A pseudoknot ribozyme structure is active in vivo and required for hepatitis delta virus RNA replication

The ribozymes of hepatitis delta virus (HDV) have so far been studied primarily in vitro. Several structural models for HDV ribozymes based on truncated HDV RNA fragments, which are different from the hammerhead or the hairpin/paperclip ribozyme model proposed for plant viroid or virusoid RNAs, have been proposed. Whether these structures actually exist in vivo and whether ribozymes actually function in the HDV replication cycle have not been demonstrated. We have now developed an in vivo ribozyme self-cleavage assay capable of detecting self-cleavage of dimer or trimer HDV RNA in vivo. By site-directed mutagenesis and compensatory mutations to disrupt and restore potential base pairing in the ribozyme domain of the full-length HDV RNA according to the various structural models, a close correlation between the detected in vivo and the predicted in vitro ribozyme activities of various mutant RNAs was demonstrated. These results suggest that the proposed in vitro ribozyme structure likely exists and functions during the HDV replication cycle in vivo. Furthermore, the pseudoknot model most likely represents the structure responsible for the ribozyme activity in vivo. All of the mutants that had lost the ribozyme activity could not replicate, indicating that the ribozyme activities are indeed required for HDV RNA replication. However, some of the compensatory mutants which have restored both the cleavage and ligation activities could not replicate, suggesting that the ribozyme domains are also involved in other unidentified functions or in the formation of an alternative structure that is required for HDV RNA replication. This study thus established that the ribozyme has important biological functions in the HDV life cycle.

Trypanosoma cruzi strains and autonomic nervous system pathology in experimental Chagas disease

Lesions involving the sympathetic (para-vertebral ganglia) and para-sympathetic ganglia of intestines (Auerbach plexus) and heart (right atrial ganglia) were comparatively analyzed in mice infected with either of three different strain types of Trypanosoma cruzi, during acute and chronic infection, in an attempt to understand the influence of parasite strain in causing autonomic nervous system pathology. Ganglionar involvement with neuronal destruction appeared related to inflammation, which most of the times extended from neighboring adipose and cardiac, smooth and striated muscular tissues. Intraganglionic parasitism was exceptional. Inflammation involving peripheral nervous tissue exhibited a focal character and its variability in the several groups examined appeared unpredictable. Although lesions were generally more severe with the Y strain, comparative qualitative study did not allow the conclusion, under the present experimental conditions, that one strain was more pathogenic to the autonomic nervous system than others. No special tropism of the parasites from any strain toward autonomic ganglia was disclosed.

Evolution of fitness in experimental populations of vesicular stomatitis virus

The evolution of fitness in experimental clonal populations of vesicular stomatitis virus (VSV) has been compared under different genetic (fitness of initial clone) and demographic (population dynamics) regimes. In spite of the high genetic heterogeneity among replicates within experiments, there is a clear effect of population dynamics on the evolution of fitness. Those populations that went through strong periodic bottlenecks showed a decreased fitness in competition experiments with wild type. Conversely, mutant populations that were transferred under the dynamics of continuous population expansions increased their fitness when compared with the same wild type. The magnitude of the observed effect depended on the fitness of the original viral clone. Thus, high fitness clones showed a larger reduction in fitness than low fitness clones under dynamics with included periodic bottleneck. In contrast, the gain in fitness was larger the lower the initial fitness of the viral clone. The quantitative genetic analysis of the trait "fitness" in the resulting populations shows that genetic variation for the trait is positively correlated with the magnitude of the change in the same trait. The results are interpreted in terms of the operation of Muller's ratchet and genetic drift as opposed to the appearance of beneficial mutations.

A nonribosomal system of peptide biosynthesis

This review covers peptide structures originating from the concerted action of enzyme systems without the direct participation of nucleic acids. Biosynthesis proceeds by formation of linear peptidyl intermediates which may be enzymatically modified as well as transformed into specific cyclic structures. The respective enzyme systems are constructed of biosynthetic modules integrated into multienzyme structures. Genetic and DNA-sequence analysis of biosynthetic gene clusters have revealed extensive similarities between prokaryotic and eukaryotic systems, conserved principles of organisation, and a unique mechanism of transport of intermediates during elongation and modification steps involving 4'-phospho-pantetheine. These similarities permit the identification of peptide synthetases and related aminoacyl-ligases and acyl-ligases from sequence data. Similarities to other biosynthetic systems involved in the assembly of polyketide metabolites are discussed.

Random removal of inserts from an RNA genome: selection against single-stranded RNA

We have monitored the evolution of insertions in two MS2 RNA regions of known secondary structure where coding pressure is negligible or absent. Base changes and shortening of the inserts proceed until the excessive nucleotides can be accommodated in the original structure. The stems of hairpins can be dramatically extended but the loops cannot, revealing natural selection against single-stranded RNA. The 3' end of the MS2 A-protein gene forms a small hairpin with an XbaI sequence in the loop. This site was used to insert XbaI fragments of various sizes. Phages produced by these MS2 cDNA clones were not wild type, nor had they retained the full insert. Instead, every revertant phage had trimmed the insert in a different way to leave a four- to seven-membered loop to the now extended stem. Similar results were obtained with inserts in the 5' untranslated region. The great number of different revertants obtained from a single starting mutant as well as sequence inspection of the crossover points suggest that the removal of redundant RNA occurs randomly. The only common feature among all revertants appears the potential to form a hairpin with a short loop, suggesting that single-stranded RNA negatively affects the viability of the phage. To test this hypothesis, we introduced XbaI fragments of 34 nucleotides that could form either a long stem with a small loop or a short stem with a large loop (26 nucleotides). The base-paired inserts were perfectly maintained for many generations, whereas the unpaired versions were quickly trimmed back to reduce the size of the loop. These data confirm that single-stranded RNA adversely affects phage fitness and is strongly selected against. The repair of the RNA genome that we describe here appears as the result of random recombination. Of the plethora of recombinants, only those able to adopt a base-paired structure survive. The frequency with which our inserts are removed seems higher than measured by others for small inserts in a reading frame in Q beta RNA. To account for this higher frequency, we suggest models in which the single-stranded nature of our inserts induces random recombination at the site of the insertion.

