Diss. (sammanfattning) Umeå : Univ., 2008. / Härtill 4 uppsatser.

For survival and successful propagation, every organism has to maintain the genomic integrity of the cell. The information content, in the form of nucleotide bases, is constantly threatened by endogenous agents and environmental pollutants. In particular, pathogenic mycobacteria are constantly exposed to DNA-damaging assaults such as reactive oxygen species (ROS) and reactive nitrogen intermediate (RNI), in their habitat which is inside host macrophage. In addition, the genome of Mycobacterium tuberculosis makes it more susceptible for guanine oxidation and cytosine deamination as it is G-C rich. Therefore DNA repair mechanisms are extremely important for the mycobacterium. An important enzyme involved in DNA repair is uracil-DNA glycosylase (Ung). To access the genomic information, during repair as well as DNA replication and recombination, dsDNA must unwind to form single stranded (ss) intermediates. ssDNA is more prone to chemical and nuclease attacks that can produce breaks or lesions and can also inappropriately self associate. In order to preserve ssDNA intermediates, cells have evolved a specialized class of ssDNA-binding proteins (SSB) that associate with ssDNA with high affinity. As part of a major programme on mycobacterial proteins in this laboratory, structural studies on mycobacterial uracil-DNA glycosylase (Ung) and single-stranded DNA binding protein (SSB) have been carried out. The structures were solved using the well-established techniques of protein X-ray crystallography. The hanging drop vapour diffusion and microbatch methods were used for crystallization in all cases. X-ray intensity data were collected on a MAR Research imaging plate mounted on a Rigaku RU200 X-ray generator. The data were processed using the HKL program suite. The structures were solved by the molecular replacement method using the program PHASER and AMoRe. Structure refinements were carried out using the programs CNS and REFMAC. Model building was carried out using COOT. PROCHECK, ALIGN, INSIGHT and NACCESS were used for structure validation and analysis of the refined structures. MD simulations were performed using the software package GROMACS v 3.3.1. Uracil-DNA glycosylase (UNG), a repair enzyme involved in the excision of uracil from DNA, from mycobacteria differs from UNGs from other sources, particularly in the sequence in the catalytically important loops. The structure of the enzyme from Mycobacterium tuberculosis (MtUng) in complex with a proteinaceous inhibitor (Ugi) has been determined by X-ray analysis of a crystal containing seven crystallographically independent copies of the complex. This structure provides the first geometric characterization of a mycobacterial UNG. A comparison of the structure with those of other UNG proteins of known structure shows that a central core region of the molecule is relatively invariant in structure and sequence, while the N- and C-terminal tails exhibit high variability. The tails are probably important in folding and stability. The mycobacterial enzyme exhibits differences in UNG-Ugi interactions compared with those involving UNG from other sources. The MtUng-DNA complex modelled on the basis of the known structure of the complex involving the human enzyme indicates a domain closure in the enzyme when binding to DNA. The binding involves a larger burial of surface area than is observed in binding by human UNG. The DNA-binding site of MtUng is characterized by the presence of a higher proportion of arginyl residues than is found in the binding site of any other UNG of known structure. In addition to the electrostatic effects produced by the arginyl residues, the hydrogen bonds in which they are involved compensate for the loss of some interactions arising from changes in amino-acid residues, particularly in the catalytic loops. The results arising from the present investigation represent unique features of the structure and interaction of mycobacterial Ungs. To gain further insights, the structure of Mycobacterium tuberculosis Ung (MtUng) in its free form was also determined. Comparison with appropriate structures indicate that the two domain enzyme slightly closes up when binding to DNA while it slightly opens up when binding to its proteinaceous inhibitor Ugi. The structural changes on complexation in the catalytic loops reflect the special features of their structure in the mycobacterial protein. A comparative analysis of available sequences of the enzyme from different sources indicates high conservation of amino acid residues in the catalytic loops. The uracil binding pocket in the structure is occupied by a citrate ion. The interactions of the citrate ion with the protein mimic those of uracil in addition to providing insights into other possible interactions that inhibitors could be involved in. SSB is an