The mechanism of type IA topoisomerases.

The topology of cellular DNA is carefully controlled by enzymes called topoisomerases. By using single-molecule techniques, we monitored the activity of two type IA topoisomerases in real time under conditions in which single relaxation events were detected. The strict one-at-a-time removal of supercoils we observed establishes that these enzymes use an enzyme-bridged strand-passage mechanism that is well suited to their physiological roles and demonstrates a mechanistic unity with type II topoisomerases.

Topological challenges to DNA replication: conformations at the fork.

The unwinding of the parental DNA duplex during replication causes a positive linking number difference, or superhelical strain, to build up around the elongating replication fork. The branching at the fork and this strain bring about different conformations from that of (-) supercoiled DNA that is not being replicated. The replicating DNA can form (+) precatenanes, in which the daughter DNAs are intertwined, and (+) supercoils. Topoisomerases have the essential role of relieving the superhelical strain by removing these structures. Stalled replication forks of molecules with a (+) superhelical strain have the additional option of regressing, forming a four-way junction at the replication fork. This four-way junction can be acted on by recombination enzymes to restart replication. Replication and chromosome folding are made easier by topological domain barriers, which sequester the substrates for topoisomerases into defined and concentrated regions. Domain barriers also allow replicated DNA to be (-) supercoiled. We discuss the importance of replicating DNA conformations and the roles of topoisomerases, focusing on recent work from our laboratory.

Bypass of heterology during strand transfer by Saccharomyces cerevisiae Rad51 protein.

During recombination-mediated repair of DNA double-strand breaks, strand transfer proteins must distinguish a homologous repair template from closely related genomic sequences. However, some tolerance by strand transfer proteins for sequence differences is also critical: too much stringency will prevent recombination between different alleles of the same gene, but too much tolerance will lead to illegitimate recombination. We characterized the heterology tolerance of Saccharomyces cerevisiae Rad51 by testing bypass of small heterologous inserts in either the single- or double-stranded substrate of an in vitro strand transfer reaction that models the early steps of homologous recombination. We found that the yeast protein is rather stringent, only tolerating heterologies up to 9 bases long. The efficiency of heterology bypass depends on whether the insert is in the single- or double-stranded substrate, as well as on the location of the insert relative to the end of the double-stranded linear substrate. Rad51 is distinct in that it can catalyze strand transfer in either the 3'-->5' or 5'-->3' direction. We found that bypass of heterology was independent of the polarity of strand transfer, suggesting that the mechanism of 5'-->3' transfer is the same as that of 3'-->5' transfer.

Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements.

We show that positively supercoiled [(+) SC] DNA is the preferred substrate for Escherichia coli topoisomerase IV (topo IV). We measured topo IV relaxation of (-) and (+) supercoils in real time on single, tethered DNA molecules to complement ensemble experiments. We find that the preference for (+) SC DNA is complete at low enzyme concentration. Otherwise, topo IV relaxed (+) supercoils at a 20-fold faster rate than (-) supercoils, due primarily to about a 10-fold increase in processivity with (+) SC DNA. The preferential cleavage of (+) SC DNA in a competition experiment showed that substrate discrimination can take place prior to strand passage in the presence or absence of ATP. We propose that topo IV discriminates between (-) and (+) supercoiled DNA by recognition of the geometry of (+) SC DNA. Our results explain how topo IV can rapidly remove (+) supercoils to support DNA replication without relaxing the essential (-) supercoils of the chromosome. They also show that the rate of supercoil relaxation by topo IV is several orders of magnitude faster than hitherto appreciated, so that a single enzyme may suffice at each replication fork.

13S condensin actively reconfigures DNA by introducing global positive writhe: implications for chromosome condensation.

Xenopus 13S condensin converts interphase chromatin into mitotic-like chromosomes, and, in the presence of ATP and a type I topoisomerase, introduces (+) supercoils into DNA. The specific production of (+) trefoil knots in the presence of condensin and a type II topoisomerase shows that condensin reconfigures DNA by introducing an ordered, global, (+) writhe. Knotting required ATP hydrolysis and cell cycle-specific phosphorylation of condensin. Condensin bound preferentially to (+) supercoiled DNA in the presence of ATP but not in its absence. Our results suggest a mechanism for the compaction of chromatin by condensin during mitosis.

The topological mechanism of phage lambda integrase.

