The tra locus of streptomycete plasmid pIJ101 mediates efficient transfer of a circular but not a linear version of the same replicon

Microbiology ◽  
2010 ◽  
Vol 156 (9) ◽  
pp. 2723-2733 ◽  
Author(s):  
Jing Wang ◽  
Gregg S. Pettis

Conjugal transfer of circular plasmids in Streptomyces involves a unique mechanism employing few plasmid-encoded loci and the transfer of double-stranded DNA by an as yet uncharacterized intercellular route. Efficient transfer of the circular streptomycete plasmid pIJ101 requires only two plasmid loci: the pIJ101 tra gene, and as a cis-acting function known as clt. Here, we compared the ability of the pIJ101 transfer apparatus to promote conjugal transfer of circular versus linear versions of the same replicon. While the pIJ101 tra locus readily transferred the circular form of the replicon, the linear version was transferred orders of magnitude less efficiently and all plasmids isolated from the transconjugants were circular, regardless of their original configuration in the donor. Additionally, relatively rare circularization of linear plasmids was detectable in the donor cells, which is consistent with the notion that this event was a prerequisite for transfer by TraB(pIJ101). Linear versions of this same replicon did transfer efficiently, in that configuration, from strains containing the conjugative linear plasmid SLP2. Our data indicate that functions necessary and sufficient for transfer of circular DNA were insufficient for transfer of a related linear DNA molecule. The results here suggest that the conjugation mechanisms of linear versus circular DNA in Streptomyces spp. are inherently different and/or that efficient transfer of linear DNA requires additional components.

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1463
Author(s):  
Lei Wei ◽  
Alexander Ploss

Hepatitis B virus (HBV) remains a major medical problem affecting at least 257 million chronically infected patients who are at risk of developing serious, frequently fatal liver diseases. HBV is a small, partially double-stranded DNA virus that goes through an intricate replication cycle in its native cellular environment: human hepatocytes. A critical step in the viral life-cycle is the conversion of relaxed circular DNA (rcDNA) into covalently closed circular DNA (cccDNA), the latter being the major template for HBV gene transcription. For this conversion, HBV relies on multiple host factors, as enzymes capable of catalyzing the relevant reactions are not encoded in the viral genome. Combinations of genetic and biochemical approaches have produced findings that provide a more holistic picture of the complex mechanism of HBV cccDNA formation. Here, we review some of these studies that have helped to provide a comprehensive picture of rcDNA to cccDNA conversion. Mechanistic insights into this critical step for HBV persistence hold the key for devising new therapies that will lead not only to viral suppression but to a cure.


2013 ◽  
Vol 41 (2) ◽  
pp. 625-629 ◽  
Author(s):  
Zuzana Benková ◽  
Peter Cifra

Understanding the mechanism of DNA extension in nanochannels is necessary for interpretation of experiments in nanofluidic channel devices that have been conducted recently with both linear and ring chains. The present article reviews the situation with linear chains and analyses the experimental results and simulations for channel-induced extension (linearization) of ring chains. Results for confined rings indicate a transition between moderate and strong confinement similar to that of linear chains. Owing to stronger self-avoidance in confined rings, the transition and chain extension is shifted relative to linear DNA. We suggest that a relationship similar to that used for the extension of linear chains may also be used for circular DNA.


1995 ◽  
Vol 28 (3) ◽  
pp. 253-313 ◽  
Author(s):  
De Witt Sumners ◽  
Claus Ernst ◽  
Sylvia J. Spengler ◽  
Nicholas R. Cozzarelli

The DNA of all organisms has a complex and essential topology. The three topological properties of naturally occurring DNA are supercoiling, catenation, and knotting. Although these properties are denned rigorously only for closed circular DNA, even linear DNA in vivo can have topological properties because it is divided into topologically separate subdomains (Drlica 1987; Roberge & Gasser, 1992). The essentiality of topological properties is demonstrated by the lethal consequence of interfering with topoisomerases, the enzymes that regulate the level of DNA supercoiling and that unlink DNA during its replication (reviewed in Wang, 1991; Bjornsti, 1991; Drlica, 1992; Ullsperger et al. 1995).


Cell ◽  
1978 ◽  
Vol 15 (4) ◽  
pp. 1383-1395 ◽  
Author(s):  
Peter R. Shank ◽  
Stephen H. Hughes ◽  
Hsing-Jien Kung ◽  
John E. Majors ◽  
Nancy Quintrell ◽  
...  

1979 ◽  
Vol 16 (04) ◽  
pp. 721-731
Author(s):  
Samuel Litwin

A linear DNA molecule may be labelled at a fixed locus by a minute complementary radioactive molecule. A collection of identical molecules is to be so labelled and each one independently cut at a random number, N, of random places, X (N Poisson, X uniform). Fragments containing the label are to be collected and assayed by length. It is shown that the recovery pattern (fragment length distribution) contains a jump discontinuity at the fixed locus and may be used to determine the distance between the attachment site and the nearest end of the molecule. The recovery pattern under the hypothesis that the collection of molecules are circularly permuted, i.e. the labelled locus is uniformly distributed over the length of the molecule, does not contain such discontinuities. The case where the labelling molecule has a non-negligible extent is also treated.


Polymers ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 84 ◽  
Author(s):  
Tomoya Kubota ◽  
Kento Lloyd ◽  
Naoto Sakashita ◽  
Seiya Minato ◽  
Kentaro Ishida ◽  
...  