essential accessory protein required during DNA replication, repair and recombination, and various other DNA transactions. Eubacteral single stranded DNA binding (SSB) proteins constitute an extensively studied family of proteins. The variability in the quaternary association in these tetrameric proteins was first demonstrated through the X-ray analysis of the crystal structure of Mycobacterium tuberculosis SSB (MtSSB) and Mycobacterium smegmatis (MsSSB) in this laboratory. Subsequent studies on these proteins elsewhere have further explored this variability, but attention was solely concentrated on the variability in the relative orientation of the two dimers that constitute the tetramer. Furthermore, the effect of this variability on the properties of the tetrameric molecule was not adequately addressed. In order to further explore this variability and strengthen structural information on mycobacterial SSBs in particular, and on SSB proteins in general, the crystal structures of two forms of Mycobacterium leprae single stranded DNA-binding protein (MlSSB) has been determined. Comparison of the structures with other eubacterial SSB structures indicates considerable variation in their quaternary association although the DNA binding domains in all of them exhibit the same OB-fold. This variation has no linear correlation with sequence variation, but it appears to correlate well with variation in protein stability. Molecular dynamics simulations have been carried out on tetrameric molecules derived from the two forms and the prototype E. coli SSB and the individual subunits of both the proteins. The X-ray studies and molecular dynamics simulations together yield information on the relatively rigid and flexible regions of the molecule and the effect of oligomerization on flexibility. The simulations provide insights into the changes in the subunit structure on oligomerization. They also provide insights into the stability and time evolution of the hydrogen bonds/water-bridges that connect two pairs of monomers in the tetramer. In continuation of our effort to understand structure-function relationships of mycobacterial SSBs, the structure of MsSSB complexed with a 31-mer polydeoxy-cytidine single stranded DNA (ssDNA) was determined. The mode of ssDNA binding in the MsSSB is different from the modes in the known structures of similar complexes of the proteins from E. coli (EcSSB) and Helicobacter pylori (HpSSB). The modes in the EcSSB and HpSSB also exhibit considerable differences between them. A comparison of the three structures reveals the promiscuity of DNA-binding to SSBs from different species in terms of symmetry and the path followed by the bound DNA chain. It also reveals commonalities within the diversity. The regions of the protein molecule involved in DNA-binding and the nature of the residues which interact with the DNA, exhibit substantial similarities. The regions which exhibit similarities are on the central core of the subunit which is unaffected by tetramerisation. The variable features of DNA binding are associated with the periphery of the subunit, which is involved in oligomerization. Thus, there is some correlation between variability in DNA-binding and the known variability in tetrameric association in SSBs. In addition to the work on Ung and SSB, the author was involved in X-ray studies on crystals of horse methemoglobin at different levels of hydration, which is described in the Appendix of the thesis. The crystal structure of high-salt horse methaemoglobin has been determined at environmental relative humidities (r.h.) of 88, 79, 75 and 66%. The molecule is in the R state in the native and the r.h. 88% crystals. At r.h.79% the molecule appears to move towards the R2 state. The crystal structure at r.h.66% is similar, but not identical, to that at r.h.75%. Thus variation in hydration leads to variation in the quaternary structure. Furthermore, partial dehydration appears to shift the structure from the R state to the R2 state. This observation is in agreement with the earlier conclusion that the changes in protein structure that accompany partial dehydration are similar to those that occur during protein action. A part of the work presented in the thesis has been reported in the following publications. 1. Singh, P., Talawar, R.K., Krishna, P.D., Varshney, U. & Vijayan, M. (2006). Overexpression, purification, crystallization and preliminary X-ray analysis of uracil N-glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor. Acta Crystallogr. F62, 1231-1234. 2. Kaushal, P.S., Talawar, R.K., Krishna, P.D., Varshney, U. & Vijayan, M. (2008). Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources. Acta Crystallogr. D64, 551-560. 3. Kaushal, P.S., Sankaranarayanan, R. & Vijayan, M. (2008). Water-mediated variability in the structure of relaxed-state haemoglobin. Acta Crystallogr. F64, 463-469.

