Biomedical subjects

Mark D Sutton

Publications and source records attributed to Mark D Sutton.

15 recordsLinked to original sources

PubMed2006

Role of Pseudomonas aeruginosa dinB-encoded DNA polymerase IV in mutagenesis.

Pseudomonas aeruginosa is a human opportunistic pathogen that chronically infects the lungs of cystic fibrosis patients and is the leading cause of morbidity and mortality of people afflicted with this disease. A striking correlation between mutagenesis and the persistence of P. aeruginosa has been reported. In other well-studied organisms, error-prone replication by Y family DNA polymerases contributes significantly to mutagenesis. Based on an analysis of the PAO1 genome sequence, P. aeruginosa contains a single Y family DNA polymerase encoded by the dinB gene. As part of an effort to understand the mechanisms of mutagenesis in P. aeruginosa, we have cloned the dinB gene of P. aeruginosa and utilized a combination of genetic and biochemical approaches to characterize the activity and regulation of the P. aeruginosa DinB protein (DinB(Pa)). Our results indicate that DinB(Pa) is a distributive DNA polymerase that lacks intrinsic proofreading activity in vitro. Modest overexpression of DinB(Pa) from a plasmid conferred a mutator phenotype in both Escherichia coli and P. aeruginosa. An examination of this mutator phenotype indicated that DinB(Pa) has a propensity to promote C-->A transversions and -1 frameshift mutations within poly(dGMP) and poly(dAMP) runs. The characterization of lexA+ and DeltalexA::aacC1 P. aeruginosa strains, together with in vitro DNA binding assays utilizing cell extracts or purified P. aeruginosa LexA protein (LexA(Pa)), indicated that the transcription of the dinB gene is regulated as part of an SOS-like response. The deletion of the dinB(Pa) gene sensitized P. aeruginosa to nitrofurazone and 4-nitroquinoline-1-oxide, consistent with a role for DinB(Pa) in translesion DNA synthesis over N2-dG adducts. Finally, P. aeruginosa exhibited a UV-inducible mutator phenotype that was independent of dinB(Pa) function and instead required polA and polC, which encode DNA polymerase I and the second DNA polymerase III enzyme, respectively. Possible roles of the P. aeruginosa dinB, polA, and polC gene products in mutagenesis are discussed.

Bacterial Proteins↗

PubMed2005

Specific amino acid residues in the beta sliding clamp establish a DNA polymerase usage hierarchy in Escherichia coli.

Escherichia coli dnaN159 strains encode a mutant form of the beta sliding clamp (beta159), causing them to display altered DNA polymerase (pol) usage. In order to better understand mechanisms of pol selection/switching in E. coli, we have further characterized pol usage in the dnaN159 strain. The dnaN159 allele contains two amino acid substitutions: G66E (glycine-66 to glutamic acid) and G174A (glycine-174 to alanine). Our results indicated that the G174A substitution impaired interaction of the beta clamp with the alpha catalytic subunit of pol III. In light of this finding, we designed two additional dnaN alleles. One of these dnaN alleles contained a G174A substitution (beta-G174A), while the other contained D173A, G174A and H175A substitutions (beta-173-175). Examination of strains bearing these different dnaN alleles indicated that each conferred a distinct UV sensitive phenotype that was dependent upon a unique combination of Delta polB (pol II), Delta dinB (pol IV) and/or Delta umuDC (pol V) alleles. Taken together, these findings indicate that mutations in the beta clamp differentially affect the functions of these three pols, and suggest that pol II, pol IV and pol V are capable of influencing each others' abilities to gain access to the replication fork. These findings are discussed in terms of a model whereby amino acid residues in the vicinity of those mutated in beta159 (G66 and G174) help to define a DNA polymerase usage hierarchy in E. coli following UV irradiation.

Amino Acid Substitution↗

PubMed2005

Metamorphosis in a Silurian barnacle.