Muller's ratchet decreases fitness of a DNA-based microbe

Muller proposed that an asexual organism will inevitably accumulate deleterious mutations, resulting in an increase of the mutational load and an inexorable, ratchet-like, loss of the least mutated class [Muller, H.J. (1964) Mutat. Res. 1, 2-9]. The operation of Muller's ratchet on real populations has been experimentally demonstrated only in RNA viruses. However, these cases are exceptional in that the mutation rates of the RNA viruses are extremely high. We have examined whether Muller's ratchet operates in Salmonella typhimurium, a DNA-based organism with a more typical genomic mutation rate. Cells were grown asexually under conditions expected to result in high genetic drift, and the increase in mutational load was determined. S. typhimurium accumulated mutations under these conditions such that after 1700 generations, 1% of the 444 lineages tested had suffered an obvious loss of fitness, as determined by decreased growth rate. These results suggest that in the absence of sex and with high genetic drift, genetic mechanisms, such as back or compensatory mutations, cannot compensate for the accumulation of deleterious mutations. In addition, we measured the appearance of auxotrophs, which allowed us to calculate an average spontaneous mutation rate of approximately 0.3-1.5 x 10(-9) mutations per base pair per generation. This rate is measured for the largest genetic target studied so far, a collection of about 200 genes.

Genetic variation in populations of kennedya yellow mosaic tymovirus

Kennedya yellow mosaic tymovirus (KYMV) occurs along the eastern Australian seaboard in the perennial legumes Desmodium triflorum and D. scorpiurus in the north, and Kennedya rubicunda in the south. The genetic variation of more than 100 isolates of KYMV, most of them from the north, has been studied using an RNA hybrid mismatch polymorphism (RHMP) method. The method clearly separated the isolates into two groups; all the northern Desmodium isolates formed one group and all the Kennedya isolates from the south another. These sub-populations were themselves variable and the Desmodium population alone was more variable than that of the related turnip yellow mosaic tymovirus in the Kosciusko alpine area.

Cytoplasmic incompatibility and mating preference in Colombian Drosophila pseudoobscura

MACRAE and ANDERSON observed a large frequency change of mitochondrial DNA (mtDNA) haplotypes in a population initiated with two allopatric strains of Drosophila pseudoobscura, BogER from Colombia and AH162 from California. They concluded that mtDNA haplotypes in D. pseudoobscura are not always selectively neutral. NIGRO and PROUT suggested, however, that a maternally transmitted incompatibility system, similar to the one they observed in two strains of D. simulans from Italy, could account for the observed mtDNA frequency changes. SINGH and HALE postulated that a mating preference between the strains BogER and AH162 in MACRAF and ANDERSON's experiment, in the form of negative assortative mating, could also account for the mtDNA frequency changes. We report two experiments designed to test the hypotheses: that a maternally transmitted cytoplasmic incompatibility system exists between D. pseudoobscura strains BogER and AH162; and, that BogER females mate preferentially with AH162 males. Our results do not support either hypothesis.

Helper-dependent vector transmission of plant viruses

A variety of noncirculatively transmitted viruses have evolved a vector transmission strategy that involves, in addition to virions, virus-encoded proteins that are not constituents of virions. These "helpers" and the genes encoding them have been characterized for viruses in the genera Potyvirus and Caulimovirus. Several lines of evidence support the hypothesis that these helpers act by mediating retention of virions in regions of the vector's alimentary tract from which they subsequently can be egested to initiate an infection. The possible advantage this convergently evolved strategy could confer to noncirculatively transmitted virus quasispecies is discussed.

Episodic selection as a force in fungal microevolution, with special reference to clonal speciation and hybrid introgression

Episodic selection encompasses any sudden environmental disturbance likely to lead to a significant alteration in a species' population structure. Such disturbances include geographical transposition, a change in substrate availability, exposure to a new host or a new vector, climate change, and pollution stress. Today, such events may often be brought about by man. Their role in the promotion of fungal microevolution is discussed. In some circumstances, episodic selection may result in the emergence of a highly fitted clone from an originally heterogeneous population, and sustained disturbance may lead to clonal speciation. Clonal speciation accompanied by loss of sexual function, whether under episodic selection or under less intensive but analagous environmental conditions, could account for the origin of many of today's imperfect taxa (Deuteromycotina). Geographical transposition, a special form of episodic selection, can lead to hybridization between previously allopatric species. This may result in modifications to existing species via the acquisition of new loci or cytoplasmic elements, in the production of new taxa via secondary speciation, or in the emergence of hybrid swarms. Episodic selection will also favour survival of novel genotypes by providing new habitats for exploitation, so encouraging novel evolutionary development. Key words: episodic selection, fungal speciation, hybridization, introgression.

A method for determining the position and size of optimal sequence regions for phylogenetic analysis

The availability of fast and accurate sequencing procedures along with the use of PCR has led to a proliferation of studies of variability at the molecular level in populations. Nevertheless, it is often impractical to examine long genomic stretches and a large number of individuals at the same time. In order to optimize this kind of study, we suggest a heuristic procedure for detection of the shortest region whose informational content can be considered sufficient for significant phylogenetic reconstruction. The method is based on the comparison of the pairwise genetic distances obtained from a set of sequences of reference to those obtained for different windows of variable size and position by means of a simple index. We also present an approach for testing whether the informative content in the stretches selected in this way is significantly different from the corresponding content shown by the larger genomic regions used as reference. Application of this test to the analysis of the VP1 protein gene of foot-and-mouth-disease type C virus allowed us to define optimal stretches whose informative content is not significantly different from that displayed by the complete VP1 sequence. We showed that the predictions made for type C sequences are valid for type O sequences, indicating that the results of the procedure are consistent.

