Properties of the Circular Plasmid-like DNA Bl from Mitochondria of Cytoplasmic Male-sterile Rice

Mitochondrial DNA from suspension-cultured cells of the cytoplasmicmale-sterile rice line, A-58 CMS, was shown to contain fourminicircular DNAs. We chose for further examination the largestminicircular DNA, designated Bl. A molecular clone containingthe complete sequence of Bl was constructed and used to probemitochondrial and nuclear genomes by Southern hybridization.No evidence was found for the existence of integrated copiesof Bl in the main mitochondrial genomes of either male-sterileor fertile rice. Sequences homologous to Bl, however, were foundin nuclear genomes of both the male-sterile and the fertilerice. The complete nudeotide sequence of Bl (2,135 bp) was determined,and found to contain sequences homologous to those in the 1,913bp plasmid-like DNA of maize. (Received May 15, 1987; Accepted July 20, 1987)     

Enhanced Methane Production from Anaerobic Digestion of Disintegrated and Deproteinized Excess Sludge

To improve biogas yield and methane content in anaerobic digestion of excess sludge from the wastewater treatment plant, the sludge was disintegrated by using various methods (sonication, alkaline and thermal treatments). Since disintegrated sludge contains a high concentration of soluble proteins, the resulting metabolite, ammonia, may inhibit methane generation. Therefore, the effects of protein removal from disintegrated sludge on methane production were also studied. As a result, an obvious enhancement of biogas generation was observed by digesting disintegrated sludge (biogas yield increased from 15 to 36 ml/g COD_added·day for the raw excess sludge and the sonicated sludge, respectively). The quality of biogas was also improved by removing proteins from the disintegrated sludge. About 50% (w/w) of soluble proteins were removed from the suspension of disintegrated sludge by salting out using 35 g MgCl₂·6H₂O/l and also by isoelectric point precipitation at pH 3.3. For deproteinized sludge, methane production increased by 19%, and its yield increased from 145 ml/g COD_removed to 325 ml/g COD_removed. Therefore, the yield and quality of biogas produced from digestion of excess sludge can be enhanced by disintegrating the sludge and subsequent protein removal. Revisions requested 14 November 2005; Revisions received 13 January 2006     

Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses

Because most extant viruses mutate rapidly and lack a true fossil record, their deep evolution and long-term substitution rates remain poorly understood. In addition to retroviruses, which rely on chromosomal integration for their replication, many other viruses replicate in the nucleus of their host''s cells and are therefore prone to endogenization, a process that involves integration of viral DNA into the host''s germline genome followed by long-term vertical inheritance. Such endogenous viruses are highly valuable as they provide a molecular fossil record of past viral invasions, which may be used to decipher the origins and long-term evolutionary characteristics of modern pathogenic viruses. Hepadnaviruses (Hepadnaviridae) are a family of small, partially double-stranded DNA viruses that include hepatitis B viruses. Here we report the discovery of endogenous hepadnaviruses in the genome of the zebra finch. We used a combination of cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds. We provide evidence that some of the avian hepadnavirus integration events are at least 19 My old, which reveals a much deeper ancestry of Hepadnaviridae than could be inferred based on the coalescence times of modern hepadnaviruses. Furthermore, the remarkable sequence similarity between endogenous and extant avian hepadnaviruses (up to 75% identity) suggests that long-term substitution rates for these viruses are on the order of 10⁻⁸ substitutions per site per year, which is a 1,000-fold slower than short-term rates estimated based on the sequences of circulating hepadnaviruses. Together, these results imply a drastic shift in our understanding of the time scale of hepadnavirus evolution, and suggest that the rapid evolutionary dynamics characterizing modern avian hepadnaviruses do not reflect their mode of evolution on a deep time scale.     