Motions of circular and linear DNA molecules of various lengths near a nanopore of 100 or 200 nm diameter were experimentally observed and investigated by fluorescence microscopy. The movement of DNA molecules through nanopores, known as translocation, is mainly driven by electric fields near and inside the pores. We found significant clogging of nanopores by DNA molecules, particularly by circular DNA and linear T4 DNA (165.65 kbp). Here, the probabilities of DNA clogging events, depending on the DNA length and shape—linear or circular—were determined. Furthermore, two distinct DNA motions were observed: clog and release by linear T4 DNA, and a reverse direction motion at the pore entrance by circular DNA, after which both molecules moved away from the pore. Finite element method-based numerical simulations were performed. The results indicated that DNA molecules with pores 100–200 nm in diameter were strongly influenced by opposing hydrodynamic streaming flow, which was further enhanced by bulky DNA configurations.


2008 ◽  
Vol 82 (9) ◽  
pp. 4595-4611 ◽  
Author(s):  
Adly M. M. Abd-Alla ◽  
François Cousserans ◽  
Andrew G. Parker ◽  
Johannes A. Jehle ◽  
Nicolas J. Parker ◽  
...  

ABSTRACT Several species of tsetse flies can be infected by the Glossina pallidipes salivary gland hypertrophy virus (GpSGHV). Infection causes salivary gland hypertrophy and also significantly reduces the fecundity of the infected flies. To better understand the molecular basis underlying the pathogenesis of this unusual virus, we sequenced and analyzed its genome. The GpSGHV genome is a double-stranded circular DNA molecule of 190,032 bp containing 160 nonoverlapping open reading frames (ORFs), which are distributed equally on both strands with a gene density of one per 1.2 kb. It has a high A+T content of 72%. About 3% of the GpSGHV genome is composed of 15 sequence repeats, distributed throughout the genome. Although sharing the same morphological features (enveloped rod-shaped nucleocapsid) as baculoviruses, nudiviruses, and nimaviruses, analysis of its genome revealed that GpSGHV differs significantly from these viruses at the level of its genes. Sequence comparisons indicated that only 23% of GpSGHV genes displayed moderate homologies to genes from other invertebrate viruses, principally baculoviruses and entomopoxviruses. Most strikingly, the GpSGHV genome encodes homologues to the four baculoviral per os infectivity factors (p74 [pif-0], pif-1, pif-2, and pif-3). The DNA polymerase encoded by GpSGHV is of type B and appears to be phylogenetically distant from all DNA polymerases encoded by large double-stranded DNA viruses. The majority of the remaining ORFs could not be assigned by sequence comparison. Furthermore, no homologues to DNA-dependent RNA polymerase subunits were detected. Taken together, these data indicate that GpSGHV is the prototype member of a novel group of insect viruses.


Blood ◽  
2006 ◽  
Vol 109 (1) ◽  
pp. 109-111 ◽  
Author(s):  
Gregory V. Priestley ◽  
Tatiana Ulyanova ◽  
Thalia Papayannopoulou

Abstract We have generated Tie2Cre+α4f/f mice with documented α4-integrin ablation in hematopoietic and endothelial cells. A prominent feature in this model is a sustained, significant increase in circulating progenitors at levels higher than the levels seen with Tie2Cre+VCAM-1f/f mice. To test whether phenotypic differences are due to contributions by ligands other than VCAM-1 in bone marrow, or to α4-deficient endothelial cells or pericytes, we carried out transplantation experiments using these mice as donors or as recipients. Changes in progenitor biodistribution after transplantation were seen only with α4-deficient donor cells, suggesting that these cells were necessary and sufficient to reproduce the phenotype with no discernible contribution by α4-deficient nonhematopoietic cells. Because several similarities are seen after transplantation between our results and those with CXCR4−/− donor cells, the data suggest that VLA4/VCAM-1 and CXCR4/CXCL12 pathways contribute to a nonredundant, ongoing signaling required for bone marrow retention of progenitor cells during homeostasis.


1972 ◽  
Vol 130 (4) ◽  
pp. 1019-1028 ◽  
Author(s):  
Douglas J. Jolly ◽  
Ailsa M. Campbell

Previous investigations on the persistence length of DNA in solution have revealed large discrepancies between hydrodynamic results and those from light-scattering techniques which have potentially a greater resolving power. The information obtained from experiments on a small circular DNA molecule has resolved these discrepancies. The non-superhelical circular double-stranded DNA molecule from bacteriophage [unk]X174-infected cells is small enough to permit accurate light-scattering extrapolations, and its solutions have negligible anisotropy. The persistence length obtained from experimental investigations on this molecule is comparable with that obtained by hydrodynamic techniques, even with variation of the excluded-volume factor.


1979 ◽  
Vol 16 (4) ◽  
pp. 721-731
Author(s):  
Samuel Litwin

A linear DNA molecule may be labelled at a fixed locus by a minute complementary radioactive molecule. A collection of identical molecules is to be so labelled and each one independently cut at a random number, N, of random places, X (N Poisson, X uniform). Fragments containing the label are to be collected and assayed by length. It is shown that the recovery pattern (fragment length distribution) contains a jump discontinuity at the fixed locus and may be used to determine the distance between the attachment site and the nearest end of the molecule.The recovery pattern under the hypothesis that the collection of molecules are circularly permuted, i.e. the labelled locus is uniformly distributed over the length of the molecule, does not contain such discontinuities. The case where the labelling molecule has a non-negligible extent is also treated.


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