Bacteriophage lambda integrase (Int) is a versatile site-specific recombinase. In concert with other proteins, it mediates phage integration into and excision out of the bacterial chromosome. Int recombines intramolecular sites in inverse or direct orientation or sites on separate DNA molecules. This wide spectrum of Int-mediated reactions has, however, hindered our understanding of the topology of Int recombination. By systematically analyzing the topology of Int reaction products and using a mathematical method called tangles, we deduce a unified model for Int recombination. We find that, even in the absence of (-) supercoiling, all Int reactions are chiral, producing one of two possible enantiomers of each product. We propose that this chirality reflects a right-handed DNA crossing within or between recombination sites in the synaptic complex that favors formation of right-handed Holliday junction intermediates. We demonstrate that the change in linking number associated with excisive inversion with relaxed DNA is equally +2 and -2, reflecting two different substrates with different topology but the same chirality. Additionally, we deduce that integrative Int recombination differs from excisive recombination only by additional plectonemic (-) DNA crossings in the synaptic complex: two with supercoiled substrates and one with relaxed substrates. The generality of our results is indicated by our finding that two other members of the integrase superfamily of recombinases, Flp of yeast and Cre of phage P1, show the same intrinsic chirality as lambda Int.

Sedimentation and electrophoretic migration of DNA knots and catenanes.

Various site-specific recombination enzymes produce different types of knots or catenanes while acting on circular DNA in vitro and in vivo. By analysing the types of knots or links produced, it is possible to reconstruct the order of events during the reaction and to deduce the molecular "architecture" of the complexes that different enzymes form with DNA. Until recently it was necessary to use laborious electron microscopy methods to identify the types of knots or catenanes that migrate in different bands on the agarose gels used to analyse the products of the reaction. We reported recently that electrophoretic migration of different knots and catenanes formed on the same size DNA molecules is simply related to the average crossing number of the ideal representations of the corresponding knots and catenanes. Here we explain this relation by demonstrating that the expected sedimentation coefficient of randomly fluctuating knotted or catenated DNA molecules in solution shows approximately linear correlation with the average crossing number of ideal configurations of the corresponding knots or catenanes.

Muscle satellite cells from dystrophic (mdx) mice have elevated levels of heparan sulphate proteoglycan receptors for fibroblast growth factor.

Skeletal muscle has the remarkable capacity to regenerate new muscle fibres in the event of injury or disease. This capacity lies in the satellite cells, which are myogenic stem cells residing in adult muscle. While the signals that activate satellite cells to divide in vivo are not fully understood, satellite cells grown in culture respond to the mitogenic action of fibroblast growth factor (FGF). Satellite cells from the dystrophic mdx mouse are more sensitive to FGF in culture than satellite cells from normal mice. In this study we investigated the basis for this heightened sensitivity of mdx satellite cells to FGF by measuring the number and affinity of protein and heparan sulphate proteoglycan (HSPG) receptors for FGF. We found that HSPG receptors were elevated over four-fold in the mdx cells compared with cells from normal animals. We supported this observation by measuring the synthesis of heparan sulphate (HS) and chondroitin sulphate (CS) by satellite cells in culture. Mdx satellite cells synthesized approximately ten times more of these sulphated glycosaminoglycans (GAGs) than did normal cells. For muscle fibroblasts, however, we found no significant difference in the number or affinity of protein or HSPG receptors, or in the amount of sulphated GAGs synthesized, between normal and mdx cells. We propose that the increase in FGF HSPG receptors is the basis for the heightened response of mdx satellite cells to FGF in culture and may reflect exposure of the cells to growth factors in the degenerating mdx muscle.

Processive recombination by wild-type gin and an enhancer-independent mutant. Insight into the mechanisms of recombination selectivity and strand exchange.

The Gin recombinase of phage Mu selectively mediates DNA inversion between two inversely oriented recombination sites (gix) and requires the assistance of three accessory factors: negative supercoiling, an enhancer sequence, and the protein Fis. Deletion and fusion reactions are proscribed. Recombination by Gin is selective because it occurs only through a particular synaptic complex tailored for inversion. A single amino acid change in Gin allows it to carry out deletion and fusion as well as inversion and to dispense with the requirement for the accessory factors. We investigated the recombination mechanism of a mutant Gin protein by analyzing the knotted products of processive recombination by electron microscopy and gel electrophoresis. We find that, in sharp contrast to wild-type Gin, mutant Gin recombines through a broad spectrum of synaptic complexes that differ topologically. We propose a model for the selectivity of wild-type Gin recombination that explains how the dependence on the accessory factors limits recombination to inversion. In addition, we show that processive recombination by wild-type Gin is not restricted by the number of base-pairs separating the gix sites from each other and from the enhancer. This result can be explained if strand exchange proceeds through alternative paths dictated by the energetics of DNA coiling.

