Damian Gawel

Role of Accessory DNA Polymerases in DNA Replication in Escherichia coli: Analysis of the dnaX36 Mutator Mutant

The dnaX36(TS) mutant of Escherichia coli confers a distinct mutator phenotype characterized by enhancement of transversion base substitutions and certain (-1) frameshift mutations. Here, we have further investigated the possible mechanism(s) underlying this mutator effect, focusing in particular on the role of the various E. coli DNA polymerases. The dnaX gene encodes the tau subunit of DNA polymerase III (Pol III) holoenzyme, the enzyme responsible for replication of the bacterial chromosome. The dnaX36 defect resides in the C-terminal domain V of tau, essential for interaction of tau with the alpha (polymerase) subunit, suggesting that the mutator phenotype is caused by an impaired or altered alpha-tau interaction. We previously proposed that the mutator activity results from aberrant processing of terminal mismatches created by Pol III insertion errors. The present results, including lack of interaction of dnaX36 with mutM, mutY, and recA defects, support our assumption that dnaX36-mediated mutations originate as errors of replication rather than DNA damage-related events. Second, an important role is described for DNA Pol II and Pol IV in preventing and producing, respectively, the mutations. In the system used, a high fraction of the mutations is dependent on the action of Pol IV in a (dinB) gene dosage-dependent manner. However, an even larger but opposing role is deduced for Pol II, revealing Pol II to be a major editor of Pol III mediated replication errors. Overall, the results provide insight into the interplay of the various DNA polymerases, and of tau subunit, in securing a high fidelity of replication.

A novel mutator of Escherichia coli carrying a defect in the dgt gene, encoding a dGTP triphosphohydrolase.

A novel mutator locus in Escherichia coli was identified from a collection of random transposon insertion mutants. Several mutators in this collection were found to have an insertion in the dgt gene, encoding a previously characterized dGTP triphosphohydrolase. The mutator activity of the dgt mutants displays an unusual specificity. Among the six possible base pair substitutions in a lacZ reversion system, the G.C-->C.G transversion and A.T-->G.C transition are strongly enhanced (10- to 50-fold), while a modest effect (two- to threefold) is also observed for the G.C-->A.T transition. Interestingly, a two- to threefold reduction in mutant frequency (antimutator effect) is observed for the G.C-->T.A transversion. In the absence of DNA mismatch repair (mutL) some of these effects are reduced or abolished, while other effects remain unchanged. Analysis of these effects, combined with the DNA sequence contexts in which the reversions take place, suggests that alterations of the dGTP pools as well as alterations in the level of some modified dNTP derivatives could affect the fidelity of in vivo DNA replication and, hence, account for the overall mutator effects.

Lack of Strand Bias in UV-Induced Mutagenesis in Escherichia coli

We have investigated whether UV-induced mutations are created with equal efficiency on the leading and lagging strands of DNA replication. We employed an assay system that permits measurement of mutagenesis in the lacZ gene in pairs of near-identical strains. Within each pair, the strains differ only in the orientation of the lacZ gene with respect to the origin of DNA replication. Depending on this orientation, any lacZ target sequence will be replicated in one orientation as a leading strand and as a lagging strand in the other orientation. In contrast to previous results obtained for mutations resulting from spontaneous replication errors or mutations resulting from the spontaneous SOS mutator effect, measurements of UV-induced mutagenesis in uvrA strains fail to show significant differences between the two target orientations. These data suggest that SOS-mediated mutagenic translesion synthesis on the Escherichia coli chromosome may occur with equal or similar probability on leading and lagging strands.

Effect of dNTP pool alterations on fidelity of leading and lagging strand DNA replication in E. coli.

The fidelity with which organisms replicate their chromosomal DNA is of considerable interest. Detailed studies in the bacterium Escherichia coli have indicated that the fidelity of leading- and lagging-strand DNA replication is not the same, based on experiments in which the orientation of certain mutational targets on the chromosome was inverted relative to the movement of the replication fork: different mutation rates for several base-pair substitutions were observed depending on this orientation. While these experiments are indicative of differential replication fidelity in the two strands, a conclusion whether leading or lagging strand is the more accurate depends on knowledge of the primary mispairing error responsible for the base substitutions in question. A broad analysis of in vitro base-pairing preferences of DNA polymerases led us to propose that lagging-strand is the more accurate strand. In the present work, we present more direct in vivo evidence in support of this proposal. We determine the orientation dependence of mutant frequencies in ndk and dcd strains, which carry defined dNTP pool alterations. As these pool alterations lead to predictable effects on the array of possible mispairing errors, they mark the strands in which the observed errors occur. The combined results support the proposed higher accuracy of lagging-strand replication in E. coli.