Exceptionally preserved fossils from the Wenlock Series (Silurian) of Herefordshire, UK, provide unique evidence of metamorphosis from free-swimming cyprid larva to attached juvenile in a Palaeozoic barnacle. The larva had large brush-like anterior limbs. The juvenile shows the head transformed into a stalk and the development of the primordial condition of five mineralized plates within the carapace. The discovery of a cyprid larva indicates that crown group cirripedes had evolved by the Silurian.

Animals↗

PubMed2005

Silurian brachiopods with soft-tissue preservation.

'Articulated' rhynchonelliformean brachiopods are abundant shelly fossils, but the direct fossil record of their soft parts was hitherto confined to a single pyritized trace possibly representing a lophophore. Anatomical knowledge of extinct rhynchonelliformeans relies heavily on analogies to extant species; these analogies are untested for stem-group clades. The Silurian Herefordshire (UK) Konservat-Lagerstätte (about 425 Myr bp) yields exceptionally preserved three-dimensional fossils that provide unrivalled insights into the palaeobiology of a variety of invertebrates. The fossils are preserved as calcitic void in-fills in carbonate concretions within a volcaniclastic horizon, and are reconstructed digitally. Here we describe a stem-group rhynchonelliformean specimen from this deposit; it most probably belongs in the order Orthida. A robust ridged pedicle with distal rootlets is preserved, together with a lophophore and other soft-tissue structures. The pedicle morphology is novel, urging caution in inferring stem-group rhynchonelliformean anatomy from that of crown-group species. Smaller brachiopods are attached to the specimen; these include a probable atrypide, with pedicle and marginal setae preserved.

Animals↗

PubMed2005

Parkin stabilizes microtubules through strong binding mediated by three independent domains.

Mutations of parkin, a protein-ubiquitin isopeptide ligase (E3), appear to be the most frequent cause of familial Parkinson's disease (PD). Our previous studies have demonstrated that parkin binds strongly to alpha/beta tubulin heterodimers and microtubules. Here we show that the strong binding between parkin and tubulin, as well as that between parkin and microtubules, was mediated by three independent domains: linker, RING1, and RING2. These redundant strong interactions made it virtually impossible to separate parkin from microtubules by high concentrations of salt (3.8 m) or urea (0.5 m). Parkin co-purified with tubulin and was found in highly purified tubulin preparation. Expression of either full-length parkin or any of its three microtubule-binding domains significantly attenuated colchicine-induced microtubule depolymerization. The abilities of parkin to bind to and stabilize microtubules were not affected by PD-linked mutations that abrogate its E3 ligase activity. Thus, the tubulin/microtubule-binding activity of parkin and its E3 ligase activity are independent. The strong binding between parkin and tubulin/microtubules through three redundant interaction domains may not only stabilize microtubules but also guarantee the anchorage of this E3 ligase on microtubules. Because many misfolded proteins are transported on microtubules, the localization of parkin on microtubules may provide an important environment for its E3 ligase activity toward misfolded substrates.

Antineoplastic Agents, Phytogenic↗

PubMed2005

Mutant forms of the Escherichia colibeta sliding clamp that distinguish between its roles in replication and DNA polymerase V-dependent translesion DNA synthesis.

The Escherichia colibeta sliding clamp is proposed to play an important role in regulating DNA polymerase traffic at the replication fork. As part of an ongoing effort to understand how organisms manage the actions of their multiple DNA polymerases, we examined the ability of several mutant forms of the beta clamp to function in DNA polymerase V- (pol V-) dependent translesion DNA synthesis (TLS) in vivo. Our results indicate that a dnaN159 strain, which expresses a temperature sensitive form of the beta clamp, was impaired for pol V-dependent TLS at the permissive temperature of 37 degrees C. This defect was complemented by a plasmid that expressed near-physiological levels of the wild-type clamp. Using a dnaN159 mutant strain, together with various plasmids expressing mutant forms of the clamp, we determined that residues H148 through R152, which comprise a portion of a solvent exposed loop, as well as position P363, which is located in the C-terminal tail of the beta clamp, are critically important for pol V-dependent TLS in vivo. In contrast, these same residues appear to be less critical for pol III-dependent replication. Taken together, these findings indicate that: (i) the beta clamp plays an essential role in pol V-dependent TLS in vivo and (ii) pol III and pol V interact with non-identical surfaces of the beta clamp.

