A Model for the Evolution of Biological Specificity: a Cross-Reacting DNA-Binding Protein Causes Plasmid Incompatibility

Few biological systems permit rigorous testing of how changes in DNA sequence give rise to adaptive phenotypes. In this study, we sought a simplified experimental system with a detailed understanding of the genotype-to-phenotype relationship that could be altered by environmental perturbations. We focused on plasmid fitness, i.e., the ability of plasmids to be stably maintained in a bacterial population, which is dictated by the plasmid''s replication and segregation machinery. Although plasmid replication depends on host proteins, the type II plasmid partitioning (Par) machinery is entirely plasmid encoded and relies solely on three components: parC, a centromere-like DNA sequence, ParR, a DNA-binding protein that interacts with parC, and ParM, which forms actin-like filaments that push two plasmids away from each other at cell division. Interactions between the Par operons of two related plasmids can cause incompatibility and the reduced transmission of one or both plasmids. We have identified segregation-dependent plasmid incompatibility between the highly divergent Par operons of plasmids pB171 and pCP301. Genetic and biochemical studies revealed that the incompatibility is due to the functional promiscuity of the DNA-binding protein ParR_pB171, which interacts with both parC DNA sequences to direct plasmid segregation, indicating that the lack of DNA binding specificity is detrimental to plasmid fitness in this environment. This study therefore successfully utilized plasmid segregation to dissect the molecular interactions between genotype, phenotype, and fitness.     

Centromere parC of plasmid R1 is curved

The centromere sequence parC of Escherichia coli low-copy-number plasmid R1 consists of two sets of 11 bp iterated sequences. Here we analysed the intrinsic sequence-directed curvature of parC by its migration anomaly in polyacrylamide gels. The 159 bp long parC is strongly curved with anomaly values (k-factors) close to 2. The properties of the parC curvature agree with those of other curved DNA sequences. parC contains two regions of 5-fold repeated iterons separated by 39 bp. We modified 4 bp within this intermediate sequence so that we could analyse the two 5-fold repeated regions independently. The analysis shows that the two repeat regions are not independently curved parts of parC but that the overall curvature is a property of the whole fragment. Since the centromere sequence of an E.coli plasmid as well as eukaryotic centromere sequences show DNA curvature, we speculate that curvature might be a general property of centromeres.     

Characterization of an active partition system for the Enterococcus faecalis pheromone-responding plasmid pAD1

Enterococcus faecalis plasmid pAD1 is a 60-kb conjugative, low-copy-number plasmid that encodes a mating response to the peptide sex pheromone cAD1 and a cytolytic exotoxin that contributes to virulence. Although aspects of conjugation have been studied extensively, relatively little is known about the control of pAD1 maintenance. Previous work on pAD1 identified a 5-kb region of DNA sufficient to support replication, copy control, and stable inheritance (K. E. Weaver, D. B. Clewell, and F. An, J. Bacteriol. 175:1900-1909, 1993), and recently, the pAD1 replication initiator (RepA) and the origin of vegetative replication (oriV) were characterized (M. V. Francia, S. Fujimoto, P. Tille, K. E. Weaver, and D. B. Clewell, J. Bacteriol. 186:5003-5016, 2004). The present study focuses on the adjacent determinants repB and repC, as well as a group of 25 8-bp direct repeats (iterons with the consensus sequence TAGTARRR) located between the divergently transcribed repA and repB. Through mutagenesis and trans-complementation experiments, RepB (a 33-kDa protein, a member of the ParA superfamily of ATPases) and RepC (a protein of 14.4 kDa) were shown to be required for maximal stabilization. Both were active in trans. The iteron region was shown to act as the pAD1 centromere-like site. Purified RepC was shown by DNA mobility shift and DNase I footprinting analyses to interact in a sequence-specific manner with the iteron repeats upstream of the repBC locus. The binding of RepC to the iteron region was shown to be modified by RepB in the presence of ATP via a possible interaction with the RepC-iteron complex. RepB did not bind to the iteron region in the absence of RepC.     