Motor unit loss estimation by the multipoint incremental MUNE method in children with spinal muscular atrophy – A preliminary study

Quantitative EMG reflects denervation of muscles after lower motor neuron degeneration in spinal muscular atrophy (SMA) but does not reflect actual motor unit loss. The aim of our study was to assess the value of the multipoint incremental motor unit number estimation (MUNE) method in the modification by Shefner in estimating motor unit loss in SMA. The number of motor units, the mean amplitude of an average surface-detected single motor unit potential (SMUP), and the amplitude of compound motor action potentials (CMAP) were estimated in 14 children with SMA in the abductor pollicis brevis (ABP). Significant differences in MUNE values and SMUP and CMAP amplitude were found between the SMA and control groups (P < 0.0001). MUNE values correlated with Hammersmith Functional Motor Scale (HFMS) scores (P < 0.05). Increased SMUP amplitude values correlated with decreased HFMS scores (P < 0.05). The study confirms that MUNE method in the modification by Shefner is a useful tool reflecting motor unit loss in SMA, and it is easy to perform and well tolerated. MUNE and SMUP amplitude seemed to be sensitive parameters reflecting motor dysfunction in SMA but a longitudinal study in a larger number of subjects is needed.

dnaX36 mutator of Escherichia coli: effects of the tau subunit of the DNA polymerase III holoenzyme on chromosomal DNA replication fidelity.

The Escherichia coli dnaX36 mutant displays a mutator effect, reflecting a fidelity function of the dnaX-encoded τ subunit of the DNA polymerase III (Pol III) holoenzyme. We have shown that this fidelity function (i) applies to both leading- and lagging-strand synthesis, (ii) is independent of Pol IV, and (iii) is limited by Pol II.

The Role of Podoplanin in the Biology of Differentiated Thyroid Cancers

Podoplanin (PDPN), a mucin-type transmembrane glycoprotein specific to the lymphatic system is expressed in a variety of human cancers, and is regarded as a factor promoting tumor progression. The purpose of this study was to elucidate the molecular role of PDPN in the biology of thyroid cancer cells. PDPN expression was evaluated in primary thyroid carcinomas and thyroid carcinoma cell lines by RT-qPCR, Western blotting, IF and IHC. To examine the role of podoplanin in determining a cells malignant potential (cellular migration, invasion, proliferation, adhesion, motility, apoptosis), a thyroid cancer cell line with silenced PDPN expression was used. We observed that PDPN was solely expressed in the cancer cells of 40% of papillary thyroid carcinoma (PTC) tissues. Moreover, PDPN mRNA and protein were highly expressed in PTC-derived TPC1 and BcPAP cell lines but were not detected in follicular thyroid cancer derived cell lines. PDPN knock-down significantly decreased cellular invasion, and modestly reduced cell migration, while proliferation and adhesion were not affected. Our results demonstrate that PDPN mediates the invasive properties of cells derived from papillary thyroid carcinomas, suggesting that podoplanin might promote PTC progression.

Structure of Escherichia coli dGTP Triphosphohydrolase: A Hexameric Enzyme With DNA Effector Molecules