Mitochondrial DNA variation and population genetic structure of the northern redbelly dace (Phoxinus eos)

Two sections of the control region and the genes coding for NADH dehydrogenase subunits 5 and 6 (ND-5/6) of mitochondrial DNA (mtDNA) were amplified from Phoxinus eos with the polymerase chain reaction. Both sections of the control region were sequenced directly while the ND-5/6 fragment was sequenced in from each end only. Additionally, the entire ND-5/6 fragment was examined for sequence variation using RFLP analysis. No sequence variation was detected in the control region among 70 individuals sampled from 18 populations across three Ontario regions (Spanish River, Madawaska R. and Cataraqui R.). To examine ND-5/6 variation, a total of 75 individuals were sampled from five populations representing two of the three regions (Madawaska River and Cataraqui R.). Six haplotypes were detected by direct sequencing and four by RFLP analysis. Estimates of population subdivision from RFLP data, sequence analysis, and the two data sets combined for the ND-5/6 fragment, suggest that gene flow is restricted within and between regions. However, estimates of sequence divergence for both sequence and RFLP analysis of this fragment suggested that populations were either founded by already differentiated populations or that populations were founded by a single stock and divergence between regions occurred prior to isolation of populations within regions. These estimates of population structure are much greater than those obtained from allozyme analysis. Additionally, high levels of heterozygosity in nuclear DNA, but low mtDNA diversity suggests that populations have experienced reductions in population size sufficient to reduce only mtDNA variation. Random lineage extinction and limited time for the accumulation of new mutations are likely responsible for low levels of mtDNA variation in ND-5/6 and the control region, while functional constraints may limit variation more than expected in the control region in dace and other fishes.

Extreme fitness differences in mammalian and insect hosts after continuous replication of vesicular stomatitis virus in sandfly cells

Continuous, persistent replication of a wild-type strain of vesicular stomatitis virus in cultured sandfly cells for 10 months profoundly decreased virus replicative fitness in mammalian cells and greatly increased fitness in sandfly cells. After persistent infection of sandfly cells, fitness was over 2,000,000-fold greater than that in mammalian cells, indicating extreme selective differences in the environmental conditions provided by insect and mammalian cells. The sandfly-adapted virus also showed extremely low fitness in mouse brain cells (comparable to that in mammalian cell cultures). It also showed an attenuated phenotype, requiring a nearly millionfold higher intracranial dose than that of its parent clone to kill mice. A single passage of this adapted virus in BHK-21 cells at 37 degrees C restored fitness to near neutrality and also restored mouse neurovirulence. These results clearly illustrate the enormous capacity of RNA viruses to adapt to changing selective environments.

Conditional hitchhiking of mitochondrial DNA: frequency shifts of Drosophila melanogaster mtDNA variants depend on nuclear genetic background

Tests were performed of the selective neutrality of mitochondrial DNA (mtDNA) variants from geographic populations of Drosophila melanogaster in Argentina (ARG) and Central Africa (CAF). The two populations were completely reproductively compatible. The two distinct mtDNA haplotypes from the two populations were competed in replicate experimental populations on three nuclear genetic backgrounds: homozygous ARG, homozygous CAF, or hybrid ARG/CAF. Mitochondrial haplotype frequencies did not change significantly on either of the two homozygous nuclear backgrounds, and there was no change after experimental perturbation of haplotype frequencies. On the hybrid background, the ARG haplotype frequency increased significantly for the first two generations in all replicate populations but then did not change in subsequent generations. After perturbation, the ARG haplotype frequency increased in only one of four replicates. There is no evidence for selective differences among mtDNA variants in homozygous nuclear contexts or for nuclear-mitochondrial coadaptation. While some "fitness" difference among mtDNA variants is required to account for the observed frequency shifts, it appears that in these hybrid populations, mtDNA is hitchhiking on fitness variation among hybrid segregating nuclear genes. These results have implications for the use of mtDNA in the study of hybrid zones and gene flow.

Molecular epidemiology of foot-and-mouth disease (FMD) in Israel in 1994 and in other Middle-Eastern countries in the years 1992-1994

The reverse transcriptase-polymerase chain reaction (RT-PCR) and direct sequencing were employed in the diagnosis and typing of foot-and-mouth disease virus (FMDV) in samples taken during the 1994 disease outbreak in Israel. Using PCR, virus isolation and serological methods it was shown that the 1994 disease outbreak in Israel and other Middle-Eastern countries was caused by O1 type virus. Direct PCR sequencing of VP1 genes and homology analysis of the virus isolates revealed that there were two distinct outbreaks in Israel. The first originated in Jordan, moved to the West Bank territory and then to the Lower Galilee. The second outbreak, caused by another virus, was responsible for disease outbreaks in South Lebanon, Upper Galilee and the Golan Heights. When viral sequences of isolates from the 1993 outbreaks in Egypt and Lebanon were included in the analysis, they showed a high degree of VP1 sequence homology between themselves, suggesting a common origin.

Speciation. Down the bottleneck?

Experiments in which laboratory populations of fruitflies have been repeatedly passed through bottlenecks fail to support 'founder-effect' models of speciation.

