Role of the N-terminal region and of beta-sheet residue Thr29 on the activity of the omega2 global regulator from the broad-host range Streptococcus pyogenes plasmid pSM19035

Distinct architectural requirements for the parS centromeric sequence of the pSM19035 plasmid partition machinery

Three-component ParABS partition systems ensure stable inheritance of many bacterial chromosomes and low-copy-number plasmids. ParA localizes to the nucleoid through its ATP-dependent nonspecific DNA-binding activity, whereas centromere-like parS-DNA and ParB form partition complexes that activate ParA-ATPase to drive the system dynamics. The essential parS sequence arrangements vary among ParABS systems, reflecting the architectural diversity of their partition complexes. Here, we focus on the pSM19035 plasmid partition system that uses a ParB_pSM of the ribbon-helix-helix (RHH) family. We show that parS_pSM with four or more contiguous ParB_pSM-binding sequence repeats is required to assemble a stable ParA_pSM-ParB_pSM complex and efficiently activate the ParA_pSM-ATPase, stimulating complex disassembly. Disruption of the contiguity of the parS_pSM sequence array destabilizes the ParA_pSM-ParB_pSM complex and prevents efficient ATPase activation. Our findings reveal the unique architecture of the pSM19035 partition complex and how it interacts with nucleoid-bound ParA_pSM-ATP.

Plasmid Replication Control by Antisense RNAs

Plasmids are selfish genetic elements that normally constitute a burden for the bacterial host cell. This burden is expected to favor plasmid loss. Therefore, plasmids have evolved mechanisms to control their replication and ensure their stable maintenance. Replication control can be either mediated by iterons or by antisense RNAs. Antisense RNAs work through a negative control circuit. They are constitutively synthesized and metabolically unstable. They act both as a measuring device and a regulator, and regulation occurs by inhibition. Increased plasmid copy numbers lead to increasing antisense-RNA concentrations, which, in turn, result in the inhibition of a function essential for replication. On the other hand, decreased plasmid copy numbers entail decreasing concentrations of the inhibiting antisense RNA, thereby increasing the replication frequency. Inhibition is achieved by a variety of mechanisms, which are discussed in detail. The most trivial case is the inhibition of translation of an essential replication initiator protein (Rep) by blockage of the rep-ribosome binding site. Alternatively, ribosome binding to a leader peptide mRNA whose translation is required for efficient Rep translation can be prevented by antisense-RNA binding. In 2004, translational attenuation was discovered. Antisense-RNA-mediated transcriptional attenuation is another mechanism that has, so far, only been detected in plasmids of Gram-positive bacteria. ColE1, a plasmid that does not need a plasmid-encoded replication initiator protein, uses the inhibition of primer formation. In other cases, antisense RNAs inhibit the formation of an activator pseudoknot that is required for efficient Rep translation.

The Interplay between Different Stability Systems Contributes to Faithful Segregation: Streptococcus pyogenes pSM19035 as a Model

The Streptococcus pyogenes pSM19035 low-copy-number θ-replicating plasmid encodes five segregation (seg) loci that contribute to plasmid maintenance. These loci map outside of the minimal replicon. The segA locus comprises β2 recombinase and two six sites, and segC includes segA and also the γ topoisomerase and two ssiA sites. Recombinase β2 plays a role both in maximizing random segregation by resolving plasmid dimers (segA) and in catalyzing inversion between two inversely oriented six sites. segA, in concert with segC, facilitates replication fork pausing at ssiA sites and overcomes the accumulation of "toxic" replication intermediates. The segB1 locus encodes ω, ε, and ζ genes. The short-lived ε2 antitoxin and the long-lived ζ toxin form an inactive ζε2ζ complex. Free ζ toxin halts cell proliferation upon decay of the ε2 antitoxin and enhances survival. If ε2 expression is not recovered, by loss of the plasmid, the toxin raises lethality. The segB2 locus comprises δ and ω genes and six parS sites. Proteins δ2 and ω2, by forming complexes with parS and chromosomal DNA, pair the plasmid copies at the nucleoid, leading to the formation of a dynamic δ2 gradient that separates the plasmids to ensure roughly equal distribution to daughter cells at cell division. The segD locus, which comprises ω2 (or ω2 plus ω22) and parS sites, coordinates expression of genes that control copy number, better-than-random segregation, faithful partition, and antibiotic resistance. The interplay of the seg loci and with the rep locus facilitates almost absolute plasmid stability.