La génétique inverse est devenue une méthode clé pour la production de virus à ARN génétiquement modifiés et pour comprendre les propriétés cellulaires et biologiques des virus. Cependant les méthodes les plus fréquemment utilisées, basées sur le clonage de génomes viraux complets dans des plasmides, sont laborieuses et imprévisibles. La première partie de cette thèse présente des études sur la mise au point d'un nouveau système de génétique inverse, appelé méthode ISA (Amplicons-Sous génomique-Infectieux), qui permet la génération, en quelques jours, de virus infectieux sauvages et génétiquement modifiés appartenant à trois familles différentes de virus à ARN simple brin de polarité positive, avec une grande maîtrise des séquences virales. Dans la deuxième partie de cette thèse, nous avons appliqué pour la première fois à un arbovirus (CHIKV), le ré-encodage des codons - une méthode développée récemment et très excitante pour le développement de vaccins vivants atténués. En utilisant une approche aléatoire de ré-encodage des codons qui attribue au hasard des codons sur la base de la séquence en acides aminés correspondante, nous avons mis en évidence des pertes importantes de fitness réplicatif sur des cellules de primates et d'arthropodes. La diminution du fitness réplicatif est en corrélation avec le degré de ré-encodage, une observation qui peut aider à la modulation de l'atténuation virale. En utilisant l'expérience acquise avec le CHIKV, nous avons transposé avec succès ce mécanisme d'atténuation au JEV et amélioré notre maîtrise du processus d'atténuation en utilisant une combinaison de la synthèse de novo et de la méthode ISA. / Reverse genetics has become a key methodology for producing genetically modified RNA viruses and deciphering cellular and viral biological properties, but the most commonly used methods, based on the preparation of plasmid-based complete viral genomes, are laborious and unpredictable. The first part of this thesis presents studies relating to the development of a new reverse genetics system, designated the ISA (Infectious-Subgenomic-Amplicons) method, which enabled the generation of both wild-type and genetically modified infectious viruses belonging to three different families of positive, single stranded RNA viruses within days with great control of the viral sequences. In the second part of this thesis, we applied for the first time to an arbovirus (CHIKV), codon re-encoding - a recently developed and very exciting method for the development of live attenuated vaccines. Using a random codon re-encoding approach which randomly attributed nucleotide codons based on their corresponding amino acid sequence, we identified major fitness losses of CHIKV in both primate and arthropod cells. The decrease of replicative fitness correlated with the extent of re-encoding, an observation that may assist in the modulation of viral attenuation. Detailed analysis of these observed replicative fitness losses indicated that they are the consequence of several independent re-encoding induced events. Using the experience acquired on the CHIKV, we successfully transposed this attenuation mechanism to JEV and improved our control of the attenuation process by using a combination of de novo synthesis and the ISA method.

No description available.