Antibody recognition of picornaviruses and escape from neutralization: a structural view

Escape of picornaviruses from neutralization by monoclonal antibodies is mediated by substitutions of very few, defined amino acid residues of the capsid, generally located on the tip of some surface-exposed loops. Substitutions at the same positions are possibly of major relevance to antigenic variation of picornaviruses in the field. Such residues tend to cluster in discrete areas, termed antigenic sites. The structure of virus-antibody and peptide-antibody complexes, determined by cryoelectron microscopy and X-ray crystallography, combined with studies using site-directed mutagenesis, are beginning to reveal new features of picornavirus epitopes. This information complements and expands the view on picornavirus antigenicity previously provided by analyses of antibody-escape mutants. In addition to amino acids found replaced in escape mutants, other surface residues which remain invariant in spite of immune pressure also participate in contacts with the antibody molecule. Some invariant residues are even critical for the antigen-antibody interaction. Escape mutations occur at the subset of antigenically critical residues which are tolerant to change because they are not essentially involved in capsid structure or function. Restrictions to variation differ among epitopes; this may contribute to explain the different number of serotypes among picornaviruses, and the frequency at which antigenically highly divergent variants occur in the field.

Evolution of the feline-subgroup parvoviruses and the control of canine host range in vivo

A related group of parvoviruses infects members of many different carnivore families. Some of those viruses differ in host range or antigenic properties, but the true relationships are poorly understood. We examined 24 VP1/VP2 and 8 NS1 gene sequences from various parvovirus isolates to determine the phylogenetic relationships between viruses isolated from cats, dogs, Asiatic raccoon dogs, mink, raccoons, and foxes. There were about 1.3% pairwise sequence differences between the VP1/VP2 genes of viruses collected up to four decades apart. Viruses from cats, mink, foxes, and raccoons were not distinguished from each other phylogenetically, but the canine or Asiatic raccoon dog isolates formed a distinct clade. Characteristic antigenic, tissue culture host range, and other properties of the canine isolates have previously been shown to be determined by differences in the VP1/VP2 gene, and we show here that there are at least 10 nucleotide sequence differences which distinguish all canine isolates from any other virus. The VP1/VP2 gene sequences grouped roughly according to the time of virus isolation, and there were similar rates of sequence divergence among the canine isolates and those from the other species. A smaller number of differences were present in the NS1 gene sequences, but a similar phylogeny was revealed. Inoculation of mutants of a feline virus isolate into dogs showed that three or four CPV-specific differences in the VP1/VP2 gene controlled the in vivo canine host range.

Identification of a retroviroid-like element from plants

The biological nature of carnation small viroid-like RNA (CarSV RNA), a 275-nt circular molecule with self-cleaving hammerhead structures in its strands of both polarities, was investigated. The lack of infectivity observed in a series of transmission assays in carnation indicates that CarSV RNA, in spite of sharing structural similarities with viroid and viroid-like satellite RNAs from plants, does not belong to either of these two groups. Additional evidence in this direction comes from the observation that CarSV RNA also exists in carnation plants as DNA tandem repeats. In this respect, CarSV RNA is similar to a small transcript of a tandemly repeated DNA sequence of the newt genome. Moreover, CarSV and newt RNAs have similarities in their sequences as well as in some characteristics of their corresponding hammerhead structures. Further analyses have revealed that CarSV DNA is found directly fused to DNA sequences of carnation etched ring caulimovirus, a pararetrovirus, most likely in the form of an extrachromosomal element. The properties of the CarSV RNA/DNA system are those of a retroviroid-like element having some features in common with viroid and viroid-like satellite RNAs from plants and others with the newt transcript.

Exponential increases of RNA virus fitness during large population transmissions

The great adaptability shown by RNA viruses is a consequence of their high mutation rates. Here we investigate the kinetics of virus fitness gains during repeated transfers of large virus populations in cell culture. Results always show that fitness increases exponentially. Low fitness clones exhibit regular increases observed as biphasic periods of exponential evolutionary improvement, while neutral clones show monophasic kinetics. These results are significant for RNA virus epidemiology, optimal handling of attenuated live virus vaccines, and routine laboratory procedures.

Molecular evolution of aphthoviruses

Aphthoviruses are an important group of animal pathogens. A combination of genetic and structural studies has revealed one of the main principles governing their evolution: severe limitations to variation imposed by functional and structural constraints, in conjunction with high mutation and recombination rates operating during genome replication. Evolution occurs by positive selection and random drift acting on complex quasispecies distributions. The mutant composition of a quasi-species (or mutant spectrum) is largely dictated by tolerance to nucleotide and amino acid substitutions in viral RNAs and proteins, which must remain functionally competent. We review recent evidence to support this proposal, and we suggest that similar concepts may apply to other RNA viruses as well.

Whole-virus vaccine development by continuous culture on a complementing host

We have evaluated an adaptive strategy for generating whole-virus vaccines using a bacteriophage model. Wildtype phage T7 was cultivated in a two-stage continuous stirred-tank reactor (CSTR) utilizing a recombinant E. coli host that constitutively expressed T7 RNA polymerase, an essential enzyme of the early viral metabolism. Over the course of 180 generations a diversity of phage variants emerged, outgrew the wildtype, and were subsequently eclipsed by yet fitter variants, based on host-ranges, restriction patterns, and one-step growth responses of isolated clones. The fittest variant, which required complementation by the recombinant host in order to grow, deleted at least 12 percent of its genome and replicated twice as fast as the wildtype. Moreover, this variant was immunogenically indistinguishable from the wildtype, based on cross-reactivities of antisera raised against both. These results suggest the feasibility of the proposed strategy for the development of safe whole-virus vaccines.