Amino Acid Sequence↗

PubMed2005

Roles of the Escherichia coli RecA protein and the global SOS response in effecting DNA polymerase selection in vivo.

The Escherichia coli beta sliding clamp protein is proposed to play an important role in effecting switches between different DNA polymerases during replication, repair, and translesion DNA synthesis. We recently described how strains bearing the dnaN159 allele, which encodes a mutant form of the beta clamp (beta159), display a UV-sensitive phenotype that is suppressed by inactivation of DNA polymerase IV (M. D. Sutton, J. Bacteriol. 186:6738-6748, 2004). As part of an ongoing effort to understand mechanisms of DNA polymerase management in E. coli, we have further characterized effects of the dnaN159 allele on polymerase usage. Three of the five E.coli DNA polymerases (II, IV, and V) are regulated as part of the global SOS response. Our results indicate that elevated expression of the dinB-encoded polymerase IV is sufficient to result in conditional lethality of the dnaN159 strain. In contrast, chronically activated RecA protein, expressed from the recA730 allele, is lethal to the dnaN159 strain, and this lethality is suppressed by mutations that either mitigate RecA730 activity (i.e., DeltarecR), or impair the activities of DNA polymerase II or DNA polymerase V (i.e., DeltapolB or DeltaumuDC). Thus, we have identified distinct genetic requirements whereby each of the three different SOS-regulated DNA polymerases are able to confer lethality upon the dnaN159 strain, suggesting the presence of multiple mechanisms by which the actions of the cell's different DNA polymerases are managed in vivo.

DNA Polymerase III↗

PubMed2004

A Silurian sea spider.

Pycnogonids (sea spiders) are marine arthropods numbering some 1,160 extant species. They are globally distributed in depths of up to 6,000 metres, and locally abundant; however, their typically delicate form and non-biomineralized cuticle has resulted in an extremely sparse fossil record that is not accepted universally. There are two opposing views of their phylogenetic position: either within Chelicerata as sister group to the euchelicerates, or as a sister taxon to all other euarthropods. The Silurian Herefordshire Konservat-Lagerstatte in England (approximately 425 million years (Myr) bp) yields exceptionally preserved three-dimensional fossils that provide unrivalled insights into the palaeobiology of a variety of invertebrates. The fossils are preserved as calcitic void in-fills in carbonate concretions within a volcaniclastic horizon, and are reconstructed digitally. Here we describe a new pycnogonid from this deposit, which is the oldest adult sea spider by approximately 35 Myr and the most completely known fossil species. The large chelate first appendage is consistent with a chelicerate affinity for the pycnogonids. Cladistic analyses place the new species near the base of the pycnogonid crown group, implying that the latter had arisen by the Silurian period.

Animals↗

PubMed2004

Identification of specific amino acid residues in the E. coli beta processivity clamp involved in interactions with DNA polymerase III, UmuD and UmuD'.

Variants of a pentapeptide sequence (QL[S/F]LF), referred to as the eubacterial clamp-binding motif, appear to be required for certain proteins to bind specifically to the Escherichia coli beta sliding clamp, apparently by making contact with a hydrophobic pocket located at the base of the C-terminal tail of each beta protomer. Although both UmuC (DNA pol V) and the alpha catalytic subunit of DNA polymerase III (pol III) each bear a reasonable match to this motif, which appears to be required for their respective interactions with the clamp, neither UmuD not UmuD' do. As part of an ongoing effort to understand how interactions involving the different E. coli umuDC gene products and components of DNA polymerase III help to coordinate DNA replication with a DNA damage checkpoint control and translesion DNA synthesis (TLS) following DNA damage, we characterized the surfaces on beta important for its interactions with the two forms of the umuD gene product. We also characterized the surface of beta important for its interaction with the alpha catalytic subunit of pol III. Our results indicate that although UmuD, UmuD' and alpha share some common contacts with beta, each also makes unique contacts with the clamp. These findings suggest that differential interactions of UmuD and UmuD' with beta impose a DNA damage-responsive conditionality on how beta interacts with the translesion DNA polymerase UmuC. This is formally analogous to how post-translational modification of the eukaryotic PCNA clamp influences mutagenesis. We discuss the implications of our findings in terms of how E. coli might coordinate the actions of the umuDC gene products with those of pol III, as well as for how organisms in general might manage the actions of their multiple DNA polymerases.

