Dynamics of protamine 1 binding to single DNA molecules.
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Protamine molecules bind to and condense DNA in the sperm of most vertebrates, packaging the sperm genome in an inactive state until it can be reactivated following fertilization. By using methods that enable the analysis of protamine binding to individual DNA molecules, we have monitored the kinetics of DNA condensation and decondensation by protamine 1 (P1) and synthetic peptides corresponding to specific segments of the bull P1 DNA binding domain. Our results show that the number of clustered arginine residues present in the DNA binding domain is the most important factor affecting the condensation and stability of the DNA-protamine complex prior to the formation of inter-protamine disulfide cross-links. The high affinity of P1 for DNA is achieved by the coordinated binding of three anchoring domains, which together in bull P1 contain 19 Arg residues. The single DNA molecule experiments show that sequences containing two or more anchoring domains have an off-rate that is at least 3 orders of magnitude slower than those containing a single domain. The use of Arg, rather than Lys residues, and the inclusion of Tyr or Phe residues in the hinge regions between anchoring domains provide additional stability to the complex. (+info)
Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy.
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A small container of several to a few hundred microm3 (i.e. bacterial cells and eukaryotic nuclei) contains extremely long genomic DNA (i.e. mm and m long, respectively) in a highly organized fashion. To understand how such genomic architecture could be achieved, Escherichia coli nucleoids were subjected to structural analyses under atomic force microscopy, and found to change their structure dynamically during cell growth, i.e. the nucleoid structure in the stationary phase was more tightly compacted than in the log phase. However, in both log and stationary phases, a fundamental fibrous structure with a diameter of approximately 80 nm was found. In addition to this '80 nm fiber', a thinner '40 nm fiber' and a higher order 'loop' structure were identified in the log phase nucleoid. In the later growth phases, the nucleoid turned into a 'coral reef structure' that also possessed the 80 nm fiber units, and, finally, into a 'tightly compacted nucleoid' that was stable in a mild lysis buffer. Mutant analysis demonstrated that these tight compactions of the nucleoid required a protein, Dps. From these results and previously available information, we propose a structural model of the E.coli nucleoid. (+info)
The portal protein plays essential roles at different steps of the SPP1 DNA packaging process.
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A large number of viruses use a specialized portal for entry of DNA to the viral capsid and for its polarized exit at the beginning of infection. These families of viruses assemble an icosahedral procapsid containing a portal protein oligomer in one of its 12 vertices. The viral ATPase (terminase) interacts with the portal vertex to form a powerful molecular motor that translocates DNA to the procapsid interior against a steep concentration gradient. The portal protein is an essential component of this DNA packaging machine. Characterization of single amino acid substitutions in the portal protein gp6 of bacteriophage SPP1 that block DNA packaging identified sequential steps in the packaging mechanism that require its action. Gp6 is essential at early steps of DNA packaging and for DNA translocation to the capsid interior, it affects the efficiency of DNA packaging, it is a central component of the headful sensor that determines the size of the packaged DNA molecule, and is essential for closure of the portal pore by the head completion proteins to prevent exit of the DNA encapsidated. Functional regions of gp6 necessary at each step are identified within its primary structure. The similarity between the architecture of portal oligomers and between the DNA packaging strategies of viruses using portals strongly suggests that the portal protein plays the same roles in a large number of viruses. (+info)
Peculiarities of the DNA of MM1, a temperate phage of Streptococcus pneumoniae.
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The abundant presence of temperate phages in the chromosomes of clinical isolates of Streptococcus pneumoniae has been well documented. The genome of MM1, a temperate phage of pneumococcus, has been isolated as a DNA-protein complex. The protein is covalently bound to the DNA, was iodinated in vitro with Na125I, and has an Mr of 22,000. Electron microscopy and enzymatic analyses revealed that the MM1 genome is a linear, circularly permuted, terminally redundant collection of double-stranded DNA molecules packaged via a headful mechanism. The location of the pac site appears to be downstream of the terminase, between orf32 and orf34 of the MM1 genome. (+info)
Complete genomic nucleotide sequence of the temperate bacteriophage Aa Phi 23 of Actinobacillus actinomycetemcomitans.