Origin and evolution of viroids and viroid-like satellite RNAs

Viroids, the smallest and simplest agents of infectious disease, cause a number of economically important diseases of crop plants. Present evidence indicates that most of these diseases originated recently (in the 20th century) by chance transfer of viroids from endemically infected wild plants or by use of viroid-infected germplasm during plant breeding. Modern agricultural practices, such as widespread monoculture of genetically identical plants, and worldwide distribution of planting material, has made it possible for the pathogens to maintain themselves in the crop plants and to conquer new territories. Phylogenetic analysis of their nucleotide sequences indicates that viroids and satellite RNAs represent a monophyletic group, with all but the two self-cleaving viroids forming one cluster and the satellite RNAs another. The two self-cleaving viroids are phylogenetically distant from either cluster; they may represent ancestral forms. Results from site-directed mutagenesis experiments indicate that, upon exposure to selective pressures, viroids can evolve extremely rapidly, with another, fitter, component of the quasi-species often becoming dominant within days or weeks. This extreme plasticity of their nucleotide sequences establishes viroids as the most rapidly evolving biological system known.

Competition between mitochondrial haplotypes in distinct nuclear genetic environments: Drosophila pseudoobscura vs. D. persimilis

A test for coadaptation of nuclear and mitochondrial genomes was performed using the sibling species, Drosophila pseudoobscura and D. persimilis. Two lines of flies with "disrupted" cytonuclear genotypes were constructed by repeated backcrossing of males from one species to females carrying mitochondrial DNA (mtDNA) from the other species. Each "disrupted" strain was competed in population cages with the original stock of each species from which the recurrent males were obtained during the backcrossing. As such, the two species' mitochondrial types were competed reciprocally in the nuclear genetic environments of each species. The trajectories of mtDNA haplotypes were followed in discrete-generation population cages using a PCR-four-cutter approach. A significant increase in the frequency of D. pseudoobscura mtDNA was observed in each of four replicate cages with a D. pseudoobscura nuclear background. In the D. persimilis nuclear background, one cage actually showed an increase in frequency of D. pseudoobscura mtDNA, although together the four replicate cages show little change in frequency. These results were repeated after frequency perturbations and reinitiation of each cage. An analysis of fitness components revealed that fertility selection greatly outweighed viability selection in these cytonuclear competition experiments. The asymmetry of the fitnesses of the mtDNA haplotypes on the two genetic backgrounds is consistent in direction with the previously reported asymmetry of female fertility in backcrosses between these two species. While our experiments do not allow us to identify mtDNA as the sole source of fitness variation, at a minimum the data indicate a fitness association between nuclear fertility factors and the D. pseudoobscura mtDNA on its own genetic background.

Size of genetic bottlenecks leading to virus fitness loss is determined by mean initial population fitness

Genetic bottlenecks are important events in the genetic diversification of organisms and colonization of new ecological niches. Repeated bottlenecking of RNA viruses often leads to fitness losses due to the operation of Muller's ratchet. Herein we use vesicular stomatitis virus to determine the transmission population size which leads to fitness decreases of virus populations. Remarkably, the effective size of a genetic bottleneck associated with fitness loss is greater when the fitness of the parental population increases. For example, for starting virus populations with low fitness, population transfers of five-clone-to-five-clone passages resulted in a fitness increase. However, when a parental population with high fitness was transferred, 30-clone-to-30-clone passages were required simply to maintain fitness values.

Evolutionary analysis of the picornavirus family

An exhaustive evolutionary analysis of the picornavirus family has been carried out using the amino acid sequences of several proteins of the viruses including: the capsid proteins (1D, 1B, and 1C) situated at the 5' end of the genome and responsible for the serotype of the viruses, and the viral polymerase (3D), located at the 3' end of the genome. The evolutionary relationships found among the viruses studied support the new classification, recently suggested, in contrast to the classical one, and the existence of a new genus for the picornavirus family. In the new taxonomic organization, five genera form the picornavirus family: (1) aphthoviruses, (2) cardioviruses, (3) hepatoviruses (previously classified as enteroviruses), (4) renteroviruses (which mainly constitute a combination of the previous genera rhinovirus and enterovirus), and (5) a new genus, with a new and unique representative: the echovirus 22. Our analysis also allowed us, for the first time, to propose the most probable sequence of speciation events to have given rise to the current picornavirus family. The bootstrap procedure was used to check the reliability of the phylogenetic trees obtained. The application of the method of the statistical geometry in distance space to internal branches of the tree revealed a high degree of evolutionary "noise," which makes the resolution of some internal branching points difficult.

Serial passage in tissue culture of mixed foot-and-mouth disease virus serotypes

The foot-and-mouth disease (FMD) virus field specimen SAU/8/88 was previously shown to consist of a mixture of O and Asia 1 serotypes [15]. In this study, plaques representing the O and Asia 1 components isolated from the original epithelial virus suspension were used to construct mixtures of known ratios, and these were serially passaged in tissue culture. After each passage, the ratio of O to Asia 1 virus was calculated. The two virus populations were shown to be cycling through time. This cycling phenomenon has not been described before for FMD virus in tissue culture, but is consistent with current population theory.

The RNA of both polarities of the peach latent mosaic viroid self-cleaves in vitro solely by single hammerhead structures

Hammerhead self-cleavage of dimeric, monomeric, truncated and mutated transcripts derived from both polarities of the peach latent mosaic viroid (PLMVd) were characterized. In contrast to some results previously published for a very close sequence variant (see ref. 1), these RNAs exhibit a virtually identical self-cleavage during transcription and after purification. By self-cleavage of dimeric transcripts with normal and mutated hammerhead domains and by complementation experiments, we show that the cleavage reactions involve only single hammerhead structures. This observation contrasts with the case of avocado sunblotch viroid (ASBVd), the other self-cleaving viroid, whose mechanism involves mostly double hammerhead structures, whereas single hammerhead cleavage is associated with viroid-like plant satellite RNAs. The difference in stability between the native secondary structures adopted by viroids and the autocatalytic structures, including the hammerhead motif, governs the efficiency of the self-cleavage reaction. The transition between these conformers is the limiting step in catalysis and is related exclusively to the left arm region of PLMVd secondary structure, which includes the hammerhead sequences. Most of the mutations between the variant we used and the sequence variant previously published are located in this left arm region, which may explain to a great extent the differences in their cleavage efficiency. No interactions with long-range sequences contributing to the autocatalytic tertiary structure were revealed in these experiments.