Amino Acids↗

PubMed2004

A new phyllocarid (Crustacea: Malacostraca) from the Silurian Fossil-Lagerstätte of Herefordshire, UK.

A new three-dimensionally preserved arthropod, Cinerocaris magnifica, from the Wenlock Series (Silurian) of Herefordshire, UK, is described and assigned to the Phyllocarida (Crustacea). The description and reconstruction are based on specimens that have been serially ground, reconstructed by computer and rendered in three dimensions as coloured virtual models. Cinerocaris magnifica displayed the tagmosis characteristic of phyllocarids, with eight thoracic and seven abdominal somites, terminating in a telson with furca. The remarkable preservation of the appendages makes this the earliest completely known malacostracan crustacean. Two pairs of antennae (the first with two flagella) were followed by a mandible and first maxilla, each with a slender palp-like ramus. The second maxilla consisted of a limb stem with endites and an endopod that tapered distally. There was no exopod. The thoracopods comprised a limb stem with six or seven endites, an arrangement previously known only in entomostracans, and an endopod with about five endites. Flap-like outer rami correspond to an exopod and epipods. The pleopods bore two long slender oar-blade-like rami. Cladistic analysis places C. magnifica as a plesion within the Echinocaridina. It provides critical evidence of the limb morphology of an early malacostracan, which will be important in understanding crustacean evolution.

Animals↗

PubMed2004

The Escherichia coli dnaN159 mutant displays altered DNA polymerase usage and chronic SOS induction.

The Escherichia coli beta sliding clamp, which is encoded by the dnaN gene, is reported to interact with a variety of proteins involved in different aspects of DNA metabolism. Recent findings indicate that many of these partner proteins interact with a common surface on the beta clamp, suggesting that competition between these partners for binding to the clamp might help to coordinate both the nature and order of the events that take place at a replication fork. The purpose of the experiments discussed in this report was to test a prediction of this model, namely, that a mutant beta clamp protein impaired for interactions with the replicative DNA polymerase (polymerase III [Pol III]) would likewise have impaired interactions with other partner proteins and hence would display pleiotropic phenotypes. Results discussed herein indicate that the dnaN159-encoded mutant beta clamp protein (beta159) is impaired for interactions with the alpha catalytic subunit of Pol III. Moreover, the dnaN159 mutant strain displayed multiple replication and repair phenotypes, including sensitivity to UV light, an absolute dependence on the polymerase activity of Pol I for viability, enhanced Pol V-dependent mutagenesis, and altered induction of the global SOS response. Furthermore, epistasis analyses indicated that the UV sensitivity of the dnaN159 mutant was suppressed by (not epistatic with) inactivation of Pol IV (dinB gene product). Taken together, these findings suggest that in the dnaN159 mutant, DNA polymerase usage, and hence DNA replication, repair, and translesion synthesis, are altered. These findings are discussed in terms of a model to describe how the beta clamp might help to coordinate protein traffic at the replication fork.

DNA Polymerase I↗

PubMed2003

An ostracode crustacean with soft parts from the Lower Silurian.

An exceptionally well-preserved ostracode from the Silurian of Herefordshire, United Kingdom, provides a rare view of the fossilized soft-part anatomy of this important group of living crustaceans and confirms that Ostracoda were extant in the Paleozoic. The fossil has striking similarity to the extant myodocopid family Cylindroleberididae, to which it is assigned, and demonstrates remarkable evolutionary stasis over 425 million years. The fossil is identified as a male on the basis of its copulatory organ.

Animals↗

PubMed2002

The arthropod Offacolus kingi (Chelicerata) from the Silurian of Herefordshire, England: computer based morphological reconstructions and phylogenetic affinities.

