DNA structures associated with autonomously replicating sequences from plants

DNA fragments capable of conferring autonomous replicating ability to plasmids inSaccharomyces cerevisiae were isolated from four different plant genomes and from the Ti plasmid ofAgrobacterium tumefaciens. The DNA structure of these autonomously replicating sequences (ARSs) as well as two from yeast were studied using retardation during polyacrylamide gel electrophoresis and computer analysis as measures of sequence-dependent DNA structures. Bent DNA was found to be associated with the ARS elements. An 11 bp ARS consensus sequence required for ARS function was also identified in the elements examined and was flanked by unusually straight structures which were rich in A+T content. These results show that the ARS elements from genomes of higher plants have structural and sequence features in common with ARS elements from yeast and higher animals.Supported by Grant 1RO1-GM41708-O1 from the National Institute of Health.     

DNA elements modulating the <Emphasis Type="Italic">KARS12</Emphasis> chromosomal replicator in <Emphasis Type="Italic">Kluyveromyces lactis</Emphasis>

Eukaryotic chromosomal DNA replication is initiated by a highly conserved set of proteins that interact with cis-acting elements on chromosomes called replicators. Despite the conservation of replication initiation proteins, replicator sequences show little similarity from species to species in the small number of organisms that have been examined. Examination of replicators in other species is likely to reveal common features of replicators. We have examined a Kluyeromyces lactis replicator, KARS12, that functions as origin of DNA replication on plasmids and in the chromosome. It contains a 50-bp region with similarity to two other K. lactis replicators, KARS101 and the pKD1 replication origin. Replacement of the 50-bp sequence with an EcoRI site completely abrogated the ability of KARS12 to support plasmid and chromosomal DNA replication origin activity, demonstrating this sequence is a common feature of K. lactis replicators and is essential for function, possibly as the initiator protein binding site. Additional sequences up to 1 kb in length are required for efficient KARS12 function. Within these sequences are a binding site for a global regulator, Abf1p, and a region of bent DNA, both of which contribute to the activity of KARS12. These elements may facilitate protein binding, protein/protein interaction and/or nucleosome positioning as has been proposed for other eukaryotic origins of DNA replication.     

Synthesis and crystal structure of a cis-oxime-oximate bridged tetra coordinated open-book shaped new dicopper(II/II) complex [Cu2(μ-Hdmg)2(Hdmg)]ClO4: First report of unusual oxime OH bridging

Reaction of Cu(ClO₄)₂ · 6H₂O with dimethylglyoxime (H₂dmg) and triethylamine (pH ∼ 4-5) at room temperature affords oxime bridged dicopper(II/II) complex of formula [Cu₂(μ-Hdmg)₂(Hdmg)]ClO₄ · H₂O (1) (H₂dmg = dimethylglyoxime). The complex has been characterized by single-crystal X-ray diffraction analysis. The structure consists of one dinuclear complex cation, [Cu₂(μ-Hdmg)₂(Hdmg)], and one anion. Two copper(II) ions at a distance of 3.558 Å are bridged by one oxime and one oximate groups in cis arrangement. The geometry around each copper atom is square planar with an overall open-book type arrangement of these planes. The average copper-oxygen distance is (1.953 Å) and the average copper-nitrogen distance is 2.003 Å. The Cu-O(oxime) distance (1.963 Å) is higher than the Cu-O(oximate) distance (1.942 Å) due to different protonation label. The room temperature value of χ_MT for the title complex (χ_M being the molar magnetic susceptibility for two copper atoms) is low (ca. 0.42 cm³ K mol⁻¹) (μ_eff = 1.52 μ_B). The UV-Vis spectrum of the complex shows a characteristic broad band at 470 nm.     

Epithelial cell proliferation and migration in the developing rat gastric mucosa

To investigate cell proliferation in developing gastric antrum and fundus, proliferating gastric epithelial cells were labeled in fetal rats by intravenously injecting mothers with [³H]thymidine. In addition 14-day postnatal (dPN) rats were given [³H]thymidine intraperitoneally. Tissue was removed 1.5 hr later, and autoradiographs were prepared to identify proliferating cells. Total epithelial labeling indices (L.I.) reached a peak at 20 days gestation (dG), coincident with the appearance of pit/glands, then declined again by 22 dG (gestation end). At 18 dG, labeled cells were distributed throughout all levels of the stratified epithelia. Between 20 and 22 dG, as pit/gland development proceeded, labeled cells became concentrated in the gland bases and were only rarely seen on the surface (L.I. of surface cells <1% at 22 dG). By 14 dPN, proliferating cells were entirely absent from the epithelial surface. Approximately 15% of the endocrine cells were labeled at 22 dG, compared to only 2% at 14 dPN; zymogen cells were labeled (～6%) at 14 dPN; parietal cells did not label at any age studied. In addition, cell migration to the epithelial surface was studied in rats labeled at 22 dG, 14 dPN, or 28 dPN, and killed 1–20 days later. Migration times were slightly shorter in the 28 dPN group and were longer in fundus than antrum in all groups.     

