Geminiviruses: a tale of a plasmid becoming a virus

Background  

Geminiviruses (family Geminiviridae) are small single-stranded (ss) DNA viruses infecting plants. Their virion morphology is unique in the known viral world – two incomplete T = 1 icosahedra are joined together to form twinned particles. Geminiviruses utilize a rolling-circle mode to replicate their genomes. A limited sequence similarity between the three conserved motifs of the rolling-circle replication initiation proteins (RCR Reps) of geminiviruses and plasmids of Gram-positive bacteria allowed Koonin and Ilyina to propose that geminiviruses descend from bacterial replicons.     

Recognition of a flipped base in a hairpinloop DNA by a small peptide

Two tiny hairpin DNAs, CORE (dAGGCTTCGGCCT) and AP2 (dAGGCTXCGGCCT; X: abasic nucleotide), fold into almost the same tetraloop hairpin structure with one exception, that is, the sixth thymine (T6) of CORE is exposed to the solvent water (Kawakami, J. et al., Chem. Lett. 2001, 258-259). In the present study, we selected small peptides that bind to CORE or AP2 from a combinatorial pentapeptide library with 2.5 x 10(6) variants. On the basis of the structural information, the selected peptide sequences should indicate the essential qualifications for recognition of the hairpin loop DNA with and without a flipped base. In the selected DNA binding peptides, aromatic amino acids such as histidine for CORE and glutamine/aspartic acid for AP2 were found to be abundant amino acids. This amino acid preference suggests that CORE-binding peptides use pi-pi stacking to recognize the target while hydrogen bonding is dominant for AP2-binding peptides. To investigate the binding properties of the selected peptide to the target, surface plasmon resonance was used. The binding constant of the interaction between CORE and a CORE-binding peptide (HWHHE) was about 1.1 x 10(6) M(-1) at 25 degrees C and the resulting binding free energy change at 25 degrees C (DeltaG degrees (25)) was -8.2 kcal mol(-1). The binding of the peptide to AP2 was also analyzed and the resulting binding constant and DeltaG degrees (25) were about 4.2 x 10(4) M(-1) and -6.3 kcal mol(-1), respectively. The difference in the binding free energy changes (DeltaDeltaG degrees (25)) of 1.9 kcal mol(-1) was comparable to the values reported in other systems and was considered a consequence of the loss of pi-pi stacking. Moreover, the stabilization effect by stacking affected the dissociation step as well as the association step. Our results suggest that the existence of an aromatic ring (T6 base) produces new dominant interactions between peptides and nucleic acids, although hydrogen bonding is the preferable mode of interaction in the absence of the flipping base. These findings regarding CORE and AP2 recognition are expected to give useful information in the design of novel artificial DNA binding peptides.     

Characterization of a neuraminidase-deficient influenza a virus as a potential gene delivery vector and a live vaccine

We recently identified a packaging signal in the neuraminidase (NA) viral RNA (vRNA) segment of an influenza A virus, allowing us to produce a mutant virus [GFP(NA)-Flu] that lacks most of the NA open reading frame but contains instead the gene encoding green fluorescent protein (GFP). To exploit the expanding knowledge of vRNA packaging signals to establish influenza virus vectors for the expression of foreign genes, we studied the replicative properties of this virus in cell culture and mice. Compared to wild-type virus, GFP(NA)-Flu was highly attenuated in normal cultured cells but was able to grow to a titer of >10(6) PFU/ml in a mutant cell line expressing reduced levels of sialic acid on the cell surface. GFP expression from this virus was stable even after five passages in the latter cells. In intranasally infected mice, GFP was detected in the epithelial cells of nasal mucosa, bronchioles, and alveoli for up to 4 days postinfection. We attribute the attenuated growth of GFP(NA)-Flu to virion aggregation at the surface of bronchiolar epithelia. In studies to test the potential of this mutant as a live attenuated influenza vaccine, all mice vaccinated with >/==" BORDER="0">10(5) PFU of GFP(NA)-Flu survived when challenged with lethal doses of the parent virus. These results suggest that influenza virus could be a useful vector for expressing foreign genes and that a sialidase-deficient virus may offer an alternative to the live influenza vaccines recently approved for human use.     