The Structure and Assembly Dynamics of Plasmid Actin AlfA Imply a Novel Mechanism of DNA Segregation

Bacterial cytoskeletal proteins participate in a variety of processes, including cell division and DNA segregation. Polymerization of one plasmid-encoded, actin-like protein, ParM, segregates DNA by pushing two plasmids in opposite directions and forms the current paradigm for understanding active plasmid segregation. An essential feature of ParM assembly is its dynamically instability, the stochastic switching between growth and disassembly. It is unclear whether dynamic instability is an essential feature of all actin-like protein-based segregation mechanisms or whether bacterial filaments can segregate plasmids by different mechanisms. We expressed and purified AlfA, a plasmid-segregating actin-like protein from Bacillus subtilis, and found that it forms filaments with a unique structure and biochemistry; AlfA nucleates rapidly, polymerizes in the presence of ATP or GTP, and forms highly twisted, ribbon-like, helical filaments with a left-handed pitch and protomer nucleotide binding pockets rotated away from the filament axis. Intriguingly, AlfA filaments spontaneously associate to form uniformly sized, mixed-polarity bundles. Most surprisingly, our biochemical characterization revealed that AlfA does not display dynamic instability and is relatively stable in the presence of diphosphate nucleotides. These results (i) show that there is remarkable structural diversity among bacterial actin filaments and (ii) indicate that AlfA filaments partition DNA by a novel mechanism.Bacteria contain multiple filament-forming proteins related to eukaryotic actin (6). These actin-like proteins have multiple cellular roles, including determination of cell shape (18), arrangement of organelles (20), and segregation of DNA (36). Little is known about the assembly dynamics of most of these proteins or about the identities and activities of the factors that regulate them. The widely expressed actin-like protein MreB, for example, has been purified and studied in vitro, but its assembly appears to be strongly inhibited by physiological concentrations of monovalent cations, suggesting that its assembly in vivo is facilitated by as-yet-unknown factors (23). At present, the best-understood actin-like protein is ParM, a plasmid-encoded protein that constructs a bipolar spindle capable of pushing plasmids to opposite poles of rod-shaped cells (5, 25). In contrast to the eukaryotic actin cytoskeleton, whose assembly and architecture are regulated by a variety of accessory factors, ParM dynamics are regulated by a single factor, a complex composed of multiple copies of the repressor protein ParR bound to a DNA locus, parC (17). The ParR/parC complex binds the ends of ParM filaments and is pushed through the cytoplasm by filament elongation (5, 14, 25). The ability of ParM to function with such minimal regulation appears to be due to its unique assembly dynamics, which are dramatically different from those of eukaryotic actins. One of the most important differences is that ParM filaments are dynamically unstable (13). That is, similar to eukaryotic microtubules, they can exist in one of two states: stably growing or rapidly (catastrophically) shrinking. This property is required for the ability of ParM to segregate DNA in vivo and appears to solve several fundamental problems associated with DNA segregation. First, spontaneous disassembly of the polymer overcomes the need for an accessory factor to take filaments apart. Second, because filaments bound to ParR/parC complexes are selectively stabilized, the catastrophic disassembly of unattached filaments provides excess monomers that can preferentially elongate them. This is significant because, if the stabilities of attached and unattached filaments were similar, the concentration of free ParM monomers would equilibrate at a level not capable of promoting DNA segregation. And finally, pairs of plasmids appear to find each other via a search-and-capture mechanism (5, 14) that is dramatically enhanced by the continual growth and shortening of filaments attached to single plasmids (16).Because we have little information on the dynamics of other actin-like proteins, it is unclear to what extent ParM''s behavior reflects general properties of bacterial actins rather than specific adaptations to its role in DNA segregation. Furthermore, it is unclear whether all plasmid-segregating actins employ the same dynamic instability-based strategy to find and transport DNA molecules. To better understand the structural and functional diversity of bacterial actins, we studied a second, recently discovered plasmid-segregating actin-like protein, AlfA (1). The AlfA gene is part of an operon (alf) that is located close to the origin of replication of a ∼70-kb, low-copy-number plasmid, pLS32. This plasmid was initially isolated from a natto strain of Bacillus subtilis used in soybean fermentation (33), but a similar plasmid with an identical alf operon is also present in a colony-forming laboratory strain of B. subtilis, strain NCIB 3610 (8, 32). The function of these plasmids is cryptic. They are present at levels of only two or three copies per chromosome equivalent (33), and maintenance of their derivatives requires both AlfA and a downstream gene, alfB (1). Becker and coworkers (1) identified AlfA as a member of the actin superfamily based on the presence of a conserved nucleotide binding fold (4), although the sequence of AlfA is as different from the sequences of ParM and MreB as all three are from the sequence of conventional eukaryotic actin (∼20% identity). These authors also showed that fluorescent derivatives of AlfA form a single filamentous structure running along the long axis of the cell. Photobleached filaments recover from both ends in approximately 1 min, indicating that the structures are composed of multiple, dynamic filaments (1). By analogy with the ParR/parC complex, AlfB might be a DNA binding protein that couples AlfA assembly to plasmid movement. To date, no centromeric sequences involved in segregation have been identified in this plasmid.We expressed and purified AlfA and characterized its assembly dynamics by using light scattering, high-speed pelleting, and fluorescence microscopy, and we determined the structure of AlfA polymers by high-resolution electron microscopy (EM). We found that in the presence of ATP and GTP, AlfA forms two-strand helical filaments and filament bundles. Like ParM filaments, AlfA filaments are left-handed two-start helices, but otherwise their filament architecture is quite different. AlfA filaments appear to be more tightly twisted and ribbon-like, and AlfA subunits have a significantly different orientation with respect to the filament axis. Unlike other actin-like proteins described thus far, AlfA spontaneously forms regularly sized, mixed-polarity filament bundles driven by electrostatic interactions between filaments, even in the absence of molecular crowding. Finally, AlfA shows no evidence of the dynamic instability crucial to the function of ParM. Thus, AlfA assembles into a unique structure with a unique set of biochemical and structural properties, suggesting a novel mechanism for DNA segregation.     