Le maintien de la stabilité du génome est essentiel pour la propagation de l’information génétique et pour la croissance et la survie des cellules. Tous les organismes possèdent des systèmes de prévention des dommages et des réarrangements de l’ADN et nos connaissances sur ces processus découlent principalement de l’étude des génomes bactériens et nucléaires. Comparativement peu de choses sont connues sur les systèmes de protection des génomes d’organelles. Cette étude révèle l’importance des protéines liant l’ADN simple-brin de la famille Whirly dans le maintien de la stabilité du génome des organelles de plantes. Nous rapportons que les Whirlies sont requis pour la stabilité du génome plastidique chez Arabidopsis thaliana et Zea mays. L’absence des Whirlies plastidiques favorise une accumulation de molécules rearrangées produites par recombinaison non-homologue médiée par des régions de microhomologie. Ce mécanisme est similaire au “microhomology-mediated break-induced replication” (MMBIR) retrouvé chez les bactéries, la levure et l’humain. Nous montrons également que les organelles de plantes peuvent réparer les bris double-brin en utilisant une voie semblable au MMBIR. La délétion de différents membres de la famille Whirly entraîne une accumulation importante de réarrangements dans le génome des organelles suite à l’induction de bris double-brin. Ces résultats indiquent que les Whirlies sont aussi importants pour la réparation fidèle des génomes d’organelles. En se basant sur des données biologiques et structurales, nous proposons un modèle où les Whirlies modulent la disponibilité de l’ADN simple-brin, régulant ainsi le choix des voies de réparation et permettant le maintien de la stabilité du génome des organelles. Les divers aspects de ce modèle seront testés au cours d’expériences futures ce qui mènera à une meilleure compréhension du maintien de la stabilité du génome des organelles. / Maintenance of genome stability is essential for the accurate propagation of genetic information and for cell growth and survival. Organisms have therefore developed efficient strategies to prevent DNA lesions and rearrangements. Much of the information concerning these strategies has been obtained through the study of bacterial and nuclear genomes. Comparatively little is known about how organelle genomes maintain a stable structure. This study implicates the single-stranded nucleic acid-binding proteins of the Whirly family in the maintenance of plant organelle genome stability. Here we report that the plastid-localized single-stranded DNA binding proteins of the Whirly family are required for plastid genome stability in Arabidopsis thaliana and Zea mays. Absence of plastidial Whirlies favors the accumulation of rearranged molecules that arise through a non-homologous recombination mechanism mediated by regions of microhomology. This mechanism is similar to the microhomology-mediated break-induced replication (MMBIR) described in bacteria, yeast and humans. Additionally we show that plant organelles can repair double-strand breaks using a MMBIR-like pathway. Plants lacking Whirly proteins accumulate elevated levels of microhomology-mediated DNA rearrangements upon double-strand break induction, indicating that Whirlies also contribute to the accurate repair of plant organelle genomes. Using biological and structural data, we propose a working model in which Whirlies modulate the access of repair proteins and complementary DNA to single-stranded regions, thereby regulating the choice of repair pathways and maintaining plant organelle genome stability. The various aspects of this model will be tested in future experiments which should allow a better understanding of the mechanisms underlying genome stability in plant organelles.

Le maintien de la stabilité du génome est essentiel pour la propagation de l’information génétique et pour la croissance et la survie des cellules. Tous les organismes possèdent des systèmes de prévention des dommages et des réarrangements de l’ADN et nos connaissances sur ces processus découlent principalement de l’étude des génomes bactériens et nucléaires. Comparativement peu de choses sont connues sur les systèmes de protection des génomes d’organelles. Cette étude révèle l’importance des protéines liant l’ADN simple-brin de la famille Whirly dans le maintien de la stabilité du génome des organelles de plantes. Nous rapportons que les Whirlies sont requis pour la stabilité du génome plastidique chez Arabidopsis thaliana et Zea mays. L’absence des Whirlies plastidiques favorise une accumulation de molécules rearrangées produites par recombinaison non-homologue médiée par des régions de microhomologie. Ce mécanisme est similaire au “microhomology-mediated break-induced replication” (MMBIR) retrouvé chez les bactéries, la levure et l’humain. Nous montrons