Inhibition of contraction of cultured muscle fibers results in increased turnover of myofibrillar proteins but not of intermediate-filament proteins.

Muscle fibers are maintained in culture in a fully contractile state and are relaxed by the addition of 10(-7) M tetrodotoxin (TTX). This toxin binds to muscle membrane Na+- channels, abolishes spontaneous contractions and causes failure of the fiber to accumulate myosin heavy chains. These effects are reversible on removal of TTX. Synthesis and accumulation kinetics have been obtained for myofibrillar and for cytoplasmic filament proteins in normal, active muscle and in TTX-relaxed muscle fibers in culture. In relaxed fibers the synthesis of most proteins remained normal or slightly elevated. However, the accumulation of all myofibrillar proteins examined was markedly inhibited in TTX-treated cultures, whereas the accumulation of cytoplasmic filament proteins was normal or slightly elevated. Myofibrillar proteins examined were alpha-actin, troponin-C, myosin fast light chain 1, myosin fast light chain 2, alpha, beta-tropomyosins and the phosphorylated forms of tropomyosin and fast light chain 2. Cytoplasmic filament proteins studied were vimentin, alpha, beta-desmin and beta, alpha-actin. We also examined the synthesis and accumulation of six unidentified muscle-specific proteins and nine unidentified nonmuscle-specific proteins. Most of these proteins showed a normal accumulation pattern in TTX-relaxed fibers. We concluded that muscle fibers made inactive by TTX display an increased instability of all myofibrillar proteins while cytoplasmic filament proteins and cytoplasmic proteins in general are relatively unaffected. We suggest that TTX interferes, in a manner as yet unidentified, with assembly and normal stability of myofibrils. Decreased assembly and/or increased instability of myofibrils would lead to increased rates of myofibrillar protein degradation.

Relation between cell activity and the distribution of cytoplasmic actin and myosin.

We documented the activity of cultured cells on time-lapse videotapes and then stained these identified cells with antibodies to actin and myosin. This experimental approach enabled us to directly correlate cellular activity with the distribution of cytoplasmic actin and myosin. When trypsinized HeLa cells spread onto a glass surface, the cortical cytoplasm was the most actively motile and random, bleb-like extensions (0.5-4.0 micrometer wide, 2-5 micrometer long) occurred over the entire surface until the cells started to spread. During spreading, ruffling membranes were found at the cell perimeter. The actin staining was found alone in the surface blebs and ruffles and together with myosin staining in the cortical cytoplasm at the bases of the blebs and ruffles. In well-spread, stationary HeLa cells most of the actin and myosin was found in stress fibers but there was also diffuse antiactin fluorescence in areas of motile cytoplasm such as leading lamellae and ruffling membranes. Similarly, all 22 of the rapidly translocating embryonic chick cells had only diffuse actin staining. Between these extremes were slow-moving HeLa cells, which had combinations of diffuse and fibrous antiactin and antimyosin staining. These results suggest that large actomyosin filament bundles are associated with nonmotile cytoplasm and that actively motile cytoplasm has a more diffuse distribution of these proteins.

Transposon-mediated conjugational transmission of nonconjugative plasmids.

When coresident with conjugative plasmid pNC21, the nonconjugative deletion F-prime pJC59, which retains the F transfer origin oriT, was transmitted to transconjugants at a frequency comparable to that of pNC21. In addition, pJC59 was transmitted as an independent plasmid, physically separate from pNC21, an example of plasmid donation. In contrast, two plasmids that are derived from F and deleted for the oriT site, pJC61 and pML31, were transmitted at frequencies 10(4) lower than that of pNC21. This low-frequency transmission was associated with the appearance of a new plasmid in the transconjugants. In the case of pML31, we determined that this new plasmid was a recombinant composed of pNC21 and pML31, the latter flanked by two copies of transposable element Tn3. We believe that this recombinant plasmid was formed as an intermediate in the transposition of Tn3 from pNC21 to pML31 and was the vehicle for conjugational transmission of pML31 genes by a process known as plasmid conduction.

Increase in conjugational transmission frequency of nonconjugative plasmids.

Addition of Eco RI fragment 6 of the Escherichia coli sex factor F to pSC101 increases the frequency of its transmission by RI-19 and ColVB. Transmission frequencies of pSC101 and two pSC101 chimeras are also increased after the putative transposition of drug resistance element Tn3 from RI-19. These increases may result from addition of an origin of conjugatinal transfer to the plasmids.