Iteron-binding ORF157 and FtsZ-like ORF156 proteins encoded by pBtoxis play a role in its replication in Bacillus thuringiensis subsp. israelensis

We recently identified a minireplicon of pBtoxis from Bacillus thuringiensis subsp. israelensis that contained an operon encoding two novel proteins (ORF156 and ORF157), both of which are required for replication. ORF157 contains a helix-turn-helix motif and shares no homology with known plasmid replication proteins (Rep), and ORF156 contains the signature motif present in FtsZ/tubulin proteins, the latter of which are known to function in cell division and chromosome segregation. Here we show that the minimal sequence composed of four 12-bp imperfect direct repeats (iterons) in the pBtoxis minireplicon was sufficient to replicate a reporter plasmid in B. thuringiensis subsp. israelensis when ORF156 and ORF157 functions were provided in trans. To further investigate the roles of ORF156 and ORF157 in pBtoxis replication, six-histidine-tagged recombinant rORF156 and rORF157 proteins were purified from Escherichia coli and used in electrophoretic mobility shift assays. Our results demonstrated that rORF157, but not rORF156, binds specifically to the pBtoxis iterons, suggesting that ORF157 functions as a Rep protein. Although rORF156 did not bind to the iteron sequence, we showed that it bound to rORF157-DNA complexes. In addition, we showed that rORF156 has GTPase activity characteristic of the FtsZ/tubulin superfamily of proteins. Taken together, these results suggest that the iterons compose the minimal replication origin (ori) of pBtoxis and that ORF157 and ORF156 are involved in the initiation of pBtoxis replication and possibly in the segregation and partitioning of this plasmid to daughter cells.     

Protein-nanocrystal conjugates support a single filament polymerization model in R1 plasmid segregation

To ensure inheritance by daughter cells, many low-copy number bacterial plasmids, including the R1 drug-resistance plasmid, encode their own DNA segregation systems. The par operon of plasmid R1 directs construction of a simple spindle structure that converts free energy of polymerization of an actin-like protein, ParM, into work required to move sister plasmids to opposite poles of rod-shaped cells. The structures of individual components have been solved, but little is known about the ultrastructure of the R1 spindle. To determine the number of ParM filaments in a minimal R1 spindle, we used DNA-gold nanocrystal conjugates as mimics of the R1 plasmid. We found that each end of a single polar ParM filament binds to a single ParR/parC-gold complex, consistent with the idea that ParM filaments bind in the hollow core of the ParR/parC ring complex. Our results further suggest that multifilament spindles observed in vivo are associated with clusters of plasmids segregating as a unit.     