The interaction of ω2 with the RNA polymerase β' subunit functions as an activation to repression switch

The ω gene is encoded in broad-host range and low-copy plasmids. It is genetically linked to antibiotic resistance genes of the major human pathogens of phylum Firmicutes. The homodimeric forms of ω (ω₂) coordinate the plasmid copy number control, faithful partition (ω₂ and δ₂) and better-than-random segregation (ζϵ₂ζ) systems. The promoter (P) of the ωϵζ operon (P_ω) transiently interacts with ω₂. Adding δ₂ facilitates the formation of stable ω₂·P_ω complexes. Here we show that limiting ω₂ interacts with the N-terminal domain of the β’ subunit of the Bacillus subtilis RNA polymerase (RNAP-σ^A) vegetative holoenzyme. In this way ω₂ recruits RNAP-σ^A onto P_ω DNA. Partial P_ω occupancy by ω₂ increases the rate at which RNAP-σ^A complex shifts from its closed (RP_C) to open (RP_O) form. This shift increases transcription activation. Adding δ₂ further increases the rate of P_ω transcription initiation, perhaps by stabilizing the ω₂·P_ω complex. In contrast, full operator occupancy by ω₂ facilitates RP_C formation, but it blocks RP_O isomerization and represses P_ω utilization. The stimulation and inhibition of RP_O formation is the mechanism whereby ω₂ mediates copy number fluctuation and stable plasmid segregation. By this mechanism, ω₂ also indirectly influences the acquisition of antibiotic resistance genes.

ParAB Partition Dynamics in Firmicutes: Nucleoid Bound ParA Captures and Tethers ParB-Plasmid Complexes

In Firmicutes, small homodimeric ParA-like (δ₂) and ParB-like (ω₂) proteins, in concert with cis-acting plasmid-borne parS and the host chromosome, secure stable plasmid inheritance in a growing bacterial population. This study shows that (ω:YFP)₂ binding to parS facilitates plasmid clustering in the cytosol. (δ:GFP)₂ requires ATP binding but not hydrolysis to localize onto the cell’s nucleoid as a fluorescent cloud. The interaction of (δ:CFP)₂ or δ₂ bound to the nucleoid with (ω:YFP)₂ foci facilitates plasmid capture, from a very broad distribution, towards the nucleoid and plasmid pairing. parS-bound ω₂ promotes redistribution of (δ:GFP)₂, leading to the dynamic release of (δ:GFP)₂ from the nucleoid, in a process favored by ATP hydrolysis and protein-protein interaction. (δD60A:GFP)₂, which binds but cannot hydrolyze ATP, also forms unstable complexes on the nucleoid. In the presence of ω₂, (δD60A:GFP)₂ accumulates foci or patched structures on the nucleoid. We propose that (δ:GFP)₂ binding to different nucleoid regions and to ω₂-parS might generate (δ:GFP)₂ gradients that could direct plasmid movement. The iterative pairing and unpairing cycles may tether plasmids equidistantly on the nucleoid to ensure faithful plasmid segregation by a mechanism compatible with the diffusion-ratchet mechanism as proposed from in vitro reconstituted systems.

Molecular Anatomy of ParA-ParA and ParA-ParB Interactions during Plasmid Partitioning

Firmicutes multidrug resistance inc18 plasmids encode parS sites and two small homodimeric ParA-like (δ2) and ParB-like (ω2) proteins to ensure faithful segregation. Protein ω2 binds to parS DNA, forming a short left-handed helix wrapped around the full parS, and interacts with δ2. Protein δ2 interacts with ω2 and, in the ATP-bound form, binds to nonspecific DNA (nsDNA), forming small clusters. Here, we have mapped the ω2·δ2 and δ2·δ2 interacting domains in the δ2 that are adjacent to but distinct from each other. The δ2 nsDNA binding domain is essential for stimulation of ω2·parS-mediated ATP hydrolysis. From the data presented here, we propose that δ2 interacts with ATP, nsDNA, and with ω2 bound to parS at near equimolar concentrations, facilitating a δ2 structural transition. This δ2 "activated" state overcomes its impediment in ATP hydrolysis, with the subsequent release of both of the proteins from nsDNA (plasmid unpairing).

Mapping of the interactions between partition proteins Delta and Omega of plasmid pSM19035 from Streptococcus pyogenes