Cytoplasmic organization of POXvirus DNA replication

Poxviruses, a family of large DNA viruses, are unique among DNA viruses, because they carry out DNA replication in the cytoplasm rather than the nucleus. This process does not occur randomly, but instead, these viruses create cytoplasmic 'mini-nuclei', distinct sites that are surrounded by membranes derived from the rough endoplasmic reticulum (ER) that support viral replication. This review summarizes how distinct steps preceding cytoplasmic DNA replication, as well as replication itself, operate in the host cell. The collective data point to an important role for both the rough ER and the microtubules and indicate that these cellular structures help to co-ordinate the virus life cycle to ensure that individual steps occur at the right time and place. In a broader sense, they emphasize how viruses have evolved sophisticated ways to use host cells to optimize their life cycles to ensure efficient production of infectious progeny.     

植物类受体胞质激酶的结构和功能

本文介绍植物类受体胞质激酶的结构及其在植物的抗病、抗逆、生长发育、自交不亲和、油菜素内酯信号转导等方面的功能。     

Circular dichroism of superhelical DNA

The circular dichroism (CD) spectra of a number of superhelical DNA's have been measured. The introduction of negative superhelical turns causes an increase in magnitude of the positive band around 280 mμ, while the trough around 250mμ is little affected. For two samples of λb2b5c DNA (20 Mdalton) containing different number of negative superhelical turns, the magnitude of the positive band relative to that of the nicked control increases with increasing number of superhelical turns. In 2M NaCl, the small (1.45 Mdalton) superhelical DNA from E. coli 15 shows an unusually large difference in CD compared with that of the same DNA with a few single-chain scissions per molecule. This large difference is not observed in a medium containing p. 0.11M NaCl. These results indicate that the double helix in a superhelical DNA is perturbed somewhat due to the bending and torsional forces in such a molecule. The magnitude of such structural alteration seems to depend on the number of superhelical turns per unit length, the size of the DNA molecule, as well as the ionic medium.     

Cytoplasmic DNA variation and relationships in cereal genomes

Summary Chloroplast (cp) and mitochondrial (mt) DNAs were isolated from four cereal genomes (cultivated wheat, rye, barley and oats) and compared by restriction nuclease analysis. Cleavage of cp and mt DNAs by Sal I, Kpn I, Xho I and EcoR I enzymes indicated that each cereal group contains specific cytoplasmic DNAs. A phylogenetic tree of cereal evolution has been obtained on the basis of cp DNA homologies. It is suggested that wheat and rye diverged after their common ancestor had diverged from the ancestor of barley. This was preceded by the divergence of the common ancestor of wheat, rye and barley and the ancestor of oats.The molecular weight of the different cp DNAs was determined from the Sal I and Kpn I patterns. cp DNAs from wheat, rye, barley and oats appeared to be characterized by a very similar molecular weight of about 80–82.10⁶ d.In the case of the mt DNAs, the great number of restriction fragments obtained with the restriction enzymes used prevented precise comparisons and determination of molecular weights.     

Alternative Splicing of the RAGE Cytoplasmic Domain Regulates Cell Signaling and Function

The Receptor for Advanced Glycation End-products (RAGE) is a multi-ligand receptor present on most cell types. Upregulation of RAGE is seen in a number of pathological states including, inflammatory and vascular disease, dementia, diabetes and various cancers. We previously demonstrated that alternative splicing of the RAGE gene is an important mechanism which regulates RAGE signaling through the production of soluble ligand decoy isoforms. However, no studies have identified any alternative splice variants within the intracellular region of RAGE, a region critical for RAGE signaling. Herein, we have cloned and characterized a novel splice variant of RAGE that has a truncated intracellular domain (RAGEΔICD). RAGEΔICD is prevalent in both human and mouse tissues including lung, brain, heart and kidney. Expression of RAGEΔICD in C6 glioma cells impaired RAGE-ligand induced signaling through various MAP kinase pathways including ERK1/2, p38 and SAPK/JNK. Moreover, RAGEΔICD significantly affected tumor cell properties through altering cell migration, invasion, adhesion and viability in C6 glioma cells. Furthermore, C6 glioma cells expressing RAGEΔICD exhibited drastic inhibition on tumorigenesis in soft agar assays. Taken together, these data indicate that RAGEΔICD represents a novel endogenous mechanism to regulate RAGE signaling. Significantly, RAGEΔICD could play an important role in RAGE related disease states through down regulation of RAGE signaling.     