Variable effects of crowding on Drosophila hosts of male-lethal and non-male-lethal spiroplasmas in laboratory populations

Male-lethal, maternally inherited spiroplasmas occur in four species of Drosophila, and persist in natural populations despite imperfect vertical transmission rates. In the field, larval crowding is thought to be sporadic, but occasionally intense. To determine whether crowding affects host persistence, I compared the population dynamics of infected females (hosts) under crowded conditions to those expected from data collected on uncrowded females. I estimated host fitness components and maternal transmission rates for individual females under uncrowded conditions in both the artificial host D. pseudoobscura (this paper) and the native host D. willistoni (previously reported). Spiroplasma infection had no effect on lifetime production of daughters in D. pseudoobscura; however, as with some D. willistoni lines, hosts may produce more of their daughters earlier in life than nonhosts. Because individual contributions to relative rates of increase calculated from these fitness data were similar for hosts and nonhosts, I expected hosts to persist in laboratory populations. Instead, three patterns were observed: rapid extinction of D. willistoni females infected with male-lethal spiroplasmas, slow decline or persistence of hosts (depending on initial frequency) in both D. pseudoobscura infected with male-lethal spiroplasmas, and D. willistoni infected with non-male-lethal spiroplasmas. Population dynamics, then, depend on host species and bacterial isolate. Fitness estimates change with host line in uncrowded D. willistoni, but host genetic background did not affect population dynamics. These and previously published results show that the interaction phenotype changes with host and parasite isolate, and that host fitness can be affected by crowding. Crowding in natural populations may therefore decrease host fitness but, in expanding populations, early reproduction in hosts may be to their advantage. Possible effects of seasonal fluctuations in population density on the fitness of infected Drosophila are discussed.

Large deletions in the 5'-untranslated region of foot-and-mouth disease virus of serotype C

Nucleotide sequences of the 5'-untranslated region (5'-UTR), at the 3'-side of the poly C tract, have been compared for 21 isolates of foot-and-mouth disease virus (FMDV) of serotype C from Europe, South America and The Philippines. A deletion of 43 nucleotides is present in the European isolates as compared with most American isolates. A larger deletion of 86 nucleotides is present in some viruses from South America and The Philippines. These deletions include the loss of one or two pseudoknot structures predicted in this region of the 5'-UTR. In addition, multiple point mutations have allowed the derivation of a phylogenetic tree which defines a grouping of isolates very similar to that derived from the capsid gene sequences of the same viruses. The study provides evidence that deletion (or addition) events must be very frequent during evolution of FMDV type C, since viruses which are phylogenetically very closely related (they belong to the same tree branch) may differ in the presence or absence of these deletions. Implications for FMDV evolution are discussed.

Overexpression of two penicillin structural genes in Aspergillus nidulans

We have placed two different penicillin structural genes from Aspergillus nidulans, ipnA (encoding isopenicillin N synthetase, IPNS) and acyA (encoding acyl-CoA:6-aminopenicillanic acid acyltransferase, AAT), under the control of the strong alcA promoter [alcA(p)]. Single copies of these transcriptional fusions were targeted to the same chromosomal location and conditions have been worked out which simultaneously allow induction of the alcA(p) and support penicillin biosynthesis. Transcriptional induction of the chimeric genes alcA(p)::ipnA or alcA(p)::acyA(cdna) in the relevant recombinant strains results in 10-fold higher levels of the ipnA or acyA transcripts than those resulting from transcription of the corresponding endogenous genes. This increase causes a 40-fold rise in IPNS activity or a 8-fold rise in AAT activity. Despite this rise in enzyme levels, forced expression of the ipnA gene results in only a modest increase in levels of exported penicillin, whereas forced expression of the acyA gene reduces penicillin production, showing that neither of these enzymes is rate-limiting for penicillin biosynthesis in A. nidulans. A genomic version of the alcA(p)::acyA fusion in which the acyA gene is interrupted by three small introns, is inducible by threonine to a lesser extent (as determined by both acyA mRNA levels and AAT enzyme levels) than the corresponding cDNA version, suggesting that processing of the introns present in the primary transcript may limit acyA expression.

Genes for beta-lactam antibiotic biosynthesis

The genes pcbAB, pcbC and penDE encoding enzymes involved in the biosynthesis of penicillin have been cloned from Penicillium chrysogenum and Aspergillus nidulans. They are clustered in chromosome I (10.4 Mb) of P. chrysogenum, but they are located in chromosome II of Penicillium notatum (9.6 Mb) and in chromosome VI (3.0 Mb) of A. nidulans. Expression studies have shown that each gene is expressed as a single transcript from separate promoters. Enzyme regulation studies and gene expression analysis have provided useful information to understand the control of gene expression leading to overexpression of the genes involved in penicillin biosynthesis. Cephalosporin genes have been studied in Cephalosporium acremonium and also in cephalosporin-producing bacteria. In C. acremonium the genes involved in cephalosporin biosynthesis are separated in at least two clusters. Cluster I (pcbAB-pcbC) encodes the first two enzymes of the cephalosporin pathway which are very similar to those involved in penicillin biosynthesis. Cluster II (cefEF-cefG), encodes the last three enzymatic activities of the cephalosporin pathway. It is unknown, at this time, if the cefD gene encoding isopenicillin epimerase is linked to any of the two clusters. In cephamycin producing bacteria the genes encoding the entire biosynthetic pathway are located in a single cluster extending for about 30 kb in Nocardia lactamdurans, and in Streptomyces clavuligerus. The cephamycin clusters of N. lactamdurans and S. clavuligerus include a gene lat which encodes lysine-6-aminotransferase an enzyme involved in formation of the precursor alpha-aminoadipic acid. The N. lactamdurans cephamycin cluster includes, in addition, a beta-lactamase (bla) gene, a penicillin binding protein (pbp), and a transmembrane protein gene (cmcT) that is probably involved in secretion of the cephamycin. Little is known however about the mechanism of control of gene expression in the different beta-lactam producers. The availability of most of the structural genes provides a good basis for further studies on gene expression. This knowledge should lead in the next decade to a rational design of strain improvement procedures. The origin and evolution of beta-lactam genes is intriguing since their nucleotide sequences are extremely conserved despite their restricted distribution in the microbial world.