également que les organelles de plantes peuvent réparer les bris double-brin en utilisant une voie semblable au MMBIR. La délétion de différents membres de la famille Whirly entraîne une accumulation importante de réarrangements dans le génome des organelles suite à l’induction de bris double-brin. Ces résultats indiquent que les Whirlies sont aussi importants pour la réparation fidèle des génomes d’organelles. En se basant sur des données biologiques et structurales, nous proposons un modèle où les Whirlies modulent la disponibilité de l’ADN simple-brin, régulant ainsi le choix des voies de réparation et permettant le maintien de la stabilité du génome des organelles. Les divers aspects de ce modèle seront testés au cours d’expériences futures ce qui mènera à une meilleure compréhension du maintien de la stabilité du génome des organelles. / Maintenance of genome stability is essential for the accurate propagation of genetic information and for cell growth and survival. Organisms have therefore developed efficient strategies to prevent DNA lesions and rearrangements. Much of the information concerning these strategies has been obtained through the study of bacterial and nuclear genomes. Comparatively little is known about how organelle genomes maintain a stable structure. This study implicates the single-stranded nucleic acid-binding proteins of the Whirly family in the maintenance of plant organelle genome stability. Here we report that the plastid-localized single-stranded DNA binding proteins of the Whirly family are required for plastid genome stability in Arabidopsis thaliana and Zea mays. Absence of plastidial Whirlies favors the accumulation of rearranged molecules that arise through a non-homologous recombination mechanism mediated by regions of microhomology. This mechanism is similar to the microhomology-mediated break-induced replication (MMBIR) described in bacteria, yeast and humans. Additionally we show that plant organelles can repair double-strand breaks using a MMBIR-like pathway. Plants lacking Whirly proteins accumulate elevated levels of microhomology-mediated DNA rearrangements upon double-strand break induction, indicating that Whirlies also contribute to the accurate repair of plant organelle genomes. Using biological and structural data, we propose a working model in which Whirlies modulate the access of repair proteins and complementary DNA to single-stranded regions, thereby regulating the choice of repair pathways and maintaining plant organelle genome stability. The various aspects of this model will be tested in future experiments which should allow a better understanding of the mechanisms underlying genome stability in plant organelles.

No description available.

No description available.

To maintain the genomic integrity, cell has evolved various DNA repair pathways. Base Excision Repair pathway (BER) is one such DNA repair pathway which is dedicated to protect DNA from small lesions such as oxidation, alkylation, deamination and loss of bases. Uracil is a promutagenic base which appears in the genome as a result of misincorporation of dUTP or due to oxidative deamination of cytosine. Uracil-DNA glycosylases (UDGs) are DNA repair enzymes that initiate multistep base excision repair (BER) pathway to excise uracil from DNA. Excision of uracil generates an abasic site (APDNA). AP-sites are cytotoxic and mutagenic to the cell. AP endonucleases act downstream to UDG in this pathway and generate substrates for DNA polymerase to fill in the correct bases. The cytotoxicity of AP-sites raises the question whether uracil excision activity is coupled to AP endonuclease activity. Also, there is transient formation of single stranded DNA (ssDNA) during DNA metabolic processes such as replication, repair and recombination. ssDNA is more prone to various nucleases and DNA damaging agents. All the living organisms encode single stranded DNA binding protein (SSB) that binds to ssDNA and protects it from various damages. In addition, SSB plays a vital role during DNA replication, repair and recombination. Studies on SSBs from prototype Escherichia coli and an important human pathogen, Mycobacterium tuberculosis have shown that despite significant variations in their quaternary structures, the DNA binding and oligomerization properties of the two are similar. My PhD thesis consists of four Chapters. Chapter 1 summarizes the relevant literature review on DNA damage and repair with an emphasis on uracil DNA glycosylase and its interacting protein, SSB. Chapters 2 and 3 describe my studies on the mechanism of uracil excision repair in E. coli. Chapter 4 describes my findings on the structure-function relationship of single stranded DNA binding proteins from E. coli and M. tuberculosis. Specific details of my research are summarized as follows: (1) Analysis of