Circular DNA from the water mold Saprolegnia

Summary Circular DNA has been investigated in the water mold Saprolegnia. This organism was shown to contain two satellite DNA components at 1.685 and 1.707 g/cm³ in addition to main band DNA at a buoyant density of 1.717 g/cm³. The component banding at a density of 1.685 g/cm³ was found to occur as closed circles of length 14 m in the relaxed form. On the basis of sucrose gradient studies this DNA is thought to be mitochondrial in origin. No other class of circular molecules was observed.     

Circular DNA Molecules in the Genus Drosophila

The satellite DNA's from the embryos of five species of Drosophila (D. melanogaster, D. simulans, D. nasuta, D. virilis and D. hydei) have been analyzed for the presence of closed circular duplex DNA molecules, as determined by CsCl-EBr gradients. Circular DNA molecules were found in every species but D. melanogaster. Analyses of cell fractions from adult Drosophila and organ fractions from Drosophila larvae show that fractions containing mitochondria are highly enriched in these molecules.     

Synthesis of Cytoplasmic Membrane-associated DNA in Lymphocyte Nucleus

The unique species of DNA associated with the cytoplasmic membranes of human lymphocytes in culture is synthesized in the nucleus during the S growth phase and then transported to the plasma membrane.     

Circular dichroism and DNA secondary structure.

The change in average rotation of the DNA helix has been determined for the transfer from 0.05 M NaCl to 3.0 M CsCl, 6.2 M LiCl and 5.4 M NH4Cl. This work, combined with data at lower salt from other laboratories, allows us to relate the intensity of the CD of DNA at 275 nm directly to the change in the number of base pairs per turn. The change in secondary structure for the transfer of DNA from 0.05 M NaCl (where it is presumably in the B-form) to high salt (where the characteristic CD has been interpreted as corresponding to C-form geometry) is found to be -0.22 (+/- 0.02) base pairs per turn. In the case of mononucleosomes, where the CD indicates the "C-form", the change in secondary structure (including temperature effects) would add -0.31 (+/- 0.03) turns about the histone core to the -1.25 turns estimated from work on SV40 chromatin. Accurate winding angles and molar extinction coefficients were determined for ethidium.     

Circular DNA in human and boar spermatozoa

Circular DNA molecules were isolated from human and boar whole spermatozoa or spermatozoal nuclei and measured for size by electron microscopy. The DNA molecules derived from both mammals were heterogeneous in size ranging from 0.07 to 17 μm; nearly 75% of the molecules were ?0.5 μm in length. The mean lengths were 1.0 μm and 1.5 μm for circular DNAs isolated from human and boar spermatozoa, respectively. The origin and function of these molecules remains unknown.     

Circular Permutations in the Molecular Evolution of DNA Methyltransferases

Circular permutations of genes during molecular evolution often are regarded as elusive, although a simple model can explain these rearrangements. The model assumes that first a gene duplication of the precursor gene occurs in such a way that both genes become fused in frame, leading to a tandem protein. After generation of a new start codon within the 5′ part of the tandem gene and a stop at an equivalent position in the 3′ part of the gene, a protein is encoded that represents a perfect circular permutation of the precursor gene product. The model is illustrated here by the molecular evolution of adenine-N⁶ DNA methyltransferases. β- and γ-type enzymes of this family can be interconverted by a single circular permutation event. Interestingly, tandem proteins, proposed as evolutionary intermediates during circular permutation, can be directly observed in the case of adenine methyltransferases, because some enzymes belonging to type IIS, like the FokI methyltransferase, are built up by two fused enzymes, both of which are active independently of each other. The mechanism for circular permutation illustrated here is very easy and applicable to every protein. Thus, circular permutation can be regarded as a normal process in molecular evolution and a changed order of conserved amino acid motifs should not be interpreted to argue against divergent evolution. Received: 17 November 1998 / Accepted: 19 February 1999