The Kinetochore

A critical requirement for mitosis is the distribution of genetic material to the two daughter cells. The central player in this process is the macromolecular kinetochore structure, which binds to both chromosomal DNA and spindle microtubule polymers to direct chromosome alignment and segregation. This review will discuss the key kinetochore activities required for mitotic chromosome segregation, including the recognition of a specific site on each chromosome, kinetochore assembly and the formation of kinetochore–microtubule connections, the generation of force to drive chromosome segregation, and the regulation of kinetochore function to ensure that chromosome segregation occurs with high fidelity.A key objective for cell division is to physically distribute the genomic material to the two new daughter cells. Achieving proper chromosome segregation requires three primary things (Fig. 1): (1) the ability to specifically recognize and detect each unit of DNA; (2) a physical connection between the DNA and other cellular structures to mediate their distribution; and (3) a force-generating mechanism to drive the spatial movement of the DNA to the daughter cells. Although this article focuses on how these processes are achieved during mitosis in eukaryotic cells, these key principles are required for DNA segregation in all organisms, including bacteria. Perhaps the simplest DNA distribution machine is the partitioning system that segregates the small, circular bacterial R1 plasmid (Fig. 1). The R1 partitioning system uses just a single component for each of the three key activities listed above (reviewed in Salje et al. 2010). First, a 160-bp sequence-specific DNA element termed parC allows the partitioning system to recognize a specific region of the plasmid. Second, the DNA-binding protein ParR associates with the parC DNA sequence. ParR can then mediate connections between the plasmid DNA and third factor—the filament forming protein ParM. ParM polymerization is capable of generating force to drive the separation of two replicated copies of the R1 plasmid. The R1 plasmid partitioning system is both simple and elegant, and it demonstrates that it is possible to achieve DNA segregation with only two proteins and a short DNA sequence.Open in a separate windowFigure 1.Core requirements for DNA segregation. Cartoon diagram showing the core activities required for DNA segregation of the bacterial R1 plasmid or eukaryotic chromosomes highlighting the recognition of DNA, physical connections, and force.In striking contrast to the R1 plasmid partitioning system, chromosome segregation in eukaryotes (Fig. 1) requires hundreds of different proteins. Given the ability of the simple R1 partitioning system to efficiently mediate DNA segregation in bacteria, it raises the question of why this added complexity is present in eukaryotes. Importantly, there are significant limitations to the bacterial system that would prevent such a system from working in eukaryotes. For example, bacteria are ∼1–2-µm long, whereas vertebrate cells can be ∼10–50 µm in diameter creating a larger spatial requirement to move the DNA (Fig. 1). In addition, although only a single R1 plasmid is present in each bacterium, human cells have 46 different units of DNA (23 from each parent), which are packaged into chromosomes. Each chromosome must be distributed properly during every cell division. Independently recognizing each of these units to ensure their accurate distribution represents a complex challenge. Indeed, adding even one additional R1 plasmid causes the system to break down, with ParM polymers acting indefinitely, pushing the two most closely positioned units of DNA apart to opposite ends of a cell (Campbell and Mullins 2007). Finally, eukaryotic cells require that chromosome segregation occur with high fidelity to ensure that the two replicated units of DNA are distributed accurately to the two new daughter cells. Even a single chromosome mis-segregation event in a multicellular organism has the potential to lead to lethality, lead to developmental disorders, or contribute to cancer progression (Holland and Cleveland 2009; Gordon et al. 2012), placing a high premium on the accuracy of this process.Despite the differences in complexity between bacterial plasmid partitioning systems and the eukaryotic chromosome segregation machinery, the fundamental requirements for distributing DNA to two new cells are remarkably similar (Fig. 1). First, it is necessary to have a region of each chromosome that is “recognized” by the chromosome segregation machinery. In eukaryotes, this region of DNA is termed the centromere. Second, a group of proteins must assemble on this DNA element to facilitate its “connections” to other structures in the cell. In eukaryotes, this physical connection is provided by a macromolecular structure termed the kinetochore. The kinetochore is an impressive molecular machine that requires the coordinated functions of more than 100 different protein components (Cheeseman and Desai 2008). Third, the kinetochore must interact with additional structures that provide the “force” to move the chromosomes. Chromosome segregation in eukaryotes requires microtubule polymers that generate force primarily through their depolymerization.In this review, I will discuss the molecular mechanisms that underlie kinetochore function, including the recognition of a specific site on each chromosome, the formation of the physical kinetochore–microtubule connections, and the forces that drive chromosome segregation during mitosis in eukaryotes, as well as the mechanisms that regulate kinetochore function.     