the impact of allelic exchange of ung with a mutant gene encoding Uracil DNA Glycosylase attenuated in AP-DNA binding in the maintenance of genomic integrity in Escherichia coli. There are five families of UDGs. Of these, Ung proteins (family 1 UDGs) represent highly efficient and evolutionary conserved enzymes. Structural and biochemical analysis of Ung proteins has identified two conserved motif, motif A (62GQDPY66) and motif B (187HPSPLS192) in E. coli that are important for the catalysis by Ung enzyme. Y66 of motif A is in van der Waals contact with the C5 position of the uracil and prevents entry of other bases. Earlier study from the laboratory showed that the Y66W and Y66H mutants of Ung were compromised by ~7 and ~170 fold, respectively in their uracil excision activities. However, unlike the wild-type and Y66H proteins, Y66W was not inhibited by its product (uracil or AP-DNA). In this study, by fluorescence anisotropy measurements I have shown that compared with the wild-type protein, the Y66W mutant is moderately compromised and attenuated in binding to AP-DNA. Allelic exchange of ung in E. coli with ung::kan, ungY66H:amp or ungY66W:amp alleles showed ~5, ~3.0 and ~2.0 fold, respectively increase in mutation frequencies. Analysis of mutations in the rifampicin resistance determining region (RRDR) of rpoB revealed that the Y66W allele resulted in an increase in A to G (or T to C) mutations. However, the increase in A to G mutations was mitigated upon expression of wild-type Ung from a plasmid borne gene. Biochemical and computational analyses showed that the Y66W mutant maintains strict specificity for uracil excision from DNA. Interestingly, a strain deficient in AP-endonucleases also showed an increase in A to G mutations. These findings have been discussed in the context of a proposal that the residency of DNA glycosylase(s) onto the AP-sites they generate shields them until recruitment of AP-endonucleases for further repair. It is proposed that an error prone replication against AP-sites (as a result of uracil excision activities on A:U pair) may result in A to G mutations. 2. Mechanism of appearance of A to G mutations in ungY66W:amp strain of Escherichia coli. In this part of my study, I have investigated the role of error prone DNA polymerases in the mutational specificity of ungY66W:amp strain. It was observed from various studies in E. coli that, DNA polymerase IV (Pol IV) and DNA polymerase V (Pol V) are involved in error-prone replication on damaged or AP-site containing DNA. E. coli strains containing deletion of either dinB (encoding DNA Pol IV) or umuDC (encoding DNA Pol V) were generated and used to study mutation frequency and mutation spectrum. Deletion of DNA Pol V resulted in a decrease in A to G mutations in ungY66W:amp E. coli strain, suggesting that increase in A to G mutations were a consequence of error prone incorporation by DNA Pol V. 3. Structure and Function studies on Single Stranded DNA Binding Proteins from Escherichia coli and Mycobacterium tuberculosis. SSB from M. tuberculosis (MtuSSB) has similar domain organization as the EcoSSB. Moreover, the biochemical properties such as oligomerization, DNA binding affinity and minimum binding site size requirements were shown to be similar to EcoSSB. However, structural studies suggested that quaternary structures of these two SSBs are variable. In this study I have used X-ray crystal structure information of these two SSBs to generate various chimeras after swapping at various regions of SSBs. Chimeras mβ1, mβ1’β2, mβ1-β5, mβ1-β6, and mβ4-β5 SSBs were generated by substituting β1 (residues 611), β1’β2 (residues 21-45), β1-β5 (residues 1 to 111), β1-β6 including a downstream sequence (residues 1 to 130), and β4-β5 (residues 74-111) regions of EcoSSB with the corresponding sequences of MtuSSB, respectively. Additionally, mβ1’β2ESWR SSB was generated by mutating the MtuSSB specific ‘PRIY’ sequence in the β2 strand of mβ1’β2 SSB to EcoSSB specific ‘ESWR’ sequence. Biochemical characterization revealed that except for mβ1 SSB, all chimeras and a control construct lacking the C-terminal domain (ΔC SSB) efficiently bound DNA in modes corresponding to limited and unlimited modes of binding. The mβ1 SSB was also hypersensitive to chymotrypsin treatment. The mβ1-β6, MtuSSB, mβ1’β2 and mβ1-β5 constructs complemented E. coli Δssb in a dose dependent manner. Complementation by the mβ1-β5 SSB was poor. In contrast, mβ1’β2ESWR SSB complemented E. coli as well as EcoSSB. Interestingly, the inefficiently functioning SSBs resulted in an elongated cell/filamentation phenotype of E. coli. Taken together, our observations suggest that specific interactions within the DNA binding domain of the homotetrameric SSBs are crucial for their biological function.

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.