Formation of the segrosome, a nucleoprotein complex crucial for proper functioning of plasmid partition systems, involves interactions between specific partition proteins (ParA-like and ParB-like), ATP and specific DNA sequences (the centromeric sites). Although partition systems have been studied for many years, details of the segrosome formation are not yet clear. Organization of the pSM19035-encoded partition system is unique; in contrast with other known par systems, here, the δ and ω genes do not constitute an operon. Moreover, Omega [a ParB-like protein which has a Ribbon-Helix-Helix (RHH) structure] recognizes multiple centromeric sequences located in the promoters of δ, ω and copS (copy-number control gene). The ParA-like protein Delta is a Walker-type ATPase. In this work, we identify the interaction domains and requirements for dimerization and hetero-interactions of the Delta and Omega proteins of pSM19035 plasmid. The RHH structures are involved in Omega dimerization in vivo and its N-terminal unstructured part is indispensable for association with Delta, both in vivo and in vitro. Omega does not need to form dimers to interact with Delta. ATP binding is not required for Delta dimerization but is important for interaction with Omega in vivo. The in vitro interaction between Delta and Omega depends on ATP but does not require the presence of specific DNA segments (the centromere) recognized by Omega. The C-terminal part of the Delta protein (aa 198-284) is indispensable for interaction with Omega. Delta most probably interacts with Omega as a dimer since two amino acid substitutions in a conserved region between the A' and B motifs abolish both the dimerization of Delta and its interaction with Omega.

Molecular anatomy of the Streptococcus pyogenes pSM19035 partition and segrosome complexes

Vancomycin or erythromycin resistance and the stability determinants, δω and ωεζ, of Enterococci and Streptococci plasmids are genetically linked. To unravel the mechanisms that promoted the stable persistence of resistance determinants, the early stages of Streptococcus pyogenes pSM19035 partitioning were biochemically dissected. First, the homodimeric centromere-binding protein, ω₂, bound parS DNA to form a short-lived partition complex 1 (PC1). The interaction of PC1 with homodimeric δ [δ₂ even in the apo form (Apo-δ₂)], significantly stimulated the formation of a long-lived ω₂·parS complex (PC2) without spreading into neighbouring DNA sequences. In the ATP·Mg²⁺ bound form, δ₂ bound DNA, without sequence specificity, to form a transient dynamic complex (DC). Second, parS bound ω₂ interacted with and promoted δ₂ redistribution to co-localize with the PC2, leading to transient segrosome complex (SC, parS·ω₂·δ₂) formation. Third, δ₂, in the SC, interacted with a second SC and promoted formation of a bridging complex (BC). Finally, increasing ω₂ concentrations stimulated the ATPase activity of δ₂ and the BC was disassembled. We propose that PC, DC, SC and BC formation were dynamic processes and that the molar ω₂:δ₂ ratio and parS DNA control their temporal and spatial assembly during partition of pSM19035 before cell division.

Plasmid pSM19035, a model to study stable maintenance in Firmicutes

pSM19035 is a low-copy-number theta-replicating plasmid, which belongs to the Inc18 family. Plasmids of this family, which show a modular organization, are functional in evolutionarily diverse bacterial species of the Firmicutes Phylum. This review summarizes our understanding, accumulated during the last 20 years, on the genetics, biochemistry, cytology and physiology of the five pSM19035 segregation (seg) loci, which map outside of the minimal replicon. The segA locus plays a role both in maximizing plasmid random segregation, and in avoiding replication fork collapses in those plasmids with long inverted repeated regions. The segB1 locus, which acts as the ultimate determinant of plasmid maintenance, encodes a short-lived epsilon(2) antitoxin protein and a long-lived zeta toxin protein, which form a complex that neutralizes zeta toxicity. The cells that do not receive a copy of the plasmid halt their proliferation upon decay of the epsilon(2) antitoxin. The segB2 locus, which encodes two trans-acting, ParA- and ParB-like proteins and six cis-acting parS centromeres, actively ensures equal or roughly equal distribution of plasmid copies to daughter cells. The segC locus includes functions that promote the shift from the use of DNA polymerase I to the replicase (PolC-PolE DNA polymerases). The segD locus, which encodes a trans-acting transcriptional repressor, omega(2), and six cis-acting cognate sites, coordinates the expression of genes that control copy number, better-than-random segregation and partition, and assures the proper balance of these different functions. Working in concert the five different loci achieve almost absolute plasmid maintenance with a minimal growth penalty.

Single-molecule analysis of proteinxDNA complexes formed during partition of newly replicated plasmid molecules in Streptococcus pyogenes

The Streptococcus pyogenes pSM19035 partition locus is ubiquitous among plasmids from vancomycin- or methicillin-resistant bacteria. An increasing understanding of this segregation system may highlight novel protein targets that could be blocked to curb bacterial proliferation. pSM19035 segregation depends on two homodimeric (delta(2) (ParA) and omega(2) (ParB)) proteins and six cis-acting centromeric noncurved parS sites. In the presence of ATPxMg(2+), delta(2) (delta x ATP x Mg(2+))(2) binds DNA in a sequence-independent manner. Protein omega(2) binds with high affinity and cooperatively to B-form parS DNA. Atomic force microscopy experiments indicate that about 10 omega(2) molecules bind parS, consisting of 10 contiguous iterons. Protein (delta x ATP x Mg(2+))(2), by interacting with the N terminus of omega(2) bound to parS, loses its association with DNA and relocalizes with omega(2).parS to form a ternary complex ((deltaxATPxMg(2+))(2) x omega(2) x parS) with the DNA remaining in straight B-form. Then, the interaction of two (delta x ATP x Mg(2+))(2).omega(2).parS complexes via delta(2) promotes pairing of a plasmid subfraction. (deltaD60A x ATP x Mg(2+))(2), which binds but does not hydrolyze ATP, leads to accumulation of pairing intermediates, suggesting that ATP hydrolysis induces plasmid separation. We propose that the molar omega(2):delta(2) ratio regulates the different stages of pSM19035 segregation, pairing, and delta(2) polymerization, before cell division.