Open strands adjacent to iterons promote the binding of the replication initiator protein (Rep) of pSC101 to the unit sequence of the iterons in vitro

The purified dimeric form of the Rep protein, a replication initiator protein of the plasmid pSC101, has a low affinity for repeated sequences, iterons, in the replication origin of the plasmid, and higher affinities for two inverted repeats in the operator region of the rep gene resulting in its functioning as an autorepressor. Studies of binding to various synthetic DNA have established that Rep can bind to duplex iteron-sequence carrying open (non-complementary) strands at one end proximal to the rep gene. Open strands at the opposite end of the iteron have no effect on Rep-binding. One open strand seems to be required in a sequence-specific fashion. A randomly sequenced duplex DNA with the open strands cannot bind to Rep but can function as a significant competitor. This suggests that Rep has some affinity for the open strands and forms a stable complex with the adjacent iteron. The mutated Rep protein, Rep1, which causes an increase in the plasmid copy number in vivo, has equally high affinity for the iteron with the open strands as wild type Rep, though it has a lower affinity for the inverted repeats than the wild type. The Rep dimer might bind to these DNA sequences with different modes.     

Bacterial actin: architecture of the ParMRC plasmid DNA partitioning complex

The R1 plasmid employs ATP-driven polymerisation of the actin-like protein ParM to move newly replicated DNA to opposite poles of a bacterial cell. This process is essential for ensuring accurate segregation of the low-copy number plasmid and is the best characterised example of DNA partitioning in prokaryotes. In vivo, ParM only forms long filaments when capped at both ends by attachment to a centromere-like region parC, through a small DNA-binding protein ParR. Here, we present biochemical and electron microscopy data leading to a model for the mechanism by which ParR-parC complexes bind and stabilise elongating ParM filaments. We propose that the open ring formed by oligomeric ParR dimers with parC DNA wrapped around acts as a rigid clamp, which holds the end of elongating ParM filaments while allowing entry of new ATP-bound monomers. We propose a processive mechanism by which cycles of ATP hydrolysis in polymerising ParM drives movement of ParR-bound parC DNA. Importantly, our model predicts that each pair of plasmids will be driven apart in the cell by just a single double helical ParM filament.     

Identification of a potent small-molecule inhibitor of bacterial DNA repair that potentiates quinolone antibiotic activity in methicillin-resistant Staphylococcus aureus

The global emergence of antibiotic resistance is one of the most serious challenges facing modern medicine. There is an urgent need for validation of new drug targets and the development of small molecules with novel mechanisms of action. We therefore sought to inhibit bacterial DNA repair mediated by the AddAB/RecBCD protein complexes as a means to sensitize bacteria to DNA damage caused by the host immune system or quinolone antibiotics. A rational, hypothesis-driven compound optimization identified IMP-1700 as a cell-active, nanomolar potency compound. IMP-1700 sensitized multidrug-resistant Staphylococcus aureus to the fluoroquinolone antibiotic ciprofloxacin, where resistance results from a point mutation in the fluoroquinolone target, DNA gyrase. Cellular reporter assays indicated IMP-1700 inhibited the bacterial SOS-response to DNA damage, and compound-functionalized Sepharose successfully pulled-down the AddAB repair complex. This work provides validation of bacterial DNA repair as a novel therapeutic target and delivers IMP-1700 as a tool molecule and starting point for therapeutic development to address the pressing challenge of antibiotic resistance.     