The small, non-biomineralized, three-dimensionally preserved arthropod Offacolus kingi Orr et al. from the Wenlock Series (Silurian) of Herefordshire, England, is re-evaluated, and the new family Offacolidae erected. This new study is based on specimens which have been serially ground, reconstructed by computer and rendered in the round as coloured models. Offacolus possesses a prosomal appendage array similar to that of Limulus, but also bears robust and setose exopods on appendages II-V which are unlike those found in any other arthropods. Opisthosomal appendages are similar in number and morphology to the book-gills of Limulus. Cladistic analysis places Offacolus basally within the Chelicerata, as a sister taxon to the eurypterids and extant chelicerates, but more derived than the Devonian Weinbergina.

Animals↗

PubMed2002

Posttranslational modification of the umuD-encoded subunit of Escherichia coli DNA polymerase V regulates its interactions with the beta processivity clamp.

The Escherichia coli umuDC (pol V) gene products participate in both a DNA damage checkpoint control and translesion DNA synthesis. Interactions of the two umuD gene products, the 139-aa UmuD and the 115-aa UmuD' proteins, with components of the replicative DNA polymerase (pol III), are important for determining which biological role the umuDC gene products will play. Here we report our biochemical characterizations of the interactions of UmuD and UmuD' with the pol III beta processivity clamp. These analyses demonstrate that UmuD possesses a higher affinity for beta than does UmuD' because of the N-terminal arm of UmuD (residues 1-39), much of which is missing in UmuD'. Furthermore, we have identified specific amino acid residues of UmuD that crosslink to beta with p-azidoiodoacetanilide, defining the domain of UmuD important for the interaction. We have recently proposed a model for the solution structure of UmuD(2) in which the N-terminal arm of each protomer makes extensive contacts with the C-terminal globular domain of its intradimer partner, masking part of each surface. Taken together, our findings suggest that UmuD(2) has a higher affinity for the beta-clamp than does UmuD'(2) because of the structures of its N-terminal arms. Viewed in this way, posttranslational modification of UmuD, which entails the removal of its N-terminal 24 residues to yield UmuD', acts in part to attenuate the affinity of the umuD gene product for the beta-clamp. Implications of these structure-function analyses for the checkpoint and translesion DNA synthesis functions of the umuDC gene products are discussed.

Acetanilides↗

PubMed2002

A model for the structure of the Escherichia coli SOS-regulated UmuD2 protein.

The ubiquitous Y-family of DNA polymerases, exemplified by the Escherichia coli UmuC protein (the catalytic subunit of DNA Pol V), possess the remarkable ability to replicate imperfect DNA templates that cannot be replicated by other types of DNA polymerases. Since this ability comes at the cost of a reduced fidelity, it is important that organisms manage these unique polymerases to coordinate their actions with those of the replication machinery. In E. coli, it is becoming evident that a sophisticated series of protein-protein interactions involving the two forms of the umuD gene product, UmuD and UmuD' and components of the replicative DNA polymerase serve to manage the actions of the umuC-encoded DNA polymerase. The purpose of this study was to better understand how structural differences between UmuD2 and UmuD2' help to determine which biological role the umuDC gene products will play; the UmuD2C complex functions as a DNA damage checkpoint effector, while the UmuD2'C complex participates in translesion DNA synthesis, which serves as the mechanistic basis for most chemical and UV light mutagenesis. Based on the results of a combination of disulfide cross-linking experiments, measurements of solvent accessibility and electron paramagnetic spin resonance (EPR) studies, we have developed a refined model for the structure of the UmuD2 homodimer. In the model that we are proposing, the N-terminal arms of UmuD (residues 1-39) form an extended interface in the UmuD2 homodimer by folding down over the globular domains of their intradimer partners. As a result, significant portions of the surface of each globular domain are buried in the UmuD2 homodimer. Based on the structure of the UmuD2' homodimer, both in the crystal and in solution, these same surfaces are exposed. Implications of these structural differences between the UmuD2 and the UmuD2' homodimers with respect to their roles in managing the actions of the umuC-encoded DNA polymerase are discussed.

Binding Sites↗