Nucleotide sequence of a hop stunt viroid variant isolated from citrus growing in Taiwan

The 303 nucleotide sequence of HSVd-citrus(T), a hop stunt viroid (HSVd) variant present in Etrog citron growing in Taiwan, was determined from cDNAs amplified by the polymerase chain reaction. HSVd-citrus(T) is very similar to several HSVd isolates previously recovered from citrus or cucumber, and exhibits microsequence heterogeneity at positions 154 and 181. Phylogenetic analysis using maximum parsimony grouped HSVd-citrus(T) with seven other isolates from citrus and cucumber in a large cluster of "citrus-type" isolates. A similar analysis revealed marked differences in both the extent and distribution of sequence variation among naturally occurring isolates of potato spindle tuber viroid.

Detection and subtyping of foot-and-mouth disease virus in infected cattle by polymerase chain reaction and amplified VP1 sequencing

Fast and accurate detection of foot-and-mouth disease (FMD) outbreaks is needed to limit spread of the disease by proper vaccination. The use of the polymerase chain reaction (PCR) has revolutionized the way in which viral diseases are diagnosed. Sequence analysis of the amplified VP1 sequence can enable the classification of FMD virus detected in the morbid animal. PCR assays were carried out to identify the virus and its serotype in suspect animals from 2 outbreaks of FMD type O virus. Sequence analysis of the amplified VP1 cDNA showed 78% homology with O1K and over 95% homology between the samples. These findings suggest that the 2 outbreaks were due to infection with the same virus serosubtype.

Paraquat resistance and starvation conditions in the selection of longevity extremes in Drosophila melanogaster populations previously selected for long and short developmental period

This paper analyzes the interaction between resistance to free radicals, development under starvation conditions, sex, and its consequences to the lifespan of Drosophila melanogaster populations selected for developmental time and longevity. Our data suggest that the interaction between these physiological and environmental parameters is modulated largely by the pre-imaginal developmental time, since the response to selection for longevity extremes depends strongly on the previous selection for developmental time extremes.

Post-transcriptional regulation of a salt-inducible alfalfa gene encoding a putative chimeric proline-rich cell wall protein

A cDNA previously shown to identify a salt-inducible root-specific transcript in Medicago sativa was used to screen an alfalfa library for the corresponding genomic sequence. One positive clone was recovered. The nucleotide sequence of a subclone contained a 329 bp 5' region upstream of the first ATG codon, a 1143 bp coding segment, and a 447 bp 3'-untranslated region interrupted by a single 475 bp intron. Translation of the coding segment, which was designated MsPRP2, suggested it encodes a chimeric 40,569 Da cell wall protein with an amino-terminal signal sequence, a repetitive proline-rich sequence, and a cysteine-rich carboxyl-terminal sequence homologous to nonspecific lipid transfer proteins. The 3'-untranslated region of MsPRP2 contained a sequence similar to one found to destabilize mRNAs transcribed from the elicitor-regulated proline-rich protein gene PvPRP1. Transcription run-on experiments using nuclei from salt-sensitive and salt-tolerant alfalfa callus suggested that the accumulation of MsPRP2 transcripts in salt-tolerant alfalfa cells grown in the presence of salt is due primarily to increased mRNA stability. The MsPRP2 gene thus may be a useful model for studying post-transcriptional salt-regulated expression of cell wall proteins.

A highly divergent antigenic site of foot-and-mouth disease virus retains its immunodominance

The ability of a highly divergent antigenic site of foot-and-mouth disease virus (FMDV) of serotype C to elicit neutralizing antibodies has been evaluated in mice and rabbits. The viruses compared, FMDV C-S8c1 and HR, differ in a single amino acid replacement in their capsid proteins, but represent two extreme antigenic specificities of the major antigenic site A of FMDV type C. Both, studies of cross-neutralization of homologous and heterologous virus, and fractionation of site A-specific antibodies by immunoaffinity chromatography suggest a similar immunodominance of antigenic site A in FMDV C-S8c1 and variant HR. This information is relevant to the formulation of synthetic peptide vaccines that ideally should consist of mixtures of peptides representing several antigenic specificities. These cocktail formulations may be required to control diseases caused by FMDV and, generally, by highly variable RNA viruses, since single specificity peptides may trigger selection of vaccine-escape viral mutants.