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The entire double-stranded DNA genome of the Actinobacillus actinomycetemcomitans bacteriophage Aa Phi 23 was sequenced. Linear DNA contained in the phage particles is circularly permuted and terminally redundant. Therefore, the physical map of the phage genome is circular. Its size is 43,033 bp with an overall molar G+C content of 42.5 mol%. Sixty-six potential open reading frames (ORFs) were identified, including an ORF resulting from a translational frameshift. A putative function could be assigned to 23 of them. Twenty-three other ORFs share homologies only with hypothetical proteins present in several bacteria or bacteriophages, and 20 ORFs seem to be specific for phage Aa Phi 23. The organization of the phage genome and several genetic functions share extensive similarities to that of the lambdoid phages. However, Aa Phi 23 encodes a DNA adenine methylase, and the DNA packaging strategy is more closely related to the P22 system. The attachment sites of Aa Phi 23 (attP) and several A. actinomycetemcomitans hosts (attB) are 49 bp long. (+info)
DNA ejection from bacteriophage T5: analysis of the kinetics and energetics.
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DNA ejection from bacteriophage T5 can be passively driven in vitro by the interaction with its specific host receptor. Light scattering was used to determine the physical parameters associated with this process. By studying the ejection kinetics at different temperatures, we demonstrate that an activation energy of the order of 70 k(B)T must be overcome to allow the complete DNA ejection. A complex shape of the kinetics was found whatever the temperature. This shape may be actually understood using a phenomenological model based on a multistep process. Passing from one stage to another requires the mentioned thermal activation of pressurized DNA inside the capsids. Both effects contribute to shorten or to lengthen the pause time between the different stages explaining why the T5 DNA ejection is so slow compared to other types of phage. (+info)
DNA recombination with a heterospecific Cre homolog identified from comparison of the pac-c1 regions of P1-related phages.
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Sequencing of the 7 kb immC region from four P1-related phages identified a novel DNA recombinase that exhibits many Cre-like characteristics, including recombination in mammalian cells, but which has a distinctly different DNA specificity. DNA sequence comparison to the P1 immC region showed that all phages had related DNA terminase, C1 repressor and DNA recombinase genes. Although these genes from phages P7, phi(w39) and p15B were highly similar to those from P1, those of phage D6 showed significant divergence. Moreover, the D6 sequence showed evidence of DNA deletion and substitution in this region relative to the other phages. Characterization of the D6 site-specific DNA recombinase (Dre) showed that it was a tyrosine recombinase closely related to the P1 Cre recombinase, but that it had a distinct DNA specificity for a 32 bp DNA site (rox). Cre and Dre are heterospecific: Cre did not catalyze recombination at rox sites and Dre did not catalyze recombination at lox sites. Like Cre, Dre catalyzed both integrative and excisive recombination and required no other phage-encoded proteins for recombination. Dre-mediated recombination in mammalian cells showed that, like Cre, no host bacterial proteins are required for efficient Dre-mediated site-specific DNA recombination. (+info)
Forces during bacteriophage DNA packaging and ejection.
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The conjunction of insights from structural biology, solution biochemistry, genetics, and single-molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a beneficiary of these experimental techniques is the study of viruses. In this article we describe how the insights obtained from such experiments can be utilized to construct physical models of processes in the viral life cycle. We focus on dsDNA bacteriophages and show that the bending elasticity of DNA and its electrostatics in solution can be combined to determine the forces experienced during packaging and ejection of the viral genome. Furthermore, we quantitatively analyze the effect of fluid viscosity and capsid expansion on the forces experienced during packaging. Finally, we present a model for DNA ejection from bacteriophages based on the hypothesis that the energy stored in the tightly packed genome within the capsid leads to its forceful ejection. The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure. (+info)