Plasmid R6K Contains Two FunctionaloriTswhich can Assemble Simultaneously in Relaxosomesin vivo

Plasmid R6K contains two functional origins or transfer (oriT), in contrast to previously characterized conjugative plasmids. TheoriTsare formed by 98 bp palindromic sequences invertedly orientated with respect to each other and located in the immediate vicinity of the α and β origins of replication. The gene for R6KoriT-nickase,taxC, was identified by transposon mutagenesis and sequenced, revealing that TaxC belongs to the VirD2 nickase family. The protein was overproduced and purified. It catalysed a cleaving-joining reaction on single-stranded DNA containing its target sequence. Identification of thenicsites suggested that the R6KoriTsbelong to the RP4/VirD2oriTfamily. Cleavage was highly specific and did not occur with oligonucleotides cleaved by related nickases like TraI of RP4 or VirD2 of the Ti plasmid.niccleavage ofin vivopre- assembled relaxation complexes was induced by incubation of plasmid cleared lysates with ethidium bromide. Nicked molecules obtained in this way were treated with snake venom phosphodiesterase to produce double strand cleavages at thenicsites. 35% of the molecules were cleaved simultaneously at bothnicsites, both in the case of R6K and of R6Kdrd1, a derepressed mutant whose frequency of transfer is 1000-fold higher. This figure represents the minimum percentage of individual R6K molecules containing two pre-assembled relaxation complexes.     

Specific and non-specific interactions of ParB with DNA: implications for chromosome segregation

The segregation of many bacterial chromosomes is dependent on the interactions of ParB proteins with centromere-like DNA sequences called parS that are located close to the origin of replication. In this work, we have investigated the binding of Bacillus subtilis ParB to DNA in vitro using a variety of biochemical and biophysical techniques. We observe tight and specific binding of a ParB homodimer to the parS sequence. Binding of ParB to non-specific DNA is more complex and displays apparent positive co-operativity that is associated with the formation of larger, poorly defined, nucleoprotein complexes. Experiments with magnetic tweezers demonstrate that non-specific binding leads to DNA condensation that is reversible by protein unbinding or force. The condensed DNA structure is not well ordered and we infer that it is formed by many looping interactions between neighbouring DNA segments. Consistent with this view, ParB is also able to stabilize writhe in single supercoiled DNA molecules and to bridge segments from two different DNA molecules in trans. The experiments provide no evidence for the promotion of non-specific DNA binding and/or condensation events by the presence of parS sequences. The implications of these observations for chromosome segregation are discussed.     

Investigations of �� Initiator Protein-mediated Interaction between Replication Origins �� and �� of the Plasmid R6K

A typical plasmid replicon of Escherichia coli, such as ori γ of R6K, contains tandem iterons (iterated initiator protein binding sites), an AT-rich region that melts upon initiator-iteron interaction, two binding sites for the bacterial initiator protein DnaA, and a binding site for the DNA-bending protein IHF. R6K also contains two structurally atypical origins called α and β that are located on either side of γ and contain a single and a half-iteron, respectively. Individually, these sites do not bind to initiator protein π but access it by DNA looping-mediated interaction with the seven π-bound γ iterons. The π protein exists in 2 interconvertible forms: inert dimers and active monomers. Initiator dimers generally function as negative regulators of replication by promoting iteron pairing (“handcuffing”) between pairs of replicons that turn off both origins. Contrary to this existing paradigm, here we show that both the dimeric and the monomeric π are necessary for ori α-driven plasmid maintenance. Furthermore, efficient looping interaction between α and γ or between 2 γ iterons in vitro also required both forms of π. Why does α-γ iteron pairing promote α activation rather than repression? We show that a weak, transitory α-γ interaction at the iteron pairs was essential for α-driven plasmid maintenance. Swapping the α iteron with one of γ without changing the original sequence context that caused enhanced looping in vitro caused a significant inhibition of α-mediated plasmid maintenance. Therefore, the affinity of α iteron for π-bound γ and not the sequence context determined whether the origin was activated or repressed.     