Replication of avocado sunblotch viroid: evidence for a symmetric pathway with two rolling circles and hammerhead ribozyme processing

The structure of a series of RNAs extracted from avocado infected by the 247-nt avocado sunblotch viroid (ASBVd) was investigated. The identification of multistranded complexes containing circular ASBVd RNAs of (+) and (-) polarity suggests that replication of ASBVd proceeds through a symmetric pathway with two rolling circles where these two circular RNAs are the templates. This is in contrast to the replication of potato spindle tuber viroid and probably of most of its related viroids, which proceeds via an asymmetric pathway where circular (+)-strand and linear multimeric (-)-strand RNAs are the two templates. Linear (+) and (-) ASBVd RNAs of subgenomic length (137 nt and about 148 nt, respectively) and one linear (+)-strand ASBVd RNA of supragenomic length (383-384 nt) were also found in viroid-infected tissue. The two linear (+)-strand RNAs have the same 5'- and 3'-terminal sequences, with the supragenomic species being a fusion product of the monomeric and subgenomic (+)-strand ASBVd RNAs. The 3' termini of these two (+)-strand molecules, which at least in the subgenomic RNA has an extra nontemplate cytidylate residue, could represent sites of either premature termination of the (+)-strands or specific initiation of the (-)-strands. The 5' termini of sub- and supragenomic (+)-strand and the 5' terminus of the subgenomic (-)-strand ASBVd RNA are identical to those produced in the in vitro self-cleavage reactions of (+) and (-) dimeric ASBVd RNAs, respectively. These observations strongly suggest that the hammerhead structures which mediate the in vitro self-cleavage reactions are also operative in vivo.

Neutral and non-neutral evolution of Drosophila mitochondrial DNA

To test hypotheses of neutral evolution of mitochondrial DNA (mtDNA), nucleotide sequences were determined for 1515 base pairs of the NADH dehydrogenase subunit 5 (ND5) gene in the mitochondrial DNA of 29 lines of Drosophila melanogaster and 9 lines of its sibling species Drosophila simulans. In contrast to the patterns for nuclear genes, where D. melanogaster generally exhibits much less nucleotide polymorphism, the number of segregating sites was slightly higher in a global sample of nine ND5 sequences in D. melanogaster (s = 8) than in the nine lines of D. simulans (s = 6). When compared to variation at nuclear loci, the mtDNA variation in D. melanogaster does not depart from neutral expectations. The ND5 sequences in D. simulans, however, show fewer than half the number of variable sites expected under neutrality when compared to sequences from the period locus. While this reduction in variation is not significant at the 5% level, HKA tests with published restriction data for mtDNA in D. simulans do show a significant reduction of variation suggesting a selective sweep of variation in the mtDNA in this species. Tests of neutral evolution based on the ratios of synonymous and replacement polymorphism and divergence are generally consistent with neutral expectations, although a significant excess of amino acid polymorphism within both species is localized in one region of the protein. The rate of mtDNA evolution has been faster in D. melanogaster than in D. simulans and the population structure of mtDNA is distinct in these species. The data reveal how different rates of mtDNA evolution between species and different histories of neutral and adaptive evolution within species can compromise historical inferences in population and evolutionary biology.

Phylogeny of the Drosophila obscura species group deduced from mitochondrial DNA sequences

Approximately 2 kb corresponding to different regions of the mtDNA of 14 different species of the obscura group of Drosophila have been sequenced. In spite of the uncertainties arising in the phylogenetic reconstruction due to a restrictive selection toward a high mtDNA A+T content, all the phylogenetic analysis carried out clearly indicate that the obscura group is formed by, at least, four well-defined lineages that would have appeared as the consequence of a rapid phyletic radiation. Two of the lineages correspond to monophyletic subgroups (i.e., affinis and pseudoobscura), whereas the obscura subgroup remains heterogeneous assemblage that could be reasonably subdivided into at least two complexes (i.e., subobscura and obscura).

Domain conservation in several volvocalean cell wall proteins

Based on our previous work demonstrating that (SerPro)x epitopes are common to extensin-like cell wall proteins in Chlamydomonas' reinhardtii, we looked for similar proteins in the distantly related species C. eugametos. Using a polyclonal antiserum against a (SerPro)10 oligopeptide, we found distinct sets of stage-specific polypeptides immunoprecipitated from in vitro translations of C. eugametos RNA. Screening of a C. eugametos cDNA expression library with the antiserum led to the isolation of a cDNA (WP6) encoding a (SerPro)x-rich multidomain wall protein. Analysis of a similarly selected cDNA (VSP-3) from a C. reinhardtii cDNA expression library revealed that it also coded for a (SerPro)x-rich multidomain wall protein. The C-terminal rod domains of VSP-3 and WP6 are highly homologous, while the N-terminal domains are dissimilar; however, the N-terminal domain of VSP-3 is homologous to the globular domain of a cell wall protein from Volvox carteri. Exon shuffling might be responsible for this example of domain conservation over 350 million years of volvocalean cell wall protein evolution.

Degree of diversity of hepatitis C virus quasispecies and progression of liver disease

We examined the quasispecies of the hepatitis C virus genome in 28 patients with liver disease of varying severity. Nucleotide sequences of the hepatitis C virus genome spanning the region from the core to envelope were used to calculate the nucleotide diversity: 0.58% +/- 0.88% in 5 patients with acute hepatitis, 0.85% +/- 0.62% in 5 patients with chronic persistent hepatitis, 1.79% +/- 0.92% in 11 patients with chronic active hepatitis, 3.05% +/- 1.26% in 4 patients with cirrhosis and 2.71% +/- 1.47% in 3 patients with cirrhosis complicated by hepatocellular carcinoma. Thus the intrapatient variation in nucleotides increased significantly with severity of liver disease (p < 0.01), except in those cases of cirrhosis complicated by hepatocellular carcinoma. Multivariate analysis including the histology, duration of infection, age, sex, history of blood transfusion and serum level of ALT at diagnosis as variables showed that the histological finding was the strongest independent factor of the nucleotide diversity (p = 0.003). Serial analysis of the genome in three patients demonstrated that the intra-patient variation in nucleotides increased with the progression of liver disease. The magnitude of the intrapatient variation in nucleotides deduced from the observed changes in the patients was correlated with the mean serum levels of ALT. These findings suggest that the degree of diversity of HCV quasispecies is related to the progression of liver disease.