively target the pathogens. The biochemical data that we have published in the above project was later supported by crystal structure and solution X-ray scattering data that we published together with Derek T. Logan`s research group.We have also studied the effect of a novel antiproliferative molecule, NSC73735, on the oligomerization of the human RNR large subunit. This collaborative research results showed that the molecule NSC73735 is the first reported non-nucleoside molecule which alters the oligomerization to inhibit human RNR and the molecule disrupts the cell cycle distribution in human leukemia cells.
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| 3. |
- Vodnala, Munender, 1977-
(author)
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Targeting the nucleotide metabolism of the mammalian pathogen Trypanosoma brucei
- 2013
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Doctoral thesis (other academic/artistic)abstract
- Trypanosoma brucei causes African sleeping sickness in humans and Nagana in cattle. There are no vaccines available against the disease and the current treatment is also not satisfactory because of inefficacy and numerous side effects of the used drugs.T. brucei lacks de novo synthesis of purine nucleosides; hence it depends on the host to make its purine nucleotides. T. brucei has a high affinity adenosine kinase (TbAK), which phosphorylates adenosine, deoxyadenosine (dAdo), inosine and their analogs. RNAi experiments confirmed that TbAK is responsible for the salvage of dAdo and the toxicity of its substrate analogs. Cell growth assays with the dAdo analogs, Ara-A and F-Ara-A, suggested that TbAK could be exploited for drug development against the disease.It has previously been shown that when T. brucei cells were cultivated in the presence of 1 mM deoxyadenosine (dAdo), they showed accumulation of dATP and depletion of ATP nucleotides. The altered nucleotide levels were toxic to the trypanosomes. However the salvage of dAdo in trypanosomes was dramatically reduced below 0.5 mM dAdo. Radiolabeled dAdo experiments showed that it (especially at low concentrations) is cleaved to adenine and converted to ATP. The recombinant methylthioadenosine phosphorylase (TbMTAP) cleaved methylthioadenosine, dAdo and adenosine into adenine and sugar-1-P in a phosphate-dependent manner. The trypanosomes became more sensitive to dAdo when TbMTAP was down-regulated in RNAi experiments. The RNAi experiments confirmed that trypanosomes avoid dATP accumulation by cleaving dAdo. The TbMTAP cleavage-resistant nucleoside analogs, FANA-A and Ara-A, successfully cured T. brucei-infected mice.The DNA building block dTTP can be synthesized either via thymidylate synthase in the de novo pathway or via thymidine kinase (TK) by salvage synthesis. We found that T. brucei and three other parasites contain a tandem TK where the gene sequence was repeated twice or four times in a single open reading frame. The recombinant T. brucei TK, which belongs to the TK1 family, showed broad substrate specificity. The enzyme phosphorylated the pyrimidine nucleosides thymidine and deoxyuridine, as well as the purine nucleosides deoxyinosine and deoxyguanosine. When the repeated sequences of the tandem TbTK were expressed individually as domains, only domain 2 was active. However, the protein could not dimerize and had a 5-fold reduced affinity to its pyrimidine substrates but a similar turnover number as the full-length enzyme. The expressed domain 1 was inactive and sequence analysis revealed that some active residues, which are needed for substrate binding and catalysis, are absent. Generally, the TK1 family enzymes form dimers or tetramers and the quaternary structure is linked to the affinity for the substrates. The covalently linked inactive domain-1 helps domain-2 to form a pseudodimer for the efficient binding of substrates. In addition, we discovered a repetition of an 89-bp sequence in both domain 1 and domain 2, which suggests a genetic exchange between the two domains.T. brucei is very dependent on de novo synthesis via ribonucleotide reductase (RNR) for the production of dNTPs. Even though T. brucei RNR belongs to the class Ia RNR family and contains an ATP-binding cone, it lacks inhibition by dATP. The mechanism behind the RNR activation by ATP and inactivation by dATP was a puzzle for a long time in the ~50 years of RNR research. We carried out oligomerization studies on mouse and E. coli RNRs, which belongs to the same family as T. brucei, to get an understanding of the molecular mechanism behind overall activity regulation. We found that the oligomerization status of RNRs and overall activity mechanism are interlinked with each other.
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