Defining a monophyletic Cardinalini: a molecular perspective

Within the New World nine-primaried oscine assemblage, feeding morphology and behavior have long been used as a guideline for assigning membership to subgroups. For example, birds with stout, conical bills capable of crushing heavy seeds have generally been placed within the tribe Cardinalini (cardinal-grosbeaks). Many workers have tried to characterize this group more definitively, using a variety of morphological characters; however, the characters used often conflicted with one another. Previous molecular studies addressing the monophyly of Cardinalini have had only limited sampling within the group. In this study, we analyze mtDNA sequence data from all genera and 34 of the 42 Cardinalini species (sensu [Sibley, C.G., Monroe, B.L., 1990. Distribution and Taxonomy of the Birds of the World, Yale University Press, New Haven, CT]) to address the monophyly of the group and to reconstruct the most complete phylogeny of this tribe published to date. We found strong support for a redefined Cardinalini that now includes some members previously placed within Thraupini (tanagers; the genera Piranga, Habia, Chlorothraupis, and Amaurospiza) and some members previously placed within the Parulini (wood-warblers; the genus Granatellus). In addition, some genera traditionally considered members of the Cardinalini are shown to have affinities with other groups (the genera Porphyrospiza, Parkerthraustes, and Saltator). Our redefined Cardinalini contains 48 species, six more than are listed in Sibley and Monroe's (1990) taxonomy of the group. Within the nine-primaried oscine assemblage, the Cardinalini are more closely related to the Thraupini (tanagers) than they are to the Emberizini (sparrows), Parulini (wood-warblers), or Icterini (blackbirds), consistently forming a monophyletic group with Thraupini across all analyses. The reconfigured Cardinalini is comprised of five well-supported, major clades: (1) a "masked" clade (Piranga, Cardinalis, Caryothraustes, Periporphyrus, and Rhodothraupis), (2) a "blue" clade (Amaurospiza, Cyanocompsa, Cyanoloxia, Passerina, and Spiza), (3) a clade containing the genera Habia and Chlorothraupis, (4) a clade containing all species of Granatellus, and (5) a clade containing only species of Pheucticus. Diversification of these five lineages from one another occurred relatively rapidly during the mid-Pliocene, around 5 or 8 million years ago. Each of these major clades includes both North and South American species; thus, a complex biogeographic history is inferred for the group.     

Metabolism of a DDT metabolite via a chloroepoxide

The 1,1,1-trichloro-2,2-bis(p-chlorophenyl)ethane (DDT) metabolic intermediate 1-chloro-2,2-bis(p-chlorophenyl)ethene (DDMU) is partially metabolized in vivo by mice to 2-hydroxy-2,2-bis(p-chlorophenyl)acetic acid (αOH-DDA) and other metabolites which are excreted in urine. The subsequent DDT metabolic intermediates 1-chloro-2,2-bis(p-chlorophenyl)ethane (DDMS) and 1,1-bis(p-chlorophenyl)ethene (DDNU) are metabolized to αOH-DDA to a much lesser extent. These results imply that DDMU may be metabolized via an α-chloroepoxide. The authentic DDMU-epoxide, which after oral administration is excreted as αOH-DDA, is mutagenic in the Ames assay, and thermally rearranges rapidly to the corresponding α-chloroaldehyde, 2,2-bis(p-chlorophenyl)-2-chloroacetaldehyde (αCl-DDCHO). As expected αCl-DDCHO yielded the same urinary metabolites as DDMU-epoxide. This suggested metabolic pathway for DDMU via a chloroepoxide intermediate may account for the tumorigenicity of DDT in mice.     