Streptococcus pyogenes pSM19035 requires dynamic assembly of ATP-bound ParA and ParB on parS DNA during plasmid segregation

The accurate partitioning of Firmicute plasmid pSM19035 at cell division depends on ATP binding and hydrolysis by homodimeric ATPase δ₂ (ParA) and binding of ω₂ (ParB) to its cognate parS DNA. The 1.83 Å resolution crystal structure of δ₂ in a complex with non-hydrolyzable ATPγS reveals a unique ParA dimer assembly that permits nucleotide exchange without requiring dissociation into monomers. In vitro, δ₂ had minimal ATPase activity in the absence of ω₂ and parS DNA. However, stoichiometric amounts of ω₂ and parS DNA stimulated the δ₂ ATPase activity and mediated plasmid pairing, whereas at high (4:1) ω₂ : δ₂ ratios, stimulation of the ATPase activity was reduced and δ₂ polymerized onto DNA. Stimulation of the δ₂ ATPase activity and its polymerization on DNA required ability of ω₂ to bind parS DNA and its N-terminus. In vivo experiments showed that δ₂ alone associated with the nucleoid, and in the presence of ω₂ and parS DNA, δ₂ oscillated between the nucleoid and the cell poles and formed spiral-like structures. Our studies indicate that the molar ω₂ : δ₂ ratio regulates the polymerization properties of (δ•ATP•Mg²⁺)₂ on and depolymerization from parS DNA, thereby controlling the temporal and spatial segregation of pSM19035 before cell division.

pSM19035-encoded zeta toxin induces stasis followed by death in a subpopulation of cells

The toxin-antitoxin operon of pSM19035 encodes three proteins: the omega global regulator, the epsilon labile antitoxin and the stable zeta toxin. Accumulation of zeta toxin free of epsilon antitoxin induced loss of cell proliferation in both Bacillus subtilis and Escherichia coli cells. Induction of a zeta variant (zetaY83C) triggered stasis, in which B. subtilis cells were viable but unable to proliferate, without selectively affecting protein translation. In E. coli cells, accumulation of free zeta toxin induced stasis, but this was fully reversed by expression of the epsilon antitoxin within a defined time window. The time window for reversion of zeta toxicity by expression of epsilon antitoxin was dependent on the initial cellular level of zeta. After 240 min of constitutive expression, or inducible expression of high levels of zeta toxin for 30 min, expression of epsilon failed to reverse the toxic effect exerted by zeta in cells growing in minimal medium. Under the latter conditions, zeta inhibited replication, transcription and translation and finally induced death in a fraction (approximately 50 %) of the cell population. These results support the view that zeta interacts with its specific target and reversibly inhibits cell proliferation, but accumulation of zeta might lead to cell death due to pleiotropic effects.

Conformation and stability of the Streptococcus pyogenes pSM19035-encoded site-specific β recombinase, and identification of a folding intermediate

Solution properties of β recombinase were studied by circular dichroism and fluorescence spectroscopy, size exclusion chromatography, analytical ultracentrifugation, denaturant-induced unfolding and thermal unfolding experiments. In high ionic strength buffer (1 M NaCl) β recombinase forms mainly dimers, and strongly tends to aggregate at ionic strength lower than 0.3 M NaCl. Urea and guanidinium chloride denaturants unfold β recombinase in a two-step process. The unfolding curves have bends at approximately 5 M and 2.2 M in urea and guanidinium chloride-containing buffers. Assuming a three-state unfolding model (N2→2I→2U), the total free energy change from 1 mol of native dimers to 2 mol of unfolded monomers amounts to ΔG tot=17.9 kcal/mol, with ΔG N2→2I=4.2 kcal/mol for the first transition and ΔG I→U=6.9 kcal/mol for the second transition. Using sedimentation-equilibrium analytical ultracentrifugation, the presence of β recombinase monomers was indicated at 5 M urea, and the urea dependence of the circular dichroism at 222 nm strongly suggests that folded monomers represent the unfolding intermediate.