Background: The Escherichia coli Dgt enzyme hydrolyzes the important DNA building block dGTP, but the cellular role of this activity is still unclear. Results: The enzyme is shown to be a hexameric structure containing regulatory DNA molecules. Conclusion: DNA mediates the regulation of dGTPase activity in the cell. Significance: This is the first demonstration of regulation of dNTPase by DNA. The Escherichia coli dgt gene encodes a dGTP triphosphohydrolase whose detailed role still remains to be determined. Deletion of dgt creates a mutator phenotype, indicating that the dGTPase has a fidelity role, possibly by affecting the cellular dNTP pool. In the present study, we have investigated the structure of the Dgt protein at 3.1-Å resolution. One of the obtained structures revealed a protein hexamer that contained two molecules of single-stranded DNA. The presence of DNA caused significant conformational changes in the enzyme, including in the catalytic site of the enzyme. Dgt preparations lacking DNA were able to bind single-stranded DNA with high affinity (Kd ∼ 50 nm). DNA binding positively affected the activity of the enzyme: dGTPase activity displayed sigmoidal (cooperative) behavior without DNA but hyperbolic (Michaelis-Menten) kinetics in its presence, consistent with a specific lowering of the apparent Km for dGTP. A mutant Dgt enzyme was also created containing residue changes in the DNA binding cleft. This mutant enzyme, whereas still active, was incapable of DNA binding and could no longer be stimulated by addition of DNA. We also created an E. coli strain containing the mutant dgt gene on the chromosome replacing the wild-type gene. The mutant also displayed a mutator phenotype. Our results provide insight into the allosteric regulation of the enzyme and support a physiologically important role of DNA binding.

Diagnostic value of blink reflex in multisystem atrophy, progressive supranuclear palsy and Parkinson disease

UNLABELLED Abnormal blink reflex (BR) is a result of reticular brainstem pathways dysfunction and seems to be one of the features of brain degenerative disorders. The aim of the study was to estimate the diagnostic value of blink reflex in neurodegenerative diseases such as: multisystem atrophy (MSA), progressive supranuclear palsy (PSP) and Parkinson disease (PD). Material consisted of 99 patients with clinically probable MSA (51), PSP (28) and PD (20). MSA patients were divided into two subgroups, with dominant cerebellar (MSA-C) and parkinsonian signs (MSA-P). The mean age of patients was 64.9 years (47-79 years); males - 55.3%. Blink reflex was obtained in a typical way. RESULTS The significant differences in mean values of blink reflex latencies between PD and other subgroups (MSA-P, MSA-C, PSP) were found, but all of them were in normal range. In individual patients with PD and PSP (50% and 18%, respectively) delayed R2 latencies were recorded. CONCLUSIONS The most frequently abnormal blink reflexes, comparing the MSA, PSP and PD groups, were present in PD patients. We postulate that this may be explained by pathological influence of nigrostriatal pathway on the circuit linking the basal ganglia, cerebellum and brainstem.

Electrophysiological features of lower motor neuron involvement in progressive supranuclear palsy

BACKGROUND Abnormalities of the spinal cord were considered uncommon in progressive supranuclear palsy (PSP), and therefore spinal symptoms were not included among PSP characteristic features. However there have been some neuropathological reports of spinal cord lesions in patients with PSP. The aim of our study was to find out if the possible lower motor neuron involvement in PSP is reflected by electromyographic (EMG) and/or electroneurographic (ENG) abnormalities. MATERIAL 24 patients with clinically probable PSP (mean age 67.5 yrs; 66% males) were included in the study. The control group for ENG studies consisted 25 age matched healthy volunteers. METHODS Nerve conduction studies in the ulnar, peroneal and sural nerves and EMG of the first interosseus dorsal and tibial anterior muscles were performed. RESULTS The only ENG abnormality observed was decreased compound muscle action potential (CMAP) and sensory nerve action potential (SNAP) amplitudes in the ulnar nerve. Such decrease was registered in 8.3% and 20% of PSP patients respectively. There was no significant difference between the values of ENG parameters between PSP patients and the control group. In EMG abnormalities suggesting chronic reinnervation were recorded in the first interosseous dorsal (FID) muscle in 45.8%, and in the tibialis anterior (TA) muscle in 37.5% of PSP patients. A significant correlation was found between the age of PSP patients and their mean motor unit potential (MUP) amplitude in TA muscle (p=0.04) and also between the age of onset and MUP amplitude in both, the TA and FID muscles (p=0.026 and p=0.03 respectively). CONCLUSIONS In PSP, neurogenic EMG abnormalities in skeletal muscles are present in nearly half the patients suggesting a loss of motor neurons in the anterior horns of the spinal cord which is in line with our histopathological findings. In contrast, electrophysiological signs of neuropathy in peripheral nerves in PSP are very rare. Concluding, although PSP is characterized by the pathological process in specific basal ganglia and brainstem areas, our electromyographic study suggests the need for broadening the spectrum of PSP for lower motor neurons degeneration.