Inactivation of C5a anaphylatoxin by a peptide that is complementary to a region of C5a

PL37 (RAARISLGPRCIKAFTE) is an antisense homology box peptide composed of aa 37-53 of C5a-anaphylatoxin and is considered to be the region essential for C5a function. Using a computer program, we designed the complementary peptides ASGAPAPGPAGPLRPMF (Pep-A) and ASTAPARAGLPRLPKFF (Pep-B). Pep-A bound to PL37 and to C5a with very slow dissociation as determined by analysis using surface plasmon resonance, whereas Pep-B failed to bind at all. C5a was inactivated by concentrations of 7 nM or more of Pep-A, and this concentration of Pep-A inhibited induction of intracellular Ca(2+) influx in neutrophils. Patch clamp electrophysiology experiments also showed the effectiveness of Pep-A in C5aR-expressing neuroblastoma cells. Furthermore, Pep-A administration prevented rats from C5a-mediated rapid lethal shock induced by an Ab to a membrane inhibitor of complement after LPS sensitization.     

Identification of a methotrexate-binding peptide from a T7 phage display screen using a QCM device

An 11-mer unique peptide sequence SIFPLCNSGAL was identified as a methotrexate (MTX)-binding peptide from a T7 phage display screen using a quartz-crystal microbalance (QCM) biosensor. The synthetic peptide displayed weak interaction with MTX (K(D) 2.23x10(-5) M) using surface plasmon resonance (SPR). Interestingly, analysis of the primary amino acid sequence of the peptide identified similarities to the MTX-binding site of dihydrofolate reductase (DHFR). Our results highlight the importance of this primary sequence for the recognition of the MTX molecule.     

Evaluation of a new apolipoprotein(a) isoform-independent assay for serum Lipoprotein(a)

The risk factor, Lipoprotein(a), [(Lp(a)], has been measured in numerous clinical studies by a variety of immunochemical assay methods. It is becoming apparent that for many of these assays antibody specificity towards the apolipoprotein(a) [apo(a)] repetitive component [the kringle 4 - type 2 repeats] and apo(a) size heterogeneity can significantly affect the accuracy of serum Lp(a) measurements. To address this issue, we investigated whether our current in house Lp(a) [Mercodia] assay showed such bias compared to a recently available assay [Apo-Tek], claiming to possess superior capability for isoform-independent measurement of Lp(a). Levels of Lipoprotein(a) by both Apo-Tek and Mercodia assays correlated inversely with apo(a) isoform sizes. No significant differences were observed between assays in ranges of Lp(a) concentration within each isoform group. The Mercodia assay exhibited similar isoform-independent behaviour to that of Apo-Tek for e quantitation of serum Lipoprotein(a). Essentially identical results were obtained by the two methods, suggesting that Mercodia assay's capture monoclonal antibody also (as is the case for Apo-Tek) does not recognize the kringle 4-type 2 repetitive domain of apo(a). Correlation of Lp(a) concentrations in patient specimens between Apo-Tek and Mercodia assays showed good agreement, although an overall higher degree of imprecision and non-linearity was noted for the Apo-Tek procedure. A change-over to the Apo-Tek assay would therefore not improve on our current assessment of risk contribution from Lp(a) for atherosclerotic vascular disease in individuals with measurable levels of circulating Lipoprotein(a).     

Active subtilisin-like protease from a hyperthermophilic archaeon in a form with a putative prosequence