Heavy metal ion interactions with deoxy nucleotides. X-ray crystal structures of orthorhombic and monoclinic forms of 2'-deoxy cytidine 5'-monophosphate complexed with Cd(II)

The crystal structures of two polymorphic complexes of Cd(II) with 2'-deoxy cytidine 5'-mono-phosphate (5'-dCMP) are reported and discussed The orthorhombic complex, [Cd(5'-dCMP) (H₂O)₂] (1), crystallizes in space group P2₁2₁2₁ with cell dimensions a = 8.422(2), b = 24.428(8), c = 7.292(2) Å, and Z = 4, the monoclinic complex, [Cd₂(5'-dCMP)₂(H₂O)₂]·3H₂O (2), crystallizes in space group C2 with a = 30.809(9), b = 5.369(2), c = 25.126(8) Å, β = 127.61(2)°, and Z = 4 Structure (1) has been solved by Patterson and Fourier methods, and structure (2) has been deduced from its isomorphous ribo-analog (J.K. Shiba and R. Bau, Inorg.Chem. 17, 3484 (1978)); and both have been refined by full-matrix least-squares methods to final R values of 0.052 for (1) and 0.103 for (2) using, respectively, 1273 and 2287 independent reflections. The orthorhombic complex (1) is three-dimensionally polymeric, with the Cd atom bound in a distorted octahedral arrangement to the cytosine base at N(3) and O(2) [Cd-N(3) 2.29(1) and Cd-O(2) 2.64(1) Å], to two phosphate oxygens of different nucleotide molecules, and to two water molecules, each phosphate group links two Cd atoms, thereby producing an infinite [-Cd-O-P-O-Cd-]_n spiraling column, which is additionally interconnected to neighboring columns via nucleotide bridges to give a layer-like polymeric structure. The monoclinic complex (2), which includes two crystallographically independent [Cd(5'-dCMP) (H2O)] units, is also three-dimensionally polymeric, with each Cd atom bound in a distorted pentagonal bipyramidal arrangement to N(3) and O(2) of the base [Cd-N(3) 2.35_av and Cd-O(2) 2.73_av Å], to four phosphate oxygens of three different nucleotide molecules, and to a water molecule, each phosphate group binds to three Cd atoms, thereby creating an infinite cross-linked spiral of sequences [-Cd-O-P-O-Cd-]_n and [-Cd-O-Cd-]_n that is further connected to adjacent spirals via nucleotide bridges to form large     

Condensation by DNA looping facilitates transfer of large DNA molecules into mammalian cells

Experimental studies of complete mammalian genes and other genetic domains are impeded by the difficulty of introducing large DNA molecules into cells in culture. Previously we have shown that GST–Z2, a protein that contains three zinc fingers and a proline-rich multimerization domain from the polydactyl zinc finger protein RIP60 fused to glutathione S-transferase (GST), mediates DNA binding and looping in vitro. Atomic force microscopy showed that GST–Z2 is able to condense 130–150 kb bacterial artificial chromosomes (BACs) into protein–DNA complexes containing multiple DNA loops. Condensation of the DNA loops onto the Z2 protein–BAC DNA core complexes with cationic lipid resulted in particles that were readily transferred into multiple cell types in culture. Transfer of total genomic linear DNA containing amplified DHFR genes into DHFR^– cells by GST–Z2 resulted in a 10-fold higher transformation rate than calcium phosphate co-precipitation. Chinese hamster ovarian cells transfected with a BAC containing the human TP53 gene locus expressed p53, showing native promoter elements are active after GST–Z2-mediated gene transfer. Because DNA condensation by GST–Z2 does not require the introduction of specific recognition sequences into the DNA substrate, condensation by the Z2 domain of RIP60 may be used in conjunction with a variety of other agents to provide a flexible and efficient non-viral platform for the delivery of large genes into mammalian cells.     

Supercoiled DNA and non-equilibrium formation of protein complexes: A quantitative model of the nucleoprotein ParBS partition complex