DNA binding and nuclease protection by the HMf histones from the hyperthermophilic archaeon Methanothermus fervidus

The DNA-binding and nuclease-protection properties of the HMf histones from the hyperthermophilic archaeon Methanothermus fervidus have been shown to be consistent with the formation of nucleosome-like structures (NLS). These proteins bind to DNA molecules as short as 20 bp and form complexes that protect DNA fragments from micrococcal nuclease (MNase) digestion that are 30 bp, ∼ 60 bp and multiples of ∼ 60 bp in length. The sequences of 49 of the ∼ 60-bp DNA fragments protected from MNase digestion by HMfA have been determined and their intrinsic curvatures calculated. A circular permutation gel mobility-shift assay was used to determine directly the curvatures for five of these sequences. HMfA bound to intrinsically curved and noncurved DNAs, but exhibited a slight preference for the model curved DNA in binding competitions with a model noncurved DNA. The results obtained are consistent with the concept that the archaeal NLS is analogous, and possibly homologous, to the central core of the eukaryal nucleosome formed by a histone (H3 + H4)2 tetramer. Received: August 11, 1996 / Accepted: November 12, 1996     

Random cloning of bent DNA segments from Saccharomyces cerevisiae and primary characterization of their structures

Summary Until recently it was assumed that any short segment of DNA could be approximated as a straight rod. Many instances, however, have been reported in which the helical axis is curved. We have devised a simple method for selective identification of DNA segments containing a sequence-directed bend (curvature), by means of a two-dimensional polyacrylamide gel electrophoresis. In order to gain general insights into the structural features and the functional significance of sequence-directed bends, a bank of plasmids carrying bent DNA inserts from the Saccharomyces cerevisiae total genomic DNA was constructed. Primary characterizations of a set of bent DNA segments randomly cloned from S. cerevisiae are presented. One of the cloned DNA segments appears to be derived from a yeast plasmid, the 2 m circle DNA.     

Structural Property of DNA That Migrates Faster in Gel Electrophoresis,as Deduced by CD Spectroscopy

Bent DNAs are known to migrate slower than ordinary DNA in non-denaturing polyacrylamide gel electrophoresis. In contrast, several satellite DNAs have been shown to migrate fast. The structural property that causes the fast migration, however, is not clarified so far on molecular basis. We have investigated the structural property of a satellite DNA, which contains consecutive purine sequences and migrates faster in gel, by CD spectroscopy. Partial formation of an A-form–like structure has been suggested. Reduction in DNA length due to the formation of the A-form–like structure may be responsible for the fast migration. The pronounced rigidity of DNA may also contribute to the behavior.     

Transgenic Plants of Creeping Bent Grass Harboring the Stress Inducible Gene, 9-cis-epoxycarotenoid dioxygenase, are Highly Tolerant to Drought and NaCl Stress

Transgenic lines of creeping bent grass were generated by Agrobacterium-mediated transformation with the VuNCED1 which was cloned from cow pea has a homology to 9-cis-epoxycarotenoid dioxygenase, which is supposed to be involved in abscisic acid (ABA) biosynthesis. ABA, a cleavage product of carotenoids, is involved in stress responses in plants. The limiting step of ABA biosynthesis in plants is presumably the cleavage of 9-cis-epoxycarotenoids, the first committed step of ABA biosynthesis. Molecular analyses of transgenic lines as performed by Southern hybridization genomic DNA-PCR revealed integration of the VuNCED1. Challenge studies performed with transgenic plants by exposure to salt stress (up to 10 dS m⁻¹) and water stress (up to 75%) for 10 weeks, revealed that more than 50% of the transgenic plants could survive NaCl and drought stress whereas wild-type was not. ABA levels were measured under drought and normal conditions, endogenous ABA was dramatically increased by drought and NaCl stress in transgenic plants. These results indicate that it is possible to manipulate ABA levels in plants by over expressing the key regulatory gene in ABA biosynthesis and that stress tolerance can be improved by increasing ABA levels. Chenna Reddy Aswath and Sun Hyung Kim - First two authors contributed equally to this work     

Organization of specific DNA sequence elements in the region of the replication origin and matrix attachment site in the chicken alpha-globin gene domain.

Summary The distribution of specific DNA sequence elements in a 2.9 kb HindIII fragment of chicken DNA containing the replication origin and the upstream matrix attachment site (MAR) of the -globin gene domain was investigated. The fragment was shown to contain a CR1-type repetitive element and two stably bent DNA sequences. One of them colocalizes with the previously described MAR element and with the recognition site for a proliferating-cell-specific, DNA-binding protein. The melting pattern of a set of subfragments of the region proved to be non random. No correlation between the distribution of readily melting sequences and bent DNA was found. The possible importance of curved, low-melting and repetitive DNA sequences for the organization of the upstream boundary of the -globin gene domain and the function of the replication origin is discussed.