The gene encoding subtilisin-like protease T. kodakaraensis subtilisin was cloned from a hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. T. kodakaraensis subtilisin is a member of the subtilisin family and composed of 422 amino acid residues with a molecular weight of 43,783. It consists of a putative presequence, prosequence, and catalytic domain. Like bacterial subtilisins, T. kodakaraensis subtilisin was overproduced in Escherichia coli in a form with a putative prosequence in inclusion bodies, solubilized in the presence of 8 M urea, and refolded and converted to an active molecule. However, unlike bacterial subtilisins, in which the prosequence was removed from the catalytic domain by autoprocessing upon refolding, T. kodakaraensis subtilisin was refolded in a form with a putative prosequence. This refolded protein of recombinant T. kodakaraensis subtilisin which is composed of 398 amino acid residues (Gly(-82) to Gly(316)), was purified to give a single band on a sodium dodecyl sulfate (SDS)-polyacrylamide gel and characterized for biochemical and enzymatic properties. The good agreement of the molecular weights estimated by SDS-polyacrylamide gel electrophoresis (44,000) and gel filtration (40,000) suggests that T. kodakaraensis subtilisin exists in a monomeric form. T. kodakaraensis subtilisin hydrolyzed the synthetic substrate N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide only in the presence of the Ca(2+) ion with an optimal pH and temperature of pH 9.5 and 80 degrees C. Like bacterial subtilisins, it showed a broad substrate specificity, with a preference for aromatic or large nonpolar P1 substrate residues. However, it was much more stable than bacterial subtilisins against heat inactivation and lost activity with half-lives of >60 min at 80 degrees C, 20 min at 90 degrees C, and 7 min at 100 degrees C.     

Nitric oxide as a cellular antioxidant: a little goes a long way

Nitric oxide (NO*) is an effective chain-breaking antioxidant in free radical-mediated lipid oxidation (LPO). It reacts rapidly with peroxyl radicals as a sacrificial chain-terminating antioxidant. The goal of this work was to determine the minimum threshold concentration of NO* required to inhibit Fe2+ -induced cellular lipid peroxidation. Using oxygen consumption as a measure of LPO, we simultaneously measured nitric oxide and oxygen concentrations with NO* and O2 electrodes. Ferrous iron and dioxygen were used to initiate LPO in docosahexaenoic acid-enriched HL-60 and U937 cells. Bolus addition of NO* (1.5 microM) inhibited LPO when the NO* concentration was greater than 50 nM. Similarly, using (Z)-1-[N-(3-ammoniopropyl)-N-(n-propyl)amino]diazen-1-ium-1,2-diolate as a NO* donor we found that an average steady-state NO* concentration of at least 72 +/- 9 nM was required to blunt LPO. As long as the concentration of NO* was above 13 +/- 8 nM the inhibition was sustained. Once the concentration of NO* fell below this value, the rate of lipid oxidation accelerated as measured by the rate of oxygen consumption. Our model suggests that a continuous production of NO* that would yield a steady-state concentration of only 10-20 nM is capable of inhibiting Fe2+ -induced LPO.     

The processing of a Benzo(a)pyrene adduct into a frameshift or a base substitution mutation requires a different set of genes in Escherichia coli

Replication through a single DNA lesion may give rise to a panel of translesion synthesis (TLS) events, which comprise error-free TLS, base substitutions and frameshift mutations. In order to determine the genetic control of the various TLS events induced by a single lesion, we have chosen the major N2-dG adduct of (+)-anti-Benzo(a)pyrene diol epoxide [(+)-anti-BPDE] adduct located within a short run of guanines as a model lesion. Within this sequence context, in addition to the major event, i.e. error-free TLS, the adduct also induces base substitutions (mostly G --> T transversions) and -1 frameshift mutations. The pathway leading to G --> T base substitution mutagenesis appears to be SOS independent, suggesting that TLS is most probably performed by the replicative Pol III holoenzyme itself. In contrast, both error-free and frameshift TLS pathways are dependent upon SOS-encoded functions that belong to the pool of inducible DNA polymerases specialized in TLS (translesional DNA polymerases), namely umuDC (Pol V) and dinB (Pol IV). It is likely that, given the diversity of conformations that can be adopted by lesion-containing replication intermediates, cells use one or several translesional DNA polymerases to achieve TLS.     