ParABS, the most widespread bacterial DNA segregation system, is composed of a centromeric sequence, parS, and two proteins, the ParA ATPase and the ParB DNA binding proteins. Hundreds of ParB proteins assemble dynamically to form nucleoprotein parS-anchored complexes that serve as substrates for ParA molecules to catalyze positioning and segregation events. The exact nature of this ParBS complex has remained elusive, what we address here by revisiting the Stochastic Binding model (SBM) introduced to explain the non-specific binding profile of ParB in the vicinity of parS. In the SBM, DNA loops stochastically bring loci inside a sharp cluster of ParB. However, previous SBM versions did not include the negative supercoiling of bacterial DNA, leading to use unphysically small DNA persistences to explain the ParB binding profiles. In addition, recent super-resolution microscopy experiments have revealed a ParB cluster that is significantly smaller than previous estimations and suggest that it results from a liquid-liquid like phase separation. Here, by simulating the folding of long (≥ 30 kb) supercoiled DNA molecules calibrated with realistic DNA parameters and by considering different possibilities for the physics of the ParB cluster assembly, we show that the SBM can quantitatively explain the ChIP-seq ParB binding profiles without any fitting parameter, aside from the supercoiling density of DNA, which, remarkably, is in accord with independent measurements. We also predict that ParB assembly results from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., ParB clusters behave like liquid-like protein condensates with unconventional “leaky” boundaries.     

Enzyme inhibitor modeling with TpZn complexes of functional hydroxamates and oximates

Salicylhydroxamic acid reacts with the enzyme model Tp^Ph,MeZn-OH to form the O,O-chelating hydroxamate complex 1. The hydrogen bonding capacity of zinc enzyme bound hydroxamates is reproduced by cocrystallization of two molecules if 1 with two molecules of methanol and by cocrystallization of one molecule of Tp^Ph,MeZn-acetohydroxamate with one molecule of 3-phenyl-5-methylpyrazole. The complex formed from Tp^Ph,MeZn-OH and N-tosylproline hydroxamic acid, according to its spectra, contains the hydroxamate as an N,N-chelating ligand. In contrast, the oximate derived from pyruvic aldehyde does not act as a chelating ligand, but is monodentate via the oximate oxygen.     

Effects of physiological self-crowding of DNA on shape and biological properties of DNA molecules with various levels of supercoiling

DNA in bacterial chromosomes and bacterial plasmids is supercoiled. DNA supercoiling is essential for DNA replication and gene regulation. However, the density of supercoiling in vivo is circa twice smaller than in deproteinized DNA molecules isolated from bacteria. What are then the specific advantages of reduced supercoiling density that is maintained in vivo? Using Brownian dynamics simulations and atomic force microscopy we show here that thanks to physiological DNA–DNA crowding DNA molecules with reduced supercoiling density are still sufficiently supercoiled to stimulate interaction between cis-regulatory elements. On the other hand, weak supercoiling permits DNA molecules to modulate their overall shape in response to physiological changes in DNA crowding. This plasticity of DNA shapes may have regulatory role and be important for the postreplicative spontaneous segregation of bacterial chromosomes.     

Preparation, characterisation and crystal structure of two zinc(II) benzoate complexes with pyridine-based ligands nicotinamide and methyl-3-pyridylcarbamate

Two benzoate complexes namely tetrakis(μ₂-benzoato-O,O^′)-bis(μ₂-benzoato-O,O)-bis(nicotinamide-N)-tri-zinc(II), [Zn₃(benz)₆(nia)₂] (I) and bis(benzoato-O)-bis(methyl-3-pyridylcarbamate-N)-zinc(II), [Zn(benz)₂(mpcm)₂] (II) (benz=benzoate anion, nia=nicotinamide, mpcm=methyl-3-pyridylcarbamate) were prepared and characterised by elemental analysis, IR spectroscopy, thermal analysis and X-ray structure determination. The structure of the complex I is centrosymmetric, formed by a linear array of three zinc atoms. The central zinc atom shows octahedral coordination and is bridged to each of the terminal zinc atoms by three benzoate anions. Two of them act as bidentate, one as monodentate ligand. By additional coordination of the nia ligand, the terminal Zn atoms adopt tetrahedral surrounding. The structure of complex II contains two crystallographically independent [Zn(benz)₂(mpcm)₂] molecules. In each molecule, the zinc atom is tetrahedrally coordinated by two monodentate benzoate and two methyl-3-pyridylcarbamate ligands. Intermolecular hydrogen bonds of the N-H?O type connect molecules in the structures of complexes I and II to form a two-dimensional network. The three different types of carboxylate binding found in the complexes were distinguished also by values of carboxylate stretching vibrations in FT-IR spectra as well as by thermal decomposition of the complexes in nitrogen.