Centromeric association of a microchromosome in a Turner syndrome patient with a pseudodicentric Y

A 12-year-old patient with Turner syndrome was found to have a complex mosaicism for a microchromosome (MC) and a psu dic(Y)(q11). The MC was smaller than Yp, appeared pale in G, C and late replicating bands, had a pair of small centromeric dots, was associated with other chromosomes in most metaphases, and was rather stable both in size and during mitosis. The psu dic(Y) was Cd-positive only at the active centromere, had two pericentromeric heterochromatic regions, and lacked the Yq12 band. No cells with both abnormal chromosomes were found. To evaluate the association of the MC with all ordinary chromosomes, 857 G-banded cells with the marker were screened. The MC was considered as associated whenever the distance between it and other chromosome(s) was equal to, or smaller than, 18p. Out of 848 associations registered, 489 (57.7%) were centromeric, 202 (23.8%) telomeric, and 157 (18.5%) interstitial; i.e., centromeric associations were overrepresented (P < 0.001) and showed a random distribution, except for an excessive involvement of chromosome 8. This association pattern, also exhibited by two similar MCs in human beings, the minute Y of a marsupial and certain B chromosomes in plants, probably reflects the Rabl orientation of chromosomes in interphase.     

Gastrointestinal stromal tumors in a baboon, a spider monkey, and a chimpanzee and a review of the literature

Background  Gastrointestinal stromal tumors (GISTs) are believed to originate from the intestinal pacemaker cells (interstitial cells of Cajal) or their progenitor cells. Spontaneous tumors have been reported in dogs, horses, rhesus, and a chimpanzee and they have been produced experimentally in mice and rats. GISTs represent a diagnostic challenge because they cannot be differentiated from non-lymphoid mesenchymal tumors without using human c-kit (CD117) immunohistochemistry.
Methods  Three neoplasms were incidental findings at necropsy in the stomachs of a baboon and a spider monkey and in the rectum of a chimpanzee.
Results  The GISTs were initially diagnosed grossly and histologically with hematoxylin and eosin as leiomyomas. Immunohistochemical analysis revealed that all three were c-kit (CD117) positive.
Conclusions  These are the first reports of GISTs in the baboon and spider monkey and the second in a chimpanzee. The occurrence of GISTs in non-human primates may provide a unique opportunity to study these tumors.     

Genetic diversity and invasibility: a test using a model system with a novel experimental design

Biological invasion is one aspect of ecosystem function that may be controlled by the biological diversity of the invaded community, and there have been a number of recent studies that investigated relationships between diversity and invasibility. Most experimental studies report that higher species or functional group diversity increases resistance to invasion, but the role of genetic diversity is unknown. We used a model organism, Arabidopsis thaliana (Brassicaceae), to investigate relationships between genotypic richness and community invasibility by creating communities with 1, 2, 4, and 8 genotypes of A. thaliana at constant low (417 plants m⁻²) and high (834 plants m⁻²) densities, that once established, were invaded with a congener, Arabidopsis suecica. To reduce the potential effects of methodological confounding related to “sampling effects,”“variance reduction effects,” or confounding of abundance with diversity, we (1) created random communities from a relatively large pool of functionally and phenotypically similar genotypes, (2) evaluated individual and community traits across richness treatments, and (3) analyzed similarity of communities within treatments (for “quasi- replication”) and between adjacent treatments (for “nestedness”). Genotypic richness had no effect on A. suecica demography (emergence, survivorship), size (biomass, rosette area), or reproductive potential (rates of bolting and fruiting or number and size of bolts). In contrast, the density of A. thaliana genotypes had strong effects on the size and reproductive potential of A. suecica, which suggests that characteristics of the recipient community other than genotypic richness (e.g. light) form the most important determinant of community invasibility. Individual- and community-level traits of community members (cover, biomass, survivorship) did not differ among richness treatments, and within- and between-treatment similarity was reduced (relative to other recent experiments) but not eliminated. We evaluate our results vis-a-vis recent analyses of diversity-invasibility experiments, and provide directions for future investigations of genetic diversity.     

Discrimination of a colony stimulating factor subclass by a specific receptor on a macrophage cell line

Utilizing the high affinity interactions between pure ¹²⁵I-L cell colony stimulating factor and its receptor(s) on the murine macrophage cell line J774, a murine radioreceptor assay (RRA) has been developed. The murine RRA selectively detects a colony stimulating factor (CSF) subclass (CSF-1) previously defined by murine radioimmunoassay (RIA) (E.R. Stanley, Proc. Nat. Acad. Sci., USA, 76:2969–2973 ('79)). CSF-1 stimulates macrophage production exclusively, and the occurrence of the CSF-1 receptor(s) appears to be restricted to cells of the mononuclear phagocytic system (L.J. Guilbert and E.R. Stanley, J. Cell Biol. 85:153–160 ('80)). The murine CSF-1 RRA failed to detect a variety of other CSF subclasses, growth factors, and hormones. In contrast to data obtained with the murine CSF-1 RIA, human CSF-1 (e.g., human urinary CSF) is detected by the mouse CSF-1 RRA almost as sensitively as murine CSF-1. In addition, there was an absolute correlation between CSF-1 levels determined by murine CSF-1 RRA and those determined by a human CSF-1 RIA for a variety of human CSF-1 sources. The murine CSF-1 RRA is a sensitive (sensitivity 5 units or 1.0 femtomole of CSF-1 protein), rapid, and highly specific assay for CSF-1 in both murine and human sources.     

Elimination of a group II intron from a plastid gene causes a mutant phenotype

Group II introns are found in bacteria and cell organelles (plastids, mitochondria) and are thought to represent the evolutionary ancestors of spliceosomal introns. It is generally believed that group II introns are selfish genetic elements that do not have any function. Here, we have scrutinized this assumption by analyzing two group II introns that interrupt a plastid gene (ycf3) involved in photosystem assembly. Using stable transformation of the plastid genome, we have generated mutant plants that lack either intron 1 or intron 2 or both. Interestingly, the deletion of intron 1 caused a strong mutant phenotype. We show that the mutants are deficient in photosystem I and that this deficiency is directly related to impaired ycf3 function. We further show that, upon deletion of intron 1, the splicing of intron 2 is strongly inhibited. Our data demonstrate that (i) the loss of a group II intron is not necessarily phenotypically neutral and (ii) the splicing of one intron can depend on the presence of another.     

Wah Soon Chow,a teacher,a friend and a colleague

Photosynthesis Research - To finish this special issue, some friends, colleagues and students of Prof. Chow (Emeritus Professor, the Research School of Biology, the Australian National University)...     

Determining a maximum-tolerated schedule of a cytotoxic agent

Most phase I clinical trials are designed to determine a maximum-tolerated dose (MTD) for one initial administration or treatment course of a cytotoxic experimental agent. Toxicity usually is defined as the indicator of whether one or more particular adverse events occur within a short time period from the start of therapy. However, physicians often administer an agent to the patient repeatedly and monitor long-term toxicity due to cumulative effects. We propose a new method for such settings. It is based on the time to toxicity rather than a binary outcome, and the goal is to determine a maximum-tolerated schedule (MTS) rather than a conventional MTD. The model and method account for a patient's entire sequence of administrations, with the overall hazard of toxicity modeled as the sum of a sequence of hazards, each associated with one administration. Data monitoring and decision making are done continuously throughout the trial. We illustrate the method with an allogeneic bone marrow transplantation (BMT) trial to determine how long a recombinant human growth factor can be administered as prophylaxis for acute graft-versus-host disease (aGVHD), and we present a simulation study in the context of this trial.     

Voltammetry of a "protein on a rope"

A periplasmic electron-transfer protein, cytochrome c(555)(m) from Aquifex aeolicus contains a 62-residue N-terminal extension by which it is anchored to the membrane--most probably via a thioester bond to its N-terminal cysteine. This linker can act as a "rope" to tether the protein close to its reaction partners. Mimicking this principle, a recombinant cytochrome c(555)(m), expressed in Escherichia coli, has been attached covalently to a gold electrode modified with 6-mercaptohexan-1-ol. The "tethered" cytochrome c(555)(m) displays remarkably fast electron-transfer kinetics, with an electrochemical exchange rate constant k(0) of 1.4 x 10(4) s(-1). The results show that fast electron transfer is associated with weak interactions: importantly, the tethered cytochrome can explore many